UCSC Genome Browser database
Names
More detailed information about this field from each metasource.
UCSC Genome Browser database
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
UCSC Genome Browser
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: UCSC Genome Browser; editing status 2021-08-24; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RK5C last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
UCSC Genome Bioinformatics
metasource: re3data.org
version: re3data.org: UCSC Genome Browser; editing status 2021-08-24; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RK5C last accessed: 2022-11-04
University of California Santa Cruz Genome Bioinformatics
metasource: re3data.org
version: re3data.org: UCSC Genome Browser; editing status 2021-08-24; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RK5C last accessed: 2022-11-04
ucsc_genome_browser
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
Names
More detailed information about this field from each metasource.
UCSC Genome Browser database
metasource: Fairsharing.orgversion: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
UCSC Genome Browser
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: UCSC Genome Browser; editing status 2021-08-24; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RK5C last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
UCSC Genome Bioinformatics
metasource: re3data.orgversion: re3data.org: UCSC Genome Browser; editing status 2021-08-24; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RK5C last accessed: 2022-11-04
University of California Santa Cruz Genome Bioinformatics
metasource: re3data.orgversion: re3data.org: UCSC Genome Browser; editing status 2021-08-24; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RK5C last accessed: 2022-11-04
ucsc_genome_browser
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:08.071742
Other names: UCSC Genome Browser, UCSC Genome Bioinformatics, University of California Santa Cruz Genome Bioinformatics, ucsc_genome_browser
Names
More detailed information about this field from each metasource.
UCSC Genome Browser database
metasource: Fairsharing.orgversion: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
UCSC Genome Browser
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: UCSC Genome Browser; editing status 2021-08-24; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RK5C last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
UCSC Genome Bioinformatics
metasource: re3data.orgversion: re3data.org: UCSC Genome Browser; editing status 2021-08-24; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RK5C last accessed: 2022-11-04
University of California Santa Cruz Genome Bioinformatics
metasource: re3data.orgversion: re3data.org: UCSC Genome Browser; editing status 2021-08-24; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RK5C last accessed: 2022-11-04
ucsc_genome_browser
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:08.071742
Genome assemblies and aligned annotations for a wide range of vertebrates and model organisms, along with an integrated tool set for visualizing, comparing, analyzing and sharing both publicly available and user-generated genomic datasets.
Description
More detailed information about this field from each metasource.
Genome assemblies and aligned annotations for a wide range of vertebrates and model organisms, along with an integrated tool set for visualizing, comparing, analyzing and sharing both publicly available and user-generated genomic datasets.
metasource: Fairsharing.orgversion: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a large collection of organisms, primarily vertebrates, with an emphasis on the human and mouse genomes. The Browser’s Web-based tools – including BLAT, the Table Browser, VisiGene, the Gene Sorter, Genome Graphs, and the Variant Annotation Integrator -- provide an integrated environment for visualizing, comparing, analyzing, and sharing both publicly available and user-generated genomic data sets. As of September 2016, the database contained genomic sequence and a basic set of annotation ‘tracks’ for 96 unique species, many with multiple assembly versions. Most genome assemblies offer mapping and sequence annotation tracks describing assembly, gap, and GC content, and alignments of mRNA, EST, and RefSeq data from GenBank. Some assemblies provide additional gene annotations and sequence alignments of selected species to facilitate comparative and evolutionary investigations. The heavily annotated human genome offers extensive conservation and evolutionary comparisons, a large collection of gene models, regulation, expression, epigenetics and tissue differentiation, variation, phenotype and disease association data, and text-mined data from publications. In addition to the native data sets local to the UCSC servers, the Genome Browser offers several options to users for viewing their own sequence and annotations: track and assembly data hubs, custom tracks, and sessions. The Genome Browser database and tools may also be installed on a local server for customized use. The full set of data, software tools, downloads, and documentation can be found on the Genome Browser website.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations. The Browser is a graphical viewer optimized to support fast interactive performance and is an open-source, web-based tool suite built on top of a MySQL database for rapid visualization, examination, and querying of the data at many levels.
metasource: re3data.orgversion: re3data.org: UCSC Genome Browser; editing status 2021-08-24; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RK5C last accessed: 2022-11-04
Large database of publicly available sequence and annotation data along with an integrated tool set for examining and comparing the genomes of organisms, aligning sequence to genomes, and displaying and sharing users own annotation data.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:08.071742
Webpage:
http://genome.ucsc.eduWebpage
More detailed information about this field from each metasource.
http://genome.ucsc.edu
metasource: Fairsharing.orgversion: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://genome.ucsc.edu/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
https://genome.ucsc.edu/
metasource: re3data.orgversion: re3data.org: UCSC Genome Browser; editing status 2021-08-24; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RK5C last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
Licence:
Name: otherLicence name
More detailed information about this field from each metasource.
other
metasource: re3data.orgversion: re3data.org: UCSC Genome Browser; editing status 2021-08-24; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RK5C last accessed: 2022-11-04
Apache-2.0
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:08.071742
Licence URL
More detailed information about this field from each metasource.
https://genome.ucsc.edu/license/gblicense.pdf
metasource: re3data.orgversion: re3data.org: UCSC Genome Browser; editing status 2021-08-24; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3RK5C last accessed: 2022-11-04
Publications:
(29)
Publications
More detailed information about this field from each metasource.
Initial sequencing and analysis of the human genome
PMID: 11237011
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
The human genome browser at UCSC
PMID: 12045153
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
BLAT--the BLAST-like alignment tool
PMID: 11932250
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
The UCSC Table Browser data retrieval tool
PMID: 14681465
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
The UCSC Genome Browser Database
PMID: 12519945
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
The UCSC Genome Browser database: update 2011
PMID: 20959295
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
The UCSC Genome Browser Database: update 2006
PMID: 16381938
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
The UCSC Genome Browser database: 2015 update
PMID: 25428374
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
The UCSC Genome Browser database: extensions and updates 2013
PMID: 23155063
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
ENCODE data in the UCSC Genome Browser: year 5 update
PMID: 23193274
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
The UCSC Genome Browser database: 2014 update
PMID: 24270787
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
The UCSC Genome Browser database: update 2010
PMID: 19906737
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
The UCSC Genome Browser database: 2019 update
PMID: 30407534
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
The UCSC Genome Browser Database: 2008 update
PMID: 18086701
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
The UCSC Genome Browser database: 2018 update
PMID: 29106570
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
The UCSC Genome Browser Database: update 2009
PMID: 18996895
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
The UCSC Genome Browser database: 2016 update
PMID: 26590259
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
The UCSC Genome Browser database: extensions and updates 2011
PMID: 22086951
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
The UCSC Genome Browser database: 2017 update
PMID: 27899642
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
ENCODE whole-genome data in the UCSC Genome Browser: update 2012
PMID: 22075998
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
The UCSC Genome Browser database: 2021 update
PMID: 33221922
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
UCSC Genome Browser enters 20th year
PMID: 31691824
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Assembly of the working draft of the human genome with GigAssembler
PMID: 11544197
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
The UCSC SARS-CoV-2 Genome Browser
PMID: 32908258
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
The UCSC Genome Browser
PMID: 23255150
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Exploring relationships and mining data with the UCSC Gene Sorter
PMID: 15867434
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
The UCSC repeat browser allows discovery and visualization of evolutionary conflict across repeat families
PMID: 32266012
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Ultrafast Sample Placement on Existing Trees (UShER) Empowers Real-Time Phylogenetics for the SARS-CoV-2 Pandemic
PMID: 33024970
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://dx.doi.org/10.1093/nar/gkv1275
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
Initial sequencing and analysis of the human genome
PMID: 11237011
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
The human genome browser at UCSC
PMID: 12045153
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
BLAT--the BLAST-like alignment tool
PMID: 11932250
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
The UCSC Table Browser data retrieval tool
PMID: 14681465
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
The UCSC Genome Browser Database
PMID: 12519945
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
The UCSC Genome Browser database: update 2011
PMID: 20959295
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
The UCSC Genome Browser Database: update 2006
PMID: 16381938
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
The UCSC Genome Browser database: 2015 update
PMID: 25428374
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
The UCSC Genome Browser database: extensions and updates 2013
PMID: 23155063
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
ENCODE data in the UCSC Genome Browser: year 5 update
PMID: 23193274
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
The UCSC Genome Browser database: 2014 update
PMID: 24270787
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
The UCSC Genome Browser database: update 2010
PMID: 19906737
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
The UCSC Genome Browser database: 2019 update
PMID: 30407534
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
The UCSC Genome Browser Database: 2008 update
PMID: 18086701
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
The UCSC Genome Browser database: 2018 update
PMID: 29106570
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
The UCSC Genome Browser Database: update 2009
PMID: 18996895
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
The UCSC Genome Browser database: 2016 update
PMID: 26590259
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
The UCSC Genome Browser database: extensions and updates 2011
PMID: 22086951
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
The UCSC Genome Browser database: 2017 update
PMID: 27899642
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
ENCODE whole-genome data in the UCSC Genome Browser: update 2012
PMID: 22075998
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:08.071742
The UCSC Genome Browser database: 2021 update
PMID: 33221922
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
UCSC Genome Browser enters 20th year
PMID: 31691824
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Assembly of the working draft of the human genome with GigAssembler
PMID: 11544197
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
The UCSC SARS-CoV-2 Genome Browser
PMID: 32908258
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
The UCSC Genome Browser
PMID: 23255150
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Exploring relationships and mining data with the UCSC Gene Sorter
PMID: 15867434
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
The UCSC repeat browser allows discovery and visualization of evolutionary conflict across repeat families
PMID: 32266012
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Ultrafast Sample Placement on Existing Trees (UShER) Empowers Real-Time Phylogenetics for the SARS-CoV-2 Pandemic
PMID: 33024970
metasource: Fairsharing.org
version: FAIRsharing.org: UCSC Genome Browser database; UCSC Genome Browser database; DOI: https://doi.org/10.25504/FAIRsharing.s22qdj; Last edited: June 30, 2021, 8:33 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://dx.doi.org/10.1093/nar/gkv1275
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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Initial sequencing and analysis of the human genome
PubMed citations: 7134.
7134 articles citing: Initial sequencing and analysis of the human genome
Four novel candidate causal variants for deficient homozygous haplotypes in Holstein cattle. PMID:35361830
Variability in Global DNA Methylation Rate Across Tissues and Over Time in Sheep. PMID:35360841
Significant Upregulation of HERV-K (HML-2) Transcription Levels in Human Lung Cancer and Cancer Cells. PMID:35359739
A beginner's guide to manual curation of transposable elements. PMID:35354491
Rethinking Protein Drug Design with Highly Accurate Structure Prediction of Anti-CRISPR Proteins. PMID:35337108
In Vitro Analysis of Biological Activity of Circulating Cell-Free DNA Isolated from Blood Plasma of Schizophrenic Patients and Healthy Controls. PMID:35328103
An Expanding Toolkit for Heterochromatin Repair Studies. PMID:35328082
IMGT®Homo sapiens IG and TR Loci, Gene Order, CNV and Haplotypes: New Concepts as a Paradigm for Jawed Vertebrates Genome Assemblies. PMID:35327572
Transposable Elements: Major Players in Shaping Genomic and Evolutionary Patterns. PMID:35326499
TrkB Truncated Isoform Receptors as Transducers and Determinants of BDNF Functions. PMID:35321093
Potential role of KRAB-ZFP binding and transcriptional states on DNA methylation of retroelements in human male germ cells. PMID:35315771
Teaching cancer imaging in the era of precision medicine: Looking at the big picture. PMID:35309874
The 103,200-arm acceleration dataset in the UK Biobank revealed a landscape of human sleep phenotypes. PMID:35302893
Short open reading frames (sORFs) and microproteins: an update on their identification and validation measures. PMID:35300685
FDA-led consortium studies advance quality control of targeted next generation sequencing assays for precision oncology. PMID:35282311
MER4 endogenous retrovirus correlated with better efficacy of anti-PD1/PD-L1 therapy in non-small cell lung cancer. PMID:35277462
Principles for the design of multicellular engineered living systems. PMID:35274072
Indicators of Successful Career Transitions from Physical Sciences and Engineering to Biomedical Research. PMID:35273460
Inter-Species Rescue of Mutant Phenotype-The Standard for Genetic Analysis of Human Genetic Disorders in Drosophila melanogaster Model. PMID:35269756
Transposable Elements and Human Diseases: Mechanisms and Implication in the Response to Environmental Pollutants. PMID:35269693
Constitutive Heterochromatin in Eukaryotic Genomes: A Mine of Transposable Elements. PMID:35269383
ALU repeat as potential molecular marker in the detection and prognosis of different cancer types: A systematic review. PMID:35251637
A novel concept of human antiviral protection: It's all about RNA (Review). PMID:35251616
Maelstrom functions in the production of Siwi-piRISC capable of regulating transposons in Bombyx germ cells. PMID:35243263
Transposable element landscapes in aging Drosophila. PMID:35239675
VPipe: an Automated Bioinformatics Platform for Assembly and Management of Viral Next-Generation Sequencing Data. PMID:35234489
Roles of transposable elements in the regulation of mammalian transcription. PMID:35228718
A guide for the diagnosis of rare and undiagnosed disease: beyond the exome. PMID:35220969
The Complexity of the Mammalian Transcriptome. PMID:35220563
Expanding Gene-Editing Potential in Crop Improvement with Pangenomes. PMID:35216392
Characterizing mobile element insertions in 5675 genomes. PMID:35212372
Low Expression of ZNF154 is Related to Poor Prognosis in Gastric Cancer. PMID:35210862
Insights into the Association Between QSER1 and M2 Macrophages and Remarkable Malignancy Characteristics in Hepatocellular Carcinoma. PMID:35210841
To Be or Not to Be Mesophilic, That Is the Question for Aeromonas salmonicida. PMID:35208695
The Ribosomal Protein RpL22 Interacts In Vitro with 5'-UTR Sequences Found in Some Drosophila melanogaster Transposons. PMID:35205350
Splicing Variants, Protein-Protein Interactions, and Drug Targeting in Hutchinson-Gilford Progeria Syndrome and Small Cell Lung Cancer. PMID:35205210
Discordant Genome Assemblies Drastically Alter the Interpretation of Single-Cell RNA Sequencing Data Which Can Be Mitigated by a Novel Integration Method. PMID:35203259
Cryo-EM advances in RNA structure determination. PMID:35197441
[Web-based gene expression analysis-paving the way to decode healthy and diseased ocular tissue]. PMID:35194679
Functional noncoding SNPs in human endothelial cells fine-map vascular trait associations. PMID:35193936
An Alu insertion map of the Indian population: identification and analysis in 1021 genomes of the IndiGen project. PMID:35178516
Particulate matter-induced hypomethylation of Alu and LINE1 in normal human bronchial epithelial cells and epidermal keratinocytes. PMID:35172897
MxB inhibits long interspersed element type 1 retrotransposition. PMID:35171907
Machine learning for multi-omics data integration in cancer. PMID:35169688
The Absence of Retroelement Activity Is Characteristic for Childhood Acute Leukemias and Adult Acute Lymphoblastic Leukemia. PMID:35163677
A Systematic Review of Expression and Immunogenicity of Human Endogenous Retroviral Proteins in Cancer and Discussion of Therapeutic Approaches. PMID:35163254
Polycystic Ovary Syndrome: An Evolutionary Adaptation to Lifestyle and the Environment. PMID:35162359
Disparities in Lung Cancer: miRNA Isoform Characterization in Lung Adenocarcinoma. PMID:35159038
Bitter taste receptors: Genes, evolution and health. PMID:35154779
Genetic variation of pharmacogenomic VIP variants in the Chinese Li population: an updated research. PMID:35146537
Emerging roles of circular RNAs in retinal diseases. PMID:35142661
Analysis of Pathogenic Pseudoexons Reveals Novel Mechanisms Driving Cryptic Splicing. PMID:35140743
Functional Precision Medicine: Putting Drugs on Patient Cancer Cells and Seeing What Happens. PMID:35140175
The mouse resource at National Resource Center for Mutant Mice. PMID:35138443
WAFNRLTG: A Novel Model for Predicting LncRNA Target Genes Based on Weighted Average Fusion Network Representation Learning Method. PMID:35127729
Translational Informatics for Natural Products as Antidepressant Agents. PMID:35127696
Mouse genomic and cellular annotations. PMID:35124726
Exposome and Skin: Part 1. Bibliometric Analysis and Review of the Impact of Exposome Approaches on Dermatology. PMID:35112325
Highly sensitive diagnostic method for colorectal cancer using the ratio of free DNA fragments in serum. PMID:35111495
ATF7ip Targets Transposable Elements for H3K9me3 Deposition to Modify CD8+ T Cell Effector and Memory Responses. PMID:35110421
Genomic deciphering of sex determination and unique immune system of a potential model species rare minnow (Gobiocypris rarus). PMID:35108042
Four groups of type 2 diabetes contribute to the etiological and clinical heterogeneity in newly diagnosed individuals: An IMI DIRECT study. PMID:35106505
LncRNA Tug1 maintains blood-testis barrier integrity by modulating Ccl2 expression in high-fat diet mice. PMID:35103851
Long Noncoding RNA Mediated Regulation in Human Embryogenesis, Pluripotency, and Reproduction. PMID:35103065
Context dependency of nucleotide probabilities and variants in human DNA. PMID:35100973
Analysis of epigenetic features characteristic of L1 loci expressed in human cells. PMID:35100410
Caenorhabditis elegans transposable elements harbor diverse transcription factor DNA-binding sites. PMID:35088854
Shaping the Innate Immune Response Through Post-Transcriptional Regulation of Gene Expression Mediated by RNA-Binding Proteins. PMID:35087521
Exploring clinical implications and role of non-coding RNAs in lung carcinogenesis. PMID:35076850
A simple guide to de novo transcriptome assembly and annotation. PMID:35076693
HERV-W Envelope Triggers Abnormal Dopaminergic Neuron Process through DRD2/PP2A/AKT1/GSK3 for Schizophrenia Risk. PMID:35062349
Endogenous Retroviruses Provide Protection Against Vaginal HSV-2 Disease. PMID:35058919
Third-Generation Sequencing: The Spearhead towards the Radical Transformation of Modern Genomics. PMID:35054423
Molecular Mechanisms in Pentanucleotide Repeat Diseases. PMID:35053321
Recent Advances in RNA Therapy and Its Carriers to Treat the Single-Gene Neurological Disorders. PMID:35052837
Genome-wide perturbations of Alu expression and Alu-associated post-transcriptional regulations distinguish oligodendroglioma from other gliomas. PMID:35042936
Balancing openness with Indigenous data sovereignty: An opportunity to leave no one behind in the journey to sequence all of life. PMID:35042810
Darwinian genomics and diversity in the tree of life. PMID:35042807
Threatened Species Initiative: Empowering conservation action using genomic resources. PMID:35042806
Standards recommendations for the Earth BioGenome Project. PMID:35042802
Why sequence all eukaryotes? PMID:35042801
LINE1 are spliced in non-canonical transcript variants to regulate T cell quiescence and exhaustion. PMID:35039641
Core promoter mutation contributes to abnormal gene expression in bladder cancer. PMID:35033028
GC content of plant genes is linked to past gene duplications. PMID:35025913
Identification of human gene research articles with wrongly identified nucleotide sequences. PMID:35022248
Using synthetic chromosome controls to evaluate the sequencing of difficult regions within the human genome. PMID:35022065
Automated prediction of the clinical impact of structural copy number variations. PMID:35017614
Canonical WNT signaling-dependent gating of MYC requires a noncanonical CTCF function at a distal binding site. PMID:35017527
Mechanism for inverted-repeat recombination induced by a replication fork barrier. PMID:35013185
PBRM1 Inactivation Promotes Upregulation of Human Endogenous Retroviruses in a HIF-Dependent Manner. PMID:35013001
Population-level genome-wide STR discovery and validation for population structure and genetic diversity assessment of Plasmodium species. PMID:35007277
The evolution of knowledge on genes associated with human diseases. PMID:35005554
Cohort Profile: The Alliance for Maternal and Newborn Health Improvement (AMANHI) biobanking study. PMID:34999881
The characteristics of early-stage research into human genes are substantially different from subsequent research. PMID:34990452
Cure and Long-Term Remission Strategies. PMID:34985678
Assessing reproducibility of inherited variants detected with short-read whole genome sequencing. PMID:34980216
Firing up Cold Tumors-Targeting the Epigenetic Machinery to Enhance Cancer Immunotherapy. PMID:34968298
Epigenetic Regulation of the Non-Coding Genome: Opportunities for Immuno-Oncology. PMID:34968293
EZH2 suppresses endogenous retroviruses and an interferon response in cancers. PMID:34966479
Structure, Activity, and Function of SETMAR Protein Lysine Methyltransferase. PMID:34947873
Chromatography-Free Purification Strategies for Large Biological Macromolecular Complexes Involving Fractionated PEG Precipitation and Density Gradients. PMID:34947821
Endogenous Retroviral Elements in Human Development and Central Nervous System Embryonal Tumors. PMID:34945804
Expression of Endogenous Retroviral RNA in Prostate Tumors has Prognostic Value and Shows Differences among Americans of African Versus European/Middle Eastern Ancestry. PMID:34944967
Methylation Markers in Cutaneous Melanoma: Unravelling the Potential Utility of Their Tracking by Liquid Biopsy. PMID:34944843
Reverse Genetic Screen for Deleterious Recessive Variants in the Local Simmental Cattle Population of Switzerland. PMID:34944310
Transgenic Model Systems Have Revolutionized the Study of Disease. PMID:34941457
Long-range promoter-enhancer contacts are conserved during evolution and contribute to gene expression robustness. PMID:34930799
Molecular Diagnostics for Ocular Infectious Diseases: LXXVIII Edward Jackson Memorial Lecture. PMID:34921773
Human endogenous retroviruses (HERV) and non-HERV viruses incorporated into the human genome and their role in the development of autoimmune diseases. PMID:34917914
Mining massive genomic data of two Swiss Braunvieh cattle populations reveals six novel candidate variants that impair reproductive success. PMID:34915862
Gauging the role and impact of drug interactions and repurposing in neurodegenerative disorders. PMID:34909657
The Vista of Application of Specific Anaphylaxis Accurate Diagnosis Based on DNA Single-Nucleotide Methylation Sites. PMID:34908915
Applications and potentials of nanopore sequencing in the (epi)genome and (epi)transcriptome era. PMID:34901902
A Method for Localizing Non-Reference Sequences to the Human Genome. PMID:34890159
Targeted insertion of large genetic payloads using cas directed LINE-1 reverse transcriptase. PMID:34880381
Transcription factor network analysis based on single cell RNA-seq identifies that Trichostatin-a reverses docetaxel resistance in prostate Cancer. PMID:34879849
DNA Profiling in Forensic Science: A Review. PMID:34877570
Human endogenous retroviruses in development and disease. PMID:34849202
Chronic cortisol differentially impacts stem cell-derived astrocytes from major depressive disorder patients. PMID:34848679
Advances in Non-Coding RNA Sequencing. PMID:34842804
DNA sequencing: an overview of solid-state and biological nanopore-based methods. PMID:34840616
From genotype to phenotype: genetics of mammalian long non-coding RNAs in vivo. PMID:34837040
Pathophysiological role of growth differentiation factor 15 (GDF15) in obesity, cancer, and cachexia. PMID:34836750
Stochastic Effects in Retrotransposon Dynamics Revealed by Modeling under Competition for Cellular Resources. PMID:34833085
Diversity-Oriented Synthesis: Amino Acetophenones as Building Blocks for the Synthesis of Natural Product Analogs. PMID:34832909
The Evolutionary Volte-Face of Transposable Elements: From Harmful Jumping Genes to Major Drivers of Genetic Innovation. PMID:34831175
Evidence of G-Protein-Coupled Receptors (GPCR) in the Parasitic Protozoa Plasmodium falciparum-Sensing the Host Environment and Coupling within Its Molecular Signaling Toolkit. PMID:34830263
Role of Non-Coding RNAs in Post-Transcriptional Regulation of Lung Diseases. PMID:34819948
Emerging roles for endogenous retroviruses in immune epigenetic regulation. PMID:34816452
Bringing precision oncology to cellular resolution with single-cell genomics. PMID:34807338
Alu insertion variants alter gene transcript levels. PMID:34799402
Inhibitor of growth protein 3 epigenetically silences endogenous retroviral elements and prevents innate immune activation. PMID:34791430
Cumulative Roles for Epstein-Barr Virus, Human Endogenous Retroviruses, and Human Herpes Virus-6 in Driving an Inflammatory Cascade Underlying MS Pathogenesis. PMID:34790199
Characterization of DNA methylation and promoter activity of long terminal repeat elements of feline endogenous retrovirus RDRS C2a. PMID:34787790
Locus-specific expression of transposable elements in single cells with CELLO-seq. PMID:34782740
Adaptive homeostasis and the p53 isoform network. PMID:34779563
Targeting Phosphatases and Kinases: How to Checkmate Cancer. PMID:34778245
Accurate long-read de novo assembly evaluation with Inspector. PMID:34775997
Mutagenesis of human genomes by endogenous mobile elements on a population scale. PMID:34772701
Histone Modification in NSCLC: Molecular Mechanisms and Therapeutic Targets. PMID:34769131
Recent development of nucleic acid nanosensors to detect sequence-specific binding interactions: From metal ions, small molecules to proteins and pathogens. PMID:34766041
AI applications in functional genomics. PMID:34765093
Computational modeling of RNase, antisense ORF0 RNA, and intracellular compartmentation and their impact on the life cycle of the line retrotransposon. PMID:34765087
Perfect and imperfect views of ultraconserved sequences. PMID:34764456
tsRFun: a comprehensive platform for decoding human tsRNA expression, functions and prognostic value by high-throughput small RNA-Seq and CLIP-Seq data. PMID:34755848
Roles and mechanisms of exosomal non-coding RNAs in human health and diseases. PMID:34753929
The transposable element-rich genome of the cereal pest Sitophilus oryzae. PMID:34749730
Post-transcriptional regulation in spermatogenesis: all RNA pathways lead to healthy sperm. PMID:34748024
The Genomic Organization of the LILR Region Remained Largely Conserved Throughout Primate Evolution: Implications for Health And Disease. PMID:34737739
Non-Coding RNAs in the Etiology and Control of Major and Neglected Human Tropical Diseases. PMID:34737736
'Omics' of suicidal behaviour: A path to personalised psychiatry. PMID:34733641
BST2 Suppresses LINE-1 Retrotransposition by Reducing the Promoter Activity of LINE-1 5' UTR. PMID:34730388
An integrative analysis of genomic and exposomic data for complex traits and phenotypic prediction. PMID:34728654
An expansion of the non-coding genome and its regulatory potential underlies vertebrate neuronal diversity. PMID:34727520
Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci. PMID:34699533
Comparative Analysis of Plasmodium falciparum Genotyping via SNP Detection, Microsatellite Profiling, and Whole-Genome Sequencing. PMID:34694871
Transposable Element Dynamics and Regulation during Zygotic Genome Activation in Mammalian Embryos and Embryonic Stem Cell Model Systems. PMID:34691189
Genetic Regulation of Immunoglobulin G Glycosylation. PMID:34687013
Integration of Epigenetic Mechanisms into Non-Genotoxic Carcinogenicity Hazard Assessment: Focus on DNA Methylation and Histone Modifications. PMID:34681626
Implications of Antigen Selection on T Cell-Based Immunotherapy. PMID:34681217
Factors Regulating the Activity of LINE1 Retrotransposons. PMID:34680956
The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock. PMID:34679854
Embryonic LTR retrotransposons supply promoter modules to somatic tissues. PMID:34675070
Alu RNA and their roles in human disease states. PMID:34672903
Pathogenic tau accelerates aging-associated activation of transposable elements in the mouse central nervous system. PMID:34670118
Comprehensive molecular characterization of lung tumors implicates AKT and MYC signaling in adenocarcinoma to squamous cell transdifferentiation. PMID:34656143
MORC3, a novel MIWI2 association partner, as an epigenetic regulator of piRNA dependent transposon silencing in male germ cells. PMID:34650118
Low-bias ncRNA libraries using ordered two-template relay: Serial template jumping by a modified retroelement reverse transcriptase. PMID:34649994
Complex Transposon Insertion as a Novel Cause of Pompe Disease. PMID:34639227
Phospho-Tau and Chromatin Landscapes in Early and Late Alzheimer's Disease. PMID:34638632
Emerging Functions for snoRNAs and snoRNA-Derived Fragments. PMID:34638533
RNA Therapeutics - Research and Clinical Advancements. PMID:34631795
Genome-wide analysis of DNA methylation in 106 schizophrenia family trios in Han Chinese. PMID:34628353
Telomere-specific chromatin capture using a pyrrole-imidazole polyamide probe for the identification of proteins and non-coding RNAs. PMID:34627342
High-quality reference genome of Fasciola gigantica: Insights into the genomic signatures of transposon-mediated evolution and specific parasitic adaption in tropical regions. PMID:34610021
Regulated splicing of large exons is linked to phase-separation of vertebrate transcription factors. PMID:34605568
Easy and fast PCR-based protocol allows characterization of breakpoints resulting from Alu/Alu-mediated genomic rearrangements. PMID:34596355
Evolutionary genetics and acclimatization in nephrology. PMID:34584272
Androgen-Binding Protein (Abp) Evolutionary History: Has Positive Selection Caused Fixation of Different Paralogs in Different Taxa of the Genus Mus? PMID:34581786
Does the Zinc Finger Antiviral Protein (ZAP) Shape the Evolution of Herpesvirus Genomes? PMID:34578438
Identification of Abundant and Functional dodecaRNAs (doRNAs) Derived from Ribosomal RNA. PMID:34575920
The Sound of Silence: How Silenced Chromatin Orchestrates the Repair of Double-Strand Breaks. PMID:34573397
Topological and Structural Plasticity of the Single Ig Fold and the Double Ig Fold Present in CD19. PMID:34572502
Phosphorylation-Mediated Molecular Pathway Changes in Human Pituitary Neuroendocrine Tumors Identified by Quantitative Phosphoproteomics. PMID:34571875
Bioinformatics and Machine Learning Approaches to Understand the Regulation of Mobile Genetic Elements. PMID:34571773
A broad analysis of splicing regulation in yeast using a large library of synthetic introns. PMID:34570750
Detection of Alu Exonization Events in Human Frontal Cortex From RNA-Seq Data. PMID:34568430
Editorial: Pathogens, Pathobionts, and Autoimmunity. PMID:34567014
The Interplay Among HIV, LINE-1, and the Interferon Signaling System. PMID:34566998
Sex, rurality and socioeconomical status in Spanish centennial population (2017). PMID:34565717
Proteomes Are of Proteoforms: Embracing the Complexity. PMID:34564541
Transposon-triggered innate immune response confers cancer resistance to the blind mole rat. PMID:34556881
Pharmaceutical drug development: high drug prices and the hidden role of public funding. PMID:34554467
The function of twister ribozyme variants in non-LTR retrotransposition in Schistosoma mansoni. PMID:34551436
Data Management and Modeling in Plant Biology. PMID:34539712
Characterization of full-length LINE-1 insertions in 154 genomes. PMID:34534648
International strategy in cancer epidemiology: Japan's involvement in global projects and future role. PMID:34532599
DNA double-strand break repair in cancer: A path to achieving precision medicine. PMID:34507781
Possible Roles of tRNA Fragments, as New Regulatory ncRNAs, in the Pathogenesis of Rheumatoid Arthritis. PMID:34502386
Proximity labeling and other novel mass spectrometric approaches for spatiotemporal protein dynamics. PMID:34496693
Endogenous Feline Leukemia Virus (FeLV) siRNA Transcription May Interfere with Exogenous FeLV Infection. PMID:34495702
A functional genomics pipeline identifies pleiotropy and cross-tissue effects within obesity-associated GWAS loci. PMID:34489471
Psi-Caller: A Lightweight Short Read-Based Variant Caller With High Speed and Accuracy. PMID:34485311
Systematic Comparison of the Performances of De Novo Genome Assemblers for Oxford Nanopore Technology Reads From Piroplasm. PMID:34485177
Shared properties and singularities of exoribonuclease-resistant RNAs in viruses. PMID:34471487
Alpha Satellite Insertion Close to an Ancestral Centromeric Region. PMID:34464971
The Propagation of Racial Disparities in Cardiovascular Genomics Research. PMID:34461749
DNA methyltransferase inhibitors combination therapy for the treatment of solid tumor: mechanism and clinical application. PMID:34452630
Advances in Computational Methodologies for Classification and Sub-Cellular Locality Prediction of Non-Coding RNAs. PMID:34445436
The Role of lncRNA in the Development of Tumors, including Breast Cancer. PMID:34445129
Suggested Absence of Horizontal Transfer of Retrotransposons between Humans and Domestic Mammal Species. PMID:34440397
Transposons-Based Clonal Diversity in Trematode Involves Parts of CR1 (LINE) in Eu- and Heterochromatin. PMID:34440303
The Key Lnc (RNA)s in Cardiac and Skeletal Muscle Development, Regeneration, and Disease. PMID:34436226
An Ancestral Retrovirus Envelope Protein Regulates Persistent Gammaherpesvirus Lifecycles. PMID:34434177
Cohort Profile: The Alliance for Maternal and Newborn Health Improvement (AMANHI) biobanking study. PMID:34426827
Unbiased proteomic mapping of the LINE-1 promoter using CRISPR Cas9. PMID:34425899
Study of lncRNA TPA in Promoting Invasion and Metastasis of Breast Cancer Mediated by TGF-β Signaling Pathway. PMID:34422811
Appropriate Clinical Genetic Testing of Hemochromatosis Type 2-4, Including Ferroportin Disease. PMID:34413666
One-carbon metabolism and global DNA methylation in mothers of individuals with Down syndrome. PMID:34410622
The Oldest Co-opted gag Gene of a Human Endogenous Retrovirus Shows Placenta-Specific Expression and Is Upregulated in Diffuse Large B-Cell Lymphomas. PMID:34410386
A comprehensive analysis of gorilla-specific LINE-1 retrotransposons. PMID:34406591
Segmental duplication as potential biomarkers for non-invasive prenatal testing of aneuploidies. PMID:34391089
A strategy for building and using a human reference pangenome. PMID:34386196
Expression of a human cDNA in moss results in spliced mRNAs and fragmentary protein isoforms. PMID:34385580
DeepG4: A deep learning approach to predict cell-type specific active G-quadruplex regions. PMID:34383754
Exploring tissue architecture using spatial transcriptomics. PMID:34381231
Genome-wide mapping of binding sites of the transposase-derived SETMAR protein in the human genome. PMID:34377368
Viral Suppression of RIPK1-Mediated Signaling. PMID:34372694
JWES: a new pipeline for whole genome/exome sequence data processing, management, and gene-variant discovery, annotation, prediction, and genotyping. PMID:34370400
Application of NGS Technology in Understanding the Pathology of Autoimmune Diseases. PMID:34362117
Signaling Pathways Regulated by UBR Box-Containing E3 Ligases. PMID:34361089
Genomic Mosaicism Formed by Somatic Variation in the Aging and Diseased Brain. PMID:34356087
Transposable elements shape the evolution of mammalian development. PMID:34354263
Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences. PMID:34337360
Current diagnostic approaches to detect two important betacoronaviruses: Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). PMID:34333398
Replication protein A: a multifunctional protein with roles in DNA replication, repair and beyond. PMID:34316690
Haplotypic Associations and Differentiation of MHC Class II Polymorphic Alu Insertions at Five Loci With HLA-DRB1 Alleles in 12 Minority Ethnic Populations in China. PMID:34305999
Role of long interspersed nuclear element-1 in the regulation of chromatin landscapes and genome dynamics. PMID:34304633
Adenosine-to-inosine Alu RNA editing controls the stability of the pro-inflammatory long noncoding RNA NEAT1 in atherosclerotic cardiovascular disease. PMID:34302813
Expanding studies of chromosome structure and function in the era of T2T genomics. PMID:34302168
Activation of Endogenous Retrovirus, Brain Infections and Environmental Insults in Neurodegeneration and Alzheimer's Disease. PMID:34298881
Discovery of genomic variation across a generation. PMID:34296264
New Genes Born-In or Invading Vertebrate Genomes. PMID:34295903
Highly accurate protein structure prediction for the human proteome. PMID:34293799
Perturbed DNA methylation by Gadd45b induces chromatin disorganization, DNA strand breaks and dopaminergic neuron death. PMID:34278264
A pooled CRISPR/AsCpf1 screen using paired gRNAs to induce genomic deletions in Chinese hamster ovary cells. PMID:34277363
Folate Deficiency Triggers the Abnormal Segregation of a Region With Large Cluster of CG-Rich Trinucleotide Repeats on Human Chromosome 2. PMID:34276797
Impact of Genetic Variation in Gene Regulatory Sequences: A Population Genomics Perspective. PMID:34276769
Distinct Retrotransposon Evolution Profile in the Genome of Rabbit (Oryctolagus cuniculus). PMID:34270728
The International Human Genome Project. PMID:34264324
Metagenomics: a path to understanding the gut microbiome. PMID:34259891
Levenshtein Distance, Sequence Comparison and Biological Database Search. PMID:34257466
Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs. PMID:34253730
A direct capture method for purification and detection of viral nucleic acid enables epidemiological surveillance of SARS-CoV-2. PMID:34252764
Markov chain Monte Carlo Gibbs sampler approach for estimating haplotype frequencies among multiple malaria infected human blood samples. PMID:34246273
Global mapping of cancers: The Cancer Genome Atlas and beyond. PMID:34245122
Single-molecule, full-length transcript isoform sequencing reveals disease-associated RNA isoforms in cardiomyocytes. PMID:34244519
Molecular mechanisms of pulmonary carcinogenesis by polycyclic aromatic hydrocarbons (PAHs): Implications for human lung cancer. PMID:34242741
Multiscale modeling of genome organization with maximum entropy optimization. PMID:34241389
Binding patterns of RNA-binding proteins to repeat-derived RNA sequences reveal putative functional RNA elements. PMID:34235430
Differential efficacies of Cas nucleases on microsatellites involved in human disorders and associated off-target mutations. PMID:34233005
Cognate restriction of transposition by piggyBac-like proteins. PMID:34232995
The RNA editing enzyme ADAR2 restricts L1 mobility. PMID:34224323
Nanopore Technology and Its Applications in Gene Sequencing. PMID:34208844
The Structural, Functional and Evolutionary Impact of Transposable Elements in Eukaryotes. PMID:34203645
Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome. PMID:34187812
Evolution of mouse circadian enhancers from transposable elements. PMID:34187518
Expression of Retroelements in Mammalian Gametes and Embryos. PMID:34182464
Lack of relationship between Alu repetitive elements in angiotensin converting enzyme and the severity of diabetic retinopathy. PMID:34177375
Man is a "Rope" Stretched Between Virosphere and Humanoid Robots: On the Urgent Need of an Ethical Code for Ecosystem Survival. PMID:34177285
A perspective on the molecular simulation of DNA from structural and functional aspects. PMID:34168783
Debugging: putting the synthetic yeast chromosome to work. PMID:34168782
Genetics of white color and iridophoroma in "Lemon Frost" leopard geckos. PMID:34166378
Genome-wide binding analysis of 195 DNA binding proteins reveals "reservoir" promoters and human specific SVA-repeat family regulation. PMID:34166368
Unraveling Genome Evolution Throughout Visual Analysis: The XCout Portal. PMID:34163150
Haplotype diversity and sequence heterogeneity of human telomeres. PMID:34162698
Viewing Victor McKusick's legacy through the lens of his bibliography. PMID:34159717
History of the methodology of disease gene identification. PMID:34159713
Endogenous reverse transcriptase and RNase H-mediated antiviral mechanism in embryonic stem cells. PMID:34158624
Mobile element insertions and associated structural variants in longitudinal breast cancer samples. PMID:34158539
Comprehensive identification of transposable element insertions using multiple sequencing technologies. PMID:34158502
Sequence determinants, function, and evolution of CpG islands. PMID:34156435
Hepatocellular adenoma in men: A nationwide assessment of pathology and correlation with clinical course. PMID:34155783
SMARCB1 deletion in atypical teratoid rhabdoid tumors results in human endogenous retrovirus K (HML-2) expression. PMID:34145313
Molecular mechanisms underlying nucleotide repeat expansion disorders. PMID:34140671
Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA. PMID:34140313
Convergent and distributed effects of the 3q29 deletion on the human neural transcriptome. PMID:34131099
Paternal MTHFR deficiency leads to hypomethylation of young retrotransposons and reproductive decline across two successive generations. PMID:34128976
Haplotype Shuffling and Dimorphic Transposable Elements in the Human Extended Major Histocompatibility Complex Class II Region. PMID:34122517
UMIc: A Preprocessing Method for UMI Deduplication and Reads Correction. PMID:34122513
Cas9 targeted enrichment of mobile elements using nanopore sequencing. PMID:34117247
Interphase Chromosomes in Replicative Senescence: Chromosome Positioning as a Senescence Biomarker and the Lack of Nuclear Motor-Driven Chromosome Repositioning in Senescent Cells. PMID:34113611
Specialty Grand Challenge for Molecular Signalling and Pathways in Molecular Neuroscience. PMID:34108865
RNA m6A modification orchestrates a LINE-1-host interaction that facilitates retrotransposition and contributes to long gene vulnerability. PMID:34108665
The pseudogene PRELID1P6 promotes glioma progression via the hnHNPH1-Akt/mTOR axis. PMID:34108621
The derepression of transposable elements in lung cells is associated with the inflammatory response and gene activation in idiopathic pulmonary fibrosis. PMID:34108012
LINE-1 transcription in round spermatids is associated with accretion of 5-carboxylcytosine in their open reading frames. PMID:34099857
Sequencing and comparative genome analysis of three Indians. PMID:34086082
The Rhox gene cluster suppresses germline LINE1 transposition. PMID:34083437
Losing DNA methylation at repetitive elements and breaking bad. PMID:34082816
Genetics, its role in preventing the pandemic of coronary artery disease. PMID:34080689
Infection by Diverse HIV-1 Subtypes Leads to Different Elevations in HERV-K Transcriptional Levels in Human T Cell Lines. PMID:34079529
Human Endogenous Retrovirus as Therapeutic Targets in Neurologic Disease. PMID:34073730
Alternate Roles of Sox Transcription Factors beyond Transcription Initiation. PMID:34073089
Triazole-Modified Nucleic Acids for the Application in Bioorganic and Medicinal Chemistry. PMID:34073038
THAP9 Transposase Cleaves DNA via Conserved Acidic Residues in an RNaseH-Like Domain. PMID:34072453
Malaria in the 'Omics Era'. PMID:34070769
Widespread Exaptation of L1 Transposons for Transcription Factor Binding in Breast Cancer. PMID:34070697
Implementing Pharmacogenomics Testing: Single Center Experience at Arkansas Children's Hospital. PMID:34064668
Proteomics, Personalized Medicine and Cancer. PMID:34063807
Ancient Adversary - HERV-K (HML-2) in Cancer. PMID:34055625
IgG and IgA autoantibodies against L1 ORF1p expressed in granulocytes correlate with granulocyte consumption and disease activity in pediatric systemic lupus erythematosus. PMID:34051843
Emerging Classes of Small Non-Coding RNAs With Potential Implications in Diabetes and Associated Metabolic Disorders. PMID:34040585
Genetic effects on liver chromatin accessibility identify disease regulatory variants. PMID:34038741
Multiomic Big Data Analysis Challenges: Increasing Confidence in the Interpretation of Artificial Intelligence Assessments. PMID:34029068
Overexpression of Endogenous Retroviruses and Malignancy Markers in Neuroblastoma Cell Lines by Medium-Induced Microenvironmental Changes. PMID:34026614
Organ-, sex- and age-dependent patterns of endogenous L1 mRNA expression at a single locus resolution. PMID:34023901
The Worldwide Invasion of Drosophila suzukii Is Accompanied by a Large Increase of Transposable Element Load and a Small Number of Putatively Adaptive Insertions. PMID:34021759
Common DNA methylation dynamics in endometriod adenocarcinoma and glioblastoma suggest universal epigenomic alterations in tumorigenesis. PMID:34021236
Chromatin-associated MRN complex protects highly transcribing genes from genomic instability. PMID:34020942
Antibodies against human endogenous retrovirus K102 envelope activate neutrophils in systemic lupus erythematosus. PMID:34019642
Structural analysis of the SRP Alu domain from Plasmodium falciparum reveals a non-canonical open conformation. PMID:34017052
Placental outcomes of phthalate exposure. PMID:34015474
Roles of long non‑coding RNA in osteoarthritis (Review). PMID:34013375
MIR-NATs repress MAPT translation and aid proteostasis in neurodegeneration. PMID:34012113
Unique evolutionary trajectories of breast cancers with distinct genomic and spatial heterogeneity. PMID:34011996
Transcriptome Analyses Implicate Endogenous Retroviruses Involved in the Host Antiviral Immune System through the Interferon Pathway. PMID:34009516
In vivo discovery of RNA proximal proteins via proximity-dependent biotinylation. PMID:34006179
Analysis of Genomic DNA from Medieval Plague Victims Suggests Long-Term Effect of Yersinia pestis on Human Immunity Genes. PMID:34002224
Identification of Differentially Expressed Human Endogenous Retrovirus Families in Human Leukemia and Lymphoma Cell Lines and Stem Cells. PMID:33996550
Enabling Genomics Pipelines in Commodity Personal Computers With Flash Storage. PMID:33995473
DoChaP: the domain change presenter. PMID:33988713
Dissecting polygenic signals from genome-wide association studies on human behaviour. PMID:33986517
Evolution of default genetic control mechanisms. PMID:33984070
High throughput quantification of short nucleic acid samples by capillary electrophoresis with automated data processing. PMID:33979658
Overexpression of ZNF460 predicts worse survival and promotes metastasis through JAK2/STAT3 signaling pathway in patient with colon cancer. PMID:33976729
The Transposable Element Environment of Human Genes Differs According to Their Duplication Status and Essentiality. PMID:33973013
Endogenous retroviruses in the origins and treatment of cancer. PMID:33971937
A Population-Specific Major Allele Reference Genome From The United Arab Emirates Population. PMID:33968136
Toward Genome-Based Selection in Asian Seabass: What Can We Learn From Other Food Fishes and Farm Animals? PMID:33968125
A Human Endogenous Bornavirus-Like Nucleoprotein Encodes a Mitochondrial Protein Associated with Cell Viability. PMID:33952640
Genomic Tackling of Human Satellite DNA: Breaking Barriers through Time. PMID:33946766
Adhesion GPR123 is an indicator for recurrence and prognosis in bladder cancer. PMID:33945147
Targeting DDX3X Triggers Antitumor Immunity via a dsRNA-Mediated Tumor-Intrinsic Type I Interferon Response. PMID:33941613
The genomic history of the Aegean palatial civilizations. PMID:33930288
The Need for a Human Pangenome Reference Sequence. PMID:33929893
The Startling Role of Mismatch Repair in Trinucleotide Repeat Expansions. PMID:33925919
The "Genomic Code": DNA Pervasively Moulds Chromatin Structures Leaving no Room for "Junk". PMID:33924668
Genetic Diversity and Population Structures in Chinese Miniature Pigs Revealed by SINE Retrotransposon Insertion Polymorphisms, a New Type of Genetic Markers. PMID:33921134
In Vivo and In Vitro Assays Evaluating the Biological Activity of Taurine, Glucose and Energetic Beverages. PMID:33920365
The Involvement of Long Non-Coding RNAs in Bone. PMID:33920083
Sequence, Chromatin and Evolution of Satellite DNA. PMID:33919233
Human Endogenous Retroviruses in Glioblastoma Multiforme. PMID:33917421
Behind the Scenes of the Human Breast Cell Atlas Project. PMID:33914224
Towards complete and error-free genome assemblies of all vertebrate species. PMID:33911273
Chromosome-scale assembly and analysis of biomass crop Miscanthus lutarioriparius genome. PMID:33911077
Virus-derived variation in diverse human genomes. PMID:33901175
MicroRNAs as theranostic markers in cardiac allograft transplantation: from murine models to clinical practice. PMID:33897899
Sensing of transposable elements by the antiviral innate immune system. PMID:33888553
Evolution of genetic networks for human creativity. PMID:33879864
Advances in epigenetic therapeutics with focus on solid tumors. PMID:33879235
FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences. PMID:33879057
Hepatitis C virus infection restricts human LINE-1 retrotransposition in hepatoma cells. PMID:33872335
Sequence deeper without sequencing more: Bayesian resolution of ambiguously mapped reads. PMID:33872311
Unearthing LTR Retrotransposon gag Genes Co-opted in the Deep Evolution of Eukaryotes. PMID:33871607
Androgen Receptor-Related Non-coding RNAs in Prostate Cancer. PMID:33869227
Role of DNA Methylation in Mediating Genetic Risk of Psychiatric Disorders. PMID:33868039
A total of 219 metagenome-assembled genomes of microorganisms from Icelandic marine waters. PMID:33859876
HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy. PMID:33858848
Mechanisms of enhancer action: the known and the unknown. PMID:33858480
Immunotherapy-induced antibodies to endogenous retroviral envelope glycoprotein confer tumor protection in mice. PMID:33857179
Integration of Transformative Platforms for the Discovery of Causative Genes in Cardiovascular Diseases. PMID:33856594
Integrated transcription factor profiling with transcriptome analysis identifies L1PA2 transposons as global regulatory modulators in a breast cancer model. PMID:33850167
Computational prediction of potential siRNA and human miRNA sequences to silence orf1ab associated genes for future therapeutics against SARS-CoV-2. PMID:33846694
DNA methylation patterns expose variations in enhancer-chromatin modifications during embryonic stem cell differentiation. PMID:33844685
Horizons in Veterinary Precision Oncology: Fundamentals of Cancer Genomics and Applications of Liquid Biopsy for the Detection, Characterization, and Management of Cancer in Dogs. PMID:33834049
Silencing of LINE-1 retrotransposons is a selective dependency of myeloid leukemia. PMID:33833453
A study of transposable element-associated structural variations (TASVs) using a de novo-assembled Korean genome. PMID:33833373
GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data. PMID:33830196
The structure, function and evolution of a complete human chromosome 8. PMID:33828295
A ride through the epigenetic landscape: aging reversal by reprogramming. PMID:33825176
PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads. PMID:33823910
Low Diversity of Human Variation Despite Mostly Mild Functional Impact of De Novo Variants. PMID:33816556
DEEPGENTM-A Novel Variant Calling Assay for Low Frequency Variants. PMID:33808158
Downfalls of Chemical Probes Acting at the Kinase ATP-Site: CK2 as a Case Study. PMID:33807474
Construction of Whole Genomes from Scaffolds Using Single Cell Strand-Seq Data. PMID:33807210
Non-Coding RNAs in Cancer Diagnosis and Therapy: Focus on Lung Cancer. PMID:33803619
How Chaotic Is Genome Chaos? PMID:33802828
Viroids and the Origin of Life. PMID:33800543
Flowering and Seed Production across the Lemnaceae. PMID:33800476
Palindromes in DNA-A Risk for Genome Stability and Implications in Cancer. PMID:33799581
The Impact of Modern Technologies on Molecular Diagnostic Success Rates, with a Focus on Inherited Retinal Dystrophy and Hearing Loss. PMID:33799353
The next horizon in precision oncology: Proteogenomics to inform cancer diagnosis and treatment. PMID:33798439
Variable number tandem repeats - Their emerging role in sickness and health. PMID:33794697
Pervasive cis effects of variation in copy number of large tandem repeats on local DNA methylation and gene expression. PMID:33794196
Large vs small genomes in Passiflora: the influence of the mobilome and the satellitome. PMID:33792791
Alternative splicing of lncRNAs in human diseases. PMID:33791145
Diversity of short interspersed nuclear elements (SINEs) in lepidopteran insects and evidence of horizontal SINE transfer between baculovirus and lepidopteran hosts. PMID:33789582
X-ray Ptychography Imaging of Human Chromosomes After Low-dose Irradiation. PMID:33786705
Genetic Risk Stratification: A Paradigm Shift in Prevention of Coronary Artery Disease. PMID:33778213
Opportunities and challenges of artificial intelligence in the medical field: current application, emerging problems, and problem-solving strategies. PMID:33771068
The evolution of patient-specific precision biomarkers to guide personalized heart-transplant care. PMID:33768160
Mechanisms of Action of Hypomethylating Agents: Endogenous Retroelements at the Epicenter. PMID:33768008
Efficacy and long-term safety of CRISPR/Cas9 genome editing in the SOD1-linked mouse models of ALS. PMID:33767386
Consequences for Pancreatic β-Cell Identity and Function of Unregulated Transcript Processing. PMID:33763030
Noncanonical immune response to the inhibition of DNA methylation by Staufen1 via stabilization of endogenous retrovirus RNAs. PMID:33762305
G-quadruplexes originating from evolutionary conserved L1 elements interfere with neuronal gene expression in Alzheimer's disease. PMID:33758195
Dissecting the transcriptome in cardiovascular disease. PMID:33757121
The functional impact of nuclear reorganization in cellular senescence. PMID:33755107
Evolutionary conservation of RNA sequence and structure. PMID:33754485
Identification of 11 candidate structured noncoding RNA motifs in humans by comparative genomics. PMID:33750298
Advancing drug discovery using the power of the human genome. PMID:33748968
Short and long-read genome sequencing methodologies for somatic variant detection; genomic analysis of a patient with diffuse large B-cell lymphoma. PMID:33742045
Exosomal Long Non-coding RNAs: Emerging Players in the Tumor Microenvironment. PMID:33738133
Genomic regions associated with microdeletion/microduplication syndromes exhibit extreme diversity of structural variation. PMID:33724415
Pinpointing the PRDM9-PRDM7 Gene Duplication Event During Primate Divergence. PMID:33719332
Reconsidering LINE-1's role in cancer: does LINE-1 function as a reporter detecting early cancer-associated epigenetic signatures? PMID:33717489
Aptardi predicts polyadenylation sites in sample-specific transcriptomes using high-throughput RNA sequencing and DNA sequence. PMID:33712618
Assessing the contribution of tumor mutational phenotypes to cancer progression risk. PMID:33711014
From the discovery of DNA to current tools for DNA editing. PMID:33710258
Retroviral Elements in Human Evolution and Neural Development. PMID:33693440
Interrogating lncRNA functions via CRISPR/Cas systems. PMID:33685382
Localization of RNAs in the nucleus: cis- and trans- regulation. PMID:33682620
Altered DNA repair creates novel Alu/Alu repeat-mediated deletions. PMID:33675284
Identification of Germline Genetic Variants that Increase Prostate Cancer Risk and Influence Development of Aggressive Disease. PMID:33673083
Meta-Analysis of Gene Popularity: Less Than Half of Gene Citations Stem from Gene Regulatory Networks. PMID:33672419
Transposable Elements and Stress in Vertebrates: An Overview. PMID:33671215
Implications of Endogenous Retroelements in the Etiopathogenesis of Systemic Lupus Erythematosus. PMID:33669709
Genetic Mechanisms Underlying Cortical Evolution in Mammals. PMID:33659245
Structural variant detection in cancer genomes: computational challenges and perspectives for precision oncology. PMID:33654267
An update of KAIKObase, the silkworm genome database. PMID:33645624
From Genome-Wide to Environment-Wide: Capturing the Environome. PMID:33645332
A Mechanism Leading to Changes in Copy Number Variations Affected by Transcriptional Level Might Be Involved in Evolution, Embryonic Development, Senescence, and Oncogenesis Mediated by Retrotransposons. PMID:33644055
Gene Size Matters: An Analysis of Gene Length in the Human Genome. PMID:33643374
VISTA: A Target to Manage the Innate Cytokine Storm. PMID:33643285
Methylation status and long-fragment cell-free DNA are prognostic biomarkers for gastric cancer. PMID:33641249
Haplotype-resolved diverse human genomes and integrated analysis of structural variation. PMID:33632895
Epigenetics of cutaneous T-cell lymphoma: biomarkers and therapeutic potentials. PMID:33628583
Closing in on a complete human genome. PMID:33619406
Elucidation of Epigenetic Landscape in Coronary Artery Disease: A Review on Basic Concept to Personalized Medicine. PMID:33598635
The Impact of Purifying and Background Selection on the Inference of Population History: Problems and Prospects. PMID:33591322
SNPC-1.3 is a sex-specific transcription factor that drives male piRNA expression in C. elegans. PMID:33587037
SARS-CoV-2 Proteins Exploit Host's Genetic and Epigenetic Mediators for the Annexation of Key Host Signaling Pathways. PMID:33585554
Mammalian Germ Cell Development: From Mechanism to In Vitro Reconstitution. PMID:33577794
Fatal perinatal mitochondrial cardiac failure caused by recurrent de novo duplications in the ATAD3 locus. PMID:33575671
A random forest-based framework for genotyping and accuracy assessment of copy number variations. PMID:33575619
Benchmark study comparing liftover tools for genome conversion of epigenome sequencing data. PMID:33575605
Five Circular RNAs in Metabolism Pathways Related to Prostate Cancer. PMID:33574834
Sense-oriented AluYRa1 elements provide a lineage-specific transcription environment for polyadenylation. PMID:33574427
Early life stress during the neonatal period alters social play and Line1 during the juvenile stage of development. PMID:33574362
LAMA: automated image analysis for the developmental phenotyping of mouse embryos. PMID:33574040
Systemic Lupus Erythematosus in Children and Young People. PMID:33569643
The broken promise that undermines human genome research. PMID:33568833
How the human genome transformed study of rare diseases. PMID:33568830
A wealth of discovery built on the Human Genome Project - by the numbers. PMID:33568828
From one human genome to a complex tapestry of ancestry. PMID:33568827
Breaking through the unknowns of the human reference genome. PMID:33568817
The Cancer Genome: Paradigm or Paradox? PMID:33567511
A mesoscopic simulator to uncover heterogeneity and evolutionary dynamics in tumors. PMID:33566821
L1 retrotransposons exploit RNA m6A modification as an evolutionary driving force. PMID:33563981
Evolution of genome structure in the Drosophila simulans species complex. PMID:33563718
RIP-seq reveals LINE-1 ORF1p association with p-body enriched mRNAs. PMID:33563338
Role of Transposable Elements in Gene Regulation in the Human Genome. PMID:33557056
Human endogenous retroviruses in cancer: Expression, regulation and function. PMID:33552242
Sea Urchin as a Universal Model for Studies of Gene Networks. PMID:33552139
Genomic Variation, Evolvability, and the Paradox of Mental Illness. PMID:33551865
Invasive and Noninvasive Nonfunctioning Gonadotroph Pituitary Tumors Differ in DNA Methylation Level of LINE-1 Repetitive Elements. PMID:33546126
Potential APOBEC-mediated RNA editing of the genomes of SARS-CoV-2 and other coronaviruses and its impact on their longer term evolution. PMID:33545556
Evolutionary dynamics of transposable elements in bdelloid rotifers. PMID:33543711
Complicated legacies: The human genome at 20. PMID:33542123
Creating artificial human genomes using generative neural networks. PMID:33539374
Benchmarking of next and third generation sequencing technologies and their associated algorithms for de novo genome assembly. PMID:33537807
Methods for Proteogenomics Data Analysis, Challenges, and Scalability Bottlenecks: A Survey. PMID:33537181
BRCA1 and RNAi factors promote repair mediated by small RNAs and PALB2-RAD52. PMID:33536619
Circular RNA circPIKfyve acts as a sponge of miR-21-3p to enhance antiviral immunity through regulating MAVS in teleost fish. PMID:33536171
Impact of short-read sequencing on the misassembly of a plant genome. PMID:33530937
Targeted next-generation sequencing-based detection of microsatellite instability in colorectal carcinomas. PMID:33524032
Homotypic clustering of L1 and B1/Alu repeats compartmentalizes the 3D genome. PMID:33514913
Noncanonical open reading frames encode functional proteins essential for cancer cell survival. PMID:33510483
tsRNAs: Novel small molecules from cell function and regulatory mechanism to therapeutic targets. PMID:33507586
Sensitive and specific multi-cancer detection and localization using methylation signatures in cell-free DNA. PMID:33506766
Complete sequences of Schizosaccharomyces pombe subtelomeres reveal multiple patterns of genome variation. PMID:33504776
The impact of purifying and background selection on the inference of population history: problems and prospects. PMID:33501439
The search for RNA-binding proteins: a technical and interdisciplinary challenge. PMID:33492363
Genomic Study of COVID-19 Corona Virus Excludes Its Origin from Recombination or Characterized Biological Sources and Suggests a Role for HERVS in Its Wide Range Symptoms. PMID:33487779
Intercellular Communication in the Nervous System Goes Viral. PMID:33485691
Machine learning as the new approach in understanding biomarkers of suicidal behavior. PMID:33485296
Estimating the accuracy of pharmacophore-based detection of cognate receptor-ligand pairs in the immunoglobulin superfamily. PMID:33483991
A comprehensive microsatellite landscape of human Y-DNA at kilobase resolution. PMID:33482734
Control of LINE-1 Expression Maintains Genome Integrity in Germline and Early Embryo Development. PMID:33481218
Epigenetic and non-coding regulation of alcohol abuse and addiction. PMID:33461665
The Texas Society of Pathologists: molded by the legacy of pathology and focused on excellence in medicine for 100 years and beyond. PMID:33456200
50th anniversary of the discovery of reverse transcriptase. PMID:33448895
Recognize Yourself-Innate Sensing of Non-LTR Retrotransposons. PMID:33445593
A Highly Conserved Circular RNA circRasGEF1B Enhances Antiviral Immunity by Regulating miR-21-3p/MITA Pathway in Lower Vertebrates. PMID:33441345
Genome diversity in Ukraine. PMID:33438729
The Dfam community resource of transposable element families, sequence models, and genome annotations. PMID:33436076
Multiple Alu Exonization in 3'UTR of a Primate-Specific Isoform of CYP20A1 Creates a Potential miRNA Sponge. PMID:33434274
Construction and integration of three de novo Japanese human genome assemblies toward a population-specific reference. PMID:33431880
Half a century of the reverse transcriptase-happy birthday! PMID:33430901
Transcriptome of nasopharyngeal samples from COVID-19 patients and a comparative analysis with other SARS-CoV-2 infection models reveal disparate host responses against SARS-CoV-2. PMID:33413422
Transposable element-derived sequences in vertebrate development. PMID:33407840
Signature changes in the expressions of protein-coding genes, lncRNAs, and repeat elements in early and late cellular senescence. PMID:33402863
TFs for TEs: the transcription factor repertoire of mammalian transposable elements. PMID:33397727
Expression profiles, biological functions and clinical significance of circRNAs in bladder cancer. PMID:33397425
Probably Correct: Rescuing Repeats with Short and Long Reads. PMID:33396198
Alu retrotransposons and COVID-19 susceptibility and morbidity. PMID:33390179
Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks. PMID:33384856
Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data. PMID:33355230
Integrative Analysis of Gene-Specific DNA Methylation and Untargeted Metabolomics Data from the ELEMENT Cohort. PMID:33354655
Gene regulation by long non-coding RNAs and its biological functions. PMID:33353982
Adaptive evolution of an essential telomere protein restricts telomeric retrotransposons. PMID:33350936
Factors that mold the nuclear landscape of HIV-1 integration. PMID:33337475
Effects of activation of the LINE-1 antisense promoter on the growth of cultured cells. PMID:33335226
Use of Genomic Information in Health Impact Assessment is Yet to Come: A Systematic Review. PMID:33334033
Involvement of DNA Repair Genes and System of Radiation-Induced Activation of Transposons in Formation of Transgenerational Effects. PMID:33329741
Antifreeze protein dispersion in eelpouts and related fishes reveals migration and climate alteration within the last 20 Ma. PMID:33320906
GAS5 regulates diabetic cardiomyopathy via miR‑221‑3p/p27 axis‑associated autophagy. PMID:33313941
Pioneer-like factor GAF cooperates with PBAP (SWI/SNF) and NURF (ISWI) to regulate transcription. PMID:33303640
Identification of Long Noncoding RNA Biomarkers for Hepatocellular Carcinoma Using Single-Sample Networks. PMID:33299877
Genotyping of Francisella tularensis subsp. holarctica from Hares in Germany. PMID:33291395
NGS-based identification and tracing of microsatellite instability from minute amounts DNA using inter-Alu-PCR. PMID:33290560
Accurate assembly of the olive baboon (Papio anubis) genome using long-read and Hi-C data. PMID:33283855
How Retroviruses and Retrotransposons in Our Genome May Contribute to Autoimmunity in Rheumatological Conditions. PMID:33281822
Epigenetic Alterations in the Gastrointestinal Tract: Current and Emerging Use for Biomarkers of Cancer. PMID:33279516
Striking heterogeneity of somatic L1 retrotransposition in single normal and cancerous gastrointestinal cells. PMID:33277430
Building genomes to understand biology. PMID:33268788
A novel computational model for predicting potential LncRNA-disease associations based on both direct and indirect features of LncRNA-disease pairs. PMID:33267800
Deep Learning in LncRNAome: Contribution, Challenges, and Perspectives. PMID:33266128
The Role of APOBECs in Viral Replication. PMID:33266042
Developmental differences in genome replication program and origin activation. PMID:33264404
FTH1 Pseudogenes in Cancer and Cell Metabolism. PMID:33260500
'There and Back Again'-Forward Genetics and Reverse Phenotyping in Pulmonary Arterial Hypertension. PMID:33256119
Evaluating the Genomic Parameters Governing rAAV-Mediated Homologous Recombination. PMID:33248247
Evaluation of the upper airway microbiome and immune response with nasal epithelial lining fluid absorption and nasal washes. PMID:33244064
CircRNAs open a new era in the study of cardiovascular disease (Review). PMID:33236162
Challenges of Precision Medicine for Atherosclerotic Cardiovascular Disease Based on Human Genome Information. PMID:33229815
Identification of the novel Np17 oncogene in human leukemia. PMID:33226963
Perversely expressed long noncoding RNAs can alter host response and viral proliferation in SARS-CoV-2 infection. PMID:33224264
Identification of high-copy number long terminal repeat retrotransposons and their expansion in Phalaenopsis orchids. PMID:33213366
Structure of the Receptor Binding Domain of EnvP(b)1, an Endogenous Retroviral Envelope Protein Expressed in Human Tissues. PMID:33203760
LC-N2G: a local consistency approach for nutrigenomics data analysis. PMID:33203358
Human Endogenous Retrovirus K Rec forms a Regulatory Loop with MITF that Opposes the Progression of Melanoma to an Invasive Stage. PMID:33202765
Hotspots of Human Mutation. PMID:33199048
Structural Mimicry Drives HIV-1 Rev-Mediated HERV-K Expression. PMID:33197463
Exploring the changing geographical pattern of international scientific collaborations through the prism of cities. PMID:33196668
Endoplasmic Reticulum Associated Protein Degradation (ERAD) in the Pathology of Diseases Related to TGFβ Signaling Pathway: Future Therapeutic Perspectives. PMID:33195419
Establishment of Quantitative PCR Assays for Active Long Interspersed Nuclear Element-1 Subfamilies in Mice and Applications to the Analysis of Aging-Associated Retrotransposition. PMID:33193604
GenomeChronicler: The Personal Genome Project UK Genomic Report Generator Pipeline. PMID:33193602
The Role of DNA Methylation in Ischemic Stroke: A Systematic Review. PMID:33193003
E3 Ubiquitin Ligases in Neurological Diseases: Focus on Gigaxonin and Autophagy. PMID:33192535
High levels of LINE-1 transposable elements expressed in Kaposi's sarcoma-associated herpesvirus-related primary effusion lymphoma. PMID:33188297
Frequency and methylation status of selected retrotransposition competent L1 loci in amyotrophic lateral sclerosis. PMID:33187550
A SINE-VNTR-Alu in the LRIG2 Promoter Is Associated with Gene Expression at the Locus. PMID:33187279
The tumor suppressor microRNA let-7 inhibits human LINE-1 retrotransposition. PMID:33177501
Lung transcriptome of a COVID-19 patient and systems biology predictions suggest impaired surfactant production which may be druggable by surfactant therapy. PMID:33173052
LINE-1 retrotransposon methylation in chorionic villi of first trimester miscarriages with aneuploidy. PMID:33170392
Modes of genetic adaptations underlying functional innovations in the rumen. PMID:33165812
Using Drosophila melanogaster To Discover Human Disease Genes: An Educational Primer for Use with "Amyotrophic Lateral Sclerosis Modifiers in Drosophila Reveal the Phospholipase D Pathway as a Potential Therapeutic Target". PMID:33158986
Clinical Interpretation and Management of Genetic Variants. PMID:33145465
Ensembl 2021. PMID:33137190
Effects of zinc finger protein 403 on the proliferation, migration and invasion abilities of prostate cancer cells. PMID:33125130
Identification of bona fide B2 SINE retrotransposon transcription through single-nucleus RNA-seq of the mouse hippocampus. PMID:33122305
Strategic vision for improving human health at The Forefront of Genomics. PMID:33116284
Raw transcriptomics data to gene specific SSRs: a validated free bioinformatics workflow for biologists. PMID:33106560
Comprehensive Transcriptome Profiling of Dairy Goat Mammary Gland Identifies Genes and Networks Crucial for Lactation and Fatty Acid Metabolism. PMID:33101357
Genomic and Transcriptomic Analyses of Bioluminescence Genes in the Enope Squid Watasenia scintillans. PMID:33098466
Beyond the RNA-dependent function of LncRNA genes. PMID:33095159
Genome streamlining in a minute herbivore that manipulates its host plant. PMID:33095158
Twenty Years Later: A Comprehensive Review of the X Chromosome Use in Forensic Genetics. PMID:33093840
A Journey through Genetic Architecture and Predisposition of Coronary Artery Disease. PMID:33093801
Genetic Aspects in Shoulder Disorders. PMID:33093716
Endogenous retroviruses drive KRAB zinc-finger protein family expression for tumor suppression. PMID:33087347
Intrinsic DNA topology as a prioritization metric in genomic fine-mapping studies. PMID:33084892
Evolutionary History of Alpha Satellite DNA Repeats Dispersed within Human Genome Euchromatin. PMID:33078196
Next Generation Sequencing Based Forward Genetic Approaches for Identification and Mapping of Causal Mutations in Crop Plants: A Comprehensive Review. PMID:33066352
An Intronic Alu Element Attenuates the Transcription of a Long Non-coding RNA in Human Cell Lines. PMID:33061937
p53 directly represses human LINE1 transposons. PMID:33060137
Whole genome sequencing data of multiple individuals of Pakistani descent. PMID:33051442
RNA editing in mesothelioma: a look forward. PMID:33050791
The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome. PMID:33021634
Posttranscriptional regulation of human endogenous retroviruses by RNA-binding motif protein 4, RBM4. PMID:33020268
New Aspects of the Epigenetics of Pancreatic Carcinogenesis. PMID:33014438
Variants of significance: medical genetics and surgical outcomes in congenital heart disease. PMID:33009125
Immunological Features with DNA Microsatellite Alterations in Patients with Colorectal Cancer. PMID:33000102
Genetic variant effects on gene expression in human pancreatic islets and their implications for T2D. PMID:32999275
RNA-cDNA hybrids mediate transposition via different mechanisms. PMID:32994470
Reconstruction of lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveals functional lncRNAs in skin cutaneous melanoma. PMID:32993558
Host Gene Regulation by Transposable Elements: The New, the Old and the Ugly. PMID:32993145
tRNA-Derived Small RNAs: Novel Epigenetic Regulators. PMID:32992597
Tissue-specific usage of transposable element-derived promoters in mouse development. PMID:32988383
The Role of Micro-RNAs and Circulating Tumor Markers as Predictors of Response to Neoadjuvant Therapy in Locally Advanced Rectal Cancer. PMID:32987896
A Model-Driven Quantitative Analysis of Retrotransposon Distributions in the Human Genome. PMID:32986810
Transposon expression in the Drosophila brain is driven by neighboring genes and diversifies the neural transcriptome. PMID:32973040
Non-Coding RNAs, a Novel Paradigm for the Management of Gastrointestinal Stromal Tumors. PMID:32972022
Connecting the Missing Dots: ncRNAs as Critical Regulators of Therapeutic Susceptibility in Breast Cancer. PMID:32967267
Prioritizing sequence variants in conserved non-coding elements in the chicken genome using chCADD. PMID:32966296
Transposon clusters as substrates for aberrant splice-site activation. PMID:32965162
Comprehensive genomic analysis reveals dynamic evolution of endogenous retroviruses that code for retroviral-like protein domains. PMID:32963593
Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing. PMID:32962098
Predicting Response to Immunotherapy in Metastatic Renal Cell Carcinoma. PMID:32961934
A multi-omics approach to solving problems in plant disease ecology. PMID:32960892
Analysis, identification and visualization of subgroups in genomics. PMID:32954413
Intronic regions of the human coagulation factor VIII gene harboring transcription factor binding sites with a strong bias towards the short-interspersed elements. PMID:32944665
Nucleotide sequencing of the HoxA gene cluster using Gorilla fosmid clones. PMID:32934753
ZBED1/DREF: A transcription factor that regulates cell proliferation. PMID:32934705
Immune activation by a multigene family of lectins with variable tandem repeats in oriental river prawn (Macrobrachium nipponense). PMID:32931720
Mouse tumor susceptibility genes identify drug combinations for multiple myeloma. PMID:32923678
Block and Lock HIV Cure Strategies to Control the Latent Reservoir. PMID:32923412
TIP_finder: An HPC Software to Detect Transposable Element Insertion Polymorphisms in Large Genomic Datasets. PMID:32917036
Mosaicism in Human Health and Disease. PMID:32916079
At the dawn of the transcriptomic medicine. PMID:32915637
Chromonomer: A Tool Set for Repairing and Enhancing Assembled Genomes Through Integration of Genetic Maps and Conserved Synteny. PMID:32912931
Differences between human and chimpanzee genomes and their implications in gene expression, protein functions and biochemical properties of the two species. PMID:32912141
Proteomic Analysis of Human Endometrial Tissues Reveals the Roles of PI3K/AKT/mTOR Pathway and Tumor Angiogenesis Molecules in the Pathogenesis of Endometrial Cancer. PMID:32908897
Evaluation of Plasma Circulating Cell Free DNA Concentration and Integrity in Patients with Prostate Cancer in Jamaica: A Preliminary Study. PMID:32906694
Next-Generation Sequencing at High Sequencing Depth as a Tool to Study the Evolution of Metastasis Driven by Genetic Change Events of Lung Squamous Cell Carcinoma. PMID:32903616
Use of an Exposome Approach to Understand the Effects of Exposures From the Natural, Built, and Social Environments on Cardio-Vascular Disease Onset, Progression, and Outcomes. PMID:32903514
An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice. PMID:32899740
Endogenous retroviruses drive species-specific germline transcriptomes in mammals. PMID:32895553
Aberrant Methylation of LINE-1 Transposable Elements: A Search for Cancer Biomarkers. PMID:32887319
Yersinia pestis strains from Latvia show depletion of the pla virulence gene at the end of the second plague pandemic. PMID:32884081
Replication stress at microsatellites causes DNA double-strand breaks and break-induced replication. PMID:32873711
Reverse Transcriptase Affects Gametogenesis and Preimplantation Development in Mouse. PMID:32871749
Characterization and Localization of Calb2 in Both the Testis and Ovary of the Japanese Flounder (Paralichthys olivaceus). PMID:32858799
Lamivudine Inhibits Alu RNA-induced Retinal Pigment Epithelium Degeneration via Anti-inflammatory and Anti-senescence Activities. PMID:32855848
Molecular Characterization of Testicular Germ Cell Tumors Using Tissue Microdissection. PMID:32852755
New Understanding of the Relevant Role of LINE-1 Retrotransposition in Human Disease and Immune Modulation. PMID:32850797
Forensic Autosomal Short Tandem Repeats and Their Potential Association With Phenotype. PMID:32849844
Background Selection Does Not Mimic the Patterns of Genetic Diversity Produced by Selective Sweeps. PMID:32847814
Potential of transposon-mediated cellular reprogramming towards cell-based therapies. PMID:32843912
Pan-genomic open reading frames: A potential supplement of single nucleotide polymorphisms in estimation of heritability and genomic prediction. PMID:32833967
A report on DNA sequence determinants in gene expression. PMID:32831525
Application of Next Generation Sequencing in Laboratory Medicine. PMID:32829577
Silencing and Transcriptional Regulation of Endogenous Retroviruses: An Overview. PMID:32823517
Untangling Data in Precision Oncology - A Model for Chronic Diseases? PMID:32823314
Identifying and Targeting Human Tumor Antigens for T Cell-Based Immunotherapy of Solid Tumors. PMID:32822573
Presence of Endogenous Viral Elements Negatively Correlates with Feline Leukemia Virus Susceptibility in Puma and Domestic Cat Cells. PMID:32817213
Cryptic genetic variation enhances primate L1 retrotransposon survival by enlarging the functional coiled coil sequence space of ORF1p. PMID:32797042
The Prospective Study of Epigenetic Regulatory Profiles in Sport and Exercise Monitored Through Chromosome Conformation Signatures. PMID:32784689
Trypanosoma cruzi Genome 15 Years Later: What Has Been Accomplished? PMID:32781761
The Long Non-coding Road to Atherosclerosis. PMID:32772181
The Human Genome Project changed everything. PMID:32770171
Polygenic risk score as clinical utility in psychiatry: a clinical viewpoint. PMID:32770057
A First NGS Investigation Suggests No Association Between Viruses and Canine Cancers. PMID:32766289
Analysis of Salmonella typhimurium Protein-Targeting in the Nucleus of Host Cells and the Implications in Colon Cancer: An in-silico Approach. PMID:32765017
Comparative genomic analysis of eutherian fibroblast growth factor genes. PMID:32758140
Whole Genome Sequencing of Four Representatives From the Admixed Population of the United Arab Emirates. PMID:32754195
Proteomics and Metabolomics for Cystic Fibrosis Research. PMID:32751630
Single-cell proteomic analysis. PMID:32748522
Genomic Diagnosis for Pediatric Disorders: Revolution and Evolution. PMID:32733828
Tumor DNA hypomethylation of LINE-1 is associated with low tumor grade of breast cancer in Tunisian patients. PMID:32724446
Human L1 Transposition Dynamics Unraveled with Functional Data Analysis. PMID:32722770
How Dietary Factors Affect DNA Methylation: Lesson from Epidemiological Studies. PMID:32722411
Endogenous Retroviruses Walk a Fine Line between Priming and Silencing. PMID:32718022
How Will Genetics Inform the Clinical Care of Atrial Fibrillation? PMID:32716712
BIOMAP: A Home for All Biology Methods. PMID:32715089
Accounting for diverse evolutionary forces reveals mosaic patterns of selection on human preterm birth loci. PMID:32709900
Consequence of Paradigm Shift with Repeat Landscapes in Reptiles: Powerful Facilitators of Chromosomal Rearrangements for Diversity and Evolution. PMID:32708239
Brain cell somatic gene recombination and its phylogenetic foundations. PMID:32699111
Prostate cancer biology & genomics. PMID:32676435
Regulation of stem cell function and neuronal differentiation by HERV-K via mTOR pathway. PMID:32669437
Human Cancers Express TRAILshort, a Dominant Negative TRAIL Splice Variant, Which Impairs Immune Effector Cell Killing of Tumor Cells. PMID:32669373
A deliberative study of public attitudes towards sharing genomic data within NHS genomic medicine services in England. PMID:32664786
Telomere-to-telomere assembly of a complete human X chromosome. PMID:32663838
Identification and Genotyping of Transposable Element Insertions From Genome Sequencing Data. PMID:32662945
Regulation of Error-Prone DNA Double-Strand Break Repair and Its Impact on Genome Evolution. PMID:32660124
Cancer systems immunology. PMID:32657757
Maximal Segmental Score Method for Localizing Recessive Disease Variants Based on Sequence Data. PMID:32655614
Enhancer Function of MicroRNA-3681 Derived from Long Terminal Repeats Represses the Activity of Variable Number Tandem Repeats in the 3' UTR of SHISA7. PMID:32655015
Cancer Associated Endogenous Retroviruses: Ideal Immune Targets for Adenovirus-Based Immunotherapy. PMID:32650622
Non-Coding RNA Editing in Cancer Pathogenesis. PMID:32650588
Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding. PMID:32649757
Higher Germline Mutagenesis of Genes with Stronger Testis Expressions Refutes the Transcriptional Scanning Hypothesis. PMID:32638015
Strategies for whole-exome sequencing analysis in a case series study of familial male infertility. PMID:32637866
Handling multi-mapped reads in RNA-seq. PMID:32637053
Transposable elements in Drosophila. PMID:32636946
mRNA Editing, Processing and Quality Control in Caenorhabditis elegans. PMID:32632025
Fully Phased Sequence of a Diploid Human Genome Determined de Novo from the DNA of a Single Individual. PMID:32631951
Comparative whole genome DNA methylation profiling across cattle tissues reveals global and tissue-specific methylation patterns. PMID:32631327
Pro-Inflammatory Signaling Upregulates a Neurotoxic Conotoxin-Like Protein Encrypted Within Human Endogenous Retrovirus-K. PMID:32629888
Nasopharyngeal Haemophilus and local immune response during infant respiratory syncytial virus infection. PMID:32628963
Breathing fresh air into respiratory research with single-cell RNA sequencing. PMID:32620586
Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures. PMID:32616928
Desiccation does not drastically increase the accessibility of exogenous DNA to nuclear genomes: evidence from the frequency of endosymbiotic DNA transfer. PMID:32611311
LDtrait: An Online Tool for Identifying Published Phenotype Associations in Linkage Disequilibrium. PMID:32606005
Long noncoding RNA H19X is a key mediator of TGF-β-driven fibrosis. PMID:32603313
Multiple Invasions of Visitor, a DD41D Family of Tc1/mariner Transposons, throughout the Evolution of Vertebrates. PMID:32602886
Retrotransposons in pluripotent stem cells. PMID:32588192
The IRI-DICE hypothesis: ionizing radiation-induced DSBs may have a functional role for non-deterministic responses at low doses. PMID:32583290
Infectious Triggers in Periodontitis and the Gut in Rheumatoid Arthritis (RA): A Complex Story About Association and Causality. PMID:32582191
Efavirenz as a potential drug for the treatment of triple-negative breast cancers. PMID:32566961
The Battle to Sequence the Bread Wheat Genome: A Tale of the Three Kingdoms. PMID:32561470
Plasma cell-free DNA predicts pediatric cerebral malaria severity. PMID:32554925
Characteristics of circular RNAs generated by human Survival Motor Neuron genes. PMID:32553550
A comparative study of long interspersed element-1 protein immunoreactivity in cutaneous malignancies. PMID:32552892
High-Throughput Sequencing is a Crucial Tool to Investigate the Contribution of Human Endogenous Retroviruses (HERVs) to Human Biology and Development. PMID:32545287
Closing Human Reference Genome Gaps: Identifying and Characterizing Gap-Closing Sequences. PMID:32532800
Multi-branch Convolutional Neural Network for Identification of Small Non-coding RNA genomic loci. PMID:32528107
Nanopore sequencing as a scalable, cost-effective platform for analyzing polyclonal vector integration sites following clinical T cell therapy. PMID:32527930
DNA methylation patterns of LINE-1 and Alu for pre-symptomatic dementia in type 2 diabetes. PMID:32525932
Single-Cell Transcriptomics Analysis Identifies Nuclear Protein 1 as a Regulator of Docetaxel Resistance in Prostate Cancer Cells. PMID:32513898
Whole-genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes. PMID:32513296
Long-read human genome sequencing and its applications. PMID:32504078
A single mutation in the ACTR8 gene associated with lineage-specific expression in primates. PMID:32503430
DNA hypomethylation promotes transposable element expression and activation of immune signaling in renal cell cancer. PMID:32493845
Education in the genomics era: Generating high-quality genome assemblies in university courses. PMID:32491162
Hagfish genome reveals parallel evolution of 7SL RNA-derived SINEs. PMID:32489435
Assembly and annotation of an Ashkenazi human reference genome. PMID:32487205
SETDB1-Mediated Silencing of Retroelements. PMID:32486217
Retrocopying expands the functional repertoire of APOBEC3 antiviral proteins in primates. PMID:32479260
The functional cooperation of 5-HT1A and mGlu4R in HEK-293 cell line. PMID:32472388
The quest to slow ageing through drug discovery. PMID:32467649
Mosaic Somatic Gene Recombination as a Potentially Unifying Hypothesis for Alzheimer's Disease. PMID:32457796
Vertical lossless genomic data compression tools for assembled genomes: A systematic literature review. PMID:32453750
Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera. PMID:32442304
Non-coding RNAs in Nervous System Development and Disease. PMID:32435641
Viral infection impacts transposable element transcript amounts in Drosophila. PMID:32434916
Reawakening the Developmental Origins of Cancer Through Transposable Elements. PMID:32432029
Mechanisms of Long Non-Coding RNAs in Cancers and Their Dynamic Regulations. PMID:32429086
Review: Understanding Rare Genetic Diseases in Low Resource Regions Like Jammu and Kashmir - India. PMID:32425985
Progress, Challenges, and Surprises in Annotating the Human Genome. PMID:32421357
Genomic Indexing by Somatic Gene Recombination of mRNA/ncRNA - Does It Play a Role in Genomic Mosaicism, Memory Formation, and Alzheimer's Disease? PMID:32411177
High Glucose Induces Lipid Accumulation via 25-Hydroxycholesterol DNA-CpG Methylation. PMID:32408171
Conserved Herpesvirus Kinase ORF36 Activates B2 Retrotransposons during Murine Gammaherpesvirus Infection. PMID:32404524
Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral. PMID:32404186
Effect of sequence depth and length in long-read assembly of the maize inbred NC358. PMID:32385271
Characterization of long G4-rich enhancer-associated genomic regions engaging in a novel loop:loop 'G4 Kissing' interaction. PMID:32383760
A single-cell transcriptomic landscape of primate arterial aging. PMID:32371953
Oxidative Stress in DNA Repeat Expansion Disorders: A Focus on NRF2 Signaling Involvement. PMID:32369911
HiC-Hiker: a probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C. PMID:32369554
The Sophisticated Transcriptional Response Governed by Transposable Elements in Human Health and Disease. PMID:32366056
Understanding the interplay between CpG island-associated gene promoters and H3K4 methylation. PMID:32360393
The Simons Genome Diversity Project: A Global Analysis of Mobile Element Diversity. PMID:32359137
Are Pathogenic Germline Variants in Metastatic Melanoma Associated with Resistance to Combined Immunotherapy? PMID:32354124
DNA methylation level in blood and relations to breast cancer, risk factors and environmental exposure in Greenlandic Inuit women. PMID:32352194
Comparison of Behavior and Genetic Structure in Populations of Family and Kenneled Beagles. PMID:32351979
Recent Trends of microRNA Significance in Pediatric Population Glioblastoma and Current Knowledge of Micro RNA Function in Glioblastoma Multiforme. PMID:32349263
Widespread and tissue-specific expression of endogenous retroelements in human somatic tissues. PMID:32345368
The functional study of human proteins using humanized yeast. PMID:32342338
Aging-regulated anti-apoptotic long non-coding RNA Sarrah augments recovery from acute myocardial infarction. PMID:32341350
The science commons in life science research: structure, function, and value of access to genetic diversity. PMID:32336774
A chromosome-scale assembly of the smallest Dothideomycete genome reveals a unique genome compaction mechanism in filamentous fungi. PMID:32326892
Insertion of Telomeric Repeats in the Human and Horse Genomes: An Evolutionary Perspective. PMID:32325780
Polygenic Scores to Assess Atherosclerotic Cardiovascular Disease Risk: Clinical Perspectives and Basic Implications. PMID:32324503
Purification of Bionanoparticles. PMID:32313384
The Biological Functions of Non-coding RNAs: From a Line to a Circle. PMID:32309571
Identification and Ranking of Biomedical Informatics Researcher Citation Statistics through a Google Scholar Scraper. PMID:32308860
Fungal evolution: cellular, genomic and metabolic complexity. PMID:32301582
RepeatModeler2 for automated genomic discovery of transposable element families. PMID:32300014
TranspoScope: interactive visualization of retrotransposon insertions. PMID:32298413
A reference map of the human binary protein interactome. PMID:32296183
Transposable elements contribute to cell and species-specific chromatin looping and gene regulation in mammalian genomes. PMID:32286261
An ancient evolutionary connection between Ribonuclease A and EndoU families. PMID:32284351
Gallop Racing Shifts Mature mRNA towards Introns: Does Exercise-Induced Stress Enhance Genome Plasticity? PMID:32283859
Tumour grade significantly correlates with total dysfunction of tumour tissue-infiltrating lymphocytes in renal cell carcinoma. PMID:32277125
Codon Usage and Splicing Jointly Influence mRNA Localization. PMID:32275854
Systems Biochemistry Approaches to Defining Mitochondrial Protein Function. PMID:32268114
Long Non-coding RNAs: Major Regulators of Cell Stress in Cancer. PMID:32266130
Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins. PMID:32252787
SAMHD1 Functions and Human Diseases. PMID:32244340
DNA methylation profiling identifies a high effect genetic variant for lipoprotein(a) levels. PMID:32237968
Reciprocal regulation between alternative splicing and the DNA damage response. PMID:32236390
Considerations for Using the Vasculature as a Coordinate System to Map All the Cells in the Human Body. PMID:32232057
Differential Responses of LINE-1 in the Dentate Gyrus, Striatum and Prefrontal Cortex to Chronic Neurotoxic Methamphetamine: A Study in Rat Brain. PMID:32231019
The genome-wide landscape of C:G > T:A polymorphism at the CpG contexts in the human population. PMID:32228436
In or Out? New Insights on Exon Recognition through Splice-Site Interdependency. PMID:32225107
Divergence-Based Introgression Polarization. PMID:32219392
Viral component of the human genome. PMID:32214476
Quantification, Dynamic Visualization, and Validation of Bias in ATAC-Seq Data with ataqv. PMID:32213349
How We Think about Targeting RNA with Small Molecules. PMID:32212706
Gene editing and CRISPR in the clinic: current and future perspectives. PMID:32207531
Pericentromeric heterochromatin is hierarchically organized and spatially contacts H3K9me2 islands in euchromatin. PMID:32203508
Long non-coding RNA GRASLND enhances chondrogenesis via suppression of the interferon type II signaling pathway. PMID:32202492
Transient DNMT3L Expression Reinforces Chromatin Surveillance to Halt Senescence Progression in Mouse Embryonic Fibroblast. PMID:32195249
Discussion of Trial Designs for Biomarker Identification and Validation Through the Use of Case Studies. PMID:32190807
Dynamic LTR retrotransposon transcriptome landscape in septic shock patients. PMID:32188504
Is Gene-Size an Issue for the Diagnosis of Skeletal Muscle Disorders? PMID:32176652
Beyond classic editing: innovative CRISPR approaches for functional studies of long non-coding RNA. PMID:32161809
Genomic Repeats Categorize Genes with Distinct Functions for Orchestrated Regulation. PMID:32160538
In Vivo Delivery of Nucleic Acid-Encoded Monoclonal Antibodies. PMID:32157600
Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes. PMID:32157095
Dynamic Signatures of the Epigenome: Friend or Foe? PMID:32156057
SECNVs: A Simulator of Copy Number Variants and Whole-Exome Sequences From Reference Genomes. PMID:32153642
Jump around: transposons in and out of the laboratory. PMID:32148769
A-to-I RNA Editing Uncovers Hidden Signals of Adaptive Genome Evolution in Animals. PMID:32145015
Genetic and Genomic Advances in Developmental Models: Applications for Nutrition Research. PMID:32135011
RETrace: simultaneous retrospective lineage tracing and methylation profiling of single cells. PMID:32127417
Dnmt3a and Dnmt3b-Decommissioned Fetal Enhancers are Linked to Kidney Disease. PMID:32127410
Does DNA Methylation Matter in FSHD? PMID:32121044
Transgene-mediated skeletal phenotypic variation in zebrafish. PMID:32112658
Integrated Mobile Element Scanning (ME-Scan) method for identifying multiple types of polymorphic mobile element insertions. PMID:32110248
Mutational Load and the Functional Fraction of the Human Genome. PMID:32108234
Data libraries - the missing element for modeling biological systems. PMID:32100391
Precision health: A nursing perspective. PMID:32099853
Villains or heroes? The raison d'être of viruses. PMID:32099651
Micro RNA Molecules as Modulators of Treatment Resistance, Immune Checkpoints Controllers and Sensitive Biomarkers in Glioblastoma Multiforme. PMID:32098401
Role of Non-Coding RNAs in the Development of Targeted Therapy and Immunotherapy Approaches for Chronic Lymphocytic Leukemia. PMID:32098192
Finding and extending ancient simple sequence repeat-derived regions in the human genome. PMID:32095164
Systematic identification of silencers in human cells. PMID:32094911
Awakening the dark side: retrotransposon activation in neurodegenerative disorders. PMID:32092528
A guide to naming human non-coding RNA genes. PMID:32090359
Minireview on the Relations between Gut Microflora and Parkinson's Disease: Further Biochemical (Oxidative Stress), Inflammatory, and Neurological Particularities. PMID:32089768
Insertion of LINE-1 Retrotransposon Inducing Exon Inversion Causes a Rotor Syndrome Phenotype. PMID:32082363
Brain Cytoplasmic RNAs in Neurons: From Biosynthesis to Function. PMID:32079202
Differential Allele-Specific Expression Uncovers Breast Cancer Genes Dysregulated by Cis Noncoding Mutations. PMID:32078798
Decoding a highly mixed Kazakh genome. PMID:32076829
Short interspersed nuclear element (SINE)-mediated post-transcriptional effects on human and mouse gene expression: SINE-UP for active duty. PMID:32075563
sRNA/L1 retrotransposition: using siRNAs and miRNAs to expand the applications of the cell culture-based LINE-1 retrotransposition assay. PMID:32075559
An atlas of transposable element-derived alternative splicing in cancer. PMID:32075558
Human transposon insertion profiling by sequencing (TIPseq) to map LINE-1 insertions in single cells. PMID:32075555
Widespread correlation of KRAB zinc finger protein binding with brain-developmental gene expression patterns. PMID:32075554
Transposable elements have contributed human regulatory regions that are activated upon bacterial infection. PMID:32075553
BlobToolKit - Interactive Quality Assessment of Genome Assemblies. PMID:32071071
Traveler, a New DD35E Family of Tc1/Mariner Transposons, Invaded Vertebrates Very Recently. PMID:32068835
Characterising a human endogenous retrovirus(HERV)-derived tumour-associated antigen: enriched RNA-Seq analysis of HERV-K(HML-2) in mantle cell lymphoma cell lines. PMID:32055257
What animals can teach us about evolution, the human genome, and human disease. PMID:32054372
Protective immunity elicited by the nematode-conserved As37 recombinant protein against Ascaris suum infection. PMID:32053593
Poly-Enrich: count-based methods for gene set enrichment testing with genomic regions. PMID:32051932
The draft genome of mandrill (Mandrillus sphinx): An Old World monkey. PMID:32051450
Re-recognition of pseudogenes: From molecular to clinical applications. PMID:32042317
Tissue and cancer-specific expression of DIEXF is epigenetically mediated by an Alu repeat. PMID:32041475
Artificial Intelligence for Cardiac Imaging-Genetics Research. PMID:32039240
Studies on the Small Body Size Mouse Developed by Mutagen N-Ethyl-N-nitrosourea. PMID:32038779
Pan-genomics in the human genome era. PMID:32034321
Human Long Noncoding RNA Interactome: Detection, Characterization and Function. PMID:32033158
Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. PMID:32024998
Genetic tests by next-generation sequencing in children with developmental delay and/or intellectual disability. PMID:32024334
Prediction of short-term neonatal complications in preterm infants using exome-wide genetic variation and gestational age: a pilot study. PMID:32023625
Precise hepatectomy in the intelligent digital era. PMID:32015674
Unveiling ncRNA regulatory axes in atherosclerosis progression. PMID:32009226
ATAC-Me Captures Prolonged DNA Methylation of Dynamic Chromatin Accessibility Loci during Cell Fate Transitions. PMID:31999955
A New Weighted Imputed Neighborhood-Regularized Tri-Factorization One-Class Collaborative Filtering Algorithm: Application to Target Gene Prediction of Transcription Factors. PMID:31995498
Towards a comprehensive catalogue of validated and target-linked human enhancers. PMID:31988385
Tetranucleotide Microsatellite Mutational Behavior Assessed in Real Time: Implications for Future Microsatellite Panels. PMID:31982570
Aberrantly High Levels of Somatic LINE-1 Expression and Retrotransposition in Human Neurological Disorders. PMID:31969897
Worldwide carrier frequency and genetic prevalence of autosomal recessive inherited retinal diseases. PMID:31964843
A potential new mechanism for pregnancy loss: considering the role of LINE-1 retrotransposons in early spontaneous miscarriage. PMID:31964400
MicroRNAs in Vascular Eye Diseases. PMID:31963809
In-Depth Mapping of the Urinary N-Glycoproteome: Distinct Signatures of ccRCC-related Progression. PMID:31963743
Idiopathic Pulmonary Fibrosis: Pathogenesis and the Emerging Role of Long Non-Coding RNAs. PMID:31947693
The Missing "lnc" between Genetics and Cardiac Disease. PMID:31947625
The Developmental Gene Hypothesis for Punctuated Equilibrium: Combined Roles of Developmental Regulatory Genes and Transposable Elements. PMID:31943266
A draft genome sequence of the elusive giant squid, Architeuthis dux. PMID:31942620
Compensating for over-production inhibition of the Hsmar1 transposon in Escherichia coli using a series of constitutive promoters. PMID:31938044
PP2A Phosphatases Take a Giant Leap in the Post-Genomics Era. PMID:31929724
Cell-free DNA donor fraction analysis in pediatric and adult heart transplant patients by multiplexed allele-specific quantitative PCR: Validation of a rapid and highly sensitive clinical test for stratification of rejection probability. PMID:31929557
How technical progress reshaped behavioral neuroendocrinology during the last 50 years… and some methodological remarks. PMID:31927020
Comparative analysis on the expression of L1 loci using various RNA-Seq preparations. PMID:31921361
A brief history of human disease genetics. PMID:31915397
The p53 family reaches the final frontier: the variegated regulation of the dark matter of the genome by the p53 family in cancer. PMID:31910062
Unzipping haplotypes in diploid and polyploid genomes. PMID:31908732
Structural variant identification and characterization. PMID:31907725
The SUMO Ligase Su(var)2-10 Controls Hetero- and Euchromatic Gene Expression via Establishing H3K9 Trimethylation and Negative Feedback Regulation. PMID:31901448
Alpha-hemoglobin-stabilizing protein (AHSP): a modulatory factor in β-thalassemia. PMID:31894534
LINE-1 ORF2p expression is nearly imperceptible in human cancers. PMID:31892958
Targeted viral vector transduction of relaxin-3 neurons in the rat nucleus incertus using a novel cell-type specific promoter. PMID:31890981
Long walk to genomics: History and current approaches to genome sequencing and assembly. PMID:31890139
A re-evaluation of LINE-1 ORF2 expression in LNCaP prostate cancer cells. PMID:31890047
Few SINEs of life: Alu elements have little evidence for biological relevance despite elevated translation. PMID:31886458
Immunotherapy and next-generation sequencing guided therapy for precision oncology: What have we learnt and what does the future hold? PMID:31886407
B2 and ALU retrotransposons are self-cleaving ribozymes whose activity is enhanced by EZH2. PMID:31871160
Epigenetic therapy of myelodysplastic syndromes connects to cellular differentiation independently of endogenous retroelement derepression. PMID:31870430
A network embedding model for pathogenic genes prediction by multi-path random walking on heterogeneous network. PMID:31865919
A unified STR profiling system across multiple species with whole genome sequencing data. PMID:31861983
Restricted and non-essential redundancy of RNAi and piRNA pathways in mouse oocytes. PMID:31860668
Nucleotide composition of transposable elements likely contributes to AT/GC compositional homogeneity of teleost fish genomes. PMID:31857829
Identification and characterization of occult human-specific LINE-1 insertions using long-read sequencing technology. PMID:31853540
Novel human sex-typing strategies based on the autism candidate gene NLGN4X and its male-specific gametologue NLGN4Y. PMID:31852540
Long non-coding RNAs in ovarian cancer: expression profile and functional spectrum. PMID:31847695
Application of DArT seq derived SNP tags for comparative genome analysis in fishes; An alternative pipeline using sequence data from a non-traditional model species, Macquaria ambigua. PMID:31830141
A primate-specific retroviral enhancer wires the XACT lncRNA into the core pluripotency network in humans. PMID:31827084
Arteria: An automation system for a sequencing core facility. PMID:31825479
TEffectR: an R package for studying the potential effects of transposable elements on gene expression with linear regression model. PMID:31824778
Targeted deep-intronic sequencing in a cohort of unexplained cases of suspected Lynch syndrome. PMID:31822864
Glyoxalase 1 gene improves the antistress capacity and reduces the immune inflammatory response. PMID:31822263
Evolutionary Forces and Codon Bias in Different Flavors of Intrinsic Disorder in the Human Proteome. PMID:31820049
Nutritional Factors Modulating Alu Methylation in an Italian Sample from The Mark-Age Study Including Offspring of Healthy Nonagenarians. PMID:31817660
Conversion of DNA Sequences: From a Transposable Element to a Tandem Repeat or to a Gene. PMID:31817529
Pharmacogenomics In Pharmacy Practice: Current Perspectives. PMID:31807435
Recapitulation-like developmental transitions of chromatin accessibility in vertebrates. PMID:31807314
Endogenous Retroviruses Activity as a Molecular Signature of Neurodevelopmental Disorders. PMID:31801288
Artificial intelligence for precision medicine in neurodevelopmental disorders. PMID:31799421
Endogenous retroviruses are associated with hippocampus-based memory impairment. PMID:31792184
High-throughput long paired-end sequencing of a Fosmid library by PacBio. PMID:31788019
The Role of SINE-VNTR-Alu (SVA) Retrotransposons in Shaping the Human Genome. PMID:31783611
Advances in genetics toward identifying pathogenic cell states of rheumatoid arthritis. PMID:31782165
Sam68 binds Alu-rich introns in SMN and promotes pre-mRNA circularization. PMID:31777926
GraphTyper2 enables population-scale genotyping of structural variation using pangenome graphs. PMID:31776332
TFIIIC Binding to Alu Elements Controls Gene Expression via Chromatin Looping and Histone Acetylation. PMID:31759822
Integrative genetic map of repetitive DNA in the sole Solea senegalensis genome shows a Rex transposon located in a proto-sex chromosome. PMID:31748593
Role of Molecular Profiling of Pancreatic Cancer After Neoadjuvant Therapy: Does it Change Practice? PMID:31745905
Snapshots of a genetic cut-and-paste. PMID:31745352
Transposable element expression in tumors is associated with immune infiltration and increased antigenicity. PMID:31745090
The Human Immunopeptidome Project: A Roadmap to Predict and Treat Immune Diseases. PMID:31744855
Comparative genomic analysis of eutherian connexin genes. PMID:31729432
Soluble PD-L1 generated by endogenous retroelement exaptation is a receptor antagonist. PMID:31729316
[Mass spectrometry-applications in pathology]. PMID:31713660
New developments on the Encyclopedia of DNA Elements (ENCODE) data portal. PMID:31713622
Synthetic lethality as an engine for cancer drug target discovery. PMID:31712683
X-ray Structures of the Post-fusion 6-Helix Bundle of the Human Syncytins and their Functional Implications. PMID:31711961
Genetics of Childhood-onset Schizophrenia 2019 Update. PMID:31708045
Dynamic DNA Energy Landscapes and Substrate Complexity in Triplet Repeat Expansion and DNA Repair. PMID:31698848
Nature at 150: evidence in pursuit of truth. PMID:31695220
Ensembl 2020. PMID:31691826
A non-coding genetic variant associated with abdominal aortic aneurysm alters ERG gene regulation. PMID:31691800
The Concomitant Expression of Human Endogenous Retroviruses and Embryonic Genes in Cancer Cells under Microenvironmental Changes is a Potential Target for Antiretroviral Drugs. PMID:31691184
Recurrent intragenic exon rearrangements of SOBP and AUTS2 in non-Hodgkin B-cell lymphoma. PMID:31686349
Roles of Topoisomerases in Heterochromatin, Aging, and Diseases. PMID:31683993
Differential regulatory network-based quantification and prioritization of key genes underlying cancer drug resistance based on time-course RNA-seq data. PMID:31682596
Widespread sex dimorphism in aging and age-related diseases. PMID:31677133
The Many Faces of Gene Regulation in Cancer: A Computational Oncogenomics Outlook. PMID:31671657
Innovating the Concept and Practice of Two-Dimensional Gel Electrophoresis in the Analysis of Proteomes at the Proteoform Level. PMID:31671630
Protein Structural Information and Evolutionary Landscape by In Vitro Evolution. PMID:31670785
Comprehensive Scanning Mutagenesis of Human Retrotransposon LINE-1 Identifies Motifs Essential for Function. PMID:31666291
A 96-multiplex capillary electrophoresis screening platform for product based evolution of P450 BM3. PMID:31664146
Human-specific tandem repeat expansion and differential gene expression during primate evolution. PMID:31659027
Molecular determinants of drug response in TNBC cell lines. PMID:31655920
Comparative Genomics Analysis Reveals High Levels of Differential Retrotransposition among Primates from the Hominidae and the Cercopithecidae Families. PMID:31651947
Deep Learning Enables Accurate Prediction of Interplay Between lncRNA and Disease. PMID:31649723
Retrotransposons spread potential cis-regulatory elements during mammary gland evolution. PMID:31642473
DNA methylation of individual repetitive elements in hepatitis C virus infection-induced hepatocellular carcinoma. PMID:31639042
Evolutionary history and classification of Micropia retroelements in Drosophilidae species. PMID:31622354
Recovery of non-reference sequences missing from the human reference genome. PMID:31619167
Five months of voluntary wheel running downregulates skeletal muscle LINE-1 gene expression in rats. PMID:31618076
Children With Autism Spectrum Disorder and Their Mothers Share Abnormal Expression of Selected Endogenous Retroviruses Families and Cytokines. PMID:31616420
Specification of the First Mammalian Cell Lineages In Vivo and In Vitro. PMID:31615786
Changing expression profiles of lncRNAs, circRNAs and mRNAs in esophageal squamous carcinoma. PMID:31612046
A Japanese history of the Human Genome Project. PMID:31611500
Novel Y-Chromosome Long Non-Coding RNAs Expressed in Human Male CNS During Early Development. PMID:31608120
Introducing the first whole genomes of nationals from the United Arab Emirates. PMID:31604968
On the Function of Trans-Splicing: No Evidence for Widespread Proteome Diversification in Trypanosomes. PMID:31599940
Evaluating Chromatin Accessibility Differences Across Multiple Primate Species Using a Joint Modeling Approach. PMID:31599933
Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0. PMID:31599596
Retroelement-Linked H3K4me1 Histone Tags Uncover Regulatory Evolution Trends of Gene Enhancers and Feature Quickly Evolving Molecular Processes in Human Physiology. PMID:31597351
Co-Localization of DNA i-Motif-Forming Sequences and 5-Hydroxymethyl-cytosines in Human Embryonic Stem Cells. PMID:31597270
Lung genotoxicity of benzo(a)pyrene in vivo involves reactivation of LINE-1 retrotransposon and early reprogramming of oncogenic regulatory networks. PMID:31596105
Functional Genomics of the Retina to Elucidate its Construction and Deconstruction. PMID:31590277
Reporting on the future of integrative structural biology ORAU workshop. PMID:31585877
Synonymous genome recoding: a tool to explore microbial biology and new therapeutic strategies. PMID:31584076
Unraveling the Heterogeneous Mutational Signature of Spontaneously Developing Tumors in MLH1-/- Mice. PMID:31581674
Break-induced replication plays a prominent role in long-range repeat-mediated deletion. PMID:31571254
Up-regulation of ZFAS1 indicates dismal prognosis for cholangiocarcinoma and promotes proliferation and metastasis by modulating USF1 via miR-296-5p. PMID:31565837
Adipose Tissue Gene Expression Associations Reveal Hundreds of Candidate Genes for Cardiometabolic Traits. PMID:31564431
Discovery of Novel Sequences in 1,000 Swedish Genomes. PMID:31560401
Large, three-generation human families reveal post-zygotic mosaicism and variability in germline mutation accumulation. PMID:31549960
RNA ligation precedes the retrotransposition of U6/LINE-1 chimeric RNA. PMID:31548405
RNA-seq as a tool for evaluating human embryo competence. PMID:31548358
Dual-Specific Protein and Lipid Phosphatase PTEN and Its Biological Functions. PMID:31548229
Chromosomal rearrangements as a source of new gene formation in Drosophila yakuba. PMID:31545792
Chromosome-level assembly of the mustache toad genome using third-generation DNA sequencing and Hi-C analysis. PMID:31544214
Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci. PMID:31537640
LTR retroelement expansion of the human cancer transcriptome and immunopeptidome revealed by de novo transcript assembly. PMID:31537638
Xist RNA in action: Past, present, and future. PMID:31537017
Tracking the Fate of Endogenous Retrovirus Segregation in Wild and Domestic Cats. PMID:31534037
Overlapping protein-coding genes in human genome and their coincidental expression in tissues. PMID:31527706
The first enhancer in an enhancer chain safeguards subsequent enhancer-promoter contacts from a distance. PMID:31514731
SKF-LDA: Similarity Kernel Fusion for Predicting lncRNA-Disease Association. PMID:31514111
Quantitative detection of ALK fusion breakpoints in plasma cell-free DNA from patients with non-small cell lung cancer using PCR-based target sequencing with a tiling primer set and two-step mapping/alignment. PMID:31513617
Mechanisms of nuclear mRNA export: A structural perspective. PMID:31513326
Current Trends in Applications of Circulatory Microchimerism Detection in Transplantation. PMID:31509957
The Evolving Field of Genetic Epidemiology: From Familial Aggregation to Genomic Sequencing. PMID:31509181
Socioeconomic status and DNA methylation from birth through mid-childhood: a prospective study in Project Viva. PMID:31509016
5-Azacytidine modulates CpG methylation levels of EZH2 and NOTCH1 in myelodysplastic syndromes. PMID:31506740
SNV identification from single-cell RNA sequencing data. PMID:31504520
Detection of Microsatellite Instability Biomarkers via Next-Generation Sequencing. PMID:31502149
The NIH Common Fund/Roadmap Epigenomics Program: Successes of a comprehensive consortium. PMID:31501771
Whole Genome Analyses of Chinese Population and De Novo Assembly of A Northern Han Genome. PMID:31494266
Functional disease architectures reveal unique biological role of transposable elements. PMID:31492842
Retrotransposon insertions can initiate colorectal cancer and are associated with poor survival. PMID:31492840
A novel evolutionary model for constructing gene coexpression networks with comprehensive features. PMID:31492104
H3K4me3, H3K9ac, H3K27ac, H3K27me3 and H3K9me3 Histone Tags Suggest Distinct Regulatory Evolution of Open and Condensed Chromatin Landmarks. PMID:31491936
Food Safety and Nutraceutical Potential of Caramel Colour Class IV Using In Vivo and In Vitro Assays. PMID:31491925
Expanding the scope and scale of microbiome research. PMID:31488207
An LTR retrotransposon-derived lncRNA interacts with RNF169 to promote homologous recombination. PMID:31486214
Clinical value of non-coding RNAs in cardiovascular, pulmonary, and muscle diseases. PMID:31483703
Transposable Elements, Inflammation, and Neurological Disease. PMID:31481926
Discovering human transcription factor physical interactions with genetic variants, novel DNA motifs, and repetitive elements using enhanced yeast one-hybrid assays. PMID:31481462
The Length of the Expressed 3' UTR Is an Intermediate Molecular Phenotype Linking Genetic Variants to Complex Diseases. PMID:31475030
Dynamical Electrical Complexity Is Reduced during Neuronal Differentiation in Autism Spectrum Disorder. PMID:31474529
Accumulation of Circulating Cell-Free CpG-Enriched Ribosomal DNA Fragments on the Background of High Endonuclease Activity of Blood Plasma in Schizophrenic Patients. PMID:31467866
Emerging epigenomic landscapes of pancreatic cancer in the era of precision medicine. PMID:31462645
A concise review of human brain methylome during aging and neurodegenerative diseases. PMID:31462381
β-mercaptoethanol assists efficient construction of sperm bacterial artificial chromosome library. PMID:31453223
Intrauterine programming of obesity and type 2 diabetes. PMID:31451874
Chromosomics: Bridging the Gap between Genomes and Chromosomes. PMID:31434289
The lncRNA Malat1 functions as a ceRNA to contribute to berberine-mediated inhibition of HMGB1 by sponging miR-181c-5p in poststroke inflammation. PMID:31431734
Identification of mutations in HEXA and HEXB in Sandhoff and Tay-Sachs diseases: a new large deletion caused by Alu elements in HEXA. PMID:31428437
Investigation of NF-κB-94ins/del ATTG and CARD8 (rs2043211) Gene Polymorphism in Acute Lymphoblastic Leukemia. PMID:31428046
TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements. PMID:31425522
Transposable element-mediated structural variation analysis in dog breeds using whole-genome sequencing. PMID:31414176
Genome-wide analysis of polymerase III-transcribed Alu elements suggests cell-type-specific enhancer function. PMID:31413151
Increased HERV-E clone 4-1 expression contributes to DNA hypomethylation and IL-17 release from CD4+ T cells via miR-302d/MBD2 in systemic lupus erythematosus. PMID:31412880
Biophysics and the Genomic Sciences. PMID:31409480
A Long Polymorphic GT Microsatellite within a Gene Promoter Mediates Non-Imprinted Allele-Specific DNA Methylation of a CpG Island in a Goldfish Inter-Strain Hybrid. PMID:31409051
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. PMID:31406327
ADAR1: "Editor-in-Chief" of Cytoplasmic Innate Immunity. PMID:31404141
Is it time to change the reference genome? PMID:31399121
Dietary Patterns are Associated with Leukocyte LINE-1 Methylation in Women: A Cross-Sectional Study in Southern Italy. PMID:31395820
A Genome Model to Explain Major Features of Neurodevelopmental Disorders in Newborns. PMID:31391780
ARID1A and PI3-kinase pathway mutations in the endometrium drive epithelial transdifferentiation and collective invasion. PMID:31391455
Correlation of long interspersed element-1 open reading frame 1 and c-Met proto-oncogene protein expression in ovarian cancer. PMID:31388980
Transmissible Cancers and Immune Downregulation in Tasmanian Devil (Sacrophilus harrisii) and Canine Populations. PMID:31387668
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. PMID:31375807
Patterns of conservation of spliceosomal intron structures and spliceosome divergence in representatives of the diplomonad and parabasalid lineages. PMID:31375061
Diseases of the nERVous system: retrotransposon activity in neurodegenerative disease. PMID:31372185
Rare and common variant discovery in complex disease: the IBD case study. PMID:31363759
Endogenous Retrovirus-Derived Long Noncoding RNA Enhances Innate Immune Responses via Derepressing RELA Expression. PMID:31363026
Microsatellite Marker Analysis for Laboratory Mice Profiling. PMID:31360681
AluMine: alignment-free method for the discovery of polymorphic Alu element insertions. PMID:31360240
FERMI: A Novel Method for Sensitive Detection of Rare Mutations in Somatic Tissue. PMID:31352405
High Prevalence and Disease Correlation of Autoantibodies Against p40 Encoded by Long Interspersed Nuclear Elements in Systemic Lupus Erythematosus. PMID:31342656
Human APOBEC3G Prevents Emergence of Infectious Endogenous Retrovirus in Mice. PMID:31341050
Heterogeneous transposable elements as silencers, enhancers and targets of meiotic recombination. PMID:31332531
Non-cell autonomous mechanism of Parkinson's disease pathology caused by G2019S LRRK2 mutation in Ashkenazi Jewish patient: Single cell analysis. PMID:31330122
Repeat-associated RNA structure and aberrant splicing. PMID:31323433
Identifying causal variants and genes using functional genomics in specialized cell types and contexts. PMID:31317254
An Evaluation of Machine Learning Approaches for the Prediction of Essential Genes in Eukaryotes Using Protein Sequence-Derived Features. PMID:31312416
GC content of vertebrate exome landscapes reveal areas of accelerated protein evolution. PMID:31311498
Fast and accurate medication identification. PMID:31304359
Sleeping beauty genetic screen identifies miR-23b::BTBD7 gene interaction as crucial for colorectal cancer metastasis. PMID:31303496
Non-Coding RNAs and their Integrated Networks. PMID:31301674
Discovery of receptor-ligand interfaces in the immunoglobulin superfamily. PMID:31298437
Transposable Elements and Their Epigenetic Regulation in Mental Disorders: Current Evidence in the Field. PMID:31293617
Identifying, understanding, and correcting technical artifacts on the sex chromosomes in next-generation sequencing data. PMID:31289836
Alu RNA Modulates the Expression of Cell Cycle Genes in Human Fibroblasts. PMID:31284509
Brain organoids and insights on human evolution. PMID:31275562
Mode and Tempo of Microsatellite Length Change in a Malaria Parasite Mutation Accumulation Experiment. PMID:31273388
Genetic Variation, Comparative Genomics, and the Diagnosis of Disease. PMID:31269367
Dynamic expression of tRNA-derived small RNAs define cellular states. PMID:31267708
Centralized scientific communities are less likely to generate replicable results. PMID:31264964
LLCLPLDA: a novel model for predicting lncRNA-disease associations. PMID:31250107
Molecular Mechanisms and Determinants of Innovative Correction Approaches in Coagulation Factor Deficiencies. PMID:31234407
Construction of JRG (Japanese reference genome) with single-molecule real-time sequencing. PMID:31231536
New pathologic mechanisms in nucleotide repeat expansion disorders. PMID:31229686
SIRT7 mediates L1 elements transcriptional repression and their association with the nuclear lamina. PMID:31226208
The role of hydrophobic matching on transmembrane helix packing in cells. PMID:31225439
Exome Sequencing in Clinical Hepatology. PMID:31222768
Expression of GCRG213p, LINE-1 endonuclease variant, significantly different in gastric complete and incomplete intestinal metaplasia. PMID:31221180
Simultaneous TE Analysis of 19 Heliconiine Butterflies Yields Novel Insights into Rapid TE-Based Genome Diversification and Multiple SINE Births and Deaths. PMID:31214686
RNA-protein interactions: disorder, moonlighting and junk contribute to eukaryotic complexity. PMID:31213136
Genetic and Epigenetic Fine Mapping of Complex Trait Associated Loci in the Human Liver. PMID:31204013
The Hunt for Degrons of the 26S Proteasome. PMID:31200568
Identification of a Retroelement-Containing Human Transcript Induced in the Nucleus by Vaccination. PMID:31200438
Using phenome-wide association studies to examine the effect of environmental exposures on human health. PMID:31200158
Early life exposures, neurodevelopmental disorders, and transposable elements. PMID:31193573
Patterns in the genome. PMID:31189906
Genome sequencing-the dawn of a game-changing era. PMID:31189904
The Potential Role of Genomic Medicine in the Therapeutic Management of Rheumatoid Arthritis. PMID:31185701
Jérôme Lejeune passed away 25 years ago. PMID:31182939
CFIm25 and alternative polyadenylation: Conflicting roles in cancer. PMID:31181319
Novel de novo frameshift variant in the ASXL3 gene in a child with microcephaly and global developmental delay. PMID:31180560
Mechanisms of genome evolution in Candida albicans. PMID:31176092
Translational Metabolomics: Current Challenges and Future Opportunities. PMID:31174372
First Responder to Genomic Information: A Guide for Primary Care Providers. PMID:31172371
Characterization of bovine (Bos taurus) imprinted genes from genomic to amino acid attributes by data mining approaches. PMID:31170205
Misassembly of long reads undermines de novo-assembled ethnicity-specific genomes: validation in a Chinese Han population. PMID:31168775
Modern technologies and algorithms for scaffolding assembled genomes. PMID:31166948
WashU Epigenome Browser update 2019. PMID:31165883
Human protein-coding genes and gene feature statistics in 2019. PMID:31164174
Negative regulation of miR-1275 by H3K27me3 is critical for glial induction of glioblastoma cells. PMID:31162799
Emerging roles of histone modifications and HDACs in RNA splicing. PMID:31162605
LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novo. PMID:31159720
RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level. PMID:31157783
The Potential for microRNA Therapeutics and Clinical Research. PMID:31156715
Variable Baseline Papio cynocephalus Endogenous Retrovirus (PcEV) Expression Is Upregulated in Acutely SIV-Infected Macaques and Correlated to STAT1 Expression in the Spleen. PMID:31156613
ERCC1/XPF Is Important for Repair of DNA Double-Strand Breaks Containing Secondary Structures. PMID:31153042
Expression dynamics of repetitive DNA in early human embryonic development. PMID:31151386
Health Disparities and Sepsis: a Systematic Review and Meta-Analysis on the Influence of Race on Sepsis-Related Mortality. PMID:31144133
Genomics and data science: an application within an umbrella. PMID:31142351
The Structural and Functional Diversity of Intrinsically Disordered Regions in Transmembrane Proteins. PMID:31139867
Tracing the history of LINE and SINE extinction in sigmodontine rodents. PMID:31139266
Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. PMID:31135340
Long noncoding-RNA component of mitochondrial RNA processing endoribonuclease is involved in the progression of cholangiocarcinoma by regulating microRNA-217. PMID:31111617
Population genetic data of 20 insertion-null allele markers in the Andalusian population. PMID:31111220
An ATAC-seq atlas of chromatin accessibility in mouse tissues. PMID:31110271
MERMAID: dedicated web server to prepare and run coarse-grained membrane protein dynamics. PMID:31106328
Molecular pattern of lncRNAs in hepatocellular carcinoma. PMID:31097003
Determination and analysis of agonist and antagonist potential of naturally occurring flavonoids for estrogen receptor (ERα) by various parameters and molecular modelling approach. PMID:31092862
c-Myc induced the regulation of long non-coding RNA RHPN1-AS1 on breast cancer cell proliferation via inhibiting P53. PMID:31089812
In silico prediction of housekeeping long intergenic non-coding RNAs reveals HKlincR1 as an essential player in lung cancer cell survival. PMID:31089191
ULTRA: A Model Based Tool to Detect Tandem Repeats. PMID:31080962
Retrotransposons evolution and impact on lncRNA and protein coding genes in pigs. PMID:31080521
Recognition of 3'-end L1, Alu, processed pseudogenes, and mRNA stem-loops in the human genome using sequence-based and structure-based machine-learning models. PMID:31076573
Centromeric Satellite DNAs: Hidden Sequence Variation in the Human Population. PMID:31072070
De novo emergence and potential function of human-specific tandem repeats in brain-related loci. PMID:31069507
Humans and Chimpanzees Display Opposite Patterns of Diversity in Arylamine N-Acetyltransferase Genes. PMID:31068377
Composite Analysis of the Virome and Bacteriome of HIV/HPV Co-Infected Women Reveals Proxies for Immunodeficiency. PMID:31067713
Diversification of Transposable Elements in Arthropods and Its Impact on Genome Evolution. PMID:31064091
Target Gene Prediction of Transcription Factor Using a New Neighborhood-regularized Tri-factorization One-class Collaborative Filtering Algorithm. PMID:31061989
Emergence of the Dedifferentiated Phenotype in Hepatocyte-Derived Tumors in Mice: Roles of Oncogene-Induced Epigenetic Alterations. PMID:31061957
Human transposons are an abundant supply of transcription factor binding sites and promoter activities in breast cancer cell lines. PMID:31061680
Using RNA-seq to characterize responses to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide resistance in waterhemp (Amaranthus tuberculatus). PMID:31060501
Birth, School, Work, Death, and Resurrection: The Life Stages and Dynamics of Transposable Element Proliferation. PMID:31058854
Systems biology in inflammatory bowel diseases: on the way to precision medicine. PMID:31040620
What viruses tell us about evolution and immunity: beyond Darwin? PMID:31032941
Dissecting Motor Neuron Disease With Drosophila melanogaster. PMID:31031583
DeePromoter: Robust Promoter Predictor Using Deep Learning. PMID:31024615
Gene Lifestyle Interactions With Relation to Obesity, Cardiometabolic, and Cardiovascular Traits Among South Asians. PMID:31024458
The impact of poly-A microsatellite heterologies in meiotic recombination. PMID:31023833
Prediction of Human Immunodeficiency Virus Type 1 Subtype-Specific Off-Target Effects Arising from CRISPR-Cas9 Gene Editing Therapy. PMID:31021222
Impact of Genetic Variation on CRISPR-Cas Targeting. PMID:31021199
Genetic Variations and Precision Medicine. PMID:31019429
Sequencing of human genomes with nanopore technology. PMID:31015479
Mouse germ line mutations due to retrotransposon insertions. PMID:31011371
miR-128 Restriction of LINE-1 (L1) Retrotransposition Is Dependent on Targeting hnRNPA1 mRNA. PMID:31010097
ChimeraMiner: An Improved Chimeric Read Detection Pipeline and Its Application in Single Cell Sequencing. PMID:31010074
Subtype classification and functional annotation of L1Md retrotransposon promoters. PMID:31007728
Genome-Wide Search for Tyrosine Phosphatases in the Human Genome Through Computational Approaches Leads to the Discovery of Few New Domain Architectures. PMID:31007525
Long Noncoding RNA and Epithelial Mesenchymal Transition in Cancer. PMID:31003545
Whole Genome Sequencing and Re-sequencing of the Sable Antelope (Hippotragus niger): A Resource for Monitoring Diversity in ex Situ and in Situ Populations. PMID:31000506
The Many Faces of EpigeneticsOxford, December 2017. PMID:30994386
Protein Structure-Guided Hidden Markov Models (HMMs) as A Powerful Method in the Detection of Ancestral Endogenous Viral Elements. PMID:30986983
HERVs, immunity, and autoimmunity: understanding the connection. PMID:30984482
Evidence for ligandable sites in structured RNA throughout the Protein Data Bank. PMID:30982658
Large-scale 3D chromatin reconstruction from chromosomal contacts. PMID:30967119
A secure SNP panel scheme using homomorphically encrypted K-mers without SNP calling on the user side. PMID:30967116
Small molecule targeting of RNA structures in neurological disorders. PMID:30964958
Genetic and epigenetic sex-specific adaptations to endurance exercise. PMID:30957644
Genome-wide de novo L1 Retrotransposition Connects Endonuclease Activity with Replication. PMID:30955886
Detailed methylation map of LINE-1 5'-promoter region reveals hypomethylated CpG hotspots associated with tumor tissue specificity. PMID:30955237
One hundred years of Drosophila cancer research: no longer in solitude. PMID:30952627
A Pipeline for Faecal Host DNA Analysis by Absolute Quantification of LINE-1 and Mitochondrial Genomic Elements Using ddPCR. PMID:30944341
Mendelian Inconsistent Signatures from 1314 Ancestrally Diverse Family Trios Distinguish Biological Variation from Sequencing Error. PMID:30942611
Viruses and Evolution - Viruses First? A Personal Perspective. PMID:30941110
Regulatory Non-coding RNAs Network in Non-alcoholic Fatty Liver Disease. PMID:30941061
Discovery of Teneurins. PMID:30941006
On the Importance to Acknowledge Transposable Elements in Epigenomic Analyses. PMID:30935103
Investigation of somatic single nucleotide variations in human endogenous retrovirus elements and their potential association with cancer. PMID:30934003
BZLF1 interacts with chromatin remodelers promoting escape from latent infections with EBV. PMID:30926617
The Genome and mRNA Transcriptome of the Cosmopolitan Calanoid Copepod Acartia tonsa Dana Improve the Understanding of Copepod Genome Size Evolution. PMID:30918947
Overlooked: Extrachromosomal DNA and Their Possible Impact on Whole Genome Sequencing. PMID:30918452
Does the Presence of Transposable Elements Impact the Epigenetic Environment of Human Duplicated Genes? PMID:30917603
GenomeWarp: an alignment-based variant coordinate transformation. PMID:30916319
Repeat-Associated Non-ATG Translation: Molecular Mechanisms and Contribution to Neurological Disease. PMID:30909783
SMARCAD1 ATPase activity is required to silence endogenous retroviruses in embryonic stem cells. PMID:30902974
Functional roles of the human ribonuclease A superfamily in RNA metabolism and membrane receptor biology. PMID:30902663
Nutrigenomics of Vitamin D. PMID:30901909
The impact of transposable element activity on therapeutically relevant human stem cells. PMID:30899334
Transposon insertion profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome. PMID:30899333
Validation of a Bioinformatics Workflow for Routine Analysis of Whole-Genome Sequencing Data and Related Challenges for Pathogen Typing in a European National Reference Center: Neisseria meningitidis as a Proof-of-Concept. PMID:30894839
Predicting mutations deleterious to function in beta-lactamase TEM1 using MM-GBSA. PMID:30889230
Amplification Dynamics of Platy-1 Retrotransposons in the Cebidae Platyrrhine Lineage. PMID:30888417
Primate piRNA Cluster Evolution Suggests Limited Relevance of Pseudogenes in piRNA-Mediated Gene Regulation. PMID:30888404
Long Noncoding RNA and Protein Interactions: From Experimental Results to Computational Models Based on Network Methods. PMID:30875752
Glass confers rhabdomeric photoreceptor identity in Drosophila, but not across all metazoans. PMID:30873275
Similarities and differences between variants called with human reference genome HG19 or HG38. PMID:30871461
Synthetic Lethality in Lung Cancer-From the Perspective of Cancer Genomics. PMID:30871030
Increased Transfection of the Easily Oxidizable GC-Rich DNA Fragments into the MCF7 Breast Cancer Cell. PMID:30867888
A comparative survey of microsatellites among wild and domestic cat provides valuable resources for marker development. PMID:30864111
KMT1 family methyltransferases regulate heterochromatin-nuclear periphery tethering via histone and non-histone protein methylation. PMID:30858340
Translating Pharmacogenetics and Pharmacogenomics to the Clinic: Progress in Human and Veterinary Medicine. PMID:30854372
Recent Progress of Polymeric Nanogels for Gene Delivery. PMID:30853837
LINE1 Derepression in Aged Wild-Type and SIRT6-Deficient Mice Drives Inflammation. PMID:30853213
DNMT1 in Six2 Progenitor Cells Is Essential for Transposable Element Silencing and Kidney Development. PMID:30850438
2018 William Allan Award: Discovering the Genes for Common Disease: From Families to Populations. PMID:30849323
A novel nonsense variant in SUPT20H gene associated with Rheumatoid Arthritis identified by Whole Exome Sequencing of multiplex families. PMID:30845214
Potential Implications of Long Noncoding RNAs in Autoimmune Diseases. PMID:30838159
From Desert to Medicine: A Review of Camel Genomics and Therapeutic Products. PMID:30838017
Tropomyosins: Potential Biomarkers for Urothelial Bladder Cancer. PMID:30836651
Endogenous double-stranded Alu RNA elements stimulate IFN-responses in relapsing remitting multiple sclerosis. PMID:30826177
Mapping the dsRNA World. PMID:30824577
Epigenetic changes during aging and their reprogramming potential. PMID:30822165
Common workflow language (CWL)-based software pipeline for de novo genome assembly from long- and short-read data. PMID:30821816
Metabolic therapies inhibit tumor growth in vivo and in silico. PMID:30816152
On the length, weight and GC content of the human genome. PMID:30813969
Insights into DNA polymerase δ's mechanism for accurate DNA replication. PMID:30810803
In-depth structural analysis of glycans in the gas phase. PMID:30809341
Circular RNAs in immune responses and immune diseases. PMID:30809295
Logic Regression Analysis of Gene Polymorphisms and HDL Levels in a Nationally Representative Sample of Iranian Adolescents: The CASPIAN-III Study. PMID:30805016
Discrimination Between Self and Non-Self-Nucleic Acids by the Innate Immune System. PMID:30798985
Cohort profile: design and methods in the eye and vision consortium of UK Biobank. PMID:30796124
Completing the genetic spectrum influencing coronary artery disease: from germline to somatic variation. PMID:30789660
Prostate-specific loss of UXT promotes cancer progression. PMID:30774773
Motor neuron disease-associated loss of nuclear TDP-43 is linked to DNA double-strand break repair defects. PMID:30770445
Endogenous Retroviruses Function as Gene Expression Regulatory Elements During Mammalian Pre-implantation Embryo Development. PMID:30759824
[Breakthrough in understanding the molecular causes of psychiatric disorders]. PMID:30758637
Molecular Signature of CAID Syndrome: Noncanonical Roles of SGO1 in Regulation of TGF-β Signaling and Epigenomics. PMID:30739867
Retroelement-Linked Transcription Factor Binding Patterns Point to Quickly Developing Molecular Pathways in Human Evolution. PMID:30736359
Precision epidemiology for infectious disease control. PMID:30728537
Estimation of duplication history under a stochastic model for tandem repeats. PMID:30727948
Inferring pathogen-host interactions between Leptospira interrogans and Homo sapiens using network theory. PMID:30723266
Profiling of LINE-1-Related Genes in Hepatocellular Carcinoma. PMID:30717368
Deficiency of the Fanconi anemia E2 ubiqitin conjugase UBE2T only partially abrogates Alu-mediated recombination in a new model of homology dependent recombination. PMID:30715513
The Lupus Susceptibility Locus Sgp3 Encodes the Suppressor of Endogenous Retrovirus Expression SNERV. PMID:30709743
Identification of human endogenous retrovirus transcripts in Hodgkin Lymphoma cells. PMID:30707417
Novel Discovery of LINE-1 in a Korean Individual by a Target Enrichment Method. PMID:30699287
Dynamic Methylation of an L1 Transduction Family during Reprogramming and Neurodifferentiation. PMID:30692270
ensembldb: an R package to create and use Ensembl-based annotation resources. PMID:30689724
Whole genome sequencing of breast cancer. PMID:30689231
A re-annotation of the Anopheles darlingi mobilome. PMID:30672977
Where is genomics going next? PMID:30670080
Characterizing the Major Structural Variant Alleles of the Human Genome. PMID:30661756
Mouse PVRIG Has CD8+ T Cell-Specific Coinhibitory Functions and Dampens Antitumor Immunity. PMID:30659055
Methylation of LINE-1 in cell-free DNA serves as a liquid biopsy biomarker for human breast cancers and dog mammary tumors. PMID:30655558
Heterochromatin suppresses gross chromosomal rearrangements at centromeres by repressing Tfs1/TFIIS-dependent transcription. PMID:30652128
Functional Interplay between RNA Viruses and Non-Coding RNA in Mammals. PMID:30646609
SQuIRE reveals locus-specific regulation of interspersed repeat expression. PMID:30624635
Growth factor signalling in osteoarthritis. PMID:30624091
Regulation of LINE-1 Elements by miR-128 Is Not Conserved in Mouse Embryonic Stem Cells. PMID:30619491
Single-Cell Applications of Next-Generation Sequencing. PMID:30617056
Expressional activation and functional roles of human endogenous retroviruses in cancers. PMID:30614117
Revealing the alternative promoter usage of SAF/MAZ gene by bichromatic fluorescent reporter construct. PMID:30610159
Frozen-hydrated chromatin from metaphase chromosomes has an interdigitated multilayer structure. PMID:30609992
Transcription of human endogenous retroviruses in human brain by RNA-seq analysis. PMID:30605476
A Novel Approach Based on a Weighted Interactive Network to Predict Associations of MiRNAs and Diseases. PMID:30597923
Prolonged neuromuscular block associated with cholinesterase deficiency. PMID:30593143
The ACCOuNT Consortium: A Model for the Discovery, Translation, and Implementation of Precision Medicine in African Americans. PMID:30592548
BC200 RNA: An Emerging Therapeutic Target and Diagnostic Marker for Human Cancer. PMID:30590906
Global analysis of tRNA and translation factor expression reveals a dynamic landscape of translational regulation in human cancers. PMID:30588513
Next-generation sequencing of circulating tumor DNA for detection of gene mutations in lung cancer: implications for precision treatment. PMID:30588023
Non-Coding RNAs in Glioma. PMID:30583549
RGAAT: A Reference-based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes. PMID:30583062
LINE-1 and EPAS1 DNA methylation associations with high-altitude exposure. PMID:30574831
Variation in proviral content among human genomes mediated by LTR recombination. PMID:30568734
Accounting for heteroscedasticity and censoring in chromosome partitioning analyses. PMID:30564443
Extensive and deep sequencing of the Venter/HuRef genome for developing and benchmarking genome analysis tools. PMID:30561434
Long-read sequence and assembly of segmental duplications. PMID:30559433
Prolactin-induced protein (PIP)-characterization and role in breast cancer progression. PMID:30555735
Long Interspersed Nuclear Element 1 Retrotransposons Become Deregulated during the Development of Ovarian Cancer Precursor Lesions. PMID:30553834
A hotspots analysis-relation discovery representation model for revealing diabetes mellitus and obesity. PMID:30547805
Genomic Interventions in Medicine. PMID:30546257
Global long terminal repeat activation participates in establishing the unique gene expression programme of classical Hodgkin lymphoma. PMID:30546079
Repetitive Fragile Sites: Centromere Satellite DNA As a Source of Genome Instability in Human Diseases. PMID:30544645
Facial Sadness Recognition is Modulated by Estrogen Receptor Gene Polymorphisms in Healthy Females. PMID:30544539
Novel three‑lncRNA signature predicts survival in patients with pancreatic cancer. PMID:30542694
The translation of non-canonical open reading frames controls mucosal immunity. PMID:30542152
Structure, clustering and functional insights of repeats configurations in the upstream promoter region of the human coding genes. PMID:30537933
Evolution of Our Understanding of the Hyperparathyroid Syndromes: A Historical Perspective. PMID:30536424
Evolution of the Yeast Recombination Landscape. PMID:30535029
Multi-level remodeling of transcriptional landscapes in aging and longevity. PMID:30526773
Deletion of the murine ortholog of the 8q24 gene desert has anti-cancer effects in transgenic mammary cancer models. PMID:30526553
Sense of Smell: Structural, Functional, Mechanistic Advancements and Challenges in Human Olfactory Research. PMID:30520376
DNA Methyltransferase 1 Controls Nephron Progenitor Cell Renewal and Differentiation. PMID:30518531
Genomic Takeover by Transposable Elements in the Strawberry Poison Frog. PMID:30517748
Centromere-associated protein E expresses a novel mRNA isoform in acute lymphoblastic leukemia. PMID:30515258
Tracking microRNA Processing Signals by Degradome Sequencing Data Analysis. PMID:30487815
CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise. PMID:30486838
Retrotransposon insertion as a novel mutational event in Bardet-Biedl syndrome. PMID:30484961
Personal Genome Project UK (PGP-UK): a research and citizen science hybrid project in support of personalized medicine. PMID:30482208
Next-Generation Sequencing Technologies. PMID:30478097
Future Promises and Concerns of Ubiquitous Next-Generation Sequencing. PMID:30478095
Deep repeat resolution-the assembly of the Drosophila Histone Complex. PMID:30476267
Amphioxus functional genomics and the origins of vertebrate gene regulation. PMID:30464347
The importance of the Neutral Theory in 1968 and 50 years on: A response to Kern and Hahn 2018. PMID:30460993
Research progresses in roles of LncRNA and its relationships with breast cancer. PMID:30459529
Mendelian Randomization Studies Promise to Shorten the Journey to FDA Approval. PMID:30456340
Assembly of a pan-genome from deep sequencing of 910 humans of African descent. PMID:30455414
ERVmap analysis reveals genome-wide transcription of human endogenous retroviruses. PMID:30455304
Testing the retroelement invasion hypothesis for the emergence of the ancestral eukaryotic cell. PMID:30455297
Widespread roles of enhancer-like transposable elements in cell identity and long-range genomic interactions. PMID:30455182
MiteFinderII: a novel tool to identify miniature inverted-repeat transposable elements hidden in eukaryotic genomes. PMID:30453969
PAVOOC: designing CRISPR sgRNAs using 3D protein structures and functional domain annotations. PMID:30445568
Sendai Virus Infection Induces Expression of Novel RNAs in Human Cells. PMID:30429577
Exploring the Impact of Single-Nucleotide Polymorphisms on Translation. PMID:30425729
One Major Challenge of Sequencing Large Plant Genomes Is to Know How Big They Really Are. PMID:30423889
A fast adaptive algorithm for computing whole-genome homology maps. PMID:30423094
Next-Generation Sequencing in Autism Spectrum Disorder. PMID:30420340
Ethanol and a rapid-acting antidepressant produce overlapping changes in exon expression in the synaptic transcriptome. PMID:30419244
Alu insertion variants alter mRNA splicing. PMID:30418605
Conserved Pbp1/Ataxin-2 regulates retrotransposon activity and connects polyglutamine expansion-driven protein aggregation to lifespan-controlling rDNA repeats. PMID:30417124
Roles of Smads Family and Alternative Splicing Variants of Smad4 in Different Cancers. PMID:30410607
AFLP-AFLP in silico-NGS approach reveals polymorphisms in repetitive elements in the malignant genome. PMID:30408048
Comparative genomics of the major parasitic worms. PMID:30397333
High-complexity regions in mammalian genomes are enriched for developmental genes. PMID:30395202
The Bermuda Triangle: The Pragmatics, Policies, and Principles for Data Sharing in the History of the Human Genome Project. PMID:30390178
The influence of Neanderthal alleles on cytotoxic response. PMID:30386687
ALPHLARD: a Bayesian method for analyzing HLA genes from whole genome sequence data. PMID:30384854
LTRs activated by Epstein-Barr virus-induced transformation of B cells alter the transcriptome. PMID:30381291
A large-scale analysis of bioinformatics code on GitHub. PMID:30379882
QTL mapping of natural variation reveals that the developmental regulator bruno reduces tolerance to P-element transposition in the Drosophila female germline. PMID:30376574
Impact of somatic and germline mutations on the outcome of systemic mastocytosis. PMID:30373888
Regulation of DNA Double-Strand Break Repair by Non-Coding RNAs. PMID:30373256
Identification of recurrent and novel mutations by whole‑genome sequencing of colorectal tumors from the Han population in Shanghai, eastern China. PMID:30365144
Atypical Parkinsonism-Dystonia Syndrome Caused by a Novel DJ1 Mutation. PMID:30363821
The Decrease in Human Endogenous Retrovirus-H Activity Runs in Parallel with Improvement in ADHD Symptoms in Patients Undergoing Methylphenidate Therapy. PMID:30360480
Transposable Elements in the Organization and Diversification of the Genome of Aegilops speltoides Tausch (Poaceae, Triticeae). PMID:30356408
LncRNA HOTAIR regulates lipopolysaccharide-induced cytokine expression and inflammatory response in macrophages. PMID:30353135
A reference haplotype panel for genome-wide imputation of short tandem repeats. PMID:30353011
Prolonged Idasanutlin (RG7388) Treatment Leads to the Generation of p53-Mutated Cells. PMID:30352966
Targeted genotyping of variable number tandem repeats with adVNTR. PMID:30352806
DNA replication and repair kinetics of Alu, LINE-1 and satellite III genomic repetitive elements. PMID:30352618
Genome-wide map of human and mouse transcription factor binding sites aggregated from ChIP-Seq data. PMID:30352610
Antiviral resistance of stem cells. PMID:30352329
Inhibition of LINE-1 Retrotransposition by Capsaicin. PMID:30347711
De novo assembly of haplotype-resolved genomes with trio binning. PMID:30346939
Cost-effective assembly of the African wild dog (Lycaon pictus) genome using linked reads. PMID:30346553
Chromosome assembly of large and complex genomes using multiple references. PMID:30341161
Special Issue Introduction: The Wonders and Mysteries Next Generation Sequencing Technologies Help Reveal. PMID:30340386
A new approach based on targeted pooled DNA sequencing identifies novel mutations in patients with Inherited Retinal Dystrophies. PMID:30337596
Human SETMAR is a DNA sequence-specific histone-methylase with a broad effect on the transcriptome. PMID:30329085
Biased antagonism of CXCR4 avoids antagonist tolerance. PMID:30327409
Next-Generation Sequencing Strategies. PMID:30323017
Single-nucleotide variants in human RNA: RNA editing and beyond. PMID:30312373
PTB/nPTB: master regulators of neuronal fate in mammals. PMID:30310857
Colocalization analyses of genomic elements: approaches, recommendations and challenges. PMID:30307532
De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data. PMID:30304863
Rapid Expansion of a Highly Germline-Expressed Mariner Element Acquired by Horizontal Transfer in the Fire Ant Genome. PMID:30304394
Crystallography and Its Impact on Carbonic Anhydrase Research. PMID:30302289
Loss of pyruvate kinase M2 limits growth and triggers innate immune signaling in endothelial cells. PMID:30301887
The placenta goes viral: Retroviruses control gene expression in pregnancy. PMID:30300353
Combinatorial Approach for Complex Disorder Prediction: Case Study of Neurodevelopmental Disorders. PMID:30297454
Assessment of Resistance to Tyrosine Kinase Inhibitors by an Interrogation of Signal Transduction Pathways by Antibody Arrays. PMID:30295648
ProteomeGenerator: A Framework for Comprehensive Proteomics Based on de Novo Transcriptome Assembly and High-Accuracy Peptide Mass Spectral Matching. PMID:30295032
Multiple serine transposase dimers assemble the transposon-end synaptic complex during IS607-family transposition. PMID:30289389
An Analysis of IS630/Tc1/mariner Transposons in the Genome of a Pacific Oyster, Crassostrea gigas. PMID:30283979
Development of an AmpliSeqTM Panel for Next-Generation Sequencing of a Set of Genetic Predictors of Persisting Pain. PMID:30283335
Functional intronic variant of SLC5A10 affects DRG2 expression and survival outcomes of early-stage non-small-cell lung cancer. PMID:30281872
Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci. PMID:30275530
NMD-degradome sequencing reveals ribosome-bound intermediates with 3'-end non-templated nucleotides. PMID:30275517
PARP1 activation increases expression of modified tumor suppressors and pathways underlying development of aggressive hepatoblastoma. PMID:30271949
Progress of analytical tools and techniques for human gut microbiome research. PMID:30267313
Darkness in the Human Gene and Protein Function Space: Widely Modest or Absent Illumination by the Life Science Literature and the Trend for Fewer Protein Function Discoveries Since 2000. PMID:30265449
Genomics research in Africa and its impact on global health: insights from African researchers. PMID:30263136
Multi-objective optimized genomic breeding strategies for sustainable food improvement. PMID:30262841
Non-coding RNA in Ischemic and Non-ischemic Cardiomyopathy. PMID:30259174
Epigenetic Effects of Drugs of Abuse. PMID:30257440
Noncoding RNAs as therapeutic targets in early stage diabetic kidney disease. PMID:30254844
Human Endogenous Retroviruses Are Ancient Acquired Elements Still Shaping Innate Immune Responses. PMID:30250470
Data-Driven Exploration of Selectivity and Off-Target Activities of Designated Chemical Probes. PMID:30249057
Personalised Medicine: The Odyssey from Hope to Practice. PMID:30248964
Influenza Virus-Host Co-evolution. A Predator-Prey Relationship? PMID:30245689
Genomic approaches for studying crop evolution. PMID:30241487
Prolonged DNA hydrolysis in water: A study on DNA stability. PMID:30238033
A Global Overview of Precision Medicine in Type 2 Diabetes. PMID:30237159
Reduced PRC2 function alters male germline epigenetic programming and paternal inheritance. PMID:30236109
Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species. PMID:30227846
Genomics, bio specimens, and other biological data: Current status and future directions. PMID:30226926
Association between Polymorphisms of Antioxidant Gene (MnSOD, CAT, and GPx1) and Risk of Coronary Artery Disease. PMID:30225256
Reviving a 60 million year old LINE-1 element. PMID:30221208
Repeat-associated non-ATG (RAN) translation. PMID:30213863
Functional Evolution of Avian RIG-I-Like Receptors. PMID:30213147
Somatic Mutagenesis in Mammals and Its Implications for Human Disease and Aging. PMID:30212236
Impacts of bisphenol A (BPA) and phthalate exposures on epigenetic outcomes in the human placenta. PMID:30210810
Whole genome sequencing data for two individuals of Pakistani descent. PMID:30204152
Finding Nemo's Genes: A chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula. PMID:30203521
Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms. PMID:30202060
Transposons, p53 and Genome Security. PMID:30195581
Early Behavioral Alterations and Increased Expression of Endogenous Retroviruses Are Inherited Across Generations in Mice Prenatally Exposed to Valproic Acid. PMID:30194517
Developmental and cancer-associated plasticity of DNA replication preferentially targets GC-poor, lowly expressed and late-replicating regions. PMID:30189101
Genomes for all. PMID:30188541
Non-coding RNAs in retinal development and function. PMID:30187163
Pairs of Adjacent Conserved Noncoding Elements Separated by Conserved Genomic Distances Act as Cis-Regulatory Units. PMID:30184074
Analysis of Genome-Wide Differentiation between Native and Introduced Populations of the Cupped Oysters Crassostrea gigas and Crassostrea angulata. PMID:30184067
From Molecules to Mechanisms: Functional Proteomics and Its Application to Renal Tubule Physiology. PMID:30182799
What Are 3' UTRs Doing? PMID:30181377
The Xenopus animal cap transcriptome: building a mucociliary epithelium. PMID:30165493
Molecular functions and specific roles of circRNAs in the cardiovascular system. PMID:30159442
Circular RNAs in the cardiovascular system. PMID:30159434
Non-coding RNAs in skeletal muscle regeneration. PMID:30159421
MinION rapid sequencing: Review of potential applications in neurosurgery. PMID:30159201
Alternative splicing of the Caenorhabditis elegans lev-11 tropomyosin gene is regulated in a tissue-specific manner. PMID:30155988
Biophysical and structural characterization of the thermostable WD40 domain of a prokaryotic protein, Thermomonospora curvata PkwA. PMID:30154510
Nomenclature for endogenous retrovirus (ERV) loci. PMID:30153831
The Gut Microbiome in Adult and Pediatric Functional Gastrointestinal Disorders. PMID:30153517
Nucleic Acid-Barcoding Technologies: Converting DNA Sequencing into a Broad-Spectrum Molecular Counter. PMID:30153374
Transposable element dysregulation in systemic lupus erythematosus and regulation by histone conformation and Hsp90. PMID:30149120
Impact of non-LTR retrotransposons in the differentiation and evolution of anatomically modern humans. PMID:30147753
Bioinformatic and biological avenues for understanding alcohol use disorder. PMID:30144960
Endogenous retrovirus expression is associated with response to immune checkpoint blockade in clear cell renal cell carcinoma. PMID:30135306
The collaborative effect of scientific meetings: A study of the International Milk Genomics Consortium. PMID:30133459
Transcriptome-wide analysis uncovers the targets of the RNA-binding protein MSI2 and effects of MSI2's RNA-binding activity on IL-6 signaling. PMID:30126842
Association of Bisphenol A Exposure with LINE-1 Hydroxymethylation in Human Semen. PMID:30126118
Open questions: How many genes do we have? PMID:30124169
Practical guidelines for rigor and reproducibility in preclinical and clinical studies on cardioprotection. PMID:30120595
Cross-disciplinary evolution of the genomics revolution. PMID:30116784
Application of genome analysis strategies in the clinical testing for pediatric diseases. PMID:30112248
Discovery of 7-hydroxyaporphines as conformationally restricted ligands for beta-1 and beta-2 adrenergic receptors. PMID:30108929
Proteomics: Clinical and research applications in respiratory diseases. PMID:30105802
A piRNA utilizes HILI and HIWI2 mediated pathway to down-regulate ferritin heavy chain 1 mRNA in human somatic cells. PMID:30102404
[The Use Of Pulmonary Gene Therapy In The Treatment Of Experimental Models Of Pneumonia And Septicemia]. PMID:30100668
Delineating inflammatory bowel disease through transcriptomic studies: current review of progress and evidence. PMID:30090036
Somatic mutations in the human brain: implications for psychiatric research. PMID:30087451
The age-regulated zinc finger factor ZNF367 is a new modulator of neuroblast proliferation during embryonic neurogenesis. PMID:30087422
Gene editing in the context of an increasingly complex genome. PMID:30086710
LINE- and Alu-containing genomic instability hotspot at 16q24.1 associated with recurrent and nonrecurrent CNV deletions causative for ACDMPV. PMID:30084155
Degradation and remobilization of endogenous retroviruses by recombination during the earliest stages of a germ-line invasion. PMID:30082403
Reconstruction of the cell entry pathway of an extinct virus. PMID:30080900
Alcohol Metabolizing Polygenic Risk for Alcohol Consumption in European American College Students. PMID:30079879
Trends to store digital data in DNA: an overview. PMID:30073589
Related Endogenous Retrovirus-K Elements Harbor Distinct Protease Active Site Motifs. PMID:30072963
De novo human genome assemblies reveal spectrum of alternative haplotypes in diverse populations. PMID:30072691
Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation. PMID:30070637
Microsatellite enhancers can be targeted to impair tumorigenesis. PMID:30068701
KAP1 regulates endogenous retroviruses in adult human cells and contributes to innate immune control. PMID:30061100
TIP60 represses activation of endogenous retroviral elements. PMID:30053221
Mobile elements contribute to the uniqueness of human genome with 15,000 human-specific insertions and 14 Mbp sequence increase. PMID:30052927
Epigenome editing of microsatellite repeats defines tumor-specific enhancer functions and dependencies. PMID:30042132
[Genetics in medicine]. PMID:30039391
Ras Suppresses TXNIP Expression by Restricting Ribosome Translocation. PMID:30037981
Non-Coding RNAs in Endometrial Physiopathology. PMID:30037059
Cellular Genomic Sites of Hepatitis B Virus DNA Integration. PMID:30037029
Investigation of epigenetic regulatory networks associated with autism spectrum disorder (ASD) by integrated global LINE-1 methylation and gene expression profiling analyses. PMID:30036398
Characterization of Glycoproteins with the Immunoglobulin Fold by X-Ray Crystallography and Biophysical Techniques. PMID:30035760
CRISPR-based reagents to study the influence of the epigenome on gene expression. PMID:30030848
The genomics of insecticide resistance: insights from recent studies in African malaria vectors. PMID:30025626
Noninvasive cancer biomarkers in solid malignancies: circulating tumor DNA-clinical utility, current limitations and future perspectives. PMID:30023396
Retrotransposon-induced mosaicism in the neural genome. PMID:30021882
Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing. PMID:30018084
GtTR: Bayesian estimation of absolute tandem repeat copy number using sequence capture and high throughput sequencing. PMID:30012093
Molecular biology as a tool for the treatment of cancer. PMID:30006681
Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes. PMID:30005633
Comparative genomic analysis of eutherian adiponectin genes. PMID:30003153
L1 retrotransposition in the soma: a field jumping ahead. PMID:30002735
HIV infection results in clonal expansions containing integrations within pathogenesis-related biological pathways. PMID:29997284
Germline DNA replication timing shapes mammalian genome composition. PMID:29986092
Gene-by-Gene or Localized Dosage Compensation on the Neo-X Chromosome in Drosophila miranda. PMID:29986000
Tetz's theory and law of longevity. PMID:29978435
Machine Learning and Radiogenomics: Lessons Learned and Future Directions. PMID:29977864
LTR-retrotransposon transcriptome modulation in response to endotoxin-induced stress in PBMCs. PMID:29976163
Reappraisal of Reported Genes for Sudden Arrhythmic Death: Evidence-Based Evaluation of Gene Validity for Brugada Syndrome. PMID:29959160
G protein-coupled receptors: the evolution of structural insight. PMID:29951585
Haplotype phasing in single-cell DNA-sequencing data. PMID:29950014
Platforms for Investigating LncRNA Functions. PMID:29945466
Ethics and Quality Assessment in Genetic Testing. PMID:29942241
Towards Automation for Molecular Diagnosis of Cancer. PMID:29942240
Engrailed homeoprotein blocks degeneration in adult dopaminergic neurons through LINE-1 repression. PMID:29941661
Multigenome analysis implicates miniature inverted-repeat transposable elements (MITEs) in metabolic diversification in eudicots. PMID:29941591
Multiscale Analysis of Independent Alzheimer's Cohorts Finds Disruption of Molecular, Genetic, and Clinical Networks by Human Herpesvirus. PMID:29937276
Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data. PMID:29936186
Identification of transposable elements fused in the exonic region of the olive flounder genome. PMID:29934806
Transverse cardiac slicing and optical imaging for analysis of transmural gradients in membrane potential and Ca2+ transients in murine heart. PMID:29928770
MALAT1: A long non-coding RNA highly associated with human cancers. PMID:29928382
Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly. PMID:29925783
A machine-learned analysis of human gene polymorphisms modulating persisting pain points to major roles of neuroimmune processes. PMID:29923268
Horizontally transferred genes in the ctenophore Mnemiopsis leidyi. PMID:29922518
RNA Degradation in Neurodegenerative Disease. PMID:29916018
Motifome comparison between modern human, Neanderthal and Denisovan. PMID:29914355
Predicting human genes susceptible to genomic instability associated with Alu/Alu-mediated rearrangements. PMID:29907612
Clinical validation of the Tempus xO assay. PMID:29899824
Human Genetics of Obesity and Type 2 Diabetes Mellitus: Past, Present, and Future. PMID:29899044
ALUminating the Path of Atherosclerosis Progression: Chaos Theory Suggests a Role for Alu Repeats in the Development of Atherosclerotic Vascular Disease. PMID:29895733
Genetic Diversity in the UV Sex Chromosomes of the Brown Alga Ectocarpus. PMID:29882839
Genetic testing and autism: Tutorial for communication sciences and disorders. PMID:29879582
Cancer epigenetics: Moving forward. PMID:29879107
RNA Editing and Retrotransposons in Neurology. PMID:29875629
Precision cancer therapy is impacted by oncogene-dependent epigenome remodeling. PMID:29872691
DACCOR-Detection, characterization, and reconstruction of repetitive regions in bacterial genomes. PMID:29868249
Long Non-coding RNAs in Endothelial Biology. PMID:29867565
Evolutionary divergence of 3' UTRs in cichlid fishes. PMID:29866078
Evolution, kidney development, and chronic kidney disease. PMID:29857053
Mining the literature for genes associated with placenta-mediated maternal diseases. PMID:29854219
Counteraction of Oxidative Stress by Vitamin E Affects Epigenetic Regulation by Increasing Global Methylation and Gene Expression of MLH1 and DNMT1 Dose Dependently in Caco-2 Cells. PMID:29854080
The Physical and Biochemical Properties of the Extracellular Matrix Regulate Cell Fate. PMID:29853174
Landscape of Microsatellite Instability Across 39 Cancer Types. PMID:29850653
Whole-Genome Sequencing in Cancer. PMID:29844223
Long-Distance Relationships: Suppression of Repeat-Mediated Deletions. PMID:29804746
Mining of potential drug targets through the identification of essential and analogous enzymes in the genomes of pathogens of Glycine max, Zea mays and Solanum lycopersicum. PMID:29799863
Prenatal Perfluorooctyl Sulfonate Exposure and Alu DNA Hypomethylation in Cord Blood. PMID:29795014
Moonshot Objectives: Catalyze New Scientific Breakthroughs-Proteogenomics. PMID:29794536
Getting up close and personal with UK genomics and beyond. PMID:29793512
Mutalisk: a web-based somatic MUTation AnaLyIS toolKit for genomic, transcriptional and epigenomic signatures. PMID:29790943
PUF60-activated exons uncover altered 3' splice-site selection by germline missense mutations in a single RRM. PMID:29788428
ZNF418 overexpression protects against gastric carcinoma and prompts a good prognosis. PMID:29785125
All I's on the RADAR: role of ADAR in gene regulation. PMID:29770436
A Next-Generation Sequencing Primer-How Does It Work and What Can It Do? PMID:29761157
Selective modulation of local linkages between active transcription and oxidative demethylation activity shapes cardiomyocyte-specific gene-body epigenetic status in mice. PMID:29747586
Transactivation of human endogenous retrovirus K (HERV-K) by KSHV promotes Kaposi's sarcoma development. PMID:29743595
Osmotic modulation of chromatin impacts on efficiency and kinetics of cell fate modulation. PMID:29740078
A deeper view into the significance of simple sequence repeats in pre-miRNAs provides clues for its possible roles in determining the function of microRNAs. PMID:29739315
Detection and analysis of ancient segmental duplications in mammalian genomes. PMID:29735604
Towards a map of cis-regulatory sequences in the human genome. PMID:29733395
Copy Number Variation Disorders. PMID:29732242
Genome Editing Redefines Precision Medicine in the Cardiovascular Field. PMID:29731778
Targeting RNA in mammalian systems with small molecules. PMID:29726113
Reconstruction of a replication-competent ancestral murine endogenous retrovirus-L. PMID:29716624
Heritable L1 Retrotransposition Events During Development: Understanding Their Origins: Examination of heritable, endogenous L1 retrotransposition in mice opens up exciting new questions and research directions. PMID:29709066
Predicting gene structure changes resulting from genetic variants via exon definition features. PMID:29701825
Nuclear Signaling of Plant MAPKs. PMID:29696029
Prostate Cancer Genomics: Recent Advances and the Prevailing Underrepresentation from Racial and Ethnic Minorities. PMID:29690565
Differential Effect of Selection against LINE Retrotransposons among Vertebrates Inferred from Whole-Genome Data and Demographic Modeling. PMID:29688421
Effective discovery of rare variants by pooled target capture sequencing: A comparative analysis with individually indexed target capture sequencing. PMID:29677560
Divergent genome evolution caused by regional variation in DNA gain and loss between human and mouse. PMID:29677183
Cell type transcriptome atlas for the planarian Schmidtea mediterranea. PMID:29674431
Stonewall and Brickwall: Two Partially Redundant Determinants Required for the Maintenance of Female Germline in Drosophila. PMID:29669801
Melanoma: What do all the mutations mean? PMID:29663336
Rare Splice Variants in Long Non-Coding RNAs. PMID:29657294
Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs. PMID:29648536
Identification and characterization of short tandem repeats in the Tibetan macaque genome based on resequencing data. PMID:29643326
L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis. PMID:29643204
Tracking the Continuous Evolutionary Processes of an Endogenous Retrovirus of the Domestic Cat: ERV-DC. PMID:29642384
Genotype imputation performance of three reference panels using African ancestry individuals. PMID:29637265
Repeat-mediated deletions can be induced by a chromosomal break far from a repeat, but multiple pathways suppress such rearrangements. PMID:29636371
DNA methylation profiles correlated to striped bass sperm fertility. PMID:29636007
Targeting IS608 transposon integration to highly specific sequences by structure-based transposon engineering. PMID:29635476
Reactivation of endogenous retroviral elements via treatment with DNMT- and HDAC-inhibitors. PMID:29633898
A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms. PMID:29632618
Relationship between Long Interspersed Nuclear Element-1 DNA Methylation in Leukocytes and Dyslipidemia in the Japanese General Population. PMID:29628482
A novel long non-coding RNA Myolinc regulates myogenesis through TDP-43 and Filip1. PMID:29618024
An Evaluation of Function of Multicopy Noncoding RNAs in Mammals Using ENCODE/FANTOM Data and Comparative Genomics. PMID:29617896
A survey and evaluation of Web-based tools/databases for variant analysis of TCGA data. PMID:29617727
The SAMHD1-mediated block of LINE-1 retroelements is regulated by phosphorylation. PMID:29610582
From "Cellular" RNA to "Smart" RNA: Multiple Roles of RNA in Genome Stability and Beyond. PMID:29600857
Protein-nucleic acid interactions of LINE-1 ORF1p. PMID:29596909
HERV Envelope Proteins: Physiological Role and Pathogenic Potential in Cancer and Autoimmunity. PMID:29593697
The influence of transcript assembly on the proteogenomics discovery of microproteins. PMID:29584760
HnRNP L represses cryptic exons. PMID:29581412
Evidence for DNA Sequence Encoding of an Accessible Nucleosomal Array across Vertebrates. PMID:29580552
Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations. PMID:29576615
In silico analysis of endogenous siRNAs associated transposable elements and NATs in Schistosoma japonicum reveals their putative roles during reproductive development. PMID:29568977
Human LINE-1 retrotransposition requires a metastable coiled coil and a positively charged N-terminus in L1ORF1p. PMID:29565245
iPS Cells-The Triumphs and Tribulations. PMID:29563461
Multispecies reconstructions uncover widespread conservation, and lineage-specific elaborations in eukaryotic mRNA metabolism. PMID:29561870
Identification of sex-specific DNA methylation changes driven by specific chemicals in cord blood in a Faroese birth cohort. PMID:29560787
The Ever-Evolving Concept of the Gene: The Use of RNA/Protein Experimental Techniques to Understand Genome Functions. PMID:29560353
Analysis of lineage-specific Alu subfamilies in the genome of the olive baboon, Papio anubis. PMID:29560044
Precision oncology in advanced cancer patients improves overall survival with lower weekly healthcare costs. PMID:29552312
Nimbus: a design-driven analyses suite for amplicon-based NGS data. PMID:29538618
Transcriptional landscape of human endogenous retroviruses (HERVs) and other repetitive elements in psoriatic skin. PMID:29531256
Global analysis of A-to-I RNA editing reveals association with common disease variants. PMID:29527417
Investigation of Endogenous Retrovirus Sequences in the Neighborhood of Genes Up-regulated in a Neuroblastoma Model after Treatment with Hypoxia-Mimetic Cobalt Chloride. PMID:29515560
Human Endogenous Retroviruses and Their Putative Role in the Development of Autoimmune Disorders Such as Multiple Sclerosis. PMID:29515547
Spliced integrated retrotransposed element (SpIRE) formation in the human genome. PMID:29505568
Reading the tea leaves: Dead transposon copies reveal novel host and transposon biology. PMID:29505560
LINE-1 ORF1 Protein Is Up-regulated by Reactive Oxygen Species and Associated with Bladder Urothelial Carcinoma Progression. PMID:29496693
DNA methylation in the pathogenesis of type 2 diabetes in humans. PMID:29496428
Elevated HERV-K Expression in Soft Tissue Sarcoma Is Associated with Worsened Relapse-Free Survival. PMID:29487589
High-Throughput Methods to Detect Long Non-Coding RNAs. PMID:29485610
Agonistic Autoantibodies to the β2-Adrenergic Receptor Involved in the Pathogenesis of Open-Angle Glaucoma. PMID:29483909
Individual retrotransposon integrants are differentially controlled by KZFP/KAP1-dependent histone methylation, DNA methylation and TET-mediated hydroxymethylation in naïve embryonic stem cells. PMID:29482634
Genetic instability associated with loop or stem-loop structures within transcription units can be independent of nucleotide excision repair. PMID:29474673
Introduction to mammalian genome special issue: the combined role of genetics and environment relevant to human disease outcomes. PMID:29460122
A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts. PMID:29447159
Glia maturation factor-β: a potential therapeutic target in neurodegeneration and neuroinflammation. PMID:29445286
Mutation in an alternative transcript of CDKL5 in a boy with early-onset seizures. PMID:29444904
Evolution of neuropeptide signalling systems. PMID:29440283
Alternative Splicing as a Target for Cancer Treatment. PMID:29439487
Toward a Tiered Model to Share Clinical Trial Data and Samples in Precision Oncology. PMID:29435448
Treatment with 5-azacitidine delay growth of glioblastoma xenografts: a potential new treatment approach for glioblastomas. PMID:29427211
OVAS: an open-source variant analysis suite with inheritance modelling. PMID:29422027
Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach. PMID:29398526
Post-transcriptional regulation of LINE-1 retrotransposition by AID/APOBEC and ADAR deaminases. PMID:29396793
Mammalian transposable elements and their impacts on genome evolution. PMID:29392473
A high throughput screen for active human transposable elements. PMID:29390960
Transcriptome-wide identification of the RNA-binding landscape of the chromatin-associated protein PARP1 reveals functions in RNA biogenesis. PMID:29387452
Co(II) Coordination in Prokaryotic Zinc Finger Domains as Revealed by UV-Vis Spectroscopy. PMID:29386985
Liver X Receptor-Binding DNA Motif Associated With Atherosclerosis-Specific DNA Methylation Profiles of Alu Elements and Neighboring CpG Islands. PMID:29386205
Illumina Library Preparation for Sequencing the GC-Rich Fraction of Heterogeneous Genomic DNA. PMID:29385572
Serum DNA integrity index as a potential molecular biomarker in endometrial cancer. PMID:29382392
Rheumatoid arthritis patient antibodies highly recognize IL-2 in the immune response pathway involving IRF5 and EBV antigens. PMID:29379122
Protecting and Diversifying the Germline. PMID:29378808
Cognitive genomics: Searching for the genetic roots of neuropsychological functioning. PMID:29376674
Intraspecific and intraorganismal copy number dynamics of retrotransposons and tandem repeat in Aegilops speltoides Tausch (Poaceae, Triticeae). PMID:29374788
Patterns of variation in cis-regulatory regions: examining evidence of purifying selection. PMID:29373957
Targeted deletion of a 170-kb cluster of LINE-1 repeats and implications for regional control. PMID:29367313
Plasmodium parasites of birds have the most AT-rich genes of eukaryotes. PMID:29360019
The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution. PMID:29358652
Reccurrent F8 Intronic Deletion Found in Mild Hemophilia A Causes Alu Exonization. PMID:29357978
Beta and Gamma Human Herpesviruses: Agonistic and Antagonistic Interactions with the Host Immune System. PMID:29354096
qPortal: A platform for data-driven biomedical research. PMID:29352322
GenomeLandscaper: Landscape analysis of genome-fingerprints maps assessing chromosome architecture. PMID:29348569
Natural antisense transcripts in diseases: From modes of action to targeted therapies. PMID:29341438
Contribution of transposable elements and distal enhancers to evolution of human-specific features of interphase chromatin architecture in embryonic stem cells. PMID:29335803
Transposable elements: genome innovation, chromosome diversity, and centromere conflict. PMID:29332159
High expression of Endogenous Retroviruses from intrauterine life to adulthood in two mouse models of Autism Spectrum Disorders. PMID:29330412
Large genomic insertion at the Shh locus results in hammer toes through enhancer adoption. PMID:29330329
Retrovirus-like Gag Protein Arc1 Binds RNA and Traffics across Synaptic Boutons. PMID:29328915
Whole-genome sequencing reveals principles of brain retrotransposition in neurodevelopmental disorders. PMID:29327725
Analysis of DNA modifications in aging research. PMID:29327208
Dissection of Myogenic Differentiation Signatures in Chickens by RNA-Seq Analysis. PMID:29324704
Investigation and identification of functional post-translational modification sites associated with drug binding and protein-protein interactions. PMID:29322920
Using Genome Sequence to Enable the Design of Medicines and Chemical Probes. PMID:29322778
Structural and Evolutionary Relationships in the Giant Sex Chromosomes of Three Microtus Species. PMID:29320452
Identification of Inherited Retinal Disease-Associated Genetic Variants in 11 Candidate Genes. PMID:29320387
Interplay between RNASEH2 and MOV10 controls LINE-1 retrotransposition. PMID:29315404
Identification of Transposable Elements Contributing to Tissue-Specific Expression of Long Non-Coding RNAs. PMID:29315213
The lncRNA-HOXA-AS2/EZH2/LSD1 oncogene complex promotes cell proliferation in pancreatic cancer. PMID:29312501
Potential Links between Hepadnavirus and Bornavirus Sequences in the Host Genome and Cancer. PMID:29312227
Physiological and Pathological Transcriptional Activation of Endogenous Retroelements Assessed by RNA-Sequencing of B Lymphocytes. PMID:29312197
The Importance of ncRNAs as Epigenetic Mechanisms in Phenotypic Variation and Organic Evolution. PMID:29312192
Novel Transcriptional Activity and Extensive Allelic Imbalance in the Human MHC Region. PMID:29311362
LINE-1 protein localization and functional dynamics during the cell cycle. PMID:29309036
Dissection of affinity captured LINE-1 macromolecular complexes. PMID:29309035
Long interspersed nuclear element-1 expression and retrotransposition in prostate cancer cells. PMID:29308092
Endogenous LINE-1 (Long Interspersed Nuclear Element-1) Reverse Transcriptase Activity in Platelets Controls Translational Events Through RNA-DNA Hybrids. PMID:29301786
The effects of transcription and recombination on mutational dynamics of short tandem repeats. PMID:29300948
The development and growth of EJHG 1995-2017. PMID:29297878
Erythrogene: a database for in-depth analysis of the extensive variation in 36 blood group systems in the 1000 Genomes Project. PMID:29296939
Alu element insertion in PKLR gene as a novel cause of pyruvate kinase deficiency in Middle Eastern patients. PMID:29288557
Overexpressed HSF1 cancer signature genes cluster in human chromosome 8q. PMID:29268782
From a retrovirus infection of mice to a long noncoding RNA that induces proto-oncogene transcription and oncogenesis via an epigenetic transcription switch. PMID:29263895
Was the Watchmaker Blind? Or Was She One-Eyed? PMID:29261138
Recognizing the SINEs of Infection: Regulation of Retrotransposon Expression and Modulation of Host Cell Processes. PMID:29258254
De-novo emergence of SINE retroposons during the early evolution of passerine birds. PMID:29255493
Single molecule sequencing of the M13 virus genome without amplification. PMID:29253901
Analysis of the Expression of Repetitive DNA Elements in Osteosarcoma. PMID:29250102
Size, Shape, and Sequence-Dependent Immunogenicity of RNA Nanoparticles. PMID:29246318
LINE-1 retrotransposons in healthy and diseased human brain. PMID:29239145
Circular RNAs: A novel type of non-coding RNA and their potential implications in antiviral immunity. PMID:29230098
Disease onset in X-linked dystonia-parkinsonism correlates with expansion of a hexameric repeat within an SVA retrotransposon in TAF1. PMID:29229810
Identification of differentially expressed genes, lncRNAs and miRNAs which are associated with tumor malignant phenotypes in hepatoblastoma patients. PMID:29228631
Age-dependent changes in mean and variance of gene expression across tissues in a twin cohort. PMID:29228364
Patient Engagement in Kidney Research: Opportunities and Challenges Ahead. PMID:29225906
Transcription coupled repair and biased insertion of human retrotransposon L1 in transcribed genes. PMID:29225704
Diagnostic and prognostic tests in systemic lupus erythematosus. PMID:29224677
Integrating 5hmC and gene expression data to infer regulatory mechanisms. PMID:29220513
Computational identification of harmful mutation regions to the activity of transposable elements. PMID:29219079
Lessons from the Human Genome Project: Modesty, Honesty, and Realism. PMID:29218057
Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators. PMID:29211708
Living Organisms Author Their Read-Write Genomes in Evolution. PMID:29211049
Whole-exome sequencing of sickle cell disease patients with hyperhemolysis syndrome suggests a role for rare variation in disease predisposition. PMID:29210071
Transposable Element Mediated Innovation in Gene Regulatory Landscapes of Cells: Re-Visiting the "Gene-Battery" Model. PMID:29206283
Detection of the LINE-1 retrotransposon RNA-binding protein ORF1p in different anatomical regions of the human brain. PMID:29201157
The rise of the genome and personalised medicine. PMID:29196356
Decontaminating eukaryotic genome assemblies with machine learning. PMID:29191179
A Multilayered Control of the Human Survival Motor Neuron Gene Expression by Alu Elements. PMID:29187847
Genomic copy number variation analysis in multiple system atrophy. PMID:29187220
Functional horizontal gene transfer from bacteria to eukaryotes. PMID:29176581
Catching hidden variation: systematic correction of reference minor allele annotation in clinical variant calling. PMID:29155419
Molecular Crosstalking among Noncoding RNAs: A New Network Layer of Genome Regulation in Cancer. PMID:29147648
The Epstein-Barr Virus Episome Maneuvers between Nuclear Chromatin Compartments during Reactivation. PMID:29142137
DNA damage responses and p53 in the aging process. PMID:29141944
The European Nucleotide Archive in 2017. PMID:29140475
Genomic structural variations lead to dysregulation of important coding and non-coding RNA species in dilated cardiomyopathy. PMID:29138229
Optimized approach for the identification of highly efficient correctors of nonsense mutations in human diseases. PMID:29131862
Improving virtual screening of G protein-coupled receptors via ligand-directed modeling. PMID:29131821
Significance of functional disease-causal/susceptible variants identified by whole-genome analyses for the understanding of human diseases. PMID:29129848
Neurobiology: A genetic cause of age-related decline. PMID:29120415
Alternative splicing regulation in tumor necrosis factor-mediated inflammation. PMID:29113151
Detection of subclonal L1 transductions in colorectal cancer by long-distance inverse-PCR and Nanopore sequencing. PMID:29109480
The first draft reference genome of the American mink (Neovison vison). PMID:29109430
Coevolution between transposable elements and recombination. PMID:29109221
RNA versatility, flexibility, and thermostability for practice in RNA nanotechnology and biomedical applications. PMID:29105333
A Role for the Mutagenic DNA Self-Catalyzed Depurination Mechanism in the Evolution of 7SL-Derived RNAs. PMID:29103173
An endosiRNA-Based Repression Mechanism Counteracts Transposon Activation during Global DNA Demethylation in Embryonic Stem Cells. PMID:29100015
Can Probiotic Supplements Improve Outcomes in Rheumatoid Arthritis? PMID:29094223
A Never Ending Story.. PMID:29090025
The shortening of leukocyte telomere length relates to DNA hypermethylation of LINE-1 in type 2 diabetes mellitus. PMID:29088760
Haplotype-specific MAPT exon 3 expression regulated by common intronic polymorphisms associated with Parkinsonian disorders. PMID:29084565
Methylation of ZNF331 is an independent prognostic marker of colorectal cancer and promotes colorectal cancer growth. PMID:29075358
BBMerge - Accurate paired shotgun read merging via overlap. PMID:29073143
Molecular determinants of beta-adrenergic signaling to voltage-gated K+ channels in the cerebral circulation. PMID:29072364
Epigenetics and precision medicine in cardiovascular patients: from basic concepts to the clinical arena. PMID:29069341
Pivotal Impacts of Retrotransposon Based Invasive RNAs on Evolution. PMID:29067016
A Review of Recent Advances in Translational Bioinformatics: Bridges from Biology to Medicine. PMID:29063562
The emerging roles of NGS-based liquid biopsy in non-small cell lung cancer. PMID:29061113
Genome-wide association study reveals genetic loci and candidate genes for average daily gain in Duroc pigs. PMID:29059722
PopHuman: the human population genomics browser. PMID:29059408
Predicting causal variants affecting expression by using whole-genome sequencing and RNA-seq from multiple human tissues. PMID:29058714
[Big Data Revolution or Data Hubris? : On the Data Positivism of Molecular Biology]. PMID:29058018
DNA methylation and hydroxymethylation analyses of the active LINE-1 subfamilies in mice. PMID:29051587
Precision medicine for all? Challenges and opportunities for a precision medicine approach to critical illness. PMID:29047353
The role of gene variants in the pathogenesis of neurodegenerative disorders as revealed by next generation sequencing studies: a review. PMID:29046784
HIV-1 Infection of Primary CD4+ T Cells Regulates the Expression of Specific Human Endogenous Retrovirus HERV-K (HML-2) Elements. PMID:29046457
Ribosome Biogenesis Modulates Ty1 Copy Number Control in Saccharomyces cerevisiae. PMID:29046400
The Antibody Repertoire of Colorectal Cancer. PMID:29046389
Integrating networks and comparative genomics reveals retroelement proliferation dynamics in hominid genomes. PMID:29043294
A plasma proteomics method reveals links between ischemic stroke and MTHFR C677T genotype. PMID:29042595
Human Genome Sequencing at the Population Scale: A Primer on High-Throughput DNA Sequencing and Analysis. PMID:29040395
Highly sensitive and specific Alu-based quantification of human cells among rodent cells. PMID:29038571
Striking a balance: regulation of transposable elements by Zfp281 and Mll2 in mouse embryonic stem cells. PMID:29036642
cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches. PMID:29036576
HOXD-AS1 functions as an oncogenic ceRNA to promote NSCLC cell progression by sequestering miR-147a. PMID:29033588
Emerging and evolving concepts in gene essentiality. PMID:29033457
Software Dedicated to Virus Sequence Analysis "Bioinformatics Goes Viral". PMID:29029728
Condensin II and GAIT complexes cooperate to restrict LINE-1 retrotransposition in epithelial cells. PMID:29028794
CRISPR/Cas9-mediated noncoding RNA editing in human cancers. PMID:29028415
High-resolution mapping of the pericentromeric region on wheat chromosome arm 5AS harbouring the Fusarium head blight resistance QTL Qfhs.ifa-5A. PMID:29024288
Adaptive self-organization in the embryo: its importance to adult anatomy and to tissue engineering. PMID:29023694
Comprehensive benchmarking of SNV callers for highly admixed tumor data. PMID:29020110
DNA sequencing at 40: past, present and future. PMID:29019985
Differential gene regulatory networks in development and disease. PMID:29018868
FACS-Assisted CRISPR-Cas9 Genome Editing Facilitates Parkinson's Disease Modeling. PMID:28988985
STRScan: targeted profiling of short tandem repeats in whole-genome sequencing data. PMID:28984185
MicroRNA miR-128 represses LINE-1 (L1) retrotransposition by down-regulating the nuclear import factor TNPO1. PMID:28974576
Human evolution: the non-coding revolution. PMID:28969617
LINC00052 upregulates EPB41L3 to inhibit migration and invasion of hepatocellular carcinoma by binding miR-452-5p. PMID:28969024
Clinical interpretation of copy number variants in the human genome. PMID:28963714
Reference genome assessment from a population scale perspective: an accurate profile of variability and noise. PMID:28961772
Multiomics Approach to Asthma: Navigating the Network. PMID:28960106
RNase H As Gene Modifier, Driver of Evolution and Antiviral Defense. PMID:28959243
Functional Mechanisms of Microsatellite DNA in Eukaryotic Genomes. PMID:28957459
Modeling GATAD1-Associated Dilated Cardiomyopathy in Adult Zebrafish. PMID:28955713
Highly Variable Genomic Landscape of Endogenous Retroviruses in the C57BL/6J Inbred Strain, Depending on Individual Mouse, Gender, Organ Type, and Organ Location. PMID:28951865
STEAK: A specific tool for transposable elements and retrovirus detection in high-throughput sequencing data. PMID:28948042
Similar Evolutionary Trajectories for Retrotransposon Accumulation in Mammals. PMID:28945883
Exosomal lncRNA GAS5 regulates the apoptosis of macrophages and vascular endothelial cells in atherosclerosis. PMID:28945793
MicroRNAs in Heart Failure, Cardiac Transplantation, and Myocardial Recovery: Biomarkers with Therapeutic Potential. PMID:28940102
Population-wide sampling of retrotransposon insertion polymorphisms using deep sequencing and efficient detection. PMID:28938719
Host Noncoding Retrotransposons Induced by DNA Viruses: a SINE of Infection? PMID:28931686
"Multi-Omics" Analyses of the Development and Function of Natural Killer Cells. PMID:28928751
Satellite DNA: An Evolving Topic. PMID:28926993
Elucidation of complexity and prediction of interactions in microbial communities. PMID:28925555
Augmented expression of polo-like kinase 1 indicates poor clinical outcome for breast patients: a systematic review and meta-analysis. PMID:28915707
Prediction of genome-wide DNA methylation in repetitive elements. PMID:28911103
Distribution, Diversity, and Long-Term Retention of Grass Short Interspersed Nuclear Elements (SINEs). PMID:28903462
Cell-free circulating DNA integrity is an independent predictor of impending breast cancer recurrence. PMID:28903362
Alu-based cell-free DNA: a novel biomarker for screening of gastric cancer. PMID:28903321
Comparative Genomic In Situ Hybridization and the Possible Role of Retroelements in the Karyotypic Evolution of Three Akodontini Species. PMID:28900618
Making a virtue of necessity: the pleiotropic role of human endogenous retroviruses in cancer. PMID:28893944
Recent Advances in Experimental Whole Genome Haplotyping Methods. PMID:28891974
Silencing of retrotransposons by SETDB1 inhibits the interferon response in acute myeloid leukemia. PMID:28887438
Bias and Correction in RNA-seq Data for Marine Species. PMID:28884399
Liquid biopsy in patients with hepatocellular carcinoma: Circulating tumor cells and cell-free nucleic acids. PMID:28883691
Deamination-independent restriction of LINE-1 retrotransposition by APOBEC3H. PMID:28883657
A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog. PMID:28879061
Non-base-contacting residues enable kaleidoscopic evolution of metazoan C2H2 zinc finger DNA binding. PMID:28877740
The Exposome: A New Frontier for Education. PMID:28867821
Fifty years in human genetics--a career retrospective. PMID:28860307
Identification of novel inhibitors against Cyclin Dependent Kinase 9/Cyclin T1 complex as: Anti cancer agent. PMID:28855816
MSDB: A Comprehensive Database of Simple Sequence Repeats. PMID:28854643
rahu is a mutant allele of Dnmt3c, encoding a DNA methyltransferase homolog required for meiosis and transposon repression in the mouse male germline. PMID:28854222
RNA biology of disease-associated microsatellite repeat expansions. PMID:28851463
The complexity of TRIM28 contribution to cancer. PMID:28851455
Falling giants and the rise of gene editing: ethics, private interests and the public good. PMID:28851444
Effect of health-belief-model-based training on performance of women in breast self-examination. PMID:28848633
Short and Long Noncoding RNAs Regulate the Epigenetic Status of Cells. PMID:28847161
Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips. PMID:28842533
Evolution viewed from physics, physiology and medicine. PMID:28839924
Biological action in Read-Write genome evolution. PMID:28839913
A new role for FBP21 as regulator of Brr2 helicase activity. PMID:28838205
Long noncoding RNAs coordinate functions between mitochondria and the nucleus. PMID:28835257
Anti-HERV-K (HML-2) capsid antibody responses in HIV elite controllers. PMID:28830571
Human Retrotransposon Insertion Polymorphisms Are Associated with Health and Disease via Gene Regulatory Phenotypes. PMID:28824558
p53 binding sites in normal and cancer cells are characterized by distinct chromatin context. PMID:28820292
Exploitation of Gene Expression and Cancer Biomarkers in Paving the Path to Era of Personalized Medicine. PMID:28813639
The Retinoblastoma (RB) Tumor Suppressor: Pushing Back against Genome Instability on Multiple Fronts. PMID:28812991
Discovery of Variants Underlying Host Susceptibility to Virus Infection Using Whole-Exome Sequencing. PMID:28808973
A psychology of the human brain-gut-microbiome axis. PMID:28804508
Silencing of Repetitive DNA Is Controlled by a Member of an Unusual Caenorhabditis elegans Gene Family. PMID:28801529
Examining non-LTR retrotransposons in the context of the evolving primate brain. PMID:28800766
Large Introns of 5 to 10 Kilo Base Pairs Can Be Spliced out in Arabidopsis. PMID:28800125
Splicing and transcription touch base: co-transcriptional spliceosome assembly and function. PMID:28792005
Human genome-microbiome interaction: metagenomics frontiers for the aetiopathology of autoimmune diseases. PMID:28785422
Genetically improved BarraCUDA. PMID:28785314
"Squirrel" Primer-Based PCR Assay for Direct and Targeted Sanger Sequencing of Short Genomic Segments. PMID:28785174
Presence of a Shared 5'-Leader Sequence in Ancestral Human and Mammalian Retroviruses and Its Transduction into Feline Leukemia Virus. PMID:28768854
Impact of Alternative Splicing on the Human Proteome. PMID:28768205
Novel copy number variation of POMGNT1 associated with muscle-eye-brain disease detected by next-generation sequencing. PMID:28765568
Machine Learning-Assisted Network Inference Approach to Identify a New Class of Genes that Coordinate the Functionality of Cancer Networks. PMID:28765560
Epigenetics of colorectal cancer: emerging circulating diagnostic and prognostic biomarkers. PMID:28758105
Mobile DNA in Health and Disease. PMID:28745987
Drosophila Histone Demethylase KDM4A Has Enzymatic and Non-enzymatic Roles in Controlling Heterochromatin Integrity. PMID:28743002
How should novelty be valued in science? PMID:28742499
Resolving the prevalence of somatic transposition in Drosophila. PMID:28742021
Dissecting evolution and disease using comparative vertebrate genomics. PMID:28736437
ATM supports gammaherpesvirus replication by attenuating type I interferon pathway. PMID:28732227
A novel isoform of IL-33 revealed by screening for transposable element promoted genes in human colorectal cancer. PMID:28715472
Regulatory Roles of Long Non-Coding RNAs in the Central Nervous System and Associated Neurodegenerative Diseases. PMID:28713244
Sensorimotor Learning: Neurocognitive Mechanisms and Individual Differences. PMID:28705227
Genomic analysis of an infant with intractable diarrhea and dilated cardiomyopathy. PMID:28701297
Systematic identification and characterization of regulatory elements derived from human endogenous retroviruses. PMID:28700586
Genetics and ALS: Cause for Optimism. PMID:28698777
Medicine's movable feast: What jumping genes can teach us about treating disease. PMID:28697180
Host genetic variation and HIV disease: from mapping to mechanism. PMID:28695282
The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics. PMID:28691345
Materials Knowledge Systems in Python - A Data Science Framework for Accelerated Development of Hierarchical Materials. PMID:28690971
LINE-1 hypomethylation is not a common event in preneoplastic stages of gastric carcinogenesis. PMID:28684753
Interpreting whole genome and exome sequencing data of individual gastric cancer samples. PMID:28683819
A Cell Fusion-Based Screening Method Identifies Glycosylphosphatidylinositol-Anchored Protein Ly6e as the Receptor for Mouse Endogenous Retroviral Envelope Syncytin-A. PMID:28679758
Spectraplakin family proteins - cytoskeletal crosslinkers with versatile roles. PMID:28679697
Modeling human disease in rodents by CRISPR/Cas9 genome editing. PMID:28677007
The Exposome Paradigm in Human Health: Lessons from the Emory Exposome Summer Course. PMID:28669935
LTRs of Endogenous Retroviruses as a Source of Tbx6 Binding Sites. PMID:28664156
Landscape and variation of novel retroduplications in 26 human populations. PMID:28662076
The Piwi-piRNA pathway: road to immortality. PMID:28653810
Haplotype phasing of whole human genomes using bead-based barcode partitioning in a single tube. PMID:28650462
Transposable elements in cancer. PMID:28642606
Managing the genomic revolution in cancer diagnostics. PMID:28639053
Differential chromosomal organization between Saguinus midas and Saguinus bicolor with accumulation of differences the repetitive sequence DNA. PMID:28634866
Increasing the reach of forensic genetics with massively parallel sequencing. PMID:28631109
Molecular mechanisms of experience-dependent maturation in cortical GABAergic inhibition. PMID:28628196
A water-soluble DsbB variant that catalyzes disulfide-bond formation in vivo. PMID:28628094
Utilization of genomic sequencing for population screening of immunodeficiencies in the newborn. PMID:28617419
Expression of HERV-K108 envelope interferes with HIV-1 production. PMID:28605635
The Genomic Impact of Gene Retrocopies: What Have We Learned from Comparative Genomics, Population Genomics, and Transcriptomic Analyses? PMID:28605529
DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats. PMID:28604729
Primate-specific Long Non-coding RNAs and MicroRNAs. PMID:28602844
Interplay between viruses and bacterial microbiota in cancer development. PMID:28602713
Genome-wide mapping and characterization of microsatellites in the swamp eel genome. PMID:28600492
Dissecting LSD1-Dependent Neuronal Maturation in the Olfactory Epithelium. PMID:28597915
Reanalysis of BRCA1/2 negative high risk ovarian cancer patients reveals novel germline risk loci and insights into missing heritability. PMID:28591191
A conserved role for the ESCRT membrane budding complex in LINE retrotransposition. PMID:28586350
Large normal-range TBP and ATXN7 CAG repeat lengths are associated with increased lifetime risk of depression. PMID:28585930
Analysis of LINE-1 Elements in DNA from Postmortem Brains of Individuals with Schizophrenia. PMID:28585566
High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. PMID:28581499
Transposable elements in Drosophila. PMID:28580197
Genome-Wide Comparative Analysis of Miniature Inverted Repeat Transposable Elements in 19 Arabidopsis thaliana Ecotype Accessions. PMID:28572566
The genetics revolution in rheumatology: large scale genomic arrays and genetic mapping. PMID:28569263
Epigenetic Control of Human Endogenous Retrovirus Expression: Focus on Regulation of Long-Terminal Repeats (LTRs). PMID:28561791
The Role of Somatic L1 Retrotransposition in Human Cancers. PMID:28561751
Clinically Focused Molecular Investigation of 1000 Consecutive Families with Inherited Retinal Disease. PMID:28559085
Genome annotation for clinical genomic diagnostics: strengths and weaknesses. PMID:28558813
A birth of bipartite exon by intragenic deletion. PMID:28546999
Refining the ideas of "ethnic" skin. PMID:28538883
Methylation Levels of LINE-1 As a Useful Marker for Venous Invasion in Both FFPE and Frozen Tumor Tissues of Gastric Cancer. PMID:28535662
Last rolls of the yoyo: Assessing the human canonical protein count. PMID:28529709
L1 retrotransposition is activated by Ten-eleven-translocation protein 1 and repressed by methyl-CpG binding proteins. PMID:28524723
Reading LINEs within the cocaine addicted brain. PMID:28523221
Identification of human short introns. PMID:28520720
DNA Sequence Analysis in Clinical Medicine, Proceeding Cautiously. PMID:28516087
Robust long-read native DNA sequencing using the ONT CsgG Nanopore system. PMID:28503666
Metazoan Ribosome Inactivating Protein encoding genes acquired by Horizontal Gene Transfer. PMID:28500327
Transposon-driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution. PMID:28500258
Relationship between regulatory pattern of gene expression level and gene function. PMID:28494005
Dynamic silencing of somatic L1 retrotransposon insertions reflects the developmental and cellular contexts of their genomic integration. PMID:28491150
Evidence for transcriptome-wide RNA editing among Sus scrofa PRE-1 SINE elements. PMID:28486975
Natural Variation in the Distribution and Abundance of Transposable Elements Across the Caenorhabditis elegans Species. PMID:28486636
Horizontal gene transfer is not a hallmark of the human genome. PMID:28482857
Soft Sweeps Are the Dominant Mode of Adaptation in the Human Genome. PMID:28482049
Comparative transcriptomics in human and mouse. PMID:28479595
Contrasting Sex-and Caste-Dependent piRNA Profiles in the Transposon Depleted Haplodiploid Honeybee Apis mellifera. PMID:28472327
Reliability of algorithmic somatic copy number alteration detection from targeted capture data. PMID:28472276
EnHERV: Enrichment analysis of specific human endogenous retrovirus patterns and their neighboring genes. PMID:28472109
Improving your four-dimensional image: traveling through a decade of light-sheet-based fluorescence microscopy research. PMID:28471459
Structural variants caused by Alu insertions are associated with risks for many human diseases. PMID:28465436
T-cell activation RhoGTPase-activating protein plays an important role in TH17-cell differentiation. PMID:28462950
A novel MERTK mutation causing retinitis pigmentosa. PMID:28462455
Epigenomic and transcriptomic approaches in the post-genomic era: path to novel targets for diagnosis and therapy of the ischaemic heart? Position Paper of the European Society of Cardiology Working Group on Cellular Biology of the Heart. PMID:28460026
LINE Insertion Polymorphisms are Abundant but at Low Frequencies across Populations of Anolis carolinensis. PMID:28450881
Coronins and their role in immunological phenomena. PMID:28450807
Construction of a map-based reference genome sequence for barley, Hordeum vulgare L. PMID:28448065
Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project. PMID:28448031
Molecular mechanisms by which HERV-K Gag interferes with HIV-1 Gag assembly and particle infectivity. PMID:28446240
Small RNA Pathways That Protect the Somatic Genome. PMID:28445427
The evolution of neuropeptide signalling: insights from echinoderms. PMID:28444138
Evolutionary history of the extant amphioxus lineage with shallow-branching diversification. PMID:28442709
Implementing an Internet-Delivered Skin Cancer Genetic Testing Intervention to Improve Sun Protection Behavior in a Diverse Population: Protocol for a Randomized Controlled Trial. PMID:28442450
Early vertebrate origin and diversification of small transmembrane regulators of cellular ion transport. PMID:28436536
Truncated ORF1 proteins can suppress LINE-1 retrotransposition in trans. PMID:28431148
Large-scale collection of full-length cDNA and transcriptome analysis in Hevea brasiliensis. PMID:28431015
Global Fecal and Plasma Metabolic Dynamics Related to Helicobacter pylori Eradication. PMID:28424674
Molecular genetics: Chaperone protein gets personal. PMID:28424517
Identification and characterization of L1-specific endo-siRNAs essential for early embryonic development in pig. PMID:28423565
Sharing Data to Build a Medical Information Commons: From Bermuda to the Global Alliance. PMID:28415857
Selective elimination of long INterspersed element-1 expressing tumour cells by targeted expression of the HSV-TK suicide gene. PMID:28415677
Long non-coding RNAs in cutaneous melanoma: clinical perspectives. PMID:28415644
Repetitive DNA loci and their modulation by the non-canonical nucleic acid structures R-loops and G-quadruplexes. PMID:28406751
Characterization of genome-wide segmental duplications reveals a common genomic feature of association with immunity among domestic animals. PMID:28403820
SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata. PMID:28403240
Co-option of an endogenous retrovirus envelope for host defense in hominid ancestors. PMID:28397686
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. PMID:28396521
Scaling by shrinking: empowering single-cell 'omics' with microfluidic devices. PMID:28392571
A comprehensive hybridization model allows whole HERV transcriptome profiling using high density microarray. PMID:28390408
DNA word analysis based on the distribution of the distances between symmetric words. PMID:28389642
Monochromosomal Hybrids and Chromosome Transfer: A Functional Approach for Gene Identification. PMID:28387649
Multi-scale chromatin state annotation using a hierarchical hidden Markov model. PMID:28387224
Precision Cardiovascular Medicine: State of Genetic Testing. PMID:28385198
Translation of Nutritional Genomics into Nutrition Practice: The Next Step. PMID:28383492
Direct determination of diploid genome sequences. PMID:28381613
Structural features embedded in G protein-coupled receptor co-crystal structures are key to their success in virtual screening. PMID:28380046
Spontaneous Mutation Rate in the Smallest Photosynthetic Eukaryotes. PMID:28379581
Widespread of horizontal gene transfer in the human genome. PMID:28376762
Milestones in pathology-from histology to molecular biology. PMID:28367253
Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation. PMID:28365736
Genome graphs and the evolution of genome inference. PMID:28360232
The double-edged sword of (re)expression of genes by hypomethylating agents: from viral mimicry to exploitation as priming agents for targeted immune checkpoint modulation. PMID:28359286
Dietary restriction protects from age-associated DNA methylation and induces epigenetic reprogramming of lipid metabolism. PMID:28351387
Reflection on Molecular Approaches Influencing State-of-the-Art Bioremediation Design: Culturing to Microbial Community Fingerprinting to Omics. PMID:28348455
Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus. PMID:28348391
INSPIIRED: A Pipeline for Quantitative Analysis of Sites of New DNA Integration in Cellular Genomes. PMID:28344990
The feasibility of genome-scale biological network inference using Graphics Processing Units. PMID:28344638
Variants in the host genome may inhibit tumour growth in devil facial tumours: evidence from genome-wide association. PMID:28341828
Schizosaccharomyces pombe MutSα and MutLα Maintain Stability of Tetra-Nucleotide Repeats and Msh3 of Hepta-Nucleotide Repeats. PMID:28341698
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. PMID:28336562
DNA Sequencing Sensors: An Overview. PMID:28335417
PML nuclear bodies contribute to the basal expression of the mTOR inhibitor DDIT4. PMID:28332630
When Should Genetic Testing Be Performed in Epilepsy Patients? PMID:28331464
Intragenic multi-exon deletion in the FBN1 gene in a child with mildly dilated aortic sinus: a retrotransposal event. PMID:28331219
Gene-based genome-wide association study identified 19p13.3 for lean body mass. PMID:28322352
Identification and Expression of Equine MER-Derived miRNAs. PMID:28320202
From Sequence Data to Returnable Results: Ethical Issues in Variant Calling and Interpretation. PMID:28306396
Y chromosome palindromes and gene conversion. PMID:28303348
Editing the genome of hiPSC with CRISPR/Cas9: disease models. PMID:28303292
Epigenetic and genetic alterations and their influence on gene regulation in chronic lymphocytic leukemia. PMID:28302063
Decoupling of DNA methylation and activity of intergenic LINE-1 promoters in colorectal cancer. PMID:28300471
ThermoAlign: a genome-aware primer design tool for tiled amplicon resequencing. PMID:28300202
Functional interrogation of non-coding DNA through CRISPR genome editing. PMID:28288828
Integration site selection by retroviruses and transposable elements in eukaryotes. PMID:28286338
The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity. PMID:28284188
Molecular Tumor Boards: Ethical Issues in the New Era of Data Medicine. PMID:28281147
Characterization of contiguous gene deletions in COL4A6 and COL4A5 in Alport syndrome-diffuse leiomyomatosis. PMID:28275241
Non-coding RNA: It's Not Junk. PMID:28271304
Precision medicine driven by cancer systems biology. PMID:28265786
Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome. PMID:28263316
Analytical Biases Associated with GC-Content in Molecular Evolution. PMID:28261263
Extracellular vesicles as trans-genomic agents: Emerging roles in disease and evolution. PMID:28256033
Genomic landscape of CpG rich elements in human. PMID:28251877
Diversity in non-repetitive human sequences not found in the reference genome. PMID:28250455
High-Throughput Proteomic Approaches to the Elucidation of Potential Biomarkers of Chronic Allograft Injury (CAI). PMID:28250402
Protein-Protein Interactions: Gene Acronym Redundancies and Current Limitations Precluding Automated Data Integration. PMID:28250396
The lncRNA XIST exhibits oncogenic properties via regulation of miR-449a and Bcl-2 in human non-small cell lung cancer. PMID:28248928
Omics Approaches for the Study of Adaptive Immunity to Staphylococcus aureus and the Selection of Vaccine Candidates. PMID:28248221
Conserved expression of transposon-derived non-coding transcripts in primate stem cells. PMID:28245871
Targeting Splicing in the Treatment of Human Disease. PMID:28245575
The Isochores as a Fundamental Level of Genome Structure and Organization: A General Overview. PMID:28243687
Role of Protein Phosphatase 2A in Osteoblast Differentiation and Function. PMID:28241467
GSA and BIGD: Filling the Gap of Bioinformatics Resource and Service in China<sup/> PMID:28235641
Evolution of Brain Active Gene Promoters in Human Lineage Towards the Increased Plasticity of Gene Regulation. PMID:28233272
ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter. PMID:28232478
Population and clinical genetics of human transposable elements in the (post) genomic era. PMID:28228978
Comparative genomic analysis of eutherian kallikrein genes. PMID:28224083
MicroRNAs in model and complex organisms. PMID:28220336
Big Data Analytics for Genomic Medicine. PMID:28212287
Alu-Derived Alternative Splicing Events Specific to Macaca Lineages in CTSF Gene. PMID:28196413
Opportunities and challenges of whole-genome and -exome sequencing. PMID:28193154
Lateral gene transfer between prokaryotes and eukaryotes. PMID:28189637
The Human Long Interspersed Element-1 Retrotransposon: An Emerging Biomarker of Neoplasia. PMID:28188229
An accurate and efficient method for large-scale SSR genotyping and applications. PMID:28184437
Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity. PMID:28178237
The Evolution of LINE-1 in Vertebrates. PMID:28175298
Dicer, a new regulator of pluripotency exit and LINE-1 elements in mouse embryonic stem cells. PMID:28174687
Hypermethylated LTR retrotransposon exhibits enhancer activity. PMID:28165867
Genome-wide mining and comparative analysis of microsatellites in three macaque species. PMID:28160080
Silencing of endogenous retroviruses by heterochromatin. PMID:28160052
Evolution and Diversity of Transposable Elements in Vertebrate Genomes. PMID:28158585
What's in a name? Context-dependent significance of 'global' methylation measures in human health and disease. PMID:28149330
MISTIC-fusion proteins as antigens for high quality membrane protein antibodies. PMID:28148968
Development of a human vasopressin V1a-receptor antagonist from an evolutionary-related insect neuropeptide. PMID:28145450
CRISPR applications in ophthalmologic genome surgery. PMID:28141764
Chicken (Gallus gallus) endogenous retrovirus generates genomic variations in the chicken genome. PMID:28138342
Evolving health care through personal genomics. PMID:28138143
Long non-coding RNAs transcribed by ERV-9 LTR retrotransposon act in cis to modulate long-range LTR enhancer function. PMID:28132025
Genetic Disorders of Dental Development: Tales from the Bony Crypt. PMID:28124261
Lifestyle and precision diabetes medicine: will genomics help optimise the prediction, prevention and treatment of type 2 diabetes through lifestyle therapy? PMID:28124081
Association of new deletion/duplication region at chromosome 1p21 with intellectual disability, severe speech deficit and autism spectrum disorder-like behavior: an all-in approach to solving the DPYD enigma. PMID:28123791
How close are we to complete annotation of metabolomes? PMID:28113135
Recent advances in understanding neuropathic pain: glia, sex differences, and epigenetics. PMID:28105313
Concise Review: Induced Pluripotent Stem Cell Research in the Era of Precision Medicine. PMID:28100040
Human transposon insertion profiling: Analysis, visualization and identification of somatic LINE-1 insertions in ovarian cancer. PMID:28096347
Cryptosporidium hominis gene catalog: a resource for the selection of novel Cryptosporidium vaccine candidates. PMID:28095366
Paracoccidioides spp. catalases and their role in antioxidant defense against host defense responses. PMID:28093309
GExplore 1.4: An expanded web interface for queries on Caenorhabditis elegans protein and gene function. PMID:28090394
The future of transposable element annotation and their classification in the light of functional genomics - what we can learn from the fables of Jean de la Fontaine? PMID:28090383
Transposable elements and circular DNAs. PMID:28090380
Clinical and biological insights from viral genome sequencing. PMID:28090077
Single genome retrieval of context-dependent variability in mutation rates for human germline. PMID:28086752
Molecular Evolution of piggyBac Superfamily: From Selfishness to Domestication. PMID:28082605
Computational Prediction of the Global Functional Genomic Landscape: Applications, Methods, and Challenges. PMID:28076869
The Anti-Warburg Effect Elicited by the cAMP-PGC1α Pathway Drives Differentiation of Glioblastoma Cells into Astrocytes. PMID:28076790
Human Endogenous Retroviruses-K (HML-2) Expression Is Correlated with Prognosis and Progress of Hepatocellular Carcinoma. PMID:28070518
Effects of Replication and Transcription on DNA Structure-Related Genetic Instability. PMID:28067787
Genetic conflicts: the usual suspects and beyond. PMID:28057823
Insertion Polymorphisms of Mobile Genetic Elements in Sexual and Asexual Populations of Daphnia pulex. PMID:28057730
Exploring the Underlying Genetics of Craniofacial Morphology through Various Sources of Knowledge. PMID:28053980
Short intron-derived ncRNAs. PMID:28053119
The Nucleotide Excision Repair Pathway Limits L1 Retrotransposition. PMID:28049704
Advancement of the Emerging Field of RNA Nanotechnology. PMID:28045501
Tumor LINE-1 Methylation Level in Association with Survival of Patients with Stage II Colon Cancer. PMID:28035987
Novel Role of 3'UTR-Embedded Alu Elements as Facilitators of Processed Pseudogene Genesis and Host Gene Capture by Viral Genomes. PMID:28033411
Barriers to Infection of Human Cells by Feline Leukemia Virus: Insights into Resistance to Zoonosis. PMID:28031367
GeneBase 1.1: a tool to summarize data from NCBI gene datasets and its application to an update of human gene statistics. PMID:28025344
Combined microfluidic-optical DNA analysis with single-base-pair sizing capability. PMID:28018736
Friend or Foe: Epigenetic Regulation of Retrotransposons in Mammalian Oogenesis and Early Development. PMID:28018140
High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE. PMID:28011790
EhNPC1 and EhNPC2 Proteins Participate in Trafficking of Exogenous Cholesterol in Entamoeba histolytica Trophozoites: Relevance for Phagocytosis. PMID:28002502
The epigenetic landscape of Alu repeats delineates the structural and functional genomic architecture of colon cancer cells. PMID:27999094
Human population-specific gene expression and transcriptional network modification with polymorphic transposable elements. PMID:27998931
Useful parasites: the evolutionary biology and biotechnology applications of transposable elements. PMID:27994207
Perspectives on the history of evo-devo and the contemporary research landscape in the genomics era. PMID:27994116
The intron-enriched HERV-K(HML-10) family suppresses apoptosis, an indicator of malignant transformation. PMID:27980690
Endogenous retroviral promoter exaptation in human cancer. PMID:27980689
Performance evaluation for rapid detection of pan-cancer microsatellite instability with MANTIS. PMID:27980218
Efficient Breeding by Genomic Mating. PMID:27965707
Engineered LINE-1 retrotransposition in nondividing human neurons. PMID:27965292
Alternate-locus aware variant calling in whole genome sequencing. PMID:27964746
Prognostic and predictive significance of long interspersed nucleotide element-1 methylation in advanced-stage colorectal cancer. PMID:27955637
Development of an in vitro human liver system for interrogating nonalcoholic steatohepatitis. PMID:27942596
Incorporate gene signature profiling into routine molecular testing. PMID:27942443
Tools for Sequence-Based miRNA Target Prediction: What to Choose? PMID:27941681
High-Throughput Next-Generation Sequencing of Polioviruses. PMID:27927929
L1Base 2: more retrotransposition-active LINE-1s, more mammalian genomes. PMID:27924012
Pseudogenes and Their Genome-Wide Prediction in Plants. PMID:27916797
Replication stalling and DNA microsatellite instability. PMID:27914716
Molecular mechanism of hepatitis B virus (HBV) on suppression of raf kinase inhibitor protein (RKIP) expression. PMID:27902472
Patterns of Transposable Element Expression and Insertion in Cancer. PMID:27900322
The BIG Data Center: from deposition to integration to translation. PMID:27899658
A comprehensive approach to expression of L1 loci. PMID:27899577
Accelerated pseudogenization on the neo-X chromosome in Drosophila miranda. PMID:27897175
Blood-based DNA methylation as biomarker for breast cancer: a systematic review. PMID:27895805
Single Amino Acid Repeats in the Proteome World: Structural, Functional, and Evolutionary Insights. PMID:27893794
An RB-EZH2 Complex Mediates Silencing of Repetitive DNA Sequences. PMID:27889452
ProtLID, a Residue-Based Pharmacophore Approach to Identify Cognate Protein Ligands in the Immunoglobulin Superfamily. PMID:27889206
An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes. PMID:27882922
Phylogenetic Diversity of Koala Retrovirus within a Wild Koala Population. PMID:27881645
Toward a new paradigm of DNA writing using a massively parallel sequencing platform and degenerate oligonucleotide. PMID:27876825
Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data. PMID:27875984
The impact of transposable elements on mammalian development. PMID:27875251
Expanding Diversity in Molecular Structures and Functions of the IL-6/IL-12 Heterodimeric Cytokine Family. PMID:27867385
Regulatory activities of transposable elements: from conflicts to benefits. PMID:27867194
From profiles to function in epigenomics. PMID:27867193
Bringing It All Together: Coupling Excision Repair to the DNA Damage Checkpoint. PMID:27861980
The Role of Next-Generation Sequencing in Enabling Personalized Oncology Therapy. PMID:27860319
Gene Therapy for Metabolic Diseases. PMID:27853673
Non-coding RNAs match the deleted genomic regions in humans. PMID:27853310
CORALINA: a universal method for the generation of gRNA libraries for CRISPR-based screening. PMID:27842490
False positives and false negatives measure less than 0.001% in labeling ssDNA with osmium tetroxide 2,2'-bipyridine. PMID:27826518
Regulation of disease-associated gene expression in the 3D genome. PMID:27826147
A Method for the Annotation of Functional Similarities of Coding DNA Sequences: the Case of a Populated Cluster of Transmembrane Proteins. PMID:27812751
The PARA-suite: PAR-CLIP specific sequence read simulation and processing. PMID:27812418
Identification of Binding Targets of a Pyrrole-Imidazole Polyamide KR12 in the LS180 Colorectal Cancer Genome. PMID:27798693
Co-existence of BRAF and NRAS driver mutations in the same melanoma cells results in heterogeneity of targeted therapy resistance. PMID:27791198
Genetics of rheumatoid arthritis: GWAS and beyond. PMID:27790002
Computational pan-genomics: status, promises and challenges. PMID:27769991
Sequencing and de novo assembly of the Asian gypsy moth transcriptome using the Illumina platform. PMID:27768153
Cardiac disease and arrhythmogenesis: Mechanistic insights from mouse models. PMID:27766308
A natural barrier to lateral gene transfer from prokaryotes to eukaryotes revealed from genomes: the 70 % rule. PMID:27751184
Epigenetic Aspects of Systemic Lupus Erythematosus. PMID:27747498
SVA retrotransposons as potential modulators of neuropeptide gene expression. PMID:27743609
Comparative Principles of DNA Methylation Reprogramming during Human and Mouse In Vitro Primordial Germ Cell Specification. PMID:27728778
Genome sequence of the basal haplorrhine primate Tarsius syrichta reveals unusual insertions. PMID:27708261
Identification and Characterization of Small Noncoding RNAs in Genome Sequences of the Edible Fungus Pleurotus ostreatus. PMID:27703969
OAHG: an integrated resource for annotating human genes with multi-level ontologies. PMID:27703231
LINEs between Species: Evolutionary Dynamics of LINE-1 Retrotransposons across the Eukaryotic Tree of Life. PMID:27702814
The Hoops, Hopes, and Hypes of Human Microbiome Research. PMID:27698620
An Ecological Framework of the Human Virome Provides Classification of Current Knowledge and Identifies Areas of Forthcoming Discovery. PMID:27698618
Rad51 and Rad54 promote noncrossover recombination between centromere repeats on the same chromatid to prevent isochromosome formation. PMID:27697832
Elements in the Development of a Production Process for Modified Vaccinia Virus Ankara. PMID:27694766
Impact of the Autism-Associated Long Noncoding RNA MSNP1AS on Neuronal Architecture and Gene Expression in Human Neural Progenitor Cells. PMID:27690106
Laboratory Medicine in the Scope of Proteomics and Genomics. PMID:27683374
Reconstructing Demography and Social Behavior During the Neolithic Expansion from Genomic Diversity Across Island Southeast Asia. PMID:27683274
The possible roles of B-cell novel protein-1 (BCNP1) in cellular signalling pathways and in cancer. PMID:27680505
Advances in diagnostics for transplant rejection. PMID:27677432
Cervantes and Quijote protect heterochromatin from aberrant recombination and lead the way to the nuclear periphery. PMID:27673416
Chocó, Colombia: a hotspot of human biodiversity. PMID:27668076
Antisense Oligonucleotides Modulating Activation of a Nonsense-Mediated RNA Decay Switch Exon in the ATM Gene. PMID:27658045
Endogenous retroviruses mobilized during friend murine leukemia virus infection. PMID:27657834
Computational Evaluation of the Strict Master and Random Template Models of Endogenous Retrovirus Evolution. PMID:27649303
Omics-Based Strategies in Precision Medicine: Toward a Paradigm Shift in Inborn Errors of Metabolism Investigations. PMID:27649151
Oxford Nanopore MinION Sequencing and Genome Assembly. PMID:27646134
Heterochromatic histone modifications at transposons in Xenopus tropicalis embryos. PMID:27639284
Annotating the Function of the Human Genome with Gene Ontology and Disease Ontology. PMID:27635398
The Flow of the Gibbon LAVA Element Is Facilitated by the LINE-1 Retrotransposition Machinery. PMID:27635049
Selection on Position of Nonsense Codons in Introns. PMID:27630196
Identifying Nuclear Matrix-Attached DNA Across the Genome. PMID:27627025
FBW7 suppression leads to SOX9 stabilization and increased malignancy in medulloblastoma. PMID:27625374
Technological advances in precision medicine and drug development. PMID:27622214
Great expectations - Epigenetics and the meandering path from bench to bedside. PMID:27621117
The 2016 Lasker~Koshland Special Achievement Award recognizes Bruce Alberts' lifelong dedication to research, policy, and education. PMID:27620537
De novo sequencing, assembly and analysis of eight different transcriptomes from the Malayan pangolin. PMID:27618997
Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing. PMID:27617755
Non-alcoholic fatty liver and the gut microbiota. PMID:27617201
Contribution of type W human endogenous retroviruses to the human genome: characterization of HERV-W proviral insertions and processed pseudogenes. PMID:27613107
Whole Genome Mapping with Feature Sets from High-Throughput Sequencing Data. PMID:27611682
Human Contamination in Public Genome Assemblies. PMID:27611326
Current Status of Long Non-Coding RNAs in Human Breast Cancer. PMID:27608009
A Retrospective Analysis of Precision Medicine Outcomes in Patients With Advanced Cancer Reveals Improved Progression-Free Survival Without Increased Health Care Costs. PMID:27601506
Silencing transposable elements in the Drosophila germline. PMID:27600679
Strategies for Genomic and Proteomic Profiling of Cancers. PMID:27594925
Discrepancies between human DNA, mRNA and protein reference sequences and their relation to single nucleotide variants in the human population. PMID:27589963
The function of homeobox genes and lncRNAs in cancer. PMID:27588114
ANGIOGENES: knowledge database for protein-coding and noncoding RNA genes in endothelial cells. PMID:27582018
Identifying wrong assemblies in de novo short read primary sequence assembly contigs. PMID:27581937
Role of pharmacogenetics in public health and clinical health care: a SWOT analysis. PMID:27577547
Regulation of CTNNB1 signaling in gastric cancer and stem cells. PMID:27574551
Circular RNAs: Unexpected outputs of many protein-coding genes. PMID:27571848
The science commons in health research: structure, function, and value. PMID:27570367
Tumor Touch Imprints as Source for Whole Genome Analysis of Neuroblastoma Tumors. PMID:27560999
An Optimal Seed Based Compression Algorithm for DNA Sequences. PMID:27555868
In silico identification of lysocin biosynthetic gene cluster from Lysobacter sp. RH2180-5. PMID:27553855
A preliminary review of influential works in data-driven discovery. PMID:27540499
Improving the Flexibility of RNA-Seq Data Analysis Pipelines. PMID:27536420
The Astrobiology Primer v2.0. PMID:27532777
Inference of Ancestral Recombination Graphs through Topological Data Analysis. PMID:27532298
A Crystallographic Examination of Predisposition versus Preorganization in de Novo Designed Metalloproteins. PMID:27532255
Detection of cis- and trans-acting Factors in DNA Structure-Induced Genetic Instability Using In silico and Cellular Approaches. PMID:27532010
Exploring cancer genomic data from the cancer genome atlas project. PMID:27530686
The Ribonuclease A Superfamily in Humans: Canonical RNases as the Buttress of Innate Immunity. PMID:27527162
Restricting retrotransposons: a review. PMID:27525044
Benchmarking computational tools for polymorphic transposable element detection. PMID:27524380
Structure and regulation of human troponin genes. PMID:27520667
IRWRLDA: improved random walk with restart for lncRNA-disease association prediction. PMID:27517318
Pharmacometabolomics informs Pharmacogenomics. PMID:27516730
Prevalent Accumulation of Non-Optimal Codons through Somatic Mutations in Human Cancers. PMID:27513638
Beyond Endometriosis Genome-Wide Association Study: From Genomics to Phenomics to the Patient. PMID:27513026
Transposable elements and miRNA: Regulation of genomic stability and plasticity. PMID:27511122
The transposable element environment of human genes is associated with histone and expression changes in cancer. PMID:27506777
The Role of Retrotransposons in Gene Family Expansions in the Human and Mouse Genomes. PMID:27503295
Genome-wide measures of DNA methylation in peripheral blood and the risk of urothelial cell carcinoma: a prospective nested case-control study. PMID:27490804
Pinpointing the vesper bat transposon revolution using the Miniopterus natalensis genome. PMID:27489570
Evolutionary dynamics of selfish DNA explains the abundance distribution of genomic subsequences. PMID:27488939
Imagining Sisyphus happy: DNA barcoding and the unnamed majority. PMID:27481781
A novel human-specific splice isoform alters the critical C-terminus of Survival Motor Neuron protein. PMID:27481219
Multiscale Modeling of Cellular Epigenetic States: Stochasticity in Molecular Networks, Chromatin Folding in Cell Nuclei, and Tissue Pattern Formation of Cells. PMID:27480462
The bright side of dark matter: lncRNAs in cancer. PMID:27479746
Evidence of selection for an accessible nucleosomal array in human. PMID:27472913
In Vivo and In Vitro Genotoxic and Epigenetic Effects of Two Types of Cola Beverages and Caffeine: A Multiassay Approach. PMID:27471731
Existence of Two Distinct Infectious Endogenous Retroviruses in Domestic Cats and Their Different Strategies for Adaptation to Transcriptional Regulation. PMID:27466428
MR1 discovery. PMID:27464703
A Canonical Correlation Analysis of AIDS Restriction Genes and Metabolic Pathways Identifies Purine Metabolism as a Key Cooperator. PMID:27462363
Reprogramming, Circular Reasoning and Self versus Non-self: One-Stop Shopping with RNA Editing. PMID:27458478
Tissue homogeneity requires inhibition of unequal gene silencing during development. PMID:27458132
Aberrant DNA methylation reprogramming in bovine SCNT preimplantation embryos. PMID:27456302
Transcriptomic analyses of the radiation response in head and neck squamous cell carcinoma subclones with different radiation sensitivity: time-course gene expression profiles and gene association networks. PMID:27455841
Splicing variants of ADAR2 and ADAR2-mediated RNA editing in glioma. PMID:27446352
Expression of evolutionarily novel genes in tumors. PMID:27437030
Liquid biopsy in patients with pancreatic cancer: Circulating tumor cells and cell-free nucleic acids. PMID:27433079
Perlman syndrome nuclease DIS3L2 controls cytoplasmic non-coding RNAs and provides surveillance pathway for maturing snRNAs. PMID:27431325
LncRNAs in pancreatic cancer. PMID:27429196
APOBEC3DE Inhibits LINE-1 Retrotransposition by Interacting with ORF1p and Influencing LINE Reverse Transcriptase Activity. PMID:27428332
On the pathogenesis of insulin-dependent diabetes mellitus: the role of microbiota. PMID:27421719
Zinc finger proteins in cancer progression. PMID:27411336
Transfer of DNA from Bacteria to Eukaryotes. PMID:27406565
CTRL+INSERT: retrotransposons and their contribution to regulation and innovation of the transcriptome. PMID:27402545
Novel Insights into Chromosome Evolution in Birds, Archosaurs, and Reptiles. PMID:27401172
Chromatin variation associated with liver metabolism is mediated by transposable elements. PMID:27398095
Preferential Protection of Genetic Fidelity within Open Chromatin by the Mismatch Repair Machinery. PMID:27382058
The Grand Challenge of Characterizing Ribonucleoprotein Networks. PMID:27376072
Comments and General Discussion on "The Anatomical Problem Posed by Brain Complexity and Size: A Potential Solution". PMID:27375436
[Treat to target and personalized medicine (precision medicine)]. PMID:27365026
Unraveling the message: insights into comparative genomics of the naked mole-rat. PMID:27364349
Comprehensive analysis of lncRNAs microarray profile and mRNA-lncRNA co-expression in oncogenic HPV-positive cervical cancer cell lines. PMID:27363024
Reverse transcriptase and intron number evolution. PMID:27358863
Analysis of tandem gene copies in maize chromosomal regions reconstructed from long sequence reads. PMID:27354512
Inherited platelet disorders: Insight from platelet genomics using next-generation sequencing. PMID:27348543
Long non-coding RNAs and complex diseases: from experimental results to computational models. PMID:27345524
Mitochondrial Epigenetics and Environmental Exposure. PMID:27344144
Integrated small copy number variations and epigenome maps of disorders of sex development. PMID:27340555
The second decade of 3C technologies: detailed insights into nuclear organization. PMID:27340173
Goodbye genome paper, hello genome report: the increasing popularity of 'genome announcements' and their impact on science. PMID:27339634
The value of genomics in dissecting the RAS-network and in guiding therapeutics for RAS-driven cancers. PMID:27338857
Nothing in Evolution Makes Sense Except in the Light of Genomics: Read-Write Genome Evolution as an Active Biological Process. PMID:27338490
MiR-4638-5p inhibits castration resistance of prostate cancer through repressing Kidins220 expression and PI3K/AKT pathway activity. PMID:27329728
Mammal madness: is the mammal tree of life not yet resolved? PMID:27325836
Inferring species divergence times using pairwise sequential Markovian coalescent modelling and low-coverage genomic data. PMID:27325835
IntNetLncSim: an integrative network analysis method to infer human lncRNA functional similarity. PMID:27323856
FMLNCSIM: fuzzy measure-based lncRNA functional similarity calculation model. PMID:27322210
Computational Tools for Stem Cell Biology. PMID:27318512
Repetitive element hypermethylation in multiple sclerosis patients. PMID:27317098
Polymorphic Alu Insertion/Deletion in Different Caste and Tribal Populations from South India. PMID:27315142
The Impact of Evolutionary Driving Forces on Human Complex Diseases: A Population Genetics Approach. PMID:27313952
Evaluation of Bioinformatic Programmes for the Analysis of Variants within Splice Site Consensus Regions. PMID:27313609
Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis. PMID:27309962
The Epithelial-to-Mesenchymal Transition (EMT), a Particular Case. PMID:27308335
phRAIDER: Pattern-Hunter based Rapid Ab Initio Detection of Elementary Repeats. PMID:27307619
Prediction of ribosome footprint profile shapes from transcript sequences. PMID:27307616
DMET™ (Drug Metabolism Enzymes and Transporters): a pharmacogenomic platform for precision medicine. PMID:27304055
Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research. PMID:27297499
PiggyBac transposon-based polyadenylation-signal trap for genome-wide mutagenesis in mice. PMID:27292714
Selection pressure on human STR loci and its relevance in repeat expansion disease. PMID:27290643
The genetic heterogeneity of colorectal cancer predisposition - guidelines for gene discovery. PMID:27279102
Ancient DNA and human history. PMID:27274045
De novo assembly and characterization of the Chinese three-keeled pond turtle (Mauremys reevesii) transcriptome: presence of longevity-related genes. PMID:27257545
CRISPR/Cas9 therapeutics: a cure for cancer and other genetic diseases. PMID:27250031
The Clustered, Regularly Interspaced, Short Palindromic Repeats-associated Endonuclease 9 (CRISPR/Cas9)-created MDM2 T309G Mutation Enhances Vitreous-induced Expression of MDM2 and Proliferation and Survival of Cells. PMID:27246850
Genome stability versus transcript diversity. PMID:27246512
Global methylation, oxidative stress, and relative telomere length in biliary atresia patients. PMID:27243754
New Trends in Aryl Hydrocarbon Receptor Biology. PMID:27243009
Links between Human LINE-1 Retrotransposons and Hepatitis Virus-Related Hepatocellular Carcinoma. PMID:27242996
ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods. PMID:27242037
Lineage-specific genomics: Frequent birth and death in the human genome: The human genome contains many lineage-specific elements created by both sequence and functional turnover. PMID:27231054
LncRNApred: Classification of Long Non-Coding RNAs and Protein-Coding Transcripts by the Ensemble Algorithm with a New Hybrid Feature. PMID:27228152
Decoding transcriptional enhancers: Evolving from annotation to functional interpretation. PMID:27224938
Clinical genomics: from a truly personal genome viewpoint. PMID:27221143
Processing and transcriptome expansion at the mRNA 3' end in health and disease: finding the right end. PMID:27220521
Prenatal Air Pollution Exposures, DNA Methyl Transferase Genotypes, and Associations with Newborn LINE1 and Alu Methylation and Childhood Blood Pressure and Carotid Intima-Media Thickness in the Children's Health Study. PMID:27219456
DNA methylation by DNMT1 and DNMT3b methyltransferases is driven by the MUC1-C oncoprotein in human carcinoma cells. PMID:27212035
Identification of human RNA editing sites: A historical perspective. PMID:27208508
The Brugada Syndrome: A Rare Arrhythmia Disorder with Complex Inheritance. PMID:27200363
Retroviral DNA Integration. PMID:27198982
Endogenous Transposase Source in Human Cells Mobilizes piggyBac Transposons. PMID:27198853
A hot L1 retrotransposon evades somatic repression and initiates human colorectal cancer. PMID:27197217
Challenges of Identifying Clinically Actionable Genetic Variants for Precision Medicine. PMID:27195526
X-Linked Candidate Genes for a Ciliopathy-Like Disorder. PMID:27194972
Conservation and Innovation of APOBEC3A Restriction Functions during Primate Evolution. PMID:27189538
LTR12 promoter activation in a broad range of human tumor cells by HDAC inhibition. PMID:27172897
P53 and the defenses against genome instability caused by transposons and repetitive elements. PMID:27172878
Angiotensin II receptors and peritoneal dialysis-induced peritoneal fibrosis. PMID:27167177
Genomic Approaches to Zebrafish Cancer. PMID:27165352
CNS repair and axon regeneration: Using genetic variation to determine mechanisms. PMID:27163547
Next-generation sequencing-based detection of germline L1-mediated transductions. PMID:27161561
Transposable elements in the mammalian embryo: pioneers surviving through stealth and service. PMID:27161170
Genomic analysis of mouse VL30 retrotransposons. PMID:27158269
Roles for retrotransposon insertions in human disease. PMID:27158268
What are We Learning and What Can We Learn from the Human Oral Microbiome Project? PMID:27152251
The potential for liquid biopsies in the precision medical treatment of breast cancer. PMID:27144060
The Dark Side of Cell Fusion. PMID:27136533
Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch. PMID:27136077
Redundans: an assembly pipeline for highly heterozygous genomes. PMID:27131372
Genes and Small RNA Transcripts Exhibit Dosage-Dependent Expression Pattern in Maize Copy-Number Alterations. PMID:27129738
A Protein Domain and Family Based Approach to Rare Variant Association Analysis. PMID:27128313
piR-651 and its function in 95-D lung cancer cells. PMID:27123245
Next-Generation Sequencing in the Genetics of Human Atrial Fibrillation. PMID:27122724
Generation, Characterization and Application of Antibodies Directed against HERV-H Gag Protein in Colorectal Samples. PMID:27119520
Metabolomics in epidemiology: from metabolite concentrations to integrative reaction networks. PMID:27118561
Challenges, Solutions, and Quality Metrics of Personal Genome Assembly in Advancing Precision Medicine. PMID:27110816
Non-negligible Occurrence of Errors in Gender Description in Public Data Sets. PMID:27103889
Application of whole genome shotgun sequencing for detection and characterization of genetically modified organisms and derived products. PMID:27100228
The endonuclease domain of the LINE-1 ORF2 protein can tolerate multiple mutations. PMID:27099633
Alu SINE analyses of 3,000-year-old human skeletal remains: a pilot study. PMID:27096009
Exosomes: The Link between GPCR Activation and Metastatic Potential? PMID:27092178
Using an integrative approach to investigate the evolution of behaviour. PMID:27087846
Protection of CpG islands from DNA methylation is DNA-encoded and evolutionarily conserved. PMID:27084945
Epigenetic regulation of bone cells. PMID:27082893
iJGVD: an integrative Japanese genome variation database based on whole-genome sequencing. PMID:27081555
Identification of novel exonic mobile element insertions in epithelial ovarian cancers. PMID:27081539
Evolution of Epigenetic Regulation in Vertebrate Genomes. PMID:27080453
Incidentalome from Genomic Sequencing: A Barrier to Personalized Medicine? PMID:27077130
Stress out the LINEs. PMID:27066303
The challenge of ORF1p phosphorylation: Effects on L1 activity and its host. PMID:27066302
Anchored pseudo-de novo assembly of human genomes identifies extensive sequence variation from unmapped sequence reads. PMID:27061184
Polymorphic tandem repeats within gene promoters act as modifiers of gene expression and DNA methylation in humans. PMID:27060133
23andMe: a new two-sided data-banking market model. PMID:27059184
What is translational bioinformatics? PMID:27054069
RNA Sequencing in Schizophrenia. PMID:27053919
Introducing precise genetic modifications into human 3PN embryos by CRISPR/Cas-mediated genome editing. PMID:27052831
Associations and prognostic implications of Eastern Cooperative Oncology Group performance status and tumoral LINE-1 methylation status in stage III colon cancer patients. PMID:27051466
Retrotransposon-associated long non-coding RNAs in mice and men. PMID:27044413
Active recombinant Tol2 transposase for gene transfer and gene discovery applications. PMID:27042235
No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini. PMID:27035985
Alu methylation serves as a biomarker for non-invasive diagnosis of glioma. PMID:27028997
ILNCSIM: improved lncRNA functional similarity calculation model. PMID:27028993
Immune responses to endogenous retroelements: taking the bad with the good. PMID:27026073
LINE-1 distribution in six rodent genomes follow a species-specific pattern. PMID:27019429
Natural Selection and Genetic Diversity in the Butterfly Heliconius melpomene. PMID:27017626
Post-Transcriptional Control of LINE-1 Retrotransposition by Cellular Host Factors in Somatic Cells. PMID:27014690
To be an author. PMID:27011823
The Gene Expression Omnibus Database. PMID:27008011
Unraveling the evolutionary scenario of the hobo element in populations of Drosophila melanogaster and D. simulans in South America using the TPE repeats as markers. PMID:27007908
Transposable Elements and Their KRAB-ZFP Controllers Regulate Gene Expression in Adult Tissues. PMID:27003935
ROBO2 gene variants in children with primary nonsyndromic vesicoureteral reflux with or without renal hypoplasia/dysplasia. PMID:27002985
What Next in Schizophrenia Genetics for the Psychiatric Genomics Consortium? PMID:26994396
The Anolis Lizard Genome: An Amniote Genome without Isochores? PMID:26992416
Global Metabolic Reconstruction and Metabolic Gene Evolution in the Cattle Genome. PMID:26992093
Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus. PMID:26989998
Horizontal transfer of β-carbonic anhydrase genes from prokaryotes to protozoans, insects, and nematodes. PMID:26983858
Suppressing H19 Modulates Tumorigenicity and Stemness in U251 and U87MG Glioma Cells. PMID:26983719
Next generation sequencing (NGS) database for tandem repeats with multiple pattern 2°-shaft multicore string matching. PMID:26981434
Recurrent Gene Duplication Diversifies Genome Defense Repertoire in Drosophila. PMID:26979388
Transcription Factors Expressed in Mouse Cochlear Inner and Outer Hair Cells. PMID:26974322
Prp8 retinitis pigmentosa mutants cause defects in the transition between the catalytic steps of splicing. PMID:26968627
Heavy Metal Exposure Influences Double Strand Break DNA Repair Outcomes. PMID:26966913
Identification and Analysis of the Role of Superoxide Dismutases Isoforms in the Pathogenesis of Paracoccidioides spp. PMID:26963091
Blood-Borne Pathogens: A Canadian Blood Services Centre for Innovation Symposium. PMID:26962008
Tracking interspecies transmission and long-term evolution of an ancient retrovirus using the genomes of modern mammals. PMID:26952212
Estrogen Receptor Alpha (ESR1) Single-Nucleotide Polymorphisms (SNPs) Affect Malignant Melanoma Susceptibility and Disease Course. PMID:26949342
Contemporary views on the genetics of anorexia nervosa. PMID:26944296
LINE retrotransposition and host DNA repair machinery. PMID:26942045
Alu elements and DNA double-strand break repair. PMID:26942043
Regulatory evolution of innate immunity through co-option of endogenous retroviruses. PMID:26941318
Forty years of The Selfish Gene are not enough. PMID:26936472
MaGuS: a tool for quality assessment and scaffolding of genome assemblies with Whole Genome Profiling™ Data. PMID:26936254
Modeling congenital disease and inborn errors of development in Drosophila melanogaster. PMID:26935104
Personalised cancer care: promises and challenges of targeted therapy. PMID:26933155
DNA methylation in human epigenomes depends on local topology of CpG sites. PMID:26932361
Gene Variant Databases and Sharing: Creating a Global Genomic Variant Database for Personalized Medicine. PMID:26931283
Mechanisms underlying structural variant formation in genomic disorders. PMID:26924765
Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing. PMID:26922242
Transcriptome Analysis in Domesticated Species: Challenges and Strategies. PMID:26917953
Discovery of a new repeat family in the Callithrix jacchus genome. PMID:26916108
Retrotransposons as regulators of gene expression. PMID:26912865
Human genetic variation database, a reference database of genetic variations in the Japanese population. PMID:26911352
Atlas of Cryptic Genetic Relatedness Among 1000 Human Genomes. PMID:26907499
The Reverse Transcriptase Encoded by LINE-1 Retrotransposons in the Genesis, Progression, and Therapy of Cancer. PMID:26904537
Ensembl comparative genomics resources. PMID:26896847
LEAP: L1 Element Amplification Protocol. PMID:26895063
Immunodetection of Human LINE-1 Expression in Cultured Cells and Human Tissues. PMID:26895059
LINE-1 Cultured Cell Retrotransposition Assay. PMID:26895052
DNA methylation variation of human-specific Alu repeats. PMID:26890526
A protein constructed de novo enables cell growth by altering gene regulation. PMID:26884172
Managing risks in drug discovery: reproducibility of published findings. PMID:26883784
Alu retrotransposons promote differentiation of human carcinoma cells through the aryl hydrocarbon receptor. PMID:26883630
Molecular features of cellular reprogramming and development. PMID:26883001
Unravelling the human genome-phenome relationship using phenome-wide association studies. PMID:26875678
A Biologist's Field Guide to Multiplexed Quantitative Proteomics. PMID:26873251
MetaSINEs: Broad Distribution of a Novel SINE Superfamily in Animals. PMID:26872770
A benchmark study on error-correction by read-pairing and tag-clustering in amplicon-based deep sequencing. PMID:26868371
Curated eutherian third party data gene data sets. PMID:26862561
The contribution of transposable elements to size variations between four teleost genomes. PMID:26862351
Biochemistry and physiology within the framework of the extended synthesis of evolutionary biology. PMID:26861860
Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome. PMID:26861146
Integrated cytogenetics and genomics analysis of transposable elements in the Nile tilapia, Oreochromis niloticus. PMID:26860923
Quantification of unmethylated Alu (QUAlu): a tool to assess global hypomethylation in routine clinical samples. PMID:26859682
Feature co-localization landscape of the human genome. PMID:26854351
Graphene nanodevices for DNA sequencing. PMID:26839258
Decoding DNA, RNA and peptides with quantum tunnelling. PMID:26839257
When Medicine Meets Engineering-Paradigm Shifts in Diagnostics and Therapeutics. PMID:26835672
SncRNA (microRNA &snoRNA) opposite expression pattern found in multiple sclerosis relapse and remission is sex dependent. PMID:26831009
Genome-Wide Analysis of Transposon and Retroviral Insertions Reveals Preferential Integrations in Regions of DNA Flexibility. PMID:26818075
An epigenetic switch ensures transposon repression upon dynamic loss of DNA methylation in embryonic stem cells. PMID:26814573
Impact of host genetic polymorphisms on vaccine induced antibody response. PMID:26809773
Classification and characterization of human endogenous retroviruses; mosaic forms are common. PMID:26800882
Next-generation sequencing as an approach to dairy starter selection. PMID:26798445
detectMITE: A novel approach to detect miniature inverted repeat transposable elements in genomes. PMID:26795595
Discordant Haplotype Sequencing Identifies Functional Variants at the 2q33 Breast Cancer Risk Locus. PMID:26795348
Human Endogenous Retroviruses as Pathogenic Factors in the Development of Schizophrenia. PMID:26793126
Infectious Entry Pathway Mediated by the Human Endogenous Retrovirus K Envelope Protein. PMID:26792739
Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. PMID:26780094
Genomic landscapes of endogenous retroviruses unveil intricate genetics of conventional and genetically-engineered laboratory mouse strains. PMID:26779669
Insertion of Retrotransposons at Chromosome Ends: Adaptive Response to Chromosome Maintenance. PMID:26779254
Transposable Elements, Polydactyl Proteins, and the Genesis of Human-Specific Transcription Networks. PMID:26763983
Different Facets of Copy Number Changes: Permanent, Transient, and Adaptive. PMID:26755558
A Molecular Perspective on Procedures and Outcomes with Assisted Reproductive Technologies. PMID:26747835
Experimental methods to preserve male fertility and treat male factor infertility. PMID:26746133
Crossing the LINE Toward Genomic Instability: LINE-1 Retrotransposition in Cancer. PMID:26734601
Pathway Analysis: State of the Art. PMID:26733877
Diagnosis of D-Bifunctional Protein Deficiency through Whole-Genome Sequencing: Implications for Cost-Effective Care. PMID:26733776
In Silico Functional Annotation of Genomic Variation. PMID:26724722
Transposable element detection from whole genome sequence data. PMID:26719777
Enhanced expression of LINE-1-encoded ORF2 protein in early stages of colon and prostate transformation. PMID:26716650
Insulated Foamy Viral Vectors. PMID:26715244
Linking short tandem repeat polymorphisms with cytosine modifications in human lymphoblastoid cell lines. PMID:26714498
Gene therapy: progress and predictions. PMID:26702034
Milk: an epigenetic amplifier of FTO-mediated transcription? Implications for Western diseases. PMID:26691922
Horizontal functional gene transfer from bacteria to fishes. PMID:26691285
Comparing genetic variants detected in the 1000 genomes project with SNPs determined by the International HapMap Consortium. PMID:26690529
5th International ACC Symposium: The New Genetics of Benign Adrenocortical Neoplasia: Hyperplasias, Adenomas, and Their Implications for Progression into Cancer. PMID:26684645
A Small RNA-Based Immune System Defends Germ Cells against Mobile Genetic Elements. PMID:26681955
Somatic mosaicism: on the road to cancer. PMID:26678315
Estradiol differentially induces progesterone receptor isoforms expression through alternative promoter regulation in a mouse embryonic hypothalamic cell line. PMID:26676302
Circulating long noncoding RNA GAS5 levels are correlated to prevalence of type 2 diabetes mellitus. PMID:26675493
L1 retrotransposition requires rapid ORF1p oligomerization, a novel coiled coil-dependent property conserved despite extensive remodeling. PMID:26673717
Expressed Sequence Tags Analysis and Design of Simple Sequence Repeats Markers from a Full-Length cDNA Library in Perilla frutescens (L.). PMID:26664999
Circulating nucleic acids: a new class of physiological mobile genetic elements. PMID:26664710
Evolution of Nine Microsatellite Loci in the Fungus Fusarium oxysporum. PMID:26661928
Exercise-conditioned plasma attenuates nuclear concentrations of DNA methyltransferase 3B in human peripheral blood mononuclear cells. PMID:26660547
The domain structure and distribution of Alu elements in long noncoding RNAs and mRNAs. PMID:26654912
Comparative genomic analysis of eutherian tumor necrosis factor ligand genes. PMID:26646413
Systems Genetic Validation of the SNP-Metabolite Association in Rice Via Metabolite-Pathway-Based Phenome-Wide Association Scans. PMID:26640468
Segmenting the Human Genome into Isochores. PMID:26640363
RNA Sequence Analysis of Human Huntington Disease Brain Reveals an Extensive Increase in Inflammatory and Developmental Gene Expression. PMID:26636579
Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell type-specific hypomethylation in the regulation of cell identity genes. PMID:26635396
Progress and challenges in bioinformatics approaches for enhancer identification. PMID:26634919
Metagenomic Classification Using an Abstraction Augmented Markov Model. PMID:26618474
Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages. PMID:26613339
Obesity-induced sperm DNA methylation changes at satellite repeats are reprogrammed in rat offspring. PMID:26608942
microRNAs as neuroregulators, biomarkers and therapeutic agents in neurodegenerative diseases. PMID:26608596
The PsychENCODE project. PMID:26605881
Aquatic adaptation and the evolution of smell and taste in whales. PMID:26605054
Transcriptome networks in the mouse retina: An exon level BXD RI database. PMID:26604663
Multinational teams and diseconomies of scale in collaborative research. PMID:26601251
Evolution and Biological Roles of Alternative 3'UTRs. PMID:26597575
Transcriptomics of diapause in an isogenic self-fertilizing vertebrate. PMID:26597228
Inferring Selective Constraint from Population Genomic Data Suggests Recent Regulatory Turnover in the Human Brain. PMID:26590212
A 3' Poly(A) Tract Is Required for LINE-1 Retrotransposition. PMID:26585388
Infection-Induced Retrotransposon-Derived Noncoding RNAs Enhance Herpesviral Gene Expression via the NF-κB Pathway. PMID:26584434
Ancestral Mutations Acquired in Refrex-1, a Restriction Factor against Feline Retroviruses, during its Cooption and Domestication. PMID:26581999
What might retrotransposons teach us about aging? PMID:26581630
Suppression of the Arboviruses Dengue and Chikungunya Using a Dual-Acting Group-I Intron Coupled with Conditional Expression of the Bax C-Terminal Domain. PMID:26580561
Transposable element polymorphisms recapitulate human evolution. PMID:26579215
Death of a dogma: eukaryotic mRNAs can code for more than one protein. PMID:26578573
KATZLDA: KATZ measure for the lncRNA-disease association prediction. PMID:26577439
Adaptive Evolution Coupled with Retrotransposon Exaptation Allowed for the Generation of a Human-Protein-Specific Coding Gene That Promotes Cancer Cell Proliferation and Metastasis in Both Haematological Malignancies and Solid Tumours: The Extraordinary Case of MYEOV Gene. PMID:26568894
Are Synonymous Sites in Primates and Rodents Functionally Constrained? PMID:26563252
Cross-Species Transmission and Differential Fate of an Endogenous Retrovirus in Three Mammal Lineages. PMID:26562410
The sequence of sequencers: The history of sequencing DNA. PMID:26554401
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. PMID:26553804
Full-length single-cell RNA-seq applied to a viral human cancer: applications to HPV expression and splicing analysis in HeLa S3 cells. PMID:26550473
Long noncoding RNA MIR31HG exhibits oncogenic property in pancreatic ductal adenocarcinoma and is negatively regulated by miR-193b. PMID:26549028
Linking Genes to Cardiovascular Diseases: Gene Action and Gene-Environment Interactions. PMID:26545598
Long noncoding RNAs in T lymphocytes. PMID:26538526
Gain of a New Exon by a Lineage-Specific Alu Element-Integration Event in the BCS1L Gene during Primate Evolution. PMID:26537194
Characteristics of α-Gal epitope, anti-Gal antibody, α1,3 galactosyltransferase and its clinical exploitation (Review). PMID:26531137
Genes and dental disorders. PMID:26527946
Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data. PMID:26525298
Expression of young HERV-H loci in the course of colorectal carcinoma and correlation with molecular subtypes. PMID:26517682
Comparing the normalization methods for the differential analysis of Illumina high-throughput RNA-Seq data. PMID:26511205
CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors. PMID:26510915
Genome-wide evolutionary and functional analysis of the Equine Repetitive Element 1: an insertion in the myostatin promoter affects gene expression. PMID:26503543
Discovery and characterization of Alu repeat sequences via precise local read assembly. PMID:26503250
Clinical prospects of long noncoding RNAs as novel biomarkers and therapeutic targets in prostate cancer. PMID:26503110
Deciphering the Developmental Dynamics of the Mouse Liver Transcriptome. PMID:26496202
Evidence of Extensive Alternative Splicing in Post Mortem Human Brain HTT Transcription by mRNA Sequencing. PMID:26496077
Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping. PMID:26492141
Role of the single deaminase domain APOBEC3A in virus restriction, retrotransposition, DNA damage and cancer. PMID:26489798
Regulation of PKR by RNA: formation of active and inactive dimers. PMID:26488609
PCR-Free Enrichment of Mitochondrial DNA from Human Blood and Cell Lines for High Quality Next-Generation DNA Sequencing. PMID:26488301
Comparison among three variant callers and assessment of the accuracy of imputation from SNP array data to whole-genome sequence level in chicken. PMID:26486989
Kuwaiti population subgroup of nomadic Bedouin ancestry-Whole genome sequence and analysis. PMID:26484159
Assessing quality standards for ChIP-seq and related massive parallel sequencing-generated datasets: When rating goes beyond avoiding the crisis. PMID:26484107
Third party annotation gene data set of eutherian lysozyme genes. PMID:26484105
Cardiac cAMP: production, hydrolysis, modulation and detection. PMID:26483685
Increased Transcript Complexity in Genes Associated with Chronic Obstructive Pulmonary Disease. PMID:26480348
Potential impact of gene regulatory mechanisms on the evolution of multicellularity in the volvocine algae. PMID:26479715
Analytical and Clinical Validation of a Digital Sequencing Panel for Quantitative, Highly Accurate Evaluation of Cell-Free Circulating Tumor DNA. PMID:26474073
Transcriptome profile of liver at different physiological stages reveals potential mode for lipid metabolism in laying hens. PMID:26452545
Current strategies for mutation detection in phenotype-driven screens utilising next generation sequencing. PMID:26449678
The Fine LINE: Methylation Drawing the Cancer Landscape. PMID:26448926
Ten Simple Rules for Writing a Reply Paper. PMID:26448197
Expression profile of long non-coding RNAs in pancreatic cancer and their clinical significance as biomarkers. PMID:26447755
Stacked thin layers of metaphase chromatin explain the geometry of chromosome rearrangements and banding. PMID:26446309
Progress of cancer genomics. PMID:26445603
Genetics of Hearing Loss: Syndromic. PMID:26443487
Genetic variation and the de novo assembly of human genomes. PMID:26442640
LINE-1 activity as molecular basis for genomic instability associated with light exposure at night. PMID:26442182
Repetitive elements regulate circular RNA biogenesis. PMID:26442181
Drawing a fine line on endogenous retroelement activity. PMID:26442176
Endogenous retrovirus-mediated genomic variations in chimpanzees. PMID:26442175
An assay to monitor the activity of DNA transposition complexes yields a general quality control measure for transpositional recombination reactions. PMID:26442171
Assembly and characterization of novel Alu inserts detected from next-generation sequencing data. PMID:26442170
The Dynamic Genome and Transcriptome of the Human Fungal Pathogen Blastomyces and Close Relative Emmonsia. PMID:26439490
Spotting the enemy within: Targeted silencing of foreign DNA in mammalian genomes by the Krüppel-associated box zinc finger protein family. PMID:26435754
Alternative Splicing QTLs in European and African Populations. PMID:26430802
Genome-wide analysis of tandem repeats in Tribolium castaneum genome reveals abundant and highly dynamic tandem repeat families with satellite DNA features in euchromatic chromosomal arms. PMID:26428853
Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data. PMID:26423047
Ultra-fast local-haplotype variant calling using paired-end DNA-sequencing data reveals somatic mosaicism in tumor and normal blood samples. PMID:26420835
Present and future challenges of induced pluripotent stem cells. PMID:26416678
Next-Generation Sequencing Approaches in Cancer: Where Have They Brought Us and Where Will They Take Us? PMID:26404381
Chromosomal Rearrangements as Barriers to Genetic Homogenization between Archaic and Modern Humans. PMID:26399483
De novo sequencing and assembly analysis of transcriptome in the Sodom apple (Calotropis gigantea). PMID:26395839
Group-based variant calling leveraging next-generation supercomputing for large-scale whole-genome sequencing studies. PMID:26395405
Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5' splice site strength. PMID:26392272
A structural approach reveals how neighbouring C2H2 zinc fingers influence DNA binding specificity. PMID:26384429
The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression. PMID:26382853
Bioinformatics in Africa: The Rise of Ghana? PMID:26378921
Exploration of Deregulated Long Non-Coding RNAs in Association with Hepatocarcinogenesis and Survival. PMID:26378581
The genome of the vervet (Chlorocebus aethiops sabaeus). PMID:26377836
Donkey genome and insight into the imprinting of fast karyotype evolution. PMID:26373886
miR-128 represses L1 retrotransposition by binding directly to L1 RNA. PMID:26367248
Adapting capillary gel electrophoresis as a sensitive, high-throughput method to accelerate characterization of nucleic acid metabolic enzymes. PMID:26365239
Short interspersed DNA elements and miRNAs: a novel hidden gene regulation layer in zebrafish? PMID:26363800
The Bottleneck in Genetic Testing. PMID:26358106
Aberrant reduction of telomere repetitive sequences in plasma cell-free DNA for early breast cancer detection. PMID:26356673
Can a few non-coding mutations make a human brain? PMID:26350501
Osteosarcoma Genetics and Epigenetics: Emerging Biology and Candidate Therapies. PMID:26349415
Genetic Susceptibility to Rhodococcus equi. PMID:26340305
Villain of Molecular Biology: Why are we not reproducible in research? PMID:26339478
EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering. PMID:26335049
LINE-1 in cancer: multifaceted functions and potential clinical implications. PMID:26334179
Utility of whole-genome sequencing for detection of newborn screening disorders in a population cohort of 1,696 neonates. PMID:26334177
Improving the Power of Structural Variation Detection by Augmenting the Reference. PMID:26322511
Sequence Analysis and Characterization of Active Human Alu Subfamilies Based on the 1000 Genomes Pilot Project. PMID:26319576
Next-generation sequencing: hype and hope for development of personalized radiation therapy? PMID:26316159
Recent advances in the study of active endogenous retrovirus envelope glycoproteins in the mammalian placenta. PMID:26311491
Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future. PMID:26309733
Aberrant RNA splicing in cancer; expression changes and driver mutations of splicing factor genes. PMID:26300000
Structural and functional liaisons between transposable elements and satellite DNAs. PMID:26293606
Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals. PMID:26292667
Tandem repeat variation in human and great ape populations and its impact on gene expression divergence. PMID:26290536
Evolutionary transitions in the Asteraceae coincide with marked shifts in transposable element abundance. PMID:26290182
The genomic landscape of human immune-mediated diseases. PMID:26290150
Oncoprotein ZNF322A transcriptionally deregulates alpha-adducin, cyclin D1 and p53 to promote tumor growth and metastasis in lung cancer. PMID:26279304
Onco-exaptation of an endogenous retroviral LTR drives IRF5 expression in Hodgkin lymphoma. PMID:26279299
Predicting lncRNA-disease associations and constructing lncRNA functional similarity network based on the information of miRNA. PMID:26278472
An Atypical AAA+ ATPase Assembly Controls Efficient Transposition through DNA Remodeling and Transposase Recruitment. PMID:26276634
RNA editing by ADAR1 prevents MDA5 sensing of endogenous dsRNA as nonself. PMID:26275108
Generalised Anxiety Disorder--A Twin Study of Genetic Architecture, Genome-Wide Association and Differential Gene Expression. PMID:26274327
Making the case for chromatin profiling: a new tool to investigate the immune-regulatory landscape. PMID:26272294
Disease-associated mutation in SRSF2 misregulates splicing by altering RNA-binding affinities. PMID:26261309
SINEUPs: A new class of natural and synthetic antisense long non-coding RNAs that activate translation. PMID:26259533
A Sparse Model Based Detection of Copy Number Variations From Exome Sequencing Data. PMID:26258935
Noncoding RNAs, Emerging Regulators of Skeletal Muscle Development and Diseases. PMID:26258142
Genome-wide profiling of DNA methylation reveals preferred sequences of DNMTs in hepatocellular carcinoma cells. PMID:26254611
Paradigm shifts in genomics through the FANTOM projects. PMID:26253466
SNP Formation Bias in the Murine Genome Provides Evidence for Parallel Evolution. PMID:26253317
Clinical exome sequencing in neurogenetic and neuropsychiatric disorders. PMID:26250888
GC-Content of Synonymous Codons Profoundly Influences Amino Acid Usage. PMID:26248983
'Cut from the same cloth': Shared microsatellite variants among cancers link to ectodermal tissues-neural tube and crest cells. PMID:26246470
A call for benchmarking transposable element annotation methods. PMID:26244060
Prenatal Programming and Toxicity (PPTOX) Introduction. PMID:26241073
Use of miRNAs in biofluids as biomarkers in dietary and lifestyle intervention studies. PMID:26233309
KLF/SP Transcription Factor Family Evolution: Expansion, Diversification, and Innovation in Eukaryotes. PMID:26232396
Big Data Analytics in Healthcare. PMID:26229957
Transcription factors, chromatin proteins and the diversification of Hemiptera. PMID:26226651
A Genome-Wide Landscape of Retrocopies in Primate Genomes. PMID:26224704
The role of Alu elements in the cis-regulation of RNA processing. PMID:26223268
Long Non-coding RNA ANRIL and Polycomb in Human Cancers and Cardiovascular Disease. PMID:26220772
Circadian disruption and breast cancer: an epigenetic link? PMID:26220712
Genomic medicine in gastroenterology: A new approach or a new specialty? PMID:26217074
Epigenetic Alterations in Colorectal Cancer: Emerging Biomarkers. PMID:26216839
Double strand break repair by capture of retrotransposon sequences and reverse-transcribed spliced mRNA sequences in mouse zygotes. PMID:26216318
An open ecosystem engagement strategy through the lens of global food safety. PMID:26213614
Glioma Association and Balancing Selection of ZFPM2. PMID:26207917
Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale. PMID:26206263
MI-PVT: A Tool for Visualizing the Chromosome-Centric Human Proteome. PMID:26204236
Cell therapies and regenerative medicine. PMID:26202498
Molecular Testing in Myelodysplastic Syndromes for the Practicing Oncologist: Will the Progress Fulfill the Promise? PMID:26194858
Marsupials and monotremes possess a novel family of MHC class I genes that is lost from the eutherian lineage. PMID:26194104
Traumatic spinal cord injury in mice with human immune systems. PMID:26193167
Regulation of protein homeostasis in neurodegenerative diseases: the role of coding and non-coding genes. PMID:26190021
Utility and limitations of exome sequencing as a genetic diagnostic tool for conditions associated with pediatric sudden cardiac arrest/sudden cardiac death. PMID:26187847
LINE-1 Retroelements Get ZAPped! PMID:26182081
Harnessing Pandemonium: The Clinical Implications of Tumor Heterogeneity in Ovarian Cancer. PMID:26175968
The NIH BD2K center for big data in translational genomics. PMID:26174866
Defining "mutation" and "polymorphism" in the era of personal genomics. PMID:26173390
Regulation of human MAPT gene expression. PMID:26170022
Long non-coding RNAs in innate and adaptive immunity. PMID:26166759
Biodiversity Meets Neuroscience: From the Sequencing Ship (Ship-Seq) to Deciphering Parallel Evolution of Neural Systems in Omic's Era. PMID:26163680
Detection of Genomic Structural Variants from Next-Generation Sequencing Data. PMID:26161383
Evaluation of BLAST-based edge-weighting metrics used for homology inference with the Markov Clustering algorithm. PMID:26160651
Long Noncoding RNA in Digestive Tract Cancers: Function, Mechanism, and Potential Biomarker. PMID:26156325
Read count-based method for high-throughput allelic genotyping of transposable elements and structural variants. PMID:26153459
Label-free DNA sequencing using Millikan detection. PMID:26151683
Comparison of Gene Coexpression Profiles and Construction of Conserved Gene Networks to Find Functional Modules. PMID:26147120
An improved understanding of cancer genomics through massively parallel sequencing. PMID:26146607
Revisiting disease genes based on whole-exome sequencing in consanguineous populations. PMID:26141664
RNA Structures as Mediators of Neurological Diseases and as Drug Targets. PMID:26139368
DNAseq Workflow in a Diagnostic Context and an Example of a User Friendly Implementation. PMID:26137478
Hydra as a tractable, long-lived model system for senescence. PMID:26136619
Somatic Mutations and Clonal Hematopoiesis in Aplastic Anemia. PMID:26132940
High-throughput RNA sequencing reveals structural differences of orthologous brain-expressed genes between western lowland gorillas and humans. PMID:26132897
Assembly and diploid architecture of an individual human genome via single-molecule technologies. PMID:26121404
Quantification of SAHA-Dependent Changes in Histone Modifications Using Data-Independent Acquisition Mass Spectrometry. PMID:26120868
The diversification of PHIS transposon superfamily in eukaryotes. PMID:26120370
Epigenetic signaling in schizophrenia. PMID:26120009
The Role of Transposable Elements in the Origin and Evolution of MicroRNAs in Human. PMID:26115450
Causes of genome instability: the effect of low dose chemical exposures in modern society. PMID:26106144
P Transposable Elements in Drosophila and other Eukaryotic Organisms. PMID:26104714
The Influence of LINE-1 and SINE Retrotransposons on Mammalian Genomes. PMID:26104698
Np9, a cellular protein of retroviral ancestry restricted to human, chimpanzee and gorilla, binds and regulates ubiquitin ligase MDM2. PMID:26103464
Engineered CRISPR-Cas9 nucleases with altered PAM specificities. PMID:26098369
Connecting the speckles: Splicing kinases and their role in tumorigenesis and treatment response. PMID:26098145
Associations between genetic variation in one-carbon metabolism and LINE-1 DNA methylation in histologically normal breast tissues. PMID:26090795
RNA Sequencing for Identification of Differentially Expressed Noncoding Transcripts during Adipogenic Differentiation of Adipose-Derived Stromal Cells. PMID:26090763
Normalization of Complete Genome Characteristics: Application to Evolution from Primitive Organisms to Homo sapiens. PMID:26085808
Long noncoding RNAs in development and cancer: potential biomarkers and therapeutic targets. PMID:26082843
Mx1 and Mx2 key antiviral proteins are surprisingly lost in toothed whales. PMID:26080416
Defining the Human Brain Proteome Using Transcriptomics and Antibody-Based Profiling with a Focus on the Cerebral Cortex. PMID:26076492
Breaking bad: The mutagenic effect of DNA repair. PMID:26073774
The epigenetics of aging and neurodegeneration. PMID:26072273
Advances in long noncoding RNAs: identification, structure prediction and function annotation. PMID:26072035
Unbalanced translocations arise from diverse mutational mechanisms including chromothripsis. PMID:26070663
Coding Microsatellite Frameshift Mutations Accumulate in Atherosclerotic Carotid Artery Lesions: Evaluation of 26 Cases and Literature Review. PMID:26070012
Optical Imaging of Paramagnetic Bead-DNA Aggregation Inhibition Allows for Low Copy Number Detection of Infectious Pathogens. PMID:26068926
Preferential Amplification of Pathogenic Sequences. PMID:26067233
Constructing lncRNA functional similarity network based on lncRNA-disease associations and disease semantic similarity. PMID:26061969
Gene therapy for cancer: present status and future perspective. PMID:26056594
Transcriptional modulator ZBED6 affects cell cycle and growth of human colorectal cancer cells. PMID:26056301
A general concept for consistent documentation of computational analyses. PMID:26055099
Differential Epigenetic Effects of Atmospheric Cold Plasma on MCF-7 and MDA-MB-231 Breast Cancer Cells. PMID:26042423
Emerging applications of read profiles towards the functional annotation of the genome. PMID:26042150
Cardiovascular genetics: technological advancements and applicability for dilated cardiomyopathy. PMID:26031632
Molecular epigenetic switches in neurodevelopment in health and disease. PMID:26029068
Comprehensive identification of genes driven by ERV9-LTRs reveals TNFRSF10B as a re-activatable mediator of testicular cancer cell death. PMID:26024393
Genome-Wide Search Identifies 1.9 Mb from the Polar Bear Y Chromosome for Evolutionary Analyses. PMID:26019166
The human transmembrane proteome. PMID:26018427
A statistical framework to predict functional non-coding regions in the human genome through integrated analysis of annotation data. PMID:26015273
Targeted Capture of Phylogenetically Informative Ves SINE Insertions in Genus Myotis. PMID:26014613
Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. PMID:26006009
De novo assembly of a haplotype-resolved human genome. PMID:26006006
The cancer cell map initiative: defining the hallmark networks of cancer. PMID:26000852
High-throughput sequencing technologies. PMID:26000844
Choosing the Right Tool for the Job: RNAi, TALEN, or CRISPR. PMID:26000843
The road from next-generation sequencing to personalized medicine. PMID:26000024
The potential role of Alu Y in the development of resistance to SN38 (Irinotecan) or oxaliplatin in colorectal cancer. PMID:25997618
Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites. PMID:25995269
The role of epidermal growth factor-like module containing mucin-like hormone receptor 2 in human cancers. PMID:25992231
Differential SINE evolution in vesper and non-vesper bats. PMID:25991928
A low-latency, big database system and browser for storage, querying and visualization of 3D genomic data. PMID:25990738
Roles of solvent accessibility and gene expression in modeling protein sequence evolution. PMID:25987828
Cardiac gene expression data and in silico analysis provide novel insights into human and mouse taste receptor gene regulation. PMID:25986534
A seven-gene CpG-island methylation panel predicts breast cancer progression. PMID:25986046
LINEs in mice: features, families, and potential roles in early development. PMID:25975894
Epigenetics and pharmacology. PMID:25966315
Division of labor between IRF1 and IRF2 in regulating different stages of transcriptional activation in cellular antiviral activities. PMID:25960866
The hidden side of unstable DNA repeats: Mutagenesis at a distance. PMID:25956860
Genome-wide comparison of Asian and African rice reveals high recent activity of DNA transposons. PMID:25954322
The Zinc-Finger Antiviral Protein ZAP Inhibits LINE and Alu Retrotransposition. PMID:25951186
Haplotype-resolved genome sequencing: experimental methods and applications. PMID:25948246
Functional significance of the sex chromosomes during spermatogenesis. PMID:25948089
The renaissance of developmental biology. PMID:25946596
Advances in genetics and genomics: use and limitations in achieving malaria elimination goals. PMID:25943157
Initial description of primate-specific cystine-knot Prometheus genes and differential gene expansions of D-dopachrome tautomerase genes. PMID:25941635
Obstruction of adaptation in diploids by recessive, strongly deleterious alleles. PMID:25941393
Genome-wide amplification of proviral sequences reveals new polymorphic HERV-K(HML-2) proviruses in humans and chimpanzees that are absent from genome assemblies. PMID:25927962
Utility of proteomics in obstetric disorders: a review. PMID:25926758
Functional classification of 15 million SNPs detected from diverse chicken populations. PMID:25926514
Alu-mediated diverse and complex pathogenic copy-number variants within human chromosome 17 at p13.3. PMID:25908615
Identification, Diversity and Evolution of MITEs in the Genomes of Microsporidian Nosema Parasites. PMID:25898273
Do larger genomes contain more diverse transposable elements? PMID:25896861
piRNA involvement in genome stability and human cancer. PMID:25895683
Sustained proliferation in cancer: Mechanisms and novel therapeutic targets. PMID:25892662
Structural variation mutagenesis of the human genome: Impact on disease and evolution. PMID:25892534
Laser capture microdissection: Big data from small samples. PMID:25892148
Whole genome sequencing of an ethnic Pathan (Pakhtun) from the north-west of Pakistan. PMID:25887915
Unraveling the 3D genome: genomics tools for multiscale exploration. PMID:25887733
Prediction of host - pathogen protein interactions between Mycobacterium tuberculosis and Homo sapiens using sequence motifs. PMID:25887594
Sequencing, identification and mapping of primed L1 elements (SIMPLE) reveals significant variation in full length L1 elements between individuals. PMID:25887476
CopywriteR: DNA copy number detection from off-target sequence data. PMID:25887352
Melatonin: an inhibitor of breast cancer. PMID:25876649
A simple strategy for reducing false negatives in calling variants from single-cell sequencing data. PMID:25876174
Evolution of genetic techniques: past, present, and beyond. PMID:25874212
AID to overcome the limitations of genomic information by introducing somatic DNA alterations. PMID:25873751
Seeking a roadmap toward neuroepigenetics. PMID:25856479
Long noncoding RNAs in cardiac development and ageing. PMID:25855606
New bioinformatic tool for quick identification of functionally relevant endogenous retroviral inserts in human genome. PMID:25853282
Evidence for Natural Selection in Nucleotide Content Relationships Based on Complete Mitochondrial Genomes: Strong Effect of Guanine Content on Separation between Terrestrial and Aquatic Vertebrates. PMID:25853054
An epigenetic hypothesis for the genomic memory of pain. PMID:25852480
A network of RNA and protein interactions in Fronto Temporal Dementia. PMID:25852467
Biochemical functional predictions for protein structures of unknown or uncertain function. PMID:25848497
The Human Alzheimer Disease Project: A New Call to Arms. PMID:25844883
Temporal and spatial rearrangements of a repetitive element array on C57BL/6J mouse genome. PMID:25839092
The mechanism of ageing: primary role of transposable elements in genome disintegration. PMID:25837999
Progress and challenges in developing metabolic footprints from diet in human gut microbial cometabolism. PMID:25833886
Non-coding RNAs and hypertension-unveiling unexpected mechanisms of hypertension by the dark matter of the genome. PMID:25828869
Whole-exome sequencing and its impact in hereditary hearing loss. PMID:25825321
Comprehensive data resources and analytical tools for pathological association of aminoacyl tRNA synthetases with cancer. PMID:25824651
The future of human cerebral cartography: a novel approach. PMID:25823868
Accurate typing of short tandem repeats from genome-wide sequencing data and its applications. PMID:25823460
Non-coding RNA: a new frontier in regulatory biology. PMID:25821635
Mobilization of LINE-1 in irradiated mammary gland tissue may potentially contribute to low dose radiation-induced genomic instability. PMID:25821563
Activation of an endogenous retrovirus-associated long non-coding RNA in human adenocarcinoma. PMID:25821520
Epigenetic regulation of intragenic transposable elements impacts gene transcription in Arabidopsis thaliana. PMID:25813042
Impacts of a biobank: Bridging the gap in translational cancer medicine. PMID:25810570
Long Non-Coding RNA Expression during Aging in the Human Subependymal Zone. PMID:25806019
Genome-wide transcript profiling reveals novel breast cancer-associated intronic sense RNAs. PMID:25798919
LINE-1 induces hTERT and ensures telomere maintenance in tumour cell lines. PMID:25798839
Personal genomes, quantitative dynamic omics and personalized medicine. PMID:25798291
Inter-locus as well as intra-locus heterogeneity in LINE-1 promoter methylation in common human cancers suggests selective demethylation pressure at specific CpGs. PMID:25798207
DNA methylation dynamics in muscle development and disease. PMID:25798107
Long noncoding RNA lincRNA-p21 is the major mediator of UVB-induced and p53-dependent apoptosis in keratinocytes. PMID:25789975
Foamy viral vector integration sites in SCID-repopulating cells after MGMTP140K-mediated in vivo selection. PMID:25786870
Human endogenous retrovirus group E and its involvement in diseases. PMID:25785516
Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes. PMID:25785303
Structure of the DNA duplex d(ATTAAT)2 with Hoogsteen hydrogen bonds. PMID:25781995
The Role of Regulatory Agencies and Intellectual Property: Part I. PMID:25775921
Altering Genomic Integrity: Heavy Metal Exposure Promotes Transposable Element-Mediated Damage. PMID:25774044
Prognostic significance of promoter CpG island hypermethylation and repetitive DNA hypomethylation in stage I lung adenocarcinoma. PMID:25772390
Cancer metabolism: strategic diversion from targeting cancer drivers to targeting cancer suppliers. PMID:25767677
Evolutionary patterns of DNA base composition and correlation to polymorphisms in DNA repair systems. PMID:25765652
Sequence and analysis of a whole genome from Kuwaiti population subgroup of Persian ancestry. PMID:25765185
U6 snRNA Pseudogenes: Markers of Retrotransposition Dynamics in Mammals. PMID:25761766
The contribution of alu elements to mutagenic DNA double-strand break repair. PMID:25761216
Evaluating historical candidate genes for schizophrenia. PMID:25754081
Landscape of insertion polymorphisms in the human genome. PMID:25745018
On bioinformatic resources. PMID:25743088
Whole genome analysis of a Vietnamese trio. PMID:25740146
SVA retrotransposition in exon 6 of the coagulation factor IX gene causing severe hemophilia B. PMID:25739383
Epigenetic Mechanisms of Serotonin Signaling. PMID:25734378
Transcriptional activity of human endogenous retroviruses in human peripheral blood mononuclear cells. PMID:25734056
Toward a magic or imaginary bullet? Ligands for drug targeting to cancer cells: principles, hopes, and challenges. PMID:25733832
The effects of chromatin organization on variation in mutation rates in the genome. PMID:25732611
Mismatch repair during homologous and homeologous recombination. PMID:25731766
Type I interferon controls propagation of long interspersed element-1. PMID:25716322
terMITEs: miniature inverted-repeat transposable elements (MITEs) in the termite genome (Blattodea: Termitoidae). PMID:25711308
Genetic changes shaping the human brain. PMID:25710529
Computational prediction of molecular pathogen-host interactions based on dual transcriptome data. PMID:25705211
Genome architecture and its roles in human copy number variation. PMID:25705150
Genetics of Vascular Dementia. PMID:25705074
Pseudogene-derived lncRNAs: emerging regulators of gene expression. PMID:25699073
The genetic regulation of infant immune responses to vaccination. PMID:25699041
Methods in molecular cardiology: in silico cloning. PMID:25696371
Methods in molecular cardiology: microarray technology. PMID:25696214
Methods in molecular cardiology: DNA sequencing. PMID:25696079
The effect of life history on retroviral genome invasions. PMID:25692467
C2H2 zinc finger proteins greatly expand the human regulatory lexicon. PMID:25690854
Personalization of the immunosuppressive treatment in renal transplant recipients: the great challenge in "omics" medicine. PMID:25690039
The Genome 10K Project: a way forward. PMID:25689317
Biomarkers in Patients with Metastatic Breast Cancer and the PRAEGNANT Study Network. PMID:25684786
Identification of the specific interactors of the human lariat RNA debranching enzyme 1 protein. PMID:25671812
Embryonic stem cell specific "master" replication origins at the heart of the loss of pluripotency. PMID:25658386
Dispersal of an ancient retroposon in the TP53 promoter of Bovidae: phylogeny, novel mechanisms, and potential implications for cow milk persistency. PMID:25653076
Utilising the resources of the International Knockout Mouse Consortium: the Australian experience. PMID:25645994
A copy number variation map of the human genome. PMID:25645873
The aging clock and circadian control of metabolism and genome stability. PMID:25642238
The decline of human endogenous retroviruses: extinction and survival. PMID:25640971
Pure interstitial dup(6)(q22.31q22.31) - a case report. PMID:25637059
Exogenous enzymes upgrade transgenesis and genetic engineering of farm animals. PMID:25636347
The role of DNA insertions in phenotypic differentiation between humans and other primates. PMID:25635043
Evolutionary histories of transposable elements in the genome of the largest living marsupial carnivore, the Tasmanian devil. PMID:25633377
First insight into divergence, representation and chromosome distribution of reverse transcriptase fragments from L1 retrotransposons in peanut and wild relative species. PMID:25633099
Next-generation sequencing for the diagnosis of cardiac arrhythmia syndromes. PMID:25625719
Post-transcriptional regulation of long noncoding RNAs in cancer. PMID:25618601
Diagnosis of an imprinted-gene syndrome by a novel bioinformatics analysis of whole-genome sequences from a family trio. PMID:25614875
Genome-wide analyses of LINE-LINE-mediated nonallelic homologous recombination. PMID:25613453
The expanding role of epigenetics. PMID:25610838
Methylation status of long interspersed element-1 in advanced gastric cancer and its prognostic implication. PMID:25609453
New concepts in breast cancer genomics and genetics. PMID:25606588
Repeated horizontal transfers of four DNA transposons in invertebrates and bats. PMID:25606061
Development of a monoclonal antibody specific to the endonuclease domain of the human LINE-1 ORF2 protein. PMID:25606060
Intragenomic distribution of RTE retroelements suggests intrachromosomal movement. PMID:25605325
A droplet digital PCR detection method for rare L1 insertions in tumors. PMID:25598847
Jumping on the Train of Personalized Medicine: A Primer for Non- Geneticist Clinicians: Part 3. Clinical Applications in the Personalized Medicine Area. PMID:25598768
The cytoplasmic tail of retroviral envelope glycoproteins. PMID:25595807
Relationship between nucleosome positioning and progesterone-induced alternative splicing in breast cancer cells. PMID:25589247
Computational cancer biology: education is a natural key to many locks. PMID:25588624
Identification of the oncogenic kinase TOPK/PBK as a master mitotic regulator of C2H2 zinc finger proteins. PMID:25575812
Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions. PMID:25572935
The expanding epigenetic landscape of non-model organisms. PMID:25568458
Diversity and impact of rare variants in genes encoding the platelet G protein-coupled receptors. PMID:25567036
Self-reported race/ethnicity in the age of genomic research: its potential impact on understanding health disparities. PMID:25563503
Why and how might genetic and phylogenetic diversity be reflected in the identification of key biodiversity areas? PMID:25561678
Identification and computational analysis of gene regulatory elements. PMID:25561628
Basic concepts and potential applications of genetics and genomics for cardiovascular and stroke clinicians: a scientific statement from the American Heart Association. PMID:25561044
Long non-coding RNAs as regulators of the endocrine system. PMID:25560704
RNA-binding proteins in pluripotency, differentiation, and reprogramming. PMID:25554730
Epigenetic effects of low perinatal doses of flame retardant BDE-47 on mitochondrial and nuclear genes in rat offspring. PMID:25533936
Biased gene conversion and GC-content evolution in the coding sequences of reptiles and vertebrates. PMID:25527834
Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes. PMID:25523484
Inhibition of autoimmune Chagas-like heart disease by bone marrow transplantation. PMID:25521296
DNA polymerases in biotechnology. PMID:25520711
Genome-wide analysis of alternative splicing in Volvox carteri. PMID:25516378
Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. PMID:25504731
Comparative genomics reveals insights into avian genome evolution and adaptation. PMID:25504712
Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes. PMID:25503085
Early mesozoic coexistence of amniotes and hepadnaviridae. PMID:25501991
Focusing on long noncoding RNA dysregulation in gastric cancer. PMID:25501508
Splicing of designer exons informs a biophysical model for exon definition. PMID:25492963
Gene expression profiling of replicative and induced senescence. PMID:25483067
Regulatory roles of LINE-1-encoded reverse transcriptase in cancer onset and progression. PMID:25478632
JTD special edition 'Hot Topics in COPD'-The microbiome in COPD. PMID:25478194
Extensive error in the number of genes inferred from draft genome assemblies. PMID:25474019
Construction and characterization of three wheat bacterial artificial chromosome libraries. PMID:25464379
Genetics of allergic diseases. PMID:25459575
Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins. PMID:25436857
Genes regulating lipid and protein metabolism are highly expressed in mammary gland of lactating dairy goats. PMID:25433708
Guanine quadruplexes are formed by specific regions of human transposable elements. PMID:25431265
Using protein-binding microarrays to study transcription factor specificity: homologs, isoforms and complexes. PMID:25431149
A pathophysiological view of the long non-coding RNA world. PMID:25428918
Autoimmune thyroid disease and rheumatoid arthritis: relationship and the role of genetics. PMID:25427993
A case study in connectomics: the history, mapping, and connectivity of the claustrum. PMID:25426062
Advances in genome editing technology and its promising application in evolutionary and ecological studies. PMID:25414792
Host control of insect endogenous retroviruses: small RNA silencing and immune response. PMID:25412365
Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution. PMID:25411453
Expression of human skin-specific genes defined by transcriptomics and antibody-based profiling. PMID:25411189
Roles of intragenic and intergenic L1s in mouse and human. PMID:25409429
Using mouse models to study function of transcriptional factors in T cell development. PMID:25408871
De-repressing LncRNA-Targeted Genes to Upregulate Gene Expression: Focus on Small Molecule Therapeutics. PMID:25405465
Identification of rare alternative splicing events in MS/MS data reveals a significant fraction of alternative translation initiation sites. PMID:25405079
Protein engineering of Cas9 for enhanced function. PMID:25398355
Intronic variants in the NFKB1 gene may influence hearing forecast in patients with unilateral sensorineural hearing loss in Meniere's disease. PMID:25397881
Clinical Management of Pediatric Genomic Testing. PMID:25396100
Gene-Lifestyle Interactions in Complex Diseases: Design and Description of the GLACIER and VIKING Studies. PMID:25396097
Stress and the dynamic genome: Steroids, epigenetics, and the transposome. PMID:25385609
Resolving the complexity of the human genome using single-molecule sequencing. PMID:25383537
Identification of candidate long noncoding RNAs associated with left ventricular hypertrophy. PMID:25382655
Particles and microfluidics merged: perspectives of highly sensitive diagnostic detection. PMID:25378716
Epidaurus: aggregation and integration analysis of prostate cancer epigenome. PMID:25378314
DEEP: a general computational framework for predicting enhancers. PMID:25378307
Multispecies coalescent analysis of the early diversification of neotropical primates: phylogenetic inference under strong gene trees/species tree conflict. PMID:25377940
Conserved sequence-specific lincRNA-steroid receptor interactions drive transcriptional repression and direct cell fate. PMID:25377354
A comparative study and a phylogenetic exploration of the compositional architectures of mammalian nuclear genomes. PMID:25375262
A novel Alu-based real-time PCR method for the quantitative detection of plasma circulating cell-free DNA: sensitivity and specificity for the diagnosis of myocardial infarction. PMID:25374065
Case-only exome sequencing and complex disease susceptibility gene discovery: study design considerations. PMID:25371537
Three-Dimensional Algebraic Models of the tRNA Code and 12 Graphs for Representing the Amino Acids. PMID:25370377
Reconceptualizing major depressive disorder as an infectious disease. PMID:25364500
AN EFFICIENT ALGORITHM FOR CHINESE POSTMAN WALK ON BI-DIRECTED DE BRUIJN GRAPHS. PMID:25364472
Human cardiac systems electrophysiology and arrhythmogenesis: iteration of experiment and computation. PMID:25362174
Diverse and widespread contamination evident in the unmapped depths of high throughput sequencing data. PMID:25354084
Investigating genomic structure using changept: A Bayesian segmentation model. PMID:25349679
Mobster: accurate detection of mobile element insertions in next generation sequencing data. PMID:25348035
Control of mammalian retrotransposons by cellular RNA processing activities. PMID:25346866
iDoComp: a compression scheme for assembled genomes. PMID:25344501
Ovarian cancer biomarker discovery based on genomic approaches. PMID:25337559
The evolution of comparative genomics. PMID:25333060
A pilot study of angiotensin converting enzyme (ACE) genotype and return of spontaneous circulation following out-of-hospital cardiac arrest. PMID:25332829
Hydrophobicity and aromaticity are primary factors shaping variation in amino acid usage of chicken proteome. PMID:25329059
In vitro, long-range sequence information for de novo genome assembly via transposase contiguity. PMID:25327137
Widespread contribution of transposable elements to the innovation of gene regulatory networks. PMID:25319995
The impact of transposable elements in genome evolution and genetic instability and their implications in various diseases. PMID:25317108
Deep sequencing reveals low incidence of endogenous LINE-1 retrotransposition in human induced pluripotent stem cells. PMID:25289675
An evaluation of regulatory and commercial barriers to stratified medicine development and adoption. PMID:25287070
Multiple Mechanisms Contribute To Telomere Maintenance. PMID:25285314
Genetic networks governing heart development. PMID:25280899
Retrotransposon-based profiling of mammalian epigenomes: DNA methylation of IAP LTRs in embryonic stem, somatic and cancer cells. PMID:25277721
LINE-1 hypomethylation in blood and tissue samples as an epigenetic marker for cancer risk: a systematic review and meta-analysis. PMID:25275447
Promoter analysis reveals globally differential regulation of human long non-coding RNA and protein-coding genes. PMID:25275320
An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons. PMID:25274305
Proliferation of endogenous retroviruses in the early stages of a host germ line invasion. PMID:25261407
Hybrid and rogue kinases encoded in the genomes of model eukaryotes. PMID:25255313
Managing, analysing, and integrating big data in medical bioinformatics: open problems and future perspectives. PMID:25254202
Comprehensive analysis of mutually exclusive alternative splicing in C. elegans. PMID:25254147
ARYANA: Aligning Reads by Yet Another Approach. PMID:25252881
A comprehensive transcriptomic analysis of infant and adult mouse ovary. PMID:25251848
Analysis of the role of homology arms in gene-targeting vectors in human cells. PMID:25250686
Genome-wide and single-cell analyses reveal a context dependent relationship between CBP recruitment and gene expression. PMID:25249627
SIRT6 represses LINE1 retrotransposons by ribosylating KAP1 but this repression fails with stress and age. PMID:25247314
Human endogenous retroviral elements promote genome instability via non-allelic homologous recombination. PMID:25246103
The scaffold protein Nde1 safeguards the brain genome during S phase of early neural progenitor differentiation. PMID:25245017
Allelic mapping bias in RNA-sequencing is not a major confounder in eQTL studies. PMID:25239376
Function and dynamics of macromolecular complexes explored by integrative structural and computational biology. PMID:25238653
Molecular characterization of common fragile sites as a strategy to discover cancer susceptibility genes. PMID:25231336
Rolling-circle transposons catalyze genomic innovation in a mammalian lineage. PMID:25223768
Random forest-based protein model quality assessment (RFMQA) using structural features and potential energy terms. PMID:25222008
Human serotonin receptor 5-HT(1A) preferentially segregates to the liquid disordered phase in synthetic lipid bilayers. PMID:25211019
Positive selection and multiple losses of the LINE-1-derived L1TD1 gene in mammals suggest a dual role in genome defense and pluripotency. PMID:25211013
We are all individuals... bioinformatics in the personalized medicine era. PMID:25204962
Direct binding of the Alu binding protein dimer SRP9/14 to 40S ribosomal subunits promotes stress granule formation and is regulated by Alu RNA. PMID:25200073
The evolution of tyrosine-recombinase elements in Nematoda. PMID:25197791
Evidence for the persistence of an active endogenous retrovirus (ERVE) in humans. PMID:25192754
Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies. PMID:25192061
Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements. PMID:25188499
Recruitment of Yoruba families from Nigeria for genetic research: experience from a multisite keloid study. PMID:25182071
Prenatal maternal immune activation causes epigenetic differences in adolescent mouse brain. PMID:25180573
Open access data sharing in genomic research. PMID:25178093
Microsatellite-centromere mapping in common carp through half-tetrad analysis in diploid meiogynogenetic families. PMID:25171918
The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development. PMID:25171416
Genomic Variation: Lessons Learned from Whole-Genome CNV Analysis. PMID:25152847
LINEs and SINEs of primate evolution. PMID:25147443
Potential for genomic instability associated with retrotranspositionally-incompetent L1 loci. PMID:25143528
Relating gene expression evolution with CpG content changes. PMID:25142157
The lncRNA-MYC regulatory network in cancer. PMID:25139102
Epidemiological studies of esophageal cancer in the era of genome-wide association studies. PMID:25133033
Current status of predictive biomarkers for neoadjuvant therapy in esophageal cancer. PMID:25133032
Environmental alterations of epigenetics prior to the birth. PMID:25131541
Discovery of common sequences absent in the human reference genome using pooled samples from next generation sequencing. PMID:25129063
Decreased LINE-1 methylation levels in aldosterone-producing adenoma. PMID:25120789
Transcriptome analysis of red swamp crawfish Procambarus clarkii reveals genes involved in gonadal development. PMID:25118947
A comprehensive reference transcriptome resource for the common house spider Parasteatoda tepidariorum. PMID:25118601
A long non-coding RNA is required for targeting centromeric protein A to the human centromere. PMID:25117489
Distinct isoform of FABP7 revealed by screening for retroelement-activated genes in diffuse large B-cell lymphoma. PMID:25114248
In silico modeling of human α2C-adrenoreceptor interaction with filamin-2. PMID:25110951
TGF- β: an important mediator of allergic disease and a molecule with dual activity in cancer development. PMID:25110717
Current technologies to identify protein kinase substrates in high throughput. PMID:25110472
Discovery of modulators of HIV-1 infection from the human peptidome. PMID:25110191
LINE-1 retrotransposons: from 'parasite' sequences to functional elements. PMID:25106509
Environmental bacteriophages: viruses of microbes in aquatic ecosystems. PMID:25104950
Histidine kinases mediate differentiation, stress response, and pathogenicity in Magnaporthe oryzae. PMID:25103193
Drafts of the human proteome. PMID:25101745
The structure and retrotransposition mechanism of LTR-retrotransposons in the asexual yeast Candida albicans. PMID:25101670
Validation of high throughput sequencing and microbial forensics applications. PMID:25101166
Generation of physical map contig-specific sequences. PMID:25101119
Improved sensitivity to detect recombination using qPCR for Dyskeratosis Congenita PGD. PMID:25099625
Dynamic regulation of human endogenous retroviruses mediates factor-induced reprogramming and differentiation potential. PMID:25097266
A high resolution map of mammalian X chromosome fragile regions assessed by large-scale comparative genomics. PMID:25086724
LIA4 encodes a chromoshadow domain protein required for genomewide DNA rearrangements in Tetrahymena thermophila. PMID:25084866
Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes. PMID:25082706
The DNA methylation landscape of human early embryos. PMID:25079557
Mammalian piRNAs: Biogenesis, function, and mysteries. PMID:25077039
The quality of methods reporting in parasitology experiments. PMID:25076044
Periodontal microbiology--the lid's off the box again. PMID:25074493
Insulin as a Bridge between Type 2 Diabetes and Alzheimer Disease - How Anti-Diabetics Could be a Solution for Dementia. PMID:25071725
The dynamic exome: acquired variants as individuals age. PMID:25063753
Microarray analysis reveals global modulation of endogenous retroelement transcription by microbes. PMID:25063042
Expression and detection of LINE-1 ORF-encoded proteins. PMID:25054082
Survey on knowledge, attitudes, and training needs of Italian residents on genetic tests for hereditary breast and colorectal cancer. PMID:25050348
Heteromerization of GPR55 and cannabinoid CB2 receptors modulates signalling. PMID:25048571
Genomic data integration for ecological and evolutionary traits in non-model organisms. PMID:25047861
Functional repeat-derived RNAs often originate from retrotransposon-propagated ncRNAs. PMID:25045147
Transcriptome analysis reveals a dynamic and differential transcriptional response to sulforaphane in normal and prostate cancer cells and suggests a role for Sp1 in chemoprevention. PMID:25044704
Noncoding RNAs and the borders of heterochromatin. PMID:25044367
De novo LINE-1 retrotransposition in HepG2 cells preferentially targets gene poor regions of chromosome 13. PMID:25043885
Unraveling recombination rate evolution using ancestral recombination maps. PMID:25043668
Parallel universes of Black Six biology. PMID:25038798
The common marmoset genome provides insight into primate biology and evolution. PMID:25038751
Larger mammalian body size leads to lower retroviral activity. PMID:25033295
Effective automated feature construction and selection for classification of biological sequences. PMID:25033270
Microsatellite interruptions stabilize primate genomes and exist as population-specific single nucleotide polymorphisms within individual human genomes. PMID:25033203
Data integration in the era of omics: current and future challenges. PMID:25032990
G-protein βγ subunit dimers modulate kidney repair after ischemia-reperfusion injury in rats. PMID:25028481
Novel diet-related mouse model of colon cancer parallels human colon cancer. PMID:25024814
Cutting edge: An antibody recognizing ancestral endogenous virus glycoproteins mediates antibody-dependent cellular cytotoxicity on HIV-1-infected cells. PMID:25024383
Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression. PMID:25018785
Conventional and genetic talent identification in sports: will recent developments trace talent? PMID:25015477
Transcriptional landscape of repetitive elements in normal and cancer human cells. PMID:25012247
Fine mapping and functional studies of risk variants for type 1 diabetes at chromosome 16p13.13. PMID:25008175
Emerging role of long non-coding RNA SOX2OT in SOX2 regulation in breast cancer. PMID:25006803
Mobile DNA elements in the generation of diversity and complexity in the brain. PMID:25005482
High-throughput targeted repeat element bisulfite sequencing (HT-TREBS): genome-wide DNA methylation analysis of IAP LTR retrotransposon. PMID:25003790
Expanding the computational toolbox for mining cancer genomes. PMID:25001846
A cross-sectional study of global DNA methylation and risk of colorectal adenoma. PMID:24998982
Exome sequencing from nanogram amounts of starting DNA: comparing three approaches. PMID:24992588
Bioinformatics education--perspectives and challenges out of Africa. PMID:24990350
Searching for repeats, as an example of using the generalised Ruzzo-Tompa algorithm to find optimal subsequences with gaps. PMID:24989859
Coherent somatic mutation in autoimmune disease. PMID:24988487
Human endogenous retrovirus-K(II) envelope induction protects neurons during HIV/AIDS. PMID:24988390
Chimpanzee-specific endogenous retrovirus generates genomic variations in the chimpanzee genome. PMID:24987855
eMERGEing progress in genomics-the first seven years. PMID:24987407
Similarities and differences between exome sequences found in a variety of tissues from the same individual. PMID:24984015
Tandem repeats and G-rich sequences are enriched at human CNV breakpoints. PMID:24983241
Systems biology in the context of big data and networks. PMID:24982882
Prenatal exposure to mixtures of xenoestrogens and repetitive element DNA methylation changes in human placenta. PMID:24980756
DNA methylation, microRNAs, and their crosstalk as potential biomarkers in hepatocellular carcinoma. PMID:24976726
Insertional hypermutation in mineral oil-induced plasmacytomas. PMID:24975032
Whole-genome sequence variation, population structure and demographic history of the Dutch population. PMID:24974849
Population distribution analyses reveal a hierarchy of molecular players underlying parallel endocytic pathways. PMID:24971745
Alu and LINE-1 hypomethylation is associated with HER2 enriched subtype of breast cancer. PMID:24971511
Panning for Long Noncoding RNAs. PMID:24970166
Comparative studies of vertebrate Beta integrin genes and proteins: ancient genes in vertebrate evolution. PMID:24970121
Reviving the dead: history and reactivation of an extinct l1. PMID:24968166
A de novo genome assembly algorithm for repeats and nonrepeats. PMID:24967398
Spy: a new group of eukaryotic DNA transposons without target site duplications. PMID:24966181
The evolution of the coding exome of the Arabidopsis species--the influences of DNA methylation, relative exon position, and exon length. PMID:24965500
Returning individual research results for genome sequences of pancreatic cancer. PMID:24963353
Epigenetic heredity of human height. PMID:24963031
BLAT-based comparative analysis for transposable elements: BLATCAT. PMID:24959585
The Role of the Transmembrane RING Finger Proteins in Cellular and Organelle Function. PMID:24957874
Mobile elements and viral integrations prompt considerations for bacterial DNA integration as a novel carcinogen. PMID:24956175
Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana. PMID:24954583
Applications of RNA interference high-throughput screening technology in cancer biology and virology. PMID:24952721
Biochemical and bioinformatic methods for elucidating the role of RNA-protein interactions in posttranscriptional regulation. PMID:24951655
Epigenetic regulation of persistent pain. PMID:24948399
Nicotine and oxidative stress induced exomic variations are concordant and overrepresented in cancer-associated genes. PMID:24947164
The strength of the strongest ties in collaborative problem solving. PMID:24946798
Digital genotyping of macrosatellites and multicopy genes reveals novel biological functions associated with copy number variation of large tandem repeats. PMID:24945355
PKR is activated by cellular dsRNAs during mitosis and acts as a mitotic regulator. PMID:24939934
Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes. PMID:24939910
Obstacles and opportunities for the future of genomic medicine. PMID:24936509
Overexpression of piRNA pathway genes in epithelial ovarian cancer. PMID:24932571
Sequencing your genome: what does it mean? PMID:24932355
No effect of weight loss on LINE-1 methylation levels in peripheral blood leukocytes from postmenopausal overweight women. PMID:24930817
Effective suppression of dengue virus using a novel group-I intron that induces apoptotic cell death upon infection through conditional expression of the Bax C-terminal domain. PMID:24927852
Whole genome wide expression profiles on germination of Verticillium dahliae microsclerotia. PMID:24927478
LINE-1 hypomethylation is associated with the risk of coronary heart disease in Chinese population. PMID:24918913
Identification of candidate long non-coding RNAs in response to myocardial infarction. PMID:24917243
Structured RNAs and synteny regions in the pig genome. PMID:24917120
Discovering functional DNA elements using population genomic information: a proof of concept using human mtDNA. PMID:24916662
Regulation of L1 expression and retrotransposition by melatonin and its receptor: implications for cancer risk associated with light exposure at night. PMID:24914052
The mechanistic role of DNA methylation in myeloid leukemogenesis. PMID:24913729
Transposable elements in cancer as a by-product of stress-induced evolvability. PMID:24910642
Last-gen nostalgia: a lighthearted rant and reflection on genome sequencing culture. PMID:24904646
Using semantic web technologies to annotate and align microarray designs. PMID:24904201
A bioinformatic and computational study of myosin phosphatase subunit diversity. PMID:24898838
Genome at juncture of early human migration: a systematic analysis of two whole genomes and thirteen exomes from Kuwaiti population subgroup of inferred Saudi Arabian tribe ancestry. PMID:24896259
Exome sequencing: new insights into lipoprotein disorders. PMID:24893940
Protein-protein interactions and genetic diseases: The interactome. PMID:24892209
Human endogenous retrovirus K and cancer: Innocent bystander or tumorigenic accomplice? PMID:24890612
Simple sequence repeats in the national longitudinal study of adolescent health: an ethnically diverse resource for genetic analysis of health and behavior. PMID:24890516
Origin of spliceosomal introns and alternative splicing. PMID:24890509
Interpreting human genetic variation with in vivo zebrafish assays. PMID:24887202
Improvement of domain-level ortholog clustering by optimizing domain-specific sum-of-pairs score. PMID:24885064
Casposons: a new superfamily of self-synthesizing DNA transposons at the origin of prokaryotic CRISPR-Cas immunity. PMID:24884953
XSAnno: a framework for building ortholog models in cross-species transcriptome comparisons. PMID:24884593
Population genetic analysis of bi-allelic structural variants from low-coverage sequence data with an expectation-maximization algorithm. PMID:24884587
Physiology of the read-write genome. PMID:24882816
Heterochromatin controls γH2A localization in Neurospora crassa. PMID:24879124
Prediction of bacterial microRNAs and possible targets in human cell transcriptome. PMID:24871974
Human genetic variation and Parkinson's disease. PMID:24868370
microRNAs and Alu elements in the p53-Mdm2-Mdm4 regulatory network. PMID:24868102
Pharmacogenomics: Current State-of-the-Art. PMID:24865298
Elevated HERV-K mRNA expression in PBMC is associated with a prostate cancer diagnosis particularly in older men and smokers. PMID:24858205
HeteroGenome: database of genome periodicity. PMID:24857969
An enhancer polymorphism at the cardiomyocyte intercalated disc protein NOS1AP locus is a major regulator of the QT interval. PMID:24857694
Targeting polycomb to pericentric heterochromatin in embryonic stem cells reveals a role for H2AK119u1 in PRC2 recruitment. PMID:24857660
The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs. PMID:24850885
Rapid evolution of piRNA pathway in the teleost fish: implication for an adaptation to transposon diversity. PMID:24846630
APOBEC3A deaminates transiently exposed single-strand DNA during LINE-1 retrotransposition. PMID:24843014
Repetitive genomic elements and overall DNA methylation changes in acute myeloid and childhood B-cell lymphoblastic leukemia patients. PMID:24841671
The birth and development of the DNA theory of inheritance: sixty years since the discovery of the structure of DNA. PMID:24840850
Blood from 'junk': the LTR chimeric transcript Pu.2 promotes erythropoiesis. PMID:24839466
CtIP maintains stability at common fragile sites and inverted repeats by end resection-independent endonuclease activity. PMID:24837675
Understanding the Dynamics of Gene Regulatory Systems; Characterisation and Clinical Relevance of cis-Regulatory Polymorphisms. PMID:24832652
Genotyping-by-Sequencing in Plants. PMID:24832503
Analysis of horse genomes provides insight into the diversification and adaptive evolution of karyotype. PMID:24828444
Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing. PMID:24823667
Global and local competition between exogenously introduced microRNAs and endogenously expressed microRNAs. PMID:24823356
Identification of Horizontally-transferred Genomic Islands and Genome Segmentation Points by Using the GC Profile Method. PMID:24822029
A Brief Review: The Z-curve Theory and its Application in Genome Analysis. PMID:24822026
Changes in Membrane Cholesterol Differentially Influence Preferential and Non-preferential Signaling of the M1 and M3 Muscarinic Acetylcholine Receptors. PMID:24821386
Genomic landscape of human, bat, and ex vivo DNA transposon integrations. PMID:24809961
Evaluation of novel design strategies for developing zinc finger nucleases tools for treating human diseases. PMID:24808958
Development of rapidly evolving intron markers to estimate multilocus species trees of rodents. PMID:24804779
Realistic artificial DNA sequences as negative controls for computational genomics. PMID:24803667
Integrating omics technologies to study pulmonary physiology and pathology at the systems level. PMID:24802001
Variants of a Thermus aquaticus DNA polymerase with increased selectivity for applications in allele- and methylation-specific amplification. PMID:24800860
From Phenotype to Genotype: Enter Genomics and Transformation of Primary Health Care around the World. PMID:24799423
Molecular tumor board: the University of California-San Diego Moores Cancer Center experience. PMID:24797821
Epigenetic control of mobile DNA as an interface between experience and genome change. PMID:24795749
Integrating genomic, transcriptomic, and interactome data to improve Peptide and protein identification in shotgun proteomics. PMID:24792918
Conserved modular domains team up to latch-open active protein kinase Cα. PMID:24790081
Long noncoding RNA: significance and potential in skin biology. PMID:24789873
To be or not to be: the regulation of mRNA fate as a survival strategy during mammalian hibernation. PMID:24789358
Pharmacomicrobiomics: the impact of human microbiome variations on systems pharmacology and personalized therapeutics. PMID:24785449
Developmental transcriptome analysis of human erythropoiesis. PMID:24781209
Genetic interactions affecting human gene expression identified by variance association mapping. PMID:24771767
Impact of alternative DNA structures on DNA damage, DNA repair, and genetic instability. PMID:24767258
The new world of RNAs. PMID:24764762
Using VAAST to Identify Disease-Associated Variants in Next-Generation Sequencing Data. PMID:24763993
Global hypomethylation and promoter methylation in small intestinal neuroendocrine tumors: an in vivo and in vitro study. PMID:24762809
Microfluidic bead suspension hopper. PMID:24761972
Key regulators control distinct transcriptional programmes in blood progenitor and mast cells. PMID:24760698
Protein-centric N-glycoproteomics analysis of membrane and plasma membrane proteins. PMID:24754784
Defining functional DNA elements in the human genome. PMID:24753594
A novel tRNA variable number tandem repeat at human chromosome 1q23.3 is implicated as a boundary element based on conservation of a CTCF motif in mouse. PMID:24753417
An expanding universe of the non-coding genome in cancer biology. PMID:24747961
The enemy within: endogenous retroelements and autoimmune disease. PMID:24747712
Towards a molecular systems model of coronary artery disease. PMID:24743898
Transcription-associated R-loop formation across the human FMR1 CGG-repeat region. PMID:24743386
Revitalizing personalized medicine: respecting biomolecular complexities beyond gene expression. PMID:24739991
DNA methylation dynamics during epigenetic reprogramming in the germline and preimplantation embryos. PMID:24736841
Long-read sequencing of chicken transcripts and identification of new transcript isoforms. PMID:24736250
Species-specific alternative splicing leads to unique expression of sno-lncRNAs. PMID:24734784
Matrix and backstage: cellular substrates for viral vaccines. PMID:24732259
Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing. PMID:24728327
A quick guide to genomics and bioinformatics training for clinical and public audiences. PMID:24722068
A short guide to long non-coding RNA gene nomenclature. PMID:24716852
Genetics of polycystic ovary syndrome. PMID:24715512
Chromatin Organization by Repetitive Elements (CORE): A Genomic Principle for the Higher-Order Structure of Chromosomes. PMID:24710208
A reverse transcriptase-dependent mechanism is essential for murine preimplantation development. PMID:24710196
Next generation DNA sequencing and the future of genomic medicine. PMID:24710010
Deep investigation of Arabidopsis thaliana junk DNA reveals a continuum between repetitive elements and genomic dark matter. PMID:24709859
Retrotransposition in tumors and brains. PMID:24708615
Identifying regulatory mechanisms underlying tumorigenesis using locus expression signature analysis. PMID:24706889
Illuminating the Transcriptome through the Genome. PMID:24705295
Association claims in the sequencing era. PMID:24705293
Genetics of Charcot-Marie-Tooth (CMT) Disease within the Frame of the Human Genome Project Success. PMID:24705285
In Vivo RNAi-Based Screens: Studies in Model Organisms. PMID:24705267
High SINE RNA Expression Correlates with Post-Transcriptional Downregulation of BRCA1. PMID:24705161
Identifying and characterizing regulatory sequences in the human genome with chromatin accessibility assays. PMID:24705081
A model of evolution of development based on germline penetration of new "no-junk" DNA. PMID:24704981
Microsatellites with macro-influence in ewing sarcoma. PMID:24704979
Transposable elements: from DNA parasites to architects of metazoan evolution. PMID:24704977
Deep sequencing to identify the causes of viral encephalitis. PMID:24699691
Mapping the structure and dynamics of genomics-related MeSH terms complex networks. PMID:24699262
A LINE-1 insertion in DLX6 is responsible for cleft palate and mandibular abnormalities in a canine model of Pierre Robin sequence. PMID:24699068
A brief history of macromolecular crystallography, illustrated by a family tree and its Nobel fruits. PMID:24698025
Characteristics of the cation cotransporter NKCC1 in human brain: alternate transcripts, expression in development, and potential relationships to brain function and schizophrenia. PMID:24695712
Transcriptional regulation of YWHAZ, the gene encoding 14-3-3ζ. PMID:24690670
Implications of human genome structural heterogeneity: functionally related genes tend to reside in organizationally similar genomic regions. PMID:24684786
Construction of a high-coverage bacterial artificial chromosome library and comprehensive genetic linkage map of yellowtail Seriola quinqueradiata. PMID:24684753
Correcting for differential transcript coverage reveals a strong relationship between alternative splicing and organism complexity. PMID:24682283
Genetic counselors' views and experiences with the clinical integration of genome sequencing. PMID:24671342
Personalized ophthalmology. PMID:24665880
Association studies of sporadic Parkinson's disease in the genomic era. PMID:24653658
A first generation BAC-based physical map of the half-smooth tongue sole (Cynoglossus semilaevis) genome. PMID:24650389
An efficient method for high-fidelity messenger RNA amplification from a small amount of total RNA. PMID:24648903
HIV-1 interacts with human endogenous retrovirus K (HML-2) envelopes derived from human primary lymphocytes. PMID:24648457
Technology: The $1,000 genome. PMID:24646979
Intellectual property rights and innovation: Evidence from the human genome. PMID:24639594
Quantitative theory of entropic forces acting on constrained nucleotide sequences applied to viruses. PMID:24639520
Nuclear function of Alus. PMID:24637839
RepARK--de novo creation of repeat libraries from whole-genome NGS reads. PMID:24634442
Missing links in cardiology: long non-coding RNAs enter the arena. PMID:24619481
Genome-wide signals of positive selection in human evolution. PMID:24619126
Billions of basepairs of recently expanded, repetitive sequences are eliminated from the somatic genome during copepod development. PMID:24618421
Multiple conserved regulatory domains promote Fezf2 expression in the developing cerebral cortex. PMID:24618363
Accommodating the load: The transposable element content of very large genomes. PMID:24616835
Diversity through duplication: whole-genome sequencing reveals novel gene retrocopies in the human population. PMID:24615986
Ty3 reverse transcriptase complexed with an RNA-DNA hybrid shows structural and functional asymmetry. PMID:24608367
Scanning of transposable elements and analyzing expression of transposase genes of sweet potato [Ipomoea batatas]. PMID:24608103
2013 Curt Stern Award Address. PMID:24607386
The challenges and importance of structural variation detection in livestock. PMID:24600474
DNA methylome in spleen of avian pathogenic Escherichia coli-challenged broilers and integration with mRNA expression. PMID:24599154
Human-specific epigenetic variation in the immunological Leukotriene B4 Receptor (LTB4R/BLT1) implicated in common inflammatory diseases. PMID:24598577
Human genetics' 50th anniversary issue. PMID:24595704
Transcriptome sequencing and De Novo analysis of Youngia japonica using the illumina platform. PMID:24595283
Data simulation in machine olfaction with the R package chemosensors. PMID:24586410
Stable C0T-1 repeat RNA is abundant and is associated with euchromatic interphase chromosomes. PMID:24581492
Deletion of Gpr128 results in weight loss and increased intestinal contraction frequency. PMID:24574718
Constraint and opportunity in genome innovation. PMID:24572460
Global patterns of apparent copy number variation in birds revealed by cross-species comparative genomic hybridization. PMID:24570127
Morphine induces redox-based changes in global DNA methylation and retrotransposon transcription by inhibition of excitatory amino acid transporter type 3-mediated cysteine uptake. PMID:24569088
Epigenetics in the pathogenesis of rheumatoid arthritis. PMID:24568138
Epigenetic modification, dehydration, and molecular crowding effects on the thermodynamics of i-motif structure formation from C-rich DNA. PMID:24564458
The synthetic biology future. PMID:24561910
Frequent L1 retrotranspositions originating from TTC28 in colorectal cancer. PMID:24553397
Variation, evolution, and correlation analysis of C+G content and genome or chromosome size in different kingdoms and phyla. PMID:24551092
GATA5 CpG island hypermethylation is an independent predictor for poor clinical outcome in renal cell carcinoma. PMID:24549248
Sequencing, assembling, and correcting draft genomes using recombinant populations. PMID:24531727
An Introduction to Functional Genomics and Systems Biology. PMID:24527360
Point-of-care technologies for molecular diagnostics using a drop of blood. PMID:24525172
Genome-guided transcriptome assembly in the age of next-generation sequencing. PMID:24524156
Prediction and classification of ncRNAs using structural information. PMID:24521294
Comparative RNAi screens in C. elegans and C. briggsae reveal the impact of developmental system drift on gene function. PMID:24516395
Endogenous retroviruses and the development of cancer. PMID:24511094
Divergent and dynamic activity of endogenous retroviruses in burn patients and their inflammatory potential. PMID:24509167
Conditionally and transiently disordered proteins: awakening cryptic disorder to regulate protein function. PMID:24502763
A simple method for gene phasing using mate pair sequencing. PMID:24502676
Small-molecule probes elucidate global enzyme activity in a proteomic context. PMID:24499666
A new genome-wide method to track horizontally transferred sequences: application to Drosophila. PMID:24497602
Twenty-first century science as a relational process: from eureka! to team science and a place for community psychology. PMID:24496718
An antisense promoter in mouse L1 retrotransposon open reading frame-1 initiates expression of diverse fusion transcripts and limits retrotransposition. PMID:24493738
Comparing DNA integration site clusters with scan statistics. PMID:24489369
Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle. PMID:24487278
Nuclear architecture as an epigenetic regulator of neural development and function. PMID:24486963
Finding the missing honey bee genes: lessons learned from a genome upgrade. PMID:24479613
A new biophysical metric for interrogating the information content in human genome sequence variation: Proof of concept. PMID:24478921
Genome-scale analysis of demographic history and adaptive selection. PMID:24474201
Trans-activation, post-transcriptional maturation, and induction of antibodies to HERV-K (HML-2) envelope transmembrane protein in HIV-1 infection. PMID:24472118
Significant overlap between human genome-wide association-study nominated breast cancer risk alleles and rat mammary cancer susceptibility loci. PMID:24467842
Long non-coding RNA H19 promotes glioma cell invasion by deriving miR-675. PMID:24466011
Neurofilament Heavy polypeptide CpG island methylation associates with prognosis of renal cell carcinoma and prediction of antivascular endothelial growth factor therapy response. PMID:24464810
Alu- and 7SL RNA Analogues Suppress MCF-7 Cell Viability through Modulating the Transcription of Endoplasmic Reticulum Stress Response Genes. PMID:24455187
Diversity of human tRNA genes from the 1000-genomes project. PMID:24448271
An empirically informed critique of Habermas' argument from human nature. PMID:24446150
Bidirectional promoters are the major source of gene activation-associated non-coding RNAs in mammals. PMID:24438357
Effects of short-term exposure to inhalable particulate matter on DNA methylation of tandem repeats. PMID:24436168
The emerging molecular architecture of schizophrenia, polygenic risk scores and the clinical implications for GxE research. PMID:24435092
Sequencing depth and coverage: key considerations in genomic analyses. PMID:24434847
The first draft of the pigeonpea genome sequence. PMID:24431589
Whole genome sequence of a Turkish individual. PMID:24416366
Toward an accurate prediction of inter-residue distances in proteins using 2D recursive neural networks. PMID:24410833
Post-genomics nanotechnology is gaining momentum: nanoproteomics and applications in life sciences. PMID:24410486
Horizontal gene transfer in the acquisition of novel traits by metazoans. PMID:24403327
A computational framework to infer human disease-associated long noncoding RNAs. PMID:24392133
An absolute index (Ab-index) to measure a researcher's useful contributions and productivity. PMID:24391941
Community-Based Participatory Research and Gene-Environment Interaction Methodologies Addressing Environmental Justice among Migrant and Seasonal Farmworker Women and Children in Texas: "From Mother to Child Project". PMID:24391476
Identification and characterisation of non-coding small RNAs in the pathogenic filamentous fungus Trichophyton rubrum. PMID:24377353
DIAMUND: direct comparison of genomes to detect mutations. PMID:24375697
Discovery of MLL1 binding units, their localization to CpG Islands, and their potential function in mitotic chromatin. PMID:24373511
Mutation discovery for Mendelian traits in non-laboratory animals: a review of achievements up to 2012. PMID:24372556
RNase L restricts the mobility of engineered retrotransposons in cultured human cells. PMID:24371271
APOBEC3G oligomerization is associated with the inhibition of both Alu and LINE-1 retrotransposition. PMID:24367644
(13)C NMR spectroscopy applications to brain energy metabolism. PMID:24367329
Zinc and the aging brain. PMID:24366781
Increased seroreactivity to HERV-K10 peptides in patients with HTLV myelopathy. PMID:24365054
Life cycle of an n-globin pseudogene microsatellite locus. PMID:24363661
A novel null homozygous mutation confirms CACNA2D2 as a gene mutated in epileptic encephalopathy. PMID:24358150
Next generation 1536-well oligonucleotide synthesizer with on-the-fly dispense. PMID:24355807
A novel recombinant retrovirus in the genomes of modern birds combines features of avian and mammalian retroviruses. PMID:24352464
Identification and biochemical characterization of protein phosphatase 5 from the cantharidin-producing blister beetle, Epicauta chinensis. PMID:24351830
CrossMap: a versatile tool for coordinate conversion between genome assemblies. PMID:24351709
A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes. PMID:24347612
A tumor-promoting mechanism mediated by retrotransposon-encoded reverse transcriptase is active in human transformed cell lines. PMID:24345856
Differential inhibition of LINE1 and LINE2 retrotransposition by vertebrate AID/APOBEC proteins. PMID:24344916
De novo assembly of a field isolate genome reveals novel Plasmodium vivax erythrocyte invasion genes. PMID:24340114
Comparative genomic analysis of eutherian ribonuclease A genes. PMID:24337645
The population history of endogenous retroviruses in mule deer (Odocoileus hemionus). PMID:24336966
An age-of-allele test of neutrality for transposable element insertions. PMID:24336751
Concepts of tissue injury and cell death in inflammation: a historical perspective. PMID:24336099
Genome sequencing: a systematic review of health economic evidence. PMID:24330507
Characterization of L1 ORF1p self-interaction and cellular localization using a mammalian two-hybrid system. PMID:24324740
Students' perspective on genomics: from sample to sequence using the case study of blueberry. PMID:24324481
DNA transposon-based gene vehicles - scenes from an evolutionary drive. PMID:24320156
The roles of genetic polymorphisms and human immunodeficiency virus infection in lipid metabolism. PMID:24319689
Structural features and mechanism of translocation of non-LTR retrotransposons in Candida albicans. PMID:24317340
The Vertebrate Genome Annotation browser 10 years on. PMID:24316575
Accurate detection of subclonal single nucleotide variants in whole genome amplified and pooled cancer samples using HaloPlex target enrichment. PMID:24314227
Enhancing systems medicine beyond genotype data by dynamic patient signatures: having information and using it too. PMID:24312119
MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations. PMID:24306534
Genetic and epigenetic determinants mediate proneness of oncogene breakpoint sites for involvement in TCR translocations. PMID:24304972
Detection limit of intragenic deletions with targeted array comparative genomic hybridization. PMID:24304607
Influence of age, sex and genetic factors on the human brain. PMID:24297733
Comparative genomics of oral isolates of Streptococcus mutans by in silico genome subtraction does not reveal accessory DNA associated with severe early childhood caries. PMID:24291226
Rapid and inexpensive screening of genomic copy number variations using a novel quantitative fluorescent PCR method. PMID:24288428
L1 retrotransposons, cancer stem cells and oncogenesis. PMID:24286172
Molecular versatility: the many faces and functions of noncoding RNA. PMID:24281974
Not so pseudo anymore: pseudogenes as therapeutic targets. PMID:24279857
Alu mobile elements: from junk DNA to genomic gems. PMID:24278713
Genome-scale technology driven advances to research into normal and malignant haematopoiesis. PMID:24278696
Whole genome sequencing of field isolates reveals a common duplication of the Duffy binding protein gene in Malagasy Plasmodium vivax strains. PMID:24278487
DNA sequences at a glance. PMID:24278218
DUX4 binding to retroelements creates promoters that are active in FSHD muscle and testis. PMID:24278031
Stable RNA nanoparticles as potential new generation drugs for cancer therapy. PMID:24270010
Systematic classification of non-coding RNAs by epigenomic similarity. PMID:24267974
Role of pathogens in multiple sclerosis. PMID:24266364
Associations between serum perfluoroalkyl acids and LINE-1 DNA methylation. PMID:24263140
Microbial diversity in the era of omic technologies. PMID:24260747
Small RNAs, big impact: small RNA pathways in transposon control and their effect on the host stress response. PMID:24254230
InvFEST, a database integrating information of polymorphic inversions in the human genome. PMID:24253300
LINE-1 activation and epigenetic silencing of suppressor genes in cancer: Causally related events? PMID:24251074
Domesticated transposable element gene products in human cancer. PMID:24251072
Association and differentiation of MHC class I and II polymorphic Alu insertions and HLA-A, -B, -C and -DRB1 alleles in the Chinese Han population. PMID:24248811
Functional clustering of immunoglobulin superfamily proteins with protein-protein interaction information calibrated hidden Markov model sequence profiles. PMID:24246499
Identification of significant features in DNA microarray data. PMID:24244802
Linear decay of retrotransposon antisense bias across genes is contingent upon tissue specificity. PMID:24244495
Retrotransposon silencing during embryogenesis: dicer cuts in LINE. PMID:24244199
A sequence-ready physical map of barley anchored genetically by two million single-nucleotide polymorphisms. PMID:24243933
Deorphanizing the human transmembrane genome: A landscape of uncharacterized membrane proteins. PMID:24241348
Human heart failure: is cell therapy a valid option? PMID:24239645
Functional microRNAs and target sites are created by lineage-specific transposition. PMID:24234653
Epigenetic regulation by long noncoding RNAs in plants. PMID:24233054
Increased expression and copy number amplification of LINE-1 and SINE B1 retrotransposable elements in murine mammary carcinoma progression. PMID:24231191
STaRRRT: a table of short tandem repeats in regulatory regions of the human genome. PMID:24228761
Metabolic mechanisms of epigenetic regulation. PMID:24228614
Epigenetic status of LINE-1 predicts clinical outcome in early-stage rectal cancer. PMID:24220694
Identification of three new Alu Yb subfamilies by source tracking of recently integrated Alu Yb elements. PMID:24216009
Discovery of recurrent structural variants in nasopharyngeal carcinoma. PMID:24214394
Epigenomic elements enriched in the promoters of autoimmunity susceptibility genes. PMID:24213554
The nature of nurture: refining the definition of the exposome. PMID:24213143
Cancer genome sequencing and its implications for personalized cancer vaccines. PMID:24213133
Retrotransposon-encoded reverse transcriptase in the genesis, progression and cellular plasticity of human cancer. PMID:24212657
Plasma proteomics, the Human Proteome Project, and cancer-associated alternative splice variant proteins. PMID:24211518
Classification of α-helical membrane proteins using predicted helix architectures. PMID:24204844
Condensin II subunit dCAP-D3 restricts retrotransposon mobilization in Drosophila somatic cells. PMID:24204294
The role of transposable elements in health and diseases of the central nervous system. PMID:24198348
Exome sequencing: one small step for malignant hyperthermia, one giant step for our specialty--why exome sequencing matters to all of us, not just the experts. PMID:24195944
Non-LTR retrotransposons and microsatellites: Partners in genomic variation. PMID:24195012
A fine-scale recombination map of the human-chimpanzee ancestor reveals faster change in humans than in chimpanzees and a strong impact of GC-biased gene conversion. PMID:24190946
Perspective: a systems approach to diabetes research. PMID:24187547
DNA methylation profiling in X;autosome translocations supports a role for L1 repeats in the spread of X chromosome inactivation. PMID:24186870
Review: Alternative Splicing (AS) of Genes As An Approach for Generating Protein Complexity. PMID:24179441
Complexity of the alternative splicing landscape in plants. PMID:24179125
A 129-kb deletion on chromosome 12 confers substantial protection against rheumatoid arthritis, implicating the gene SLC2A3. PMID:24178905
The genomics of schizophrenia: update and implications. PMID:24177465
Intronic deletions in the SLC34A3 gene: a cautionary tale for mutation analysis of hereditary hypophosphatemic rickets with hypercalciuria. PMID:24176905
Old world monkeys and new age science: the evolution of nonhuman primate systems virology. PMID:24174440
Improving genome assemblies and annotations for nonhuman primates. PMID:24174438
Genetic and molecular alterations in pancreatic cancer: implications for personalized medicine. PMID:24172537
Functional transcriptomics in the post-ENCODE era. PMID:24172201
Gene regulation by non-coding RNAs. PMID:24164576
An emerging place for lung cancer genomics in 2013. PMID:24163742
Mutagenesis and phenotyping resources in zebrafish for studying development and human disease. PMID:24162064
Intron retention in the alternatively spliced region of RON results from weak 3' splice site recognition. PMID:24155930
Differential L1 regulation in pluripotent stem cells of humans and apes. PMID:24153179
Potential Antibacterial Targets in Bacterial Central Metabolism. PMID:24151543
Clinical implications of the LINE-1 methylation levels in patients with gastrointestinal cancer. PMID:24150097
The challenges, advantages and future of phenome-wide association studies. PMID:24147732
A review of bacteria-animal lateral gene transfer may inform our understanding of diseases like cancer. PMID:24146634
Next-generation sequencing for mitochondrial disorders. PMID:24138576
Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. PMID:24136355
Human genome replication proceeds through four chromatin states. PMID:24130466
Lessons from postgenome-wide association studies: functional analysis of cancer predisposition loci. PMID:24127939
Structure and Expression Analyses of SVA Elements in Relation to Functional Genes. PMID:24124410
Long noncoding RNA HOTTIP/HOXA13 expression is associated with disease progression and predicts outcome in hepatocellular carcinoma patients. PMID:24114970
Strong heterogeneity in mutation rate causes misleading hallmarks of natural selection on indel mutations in the human genome. PMID:24113537
De novo identification of VRC01 class HIV-1-neutralizing antibodies by next-generation sequencing of B-cell transcripts. PMID:24106303
Cancer genomics identifies disrupted epigenetic genes. PMID:24104525
"Conferring authorship": biobank stakeholders' experiences with publication credit in collaborative research. PMID:24098803
A novel actin mRNA splice variant regulates ACTG1 expression. PMID:24098136
Exploring mechanisms of human disease through structurally resolved protein interactome networks. PMID:24096645
Transposable elements and their potential role in complex lung disorder. PMID:24093510
BLUEPRINT: mapping human blood cell epigenomes. PMID:24091925
LINE-1 retrotransposable element DNA accumulates in HIV-1-infected cells. PMID:24089548
Guanine holes are prominent targets for mutation in cancer and inherited disease. PMID:24086153
Alu elements: an intrinsic source of human genome instability. PMID:24080407
Utilization of transposable element mPing as a novel genetic tool for modification of the stress response in rice. PMID:24078785
Mapping human epigenomes. PMID:24074860
Mass fingerprinting of complex mixtures: protein inference from high-resolution peptide masses and predicted retention times. PMID:24074221
Transcriptome profile of the green odorous frog (Odorrana margaretae). PMID:24073255
Lineage-specific duplications of Muroidea Faim and Spag6 genes and atypical accelerated evolution of the parental Spag6 gene. PMID:24071998
Contamination of live attenuated vaccines with an infectious feline endogenous retrovirus (RD-114 virus). PMID:24068581
Punctuated emergences of genetic and phenotypic innovations in eumetazoan, bilaterian, euteleostome, and hominidae ancestors. PMID:24065732
Splicing and alternative splicing in rice and humans. PMID:24064058
Association of endogenous retroviruses and long terminal repeats with human disorders. PMID:24062987
The genetics of NAFLD. PMID:24061205
Information measure for long-range correlated sequences: the case of the 24 human chromosomes. PMID:24056670
DNA sequencing methods in human genetics and disease research. PMID:24049638
Defending the genome from the enemy within: mechanisms of retrotransposon suppression in the mouse germline. PMID:24045705
The Human Genome Project: big science transforms biology and medicine. PMID:24040834
In vitro screening for compounds that enhance human L1 mobilization. PMID:24040300
Proteasome inhibitors block DNA repair and radiosensitize non-small cell lung cancer. PMID:24040035
Long non-coding RNAs and complex human diseases. PMID:24036441
Modulation of LINE-1 and Alu/SVA retrotransposition by Aicardi-Goutières syndrome-related SAMHD1. PMID:24035396
LINEs of evidence: noncanonical DNA replication as an epigenetic determinant. PMID:24034780
Genotyping of human neutrophil antigens (HNA) from whole genome sequencing data. PMID:24028078
CFTR activity and mitochondrial function. PMID:24024153
Insights into the loblolly pine genome: characterization of BAC and fosmid sequences. PMID:24023741
The relationship between gene isoform multiplicity, number of exons and protein divergence. PMID:24023641
Massively parallel sequencing: the new frontier of hematologic genomics. PMID:24021669
From helix to hematology: introduction to a collection of reviews on the emerging role of next-generation sequencing in hematology. PMID:24016460
Predicting whole genome protein interaction networks from primary sequence data in model and non-model organisms using ENTS. PMID:24015873
Lizards and LINEs: selection and demography affect the fate of L1 retrotransposons in the genome of the green anole (Anolis carolinensis). PMID:24013105
Splice variants of zinc finger protein 695 mRNA associated to ovarian cancer. PMID:24007497
Microbes, metagenomes and marine mammals: enabling the next generation of scientist to enter the genomic era. PMID:24007365
Population genetics and molecular evolution of DNA sequences in transposable elements. I. A simulation framework. PMID:24002643
Effect of heavy metals on silencing of engineered long interspersed element-1 retrotransposon in nondividing neuroblastoma cell line. PMID:23999712
The MaSuRCA genome assembler. PMID:23990416
Population genomics of cardiometabolic traits: design of the University College London-London School of Hygiene and Tropical Medicine-Edinburgh-Bristol (UCLEB) Consortium. PMID:23977022
Refrex-1, a soluble restriction factor against feline endogenous and exogenous retroviruses. PMID:23966402
Towards precision medicine: advances in computational approaches for the analysis of human variants. PMID:23962656
Segmenting the human genome based on states of neutral genetic divergence. PMID:23959903
Plasma S-adenosylmethionine, DNMT polymorphisms, and peripheral blood LINE-1 methylation among healthy Chinese adults in Singapore. PMID:23957506
Use of single nucleotide polymorphism array technology to improve the identification of chromosomal lesions in leukemia. PMID:23941516
Prolonged treatment with DNMT inhibitors induces distinct effects in promoters and gene-bodies. PMID:23940695
Hydroquinone increases 5-hydroxymethylcytosine formation through ten eleven translocation 1 (TET1) 5-methylcytosine dioxygenase. PMID:23940045
Paleovirology of 'syncytins', retroviral env genes exapted for a role in placentation. PMID:23938756
Exploring the effects of immunity and life history on the dynamics of an endogenous retrovirus. PMID:23938754
'There and back again': revisiting the pathophysiological roles of human endogenous retroviruses in the post-genomic era. PMID:23938753
Comprehensive analysis of endogenous bornavirus-like elements in eukaryote genomes. PMID:23938751
Visualized computational predictions of transcriptional effects by intronic endogenous retroviruses. PMID:23936536
Genistein inhibits prostate cancer cell growth by targeting miR-34a and oncogenic HOTAIR. PMID:23936419
Mitogenomes from two uncommon haplogroups mark late glacial/postglacial expansions from the near east and neolithic dispersals within Europe. PMID:23936216
The Profile of Human Sperm Proteome; A Mini-review. PMID:23926502
The nuage mediates retrotransposon silencing in mouse primordial ovarian follicles. PMID:23924633
Evaluation of genome sequencing quality in selected plant species using expressed sequence tags. PMID:23922843
Detecting Alu insertions from high-throughput sequencing data. PMID:23921633
Progress toward personalized medicine for glaucoma. PMID:23914252
Identification of cis-regulatory modules in promoters of human genes exploiting mutual positioning of transcription factors. PMID:23913413
The Future of Children's Health in the Genomic Era. PMID:23908811
The application of next-generation sequencing in the autozygosity mapping of human recessive diseases. PMID:23907654
Locating Pb2+ and Zn2+ in zinc finger-like peptides using mass spectrometry. PMID:23907592
Profiling the immune stromal interface in breast cancer and its potential for clinical impact. PMID:23904829
Organelle targeting: third level of drug targeting. PMID:23898223
Single-cell sequencing-based technologies will revolutionize whole-organism science. PMID:23897237
Epigenetic signature and enhancer activity of the human APOE gene. PMID:23892237
REViewer: a tool for linear visualization of repetitive elements within a sequence query. PMID:23891933
Detecting and comparing non-coding RNAs in the high-throughput era. PMID:23887659
Unraveling genomic variation from next generation sequencing data. PMID:23885890
Rates and patterns of great ape retrotransposition. PMID:23884656
Cigarette smoking and DNA methylation. PMID:23882278
Genomics of lymphoid malignancies reveal major activation pathways in lymphocytes. PMID:23880067
Recurrent HERV-H-mediated 3q13.2-q13.31 deletions cause a syndrome of hypotonia and motor, language, and cognitive delays. PMID:23878096
Hypomethylation of long interspersed nuclear element-1 promoter is associated with poor outcomes for curative resected hepatocellular carcinoma. PMID:23875825
Translational genetics for diagnosis of human disorders of sex development. PMID:23875799
A superfamily of DNA transposons targeting multicopy small RNA genes. PMID:23874566
Lessons from next-generation sequencing analysis in hematological malignancies. PMID:23872706
Evolution: life has evolved to evolve: comment on "How life changes itself: the Read-Write (RW) genome" by James Shapiro. PMID:23871431
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. PMID:23870653
Spatial localization of genes determined by intranuclear DNA fragmentation with the fusion proteins lamin KRED and histone KRED und visible light. PMID:23869190
Generation of transgenic mice with megabase-sized human yeast artificial chromosomes by yeast spheroplast-embryonic stem cell fusion. PMID:23868074
Global DNA methylation in a population with aflatoxin B1 exposure. PMID:23867725
Down's syndrome, neuroinflammation, and Alzheimer neuropathogenesis. PMID:23866266
Are human endogenous retroviruses pathogenic? An approach to testing the hypothesis. PMID:23864388
A versatile microsatellite instability reporter system in human cells. PMID:23861444
Dominant form of congenital hyperinsulinism maps to HK1 region on 10q. PMID:23859901
Evolutionary age of repetitive element subfamilies and sensitivity of DNA methylation to airborne pollutants. PMID:23855992
The sequence signature of an Ig-fold. PMID:23842991
Periodic distribution of a putative nucleosome positioning motif in human, nonhuman primates, and archaea: mutual information analysis. PMID:23841049
Bacteria-human somatic cell lateral gene transfer is enriched in cancer samples. PMID:23840181
The Mighty Mouse: the impact of rodents on advances in biomedical research. PMID:23829104
STAU1 binding 3' UTR IRAlus complements nuclear retention to protect cells from PKR-mediated translational shutdown. PMID:23824540
CluGene: A Bioinformatics Framework for the Identification of Co-Localized, Co-Expressed and Co-Regulated Genes Aimed at the Investigation of Transcriptional Regulatory Networks from High-Throughput Expression Data. PMID:23823315
Homoeologous chromosomes of Xenopus laevis are highly conserved after whole-genome duplication. PMID:23820579
Controlled insertional mutagenesis using a LINE-1 (ORFeus) gene-trap mouse model. PMID:23818630
Understanding the regulatory and transcriptional complexity of the genome through structure. PMID:23817049
Comparative genomics as a tool to understand evolution and disease. PMID:23817047
Jenner-predict server: prediction of protein vaccine candidates (PVCs) in bacteria based on host-pathogen interactions. PMID:23815072
Copy number variation of transposable elements in Triticum-Aegilops genus suggests evolutionary and revolutionary dynamics following allopolyploidization. PMID:23807536
Genomic analysis of ERVWE2 locus in patients with multiple sclerosis: absence of genetic association but potential role of human endogenous retrovirus type W elements in molecular mimicry with myelin antigen. PMID:23805135
The intertwining of transposable elements and non-coding RNAs. PMID:23803660
Enhancers. PMID:23801531
RNA-seq in the tetraploid Xenopus laevis enables genome-wide insight in a classic developmental biology model organism. PMID:23792920
The impact of natural selection on health and disease: uses of the population genetics approach in humans. PMID:23789027
Epigenetic mechanisms in fetal origins of health and disease. PMID:23787712
Crystal structures and RNA-binding properties of the RNA recognition motifs of heterogeneous nuclear ribonucleoprotein L: insights into its roles in alternative splicing regulation. PMID:23782695
GAT: a simulation framework for testing the association of genomic intervals. PMID:23782611
Evolution of the correlation between expression divergence and protein divergence in mammals. PMID:23781097
Special considerations in prognostic research in cancer involving genetic polymorphisms. PMID:23773794
Analysis of 8 X-chromosomal markers in the population of central Croatia. PMID:23771754
On guard: coronin proteins in innate and adaptive immunity. PMID:23765056
QualComp: a new lossy compressor for quality scores based on rate distortion theory. PMID:23758828
Passive and active DNA methylation and the interplay with genetic variation in gene regulation. PMID:23755361
A comparison of 100 human genes using an alu element-based instability model. PMID:23755193
Storage conditions and stability of global DNA methylation in placental tissue. PMID:23750648
The role of recombination in the origin and evolution of Alu subfamilies. PMID:23750218
Statistical analysis of pentose phosphate pathway genes from eubacteria and eukarya reveals translational selection as a major force in shaping codon usage pattern. PMID:23750079
Mapping the LINE1 ORF1 protein interactome reveals associated inhibitors of human retrotransposition. PMID:23749060
Cancer epigenetics: a brief review. PMID:23744972
Overview of high throughput sequencing technologies to elucidate molecular pathways in cardiovascular diseases. PMID:23743227
Integrated platform for genome-wide screening and construction of high-density genetic interaction maps in mammalian cells. PMID:23739767
Next-generation sequencing in genetic hearing loss. PMID:23738631
Transposable element invasions. PMID:23734297
Studying recombination with high-throughput sequencing: an educational primer for use with "fine-scale heterogeneity in crossover rate in the garnet-scalloped region of the Drosophila melanogaster X chromosome". PMID:23733850
Expansion of the pseudo-autosomal region and ongoing recombination suppression in the Silene latifolia sex chromosomes. PMID:23733786
Genomics and genetics in the biology of adaptation to exercise. PMID:23733655
LINE-1 and Alu retrotransposition exhibit clonal variation. PMID:23732044
Improved coverage and accuracy with strand-conserving sequence enrichment. PMID:23731654
Machine learning and genome annotation: a match meant to be? PMID:23731483
Enzymatic production of 'monoclonal stoichiometric' single-stranded DNA oligonucleotides. PMID:23727986
The epigenetic regulator PLZF represses L1 retrotransposition in germ and progenitor cells. PMID:23727884
Survival analysis with incomplete genetic data. PMID:23722305
High-throughput sequencing reveals principles of adeno-associated virus serotype 2 integration. PMID:23720718
Genome-wide characterization of endogenous retroviruses in the bat Myotis lucifugus reveals recent and diverse infections. PMID:23720713
The role of retrotransposons in gene family expansions: insights from the mouse Abp gene family. PMID:23718880
Expression of a LINE-1 endonuclease variant in gastric cancer: its association with clinicopathological parameters. PMID:23718141
Alu elements in primates are preferentially lost from areas of high GC content. PMID:23717800
ZNF408 is mutated in familial exudative vitreoretinopathy and is crucial for the development of zebrafish retinal vasculature. PMID:23716654
Posttranscriptional regulation by RNA-binding proteins during epithelial-to-mesenchymal transition. PMID:23715860
REAPR: a universal tool for genome assembly evaluation. PMID:23710727
Emerging tools for synthetic genome design. PMID:23708771
DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. PMID:23708189
Retroviruses and amyotrophic lateral sclerosis. PMID:23707220
HPV 5 and 8 E6 expression reduces ATM protein levels and attenuates LINE-1 retrotransposition. PMID:23706308
PeSV-Fisher: identification of somatic and non-somatic structural variants using next generation sequencing data. PMID:23704902
Identification of a novel PNMA-MS1 gene in marsupials suggests the LTR retrotransposon-derived PNMA genes evolved differently in marsupials and eutherians. PMID:23704700
Expression of a large LINE-1-driven antisense RNA is linked to epigenetic silencing of the metastasis suppressor gene TFPI-2 in cancer. PMID:23703216
Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data. PMID:23698863
Footprint of APOBEC3 on the genome of human retroelements. PMID:23698293
Comparative genomic and transcriptomic analysis of tandemly and segmentally duplicated genes in rice. PMID:23696832
Human monogenic disease genes have frequently functionally redundant paralogs. PMID:23696728
Enrichment of processed pseudogene transcripts in L1-ribonucleoprotein particles. PMID:23696454
Rapid multiplexed genotyping of simple tandem repeats using capture and high-throughput sequencing. PMID:23696428
On the classification of long non-coding RNAs. PMID:23696037
ABC transporters in multidrug resistance and pharmacokinetics, and strategies for drug development. PMID:23688078
Structural and functional annotation of the porcine immunome. PMID:23676093
A human anti-c-Met Fab fragment conjugated with doxorubicin as targeted chemotherapy for hepatocellular carcinoma. PMID:23675455
The specificity and flexibility of l1 reverse transcription priming at imperfect T-tracts. PMID:23675310
Genetic variation and its role in malignancy. PMID:23675233
Overlapping of genes in the human genome. PMID:23675016
Information theory, gene expression, and combinatorial regulation: a quantitative analysis. PMID:23674094
GATA simple sequence repeats function as enhancer blocker boundaries. PMID:23673629
Molecular evolution of peptidergic signaling systems in bilaterians. PMID:23671109
eQTL Mapping Using RNA-seq Data. PMID:23667399
Retrotransposons: a new and credible source of inherited and somatically acquired hepatocellular carcinoma mutations. PMID:23665280
A gene expression restriction network mediated by sense and antisense Alu sequences located on protein-coding messenger RNAs. PMID:23663499
Multiple suboptimal solutions for prediction rules in gene expression data. PMID:23662163
Detection of serum Alu element hypomethylation for the diagnosis and prognosis of glioma. PMID:23657981
Multiple sclerosis: autoimmunity and viruses. PMID:23656710
Digital quantitation of potential therapeutic target RNAs. PMID:23656494
Sixty years of genome biology. PMID:23651518
DNA methylation: the future of crime scene investigation? PMID:23649761
Identification of multiple binding sites for the THAP domain of the Galileo transposase in the long terminal inverted-repeats. PMID:23648487
Reprogramming of the HepG2 genome by long interspersed nuclear element-1. PMID:23648019
Long noncoding RNAs in biology and hematopoiesis. PMID:23645840
Genomic dynamics of transposable elements in the western clawed frog (Silurana tropicalis). PMID:23645600
Genomic resources for multiple species in the Drosophila ananassae species group. PMID:23639891
Influence of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors. PMID:23638344
Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PMID:23637635
Role of the human endogenous retrovirus HERV-K18 in autoimmune disease susceptibility: study in the Spanish population and meta-analysis. PMID:23634223
Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq. PMID:23629695
Systematic biases in DNA copy number originate from isolation procedures. PMID:23618369
Genetics of coronary artery disease and myocardial infarction--2013. PMID:23616109
Genome-wide analysis of alternative splicing during dendritic cell response to a bacterial challenge. PMID:23613991
Sequence and structure-specific elements of HERG mRNA determine channel synthesis and trafficking efficiency. PMID:23608144
The challenge of increasing Pfam coverage of the human proteome. PMID:23603847
Innovations in proteomic profiling of cancers: alternative splice variants as a new class of cancer biomarker candidates and bridging of proteomics with structural biology. PMID:23603631
The human qualities needed to complete the global eradication of polio. PMID:23599552
Mobile element scanning (ME-Scan) identifies thousands of novel Alu insertions in diverse human populations. PMID:23599355
Are results of targeted gene sequencing ready to be used for clinical decision making for patients with acute myelogenous leukemia? PMID:23595294
Computational solutions for omics data. PMID:23594911
Cancer genome-sequencing study design. PMID:23594910
Human-specific HERV-K insertion causes genomic variations in the human genome. PMID:23593260
Revising a personal genome by comparing and combining data from two different sequencing platforms. PMID:23593254
Identification of optimum sequencing depth especially for de novo genome assembly of small genomes using next generation sequencing data. PMID:23593174
Improving mammalian genome scaffolding using large insert mate-pair next-generation sequencing. PMID:23590730
Existing and emerging technologies for tumor genomic profiling. PMID:23589546
Mathematical modeling of complex biological systems: from parts lists to understanding systems behavior. PMID:23584751
IMACULAT - an open access package for the quantitative analysis of chromosome localization in the nucleus. PMID:23577217
The use of RelocaTE and unassembled short reads to produce high-resolution snapshots of transposable element generated diversity in rice. PMID:23576519
Searching microsatellites in DNA sequences: approaches used and tools developed. PMID:23573036
Comprehensively identifying and characterizing the missing gene sequences in human reference genome with integrated analytic approaches. PMID:23572138
From the genetic code to neuromics. PMID:23571821
Understanding neurological disease mechanisms in the era of epigenetics. PMID:23571666
What contemporary viruses tell us about evolution: a personal view. PMID:23568292
Analysis of copy number variations in the sheep genome using 50K SNP BeadChip array. PMID:23565757
Horizontal transfer and evolution of prokaryote transposable elements in eukaryotes. PMID:23563966
Evolutionarily conserved long intergenic non-coding RNAs in the eye. PMID:23562822
Impact of GC content on gene expression pattern in chicken. PMID:23557030
Transduction-specific ATLAS reveals a cohort of highly active L1 retrotransposons in human populations. PMID:23553801
Diversity of transposable elements and repeats in a 600 kb region of the fly Calliphora vicina. PMID:23552491
On the transposon origins of mammalian SCAND3 and KRBA2, two zinc-finger genes carrying an integrase/transposase domain. PMID:23550032
Characterization of a new high copy Stowaway family MITE, BRAMI-1 in Brassica genome. PMID:23547712
Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. PMID:23540693
The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. PMID:23537068
Cancer epigenetics: new therapies and new challenges. PMID:23533770
Structure prediction and analysis of DNA transposon and LINE retrotransposon proteins. PMID:23530042
Cancer pharmacogenomics in children: research initiatives and progress to date. PMID:23529868
GWAS in autoimmune thyroid disease: redefining our understanding of pathogenesis. PMID:23529038
Lifeomics leads the age of grand discoveries. PMID:23526385
Genomics in cardiovascular disease. PMID:23524054
Intron retention and transcript chimerism conserved across mammals: Ly6g5b and Csnk2b-Ly6g5b as examples. PMID:23521802
Crystallization and preliminary X-ray crystallographic analysis of the human CKIP-1 pleckstrin homology domain. PMID:23519814
Elevated rate of fixation of endogenous retroviral elements in Haplorhini TRIM5 and TRIM22 genomic sequences: impact on transcriptional regulation. PMID:23516500
Microhomology-mediated mechanisms underlie non-recurrent disease-causing microdeletions of the FOXL2 gene or its regulatory domain. PMID:23516377
Functional proteomics of barley and barley chloroplasts - strategies, methods and perspectives. PMID:23515231
Decoding retinitis pigmentosa. PMID:23514641
Significantly fewer protein functional changing variants for lipid metabolism in Africans than in Europeans. PMID:23514131
LINE-1 and Alu hypomethylation in mucoepidermoid carcinoma. PMID:23510117
Hunting human disease genes: lessons from the past, challenges for the future. PMID:23504071
Genomic and epigenomic insights into nutrition and brain disorders. PMID:23503168
The Promises and Pitfalls of Genoeconomics*. PMID:23482589
A tale of an A-tail: The lifeline of a SINE. PMID:23481375
The 2010 ESPEN Sir David Cuthbertson Lecture: new and old proteins: clinical implications. PMID:23481224
Clopidogrel and warfarin pharmacogenetic tests: what is the evidence for use in clinical practice? PMID:23478884
Increased genome instability in human DNA segments with self-chains: homology-induced structural variations via replicative mechanisms. PMID:23474816
The hierarchy of the 3D genome. PMID:23473598
Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities. PMID:23469896
Genes, environments, and developmental research: methods for a multi-site study of early substance abuse. PMID:23461817
Reduced syncytin-1 expression levels in placental syndromes correlates with epigenetic hypermethylation of the ERVW-1 promoter region. PMID:23457515
High-throughput cloning and expression library creation for functional proteomics. PMID:23457047
DNA methylation dynamics in blood after hematopoietic cell transplant. PMID:23451113
Causes and implications of codon usage bias in RNA viruses. PMID:23451064
Accurate identification and analysis of human mRNA isoforms using deep long read sequencing. PMID:23450794
Current genomics in cardiovascular medicine. PMID:23450299
Mercury biomarkers and DNA methylation among Michigan dental professionals. PMID:23444121
Long non-coding RNA in cancer. PMID:23443164
Regulatory genomics: Insights from the zebrafish. PMID:23440612
Protein analysis by shotgun/bottom-up proteomics. PMID:23438204
Evaluating rare variants in complex disorders using next-generation sequencing. PMID:23435969
Mutation screen and RNA analysis disclose the changed splicing of the E-cadherin transcription in gastric cancer. PMID:23435907
Using population admixture to help complete maps of the human genome. PMID:23435088
Probing a coral genome for components of the photoprotective scytonemin biosynthetic pathway and the 2-aminoethylphosphonate pathway. PMID:23434798
Intrinsic immunity against retrotransposons by APOBEC cytidine deaminases. PMID:23431045
On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. PMID:23431001
Emergence of novel domains in proteins. PMID:23425224
SPPS resins impact the PNA-syntheses' improvement. PMID:23423830
Assessment of clinical analytical sensitivity and specificity of next-generation sequencing for detection of simple and complex mutations. PMID:23418865
PBOV1 is a human de novo gene with tumor-specific expression that is associated with a positive clinical outcome of cancer. PMID:23418531
Genome-Level Analysis of Selective Constraint without Apparent Sequence Conservation. PMID:23418180
A library of TAL effector nucleases spanning the human genome. PMID:23417094
Transposable elements as genetic regulatory substrates in early development. PMID:23411159
New clinical and molecular insights on Barth syndrome. PMID:23409742
Transposon variants and their effects on gene expression in Arabidopsis. PMID:23408902
The developmental brain gene NPAS3 contains the largest number of accelerated regulatory sequences in the human genome. PMID:23408798
Noncoding RNAs and Cancer. PMID:23407615
The Role of MicroRNAs in Human Diseases. PMID:23407304
Comparison of sequencing platforms for single nucleotide variant calls in a human sample. PMID:23405114
Microsatellite instability in sarcoma: fact or fiction? PMID:23401795
A proteomics view of the molecular mechanisms and biomarkers of glaucomatous neurodegeneration. PMID:23396249
The repertoires of ubiquitinating and deubiquitinating enzymes in eukaryotic genomes. PMID:23393154
Comparative analysis of de novo transcriptome assembly. PMID:23393031
Multiple tandem splicing silencer elements suppress aberrant splicing within the long exon 26 of the human Apolipoprotein B gene. PMID:23391187
Genetics and epigenetics of rheumatoid arthritis. PMID:23381558
p53 promotes repair of heterochromatin DNA by regulating JMJD2b and SUV39H1 expression. PMID:23376847
Discovery of novel non-synonymous SNP variants in 988 candidate genes from 6 centenarians by target capture and next-generation sequencing. PMID:23376243
Striking structural dynamism and nucleotide sequence variation of the transposon Galileo in the genome of Drosophila mojavensis. PMID:23374229
What role (if any) does the highly conserved CSB-PGBD3 fusion protein play in Cockayne syndrome? PMID:23369858
Host genomic influences on HIV/AIDS. PMID:23369251
A novel subgradient-based optimization algorithm for blockmodel functional module identification. PMID:23368964
The genome-defence gene Tex19.1 suppresses LINE-1 retrotransposons in the placenta and prevents intra-uterine growth retardation in mice. PMID:23364048
NEAT1 long noncoding RNA and paraspeckle bodies modulate HIV-1 posttranscriptional expression. PMID:23362321
Estimation of data-specific constitutive exons with RNA-Seq data. PMID:23360225
Development of a cytokine-modified allogeneic whole cell pancreatic cancer vaccine. PMID:23359154
A lower degree of PBMC L1 methylation is associated with excess body weight and higher HOMA-IR in the presence of lower concentrations of plasma folate. PMID:23358786
Transposable elements re-wire and fine-tune the transcriptome. PMID:23358118
The human THAP9 gene encodes an active P-element DNA transposase. PMID:23349291
Quantitation of HIV DNA integration: effects of differential integration site distributions on Alu-PCR assays. PMID:23348058
Mechanisms and dynamics of orphan gene emergence in insect genomes. PMID:23348040
Transposable Elements: No More 'Junk DNA'. PMID:23346034
A short history of the genome-wide association study: where we were and where we are going. PMID:23346033
A 21(st) Century View of Evolution. PMID:23345811
Turning gold into 'junk': transposable elements utilize central proteins of cellular networks. PMID:23341038
Evolutionary rate of human tissue-specific genes are related with transposable element insertions. PMID:23337972
The sum of many small changes: microRNAs are specifically and potentially globally altered by vitamin D3 metabolites. PMID:23333596
Rat mir-155 generated from the lncRNA Bic is 'hidden' in the alternate genomic assembly and reveals the existence of novel mammalian miRNAs and clusters. PMID:23329697
ENCODE and its first impractical application. PMID:23327603
Physiology of SLC12 transporters: lessons from inherited human genetic mutations and genetically engineered mouse knockouts. PMID:23325410
Paraspeckle formation during the biogenesis of long non-coding RNAs. PMID:23324609
Hsa-mir-124-3 CpG island methylation is associated with advanced tumours and disease recurrence of patients with clear cell renal cell carcinoma. PMID:23321515
How do mammalian transposons induce genetic variation? A conceptual framework: the age, structure, allele frequency, and genome context of transposable elements may define their wide-ranging biological impacts. PMID:23319453
Personalized medicine: Has it started yet? A reconstruction of the early history. PMID:23316213
Evaluating risks of insertional mutagenesis by DNA transposons in gene therapy. PMID:23313630
Mobile element biology: new possibilities with high-throughput sequencing. PMID:23312846
Homopolymer tail-mediated ligation PCR: a streamlined and highly efficient method for DNA cloning and library construction. PMID:23311318
Effective preparation of Plasmodium vivax field isolates for high-throughput whole genome sequencing. PMID:23308154
Locus-specific DNA methylation reprogramming during early porcine embryogenesis. PMID:23303676
Inference of the protokaryotypes of amniotes and tetrapods and the evolutionary processes of microchromosomes from comparative gene mapping. PMID:23300852
Single-stranded annealing induced by re-initiation of replication origins provides a novel and efficient mechanism for generating copy number expansion via non-allelic homologous recombination. PMID:23300490
Chapter 12: Human microbiome analysis. PMID:23300406
Role of DNA secondary structures in fragile site breakage along human chromosome 10. PMID:23297364
High-throughput sequencing and rare genetic diseases. PMID:23293577
Revisiting the evolution of mouse LINE-1 in the genomic era. PMID:23286374
A novel family of terminal-repeat retrotransposon in miniature (TRIM) in the genome of the red harvester ant, Pogonomyrmex barbatus. PMID:23285291
Establishment of a TGFβ-induced post-transcriptional EMT gene signature. PMID:23285117
HTS-PEG: a method for high throughput sequencing of the paired-ends of genomic libraries. PMID:23284958
Reevaluating assembly evaluations with feature response curves: GAGE and assemblathons. PMID:23284938
A genome-wide perspective of human diversity and its implications in infectious disease. PMID:23284079
Human endogenous retroviruses and cancer prevention: evidence and prospects. PMID:23282240
Reconstructing the evolutionary history of transposable elements. PMID:23275488
Population-scale analysis of human microsatellites reveals novel sources of exonic variation. PMID:23274653
The ADAR protein family. PMID:23273215
Proteomics meets the scientific method. PMID:23269373
Omics Screening for Pharmaceutical Efficacy and Safety in Clinical Practice. PMID:23264882
Host restriction factors in retroviral infection: promises in virus-host interaction. PMID:23254112
Selection-driven extinction dynamics for group II introns in Enterobacteriales. PMID:23251705
Genome-wide analysis of DNA methylation differences in muscle and fat from monozygotic twins discordant for type 2 diabetes. PMID:23251491
Bioinformatics of Cancer ncRNA in High Throughput Sequencing: Present State and Challenges. PMID:23251139
Detecting rare variants for psychiatric disorders using next generation sequencing: a methods primer. PMID:23250814
miRNA-mediated risk for schizophrenia in 22q11.2 deletion syndrome. PMID:23248646
Functional characterization of piggyBat from the bat Myotis lucifugus unveils an active mammalian DNA transposon. PMID:23248290
Latent regulatory potential of human-specific repetitive elements. PMID:23246434
Conservation of the three-dimensional structure in non-homologous or unrelated proteins. PMID:23244440
Distinct mutational behaviors differentiate short tandem repeats from microsatellites in the human genome. PMID:23241442
Histone demethylase Jumonji D3 (JMJD3) as a tumor suppressor by regulating p53 protein nuclear stabilization. PMID:23236496
Sequences associated with centromere competency in the human genome. PMID:23230266
Horizontal transfer and the evolution of host-pathogen interactions. PMID:23227424
The yin and yang of repair mechanisms in DNA structure-induced genetic instability. PMID:23219604
The evolution of ultraconserved elements with different phylogenetic origins. PMID:23217155
LINE-1 methylation shows little intra-patient heterogeneity in primary and synchronous metastatic colorectal cancer. PMID:23216958
Nonallelic homologous recombination between retrotransposable elements is a driver of de novo unbalanced translocations. PMID:23212949
A fast and accurate SNP detection algorithm for next-generation sequencing data. PMID:23212387
Evolution of hemoglobin and its genes. PMID:23209182
Large-scale isolation of microsatellites from Chinese Mitten Crab Eriocheir sinensis via a Solexa Genomic Survey. PMID:23208373
Next generation sequencing of CLU, PICALM and CR1: pitfalls and potential solutions. PMID:23205178
Genomics in cardiovascular diseases: analysis of the importance of the toll-like receptor signaling pathway. PMID:23204853
Overview of micro- and nano-technology tools for stem cell applications: micropatterned and microelectronic devices. PMID:23202240
In vitro selection of proteins with desired characteristics using mRNA-display. PMID:23201412
Next generation sequencing for neurological diseases: new hope or new hype? PMID:23200550
Molecular genetics of AML. PMID:23200536
Developing biobanks in developing countries. PMID:23198094
H-InvDB in 2013: an omics study platform for human functional gene and transcript discovery. PMID:23197657
Identification of a group of Mus dunni endogenous virus-like endogenous retroviruses from the C57BL/6J mouse genome: proviral genomes, strain distribution, expression characteristics, and genomic integration profile. PMID:23197326
Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system. PMID:23193282
Bioinformatics. Introduction. PMID:23189382
Coinciding revolutions: how discovery of non-coding DNA and RNA can change our understanding of addiction. PMID:23189086
Endogenous hepatitis C virus homolog fragments in European rabbit and hare genomes replicate in cell culture. PMID:23185448
Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PMID:23185243
Transposable elements reveal a stem cell-specific class of long noncoding RNAs. PMID:23181609
Genomic sequencing in cancer. PMID:23178448
Somatic transposition in the brain has the potential to influence the biosynthesis of metabolites involved in Parkinson's disease and schizophrenia. PMID:23176288
NANOGP8: evolution of a human-specific retro-oncogene. PMID:23173096
Epigenome remodelling in breast cancer: insights from an early in vitro model of carcinogenesis. PMID:23168266
Comparative analysis of the recently discovered hAT transposon TcBuster in human cells. PMID:23166581
Is there a role for endogenous retroviruses to mediate long-term adaptive phenotypic response upon environmental inputs? PMID:23166400
piRNA and spermatogenesis in mice. PMID:23166399
HERVs expression in Autism Spectrum Disorders. PMID:23155411
Human endogenous retroviruses and cancer: causality and therapeutic possibilities. PMID:23155332
First all-in-one diagnostic tool for DNA intelligence: genome-wide inference of biogeographic ancestry, appearance, relatedness, and sex with the Identitas v1 Forensic Chip. PMID:23149900
Genome sequences of wild and domestic bactrian camels. PMID:23149746
Adaptive efficient compression of genomes. PMID:23146997
Active transposition in genomes. PMID:23145912
A non-synonymous single nucleotide polymorphism in an OPRM1 splice variant is associated with fentanyl-induced emesis in women undergoing minor gynaecological surgery. PMID:23144877
Ribonuclease 4 protects neuron degeneration by promoting angiogenesis, neurogenesis, and neuronal survival under stress. PMID:23143660
HERV-K-specific T cells eliminate diverse HIV-1/2 and SIV primary isolates. PMID:23143309
Amino termini of many yeast proteins map to downstream start codons. PMID:23140384
FungiQuant: a broad-coverage fungal quantitative real-time PCR assay. PMID:23136846
Impact of retrotransposons in pluripotent stem cells. PMID:23135636
Epigenetic regulation of human embryonic stem cells. PMID:23133442
The correlation of genome size and DNA methylation rate in metazoans. PMID:23132463
LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons. PMID:23131050
Physical mapping resources for large plant genomes: radiation hybrids for wheat D-genome progenitor Aegilops tauschii. PMID:23127207
LINE-1-derived poly(A) microsatellites undergo rapid shortening and create somatic and germline mosaicism in mice. PMID:23125228
General survey of hAT transposon superfamily with highlight on hobo element in Drosophila. PMID:23111927
Functional analysis of splice variant expression of MADS AFFECTING FLOWERING 2 of Arabidopsis thaliana. PMID:23111501
Exclusion of exon 2 is a common mRNA splice variant of primate telomerase reverse transcriptases. PMID:23110161
When a domain is not a domain, and why it is important to properly filter proteins in databases: conflicting definitions and fold classification systems for structural domains make filtering of such databases imperative. PMID:23108912
Multifaceted roles of Arabidopsis PP6 phosphatase in regulating cellular signaling and plant development. PMID:23104112
Distinct groups of repetitive families preserved in mammals correspond to different periods of regulatory innovations in vertebrates. PMID:23098210
The roles of gene duplication, gene conversion and positive selection in rodent Esp and Mup pheromone gene families with comparison to the Abp family. PMID:23094077
MOV10 RNA helicase is a potent inhibitor of retrotransposition in cells. PMID:23093941
Coordinated repression of cell cycle genes by KDM5A and E2F4 during differentiation. PMID:23093672
A resurrected mammalian hAT transposable element and a closely related insect element are highly active in human cell culture. PMID:23091042
Functional eukaryotic nuclear localization signals are widespread in terminal proteins of bacteriophages. PMID:23091024
Targeting the transposase domain of the DNA repair component Metnase to enhance chemotherapy. PMID:23090115
A functional selection model explains evolutionary robustness despite plasticity in regulatory networks. PMID:23089682
Alu elements and human common diseases like obesity. PMID:23087845
Protein phosphatase 1γ isoforms linked interactions in the brain. PMID:23080069
The dual roles of homeobox genes in vascularization and wound healing. PMID:23076135
Alu and LINE-1 methylation and lung function in the normative ageing study. PMID:23075571
Genome-wide association studies in myocardial infarction and coronary artery disease. PMID:23074578
Gypsy, RTE and Mariner transposable elements populate Eyprepocnemis plorans genome. PMID:23073915
The SLEEPER genes: a transposase-derived angiosperm-specific gene family. PMID:23067104
DICER- and AGO3-dependent generation of retinoic acid-induced DR2 Alu RNAs regulates human stem cell proliferation. PMID:23064648
Long interspersed nuclear elements (LINEs) show tissue-specific, mosaic genome and methylation-unrestricted, widespread expression of noncoding RNAs in somatic tissues of the rat. PMID:23064113
Intronic retroelements: Not just "speed bumps" for RNA polymerase II. PMID:23061024
Distribution of MGEs and their insertion sites in the Macaca mulatta genome. PMID:23061019
A repetitive elements perspective in Polycomb epigenetics. PMID:23060903
Association of BLCA-4 hypomethylation in blood leukocyte DNA and the risk of bladder cancer in a Chinese population. PMID:23055020
N-terminal horseshoe conformation of DCC is functionally required for axon guidance and might be shared by other neural receptors. PMID:23038776
The landscape of DNA repeat elements in human heart failure. PMID:23034148
Epigenetic interplay between mouse endogenous retroviruses and host genes. PMID:23034137
Paired-end sequencing of long-range DNA fragments for de novo assembly of large, complex Mammalian genomes by direct intra-molecule ligation. PMID:23029438
Patterns and possible roles of LINE-1 methylation changes in smoke-exposed epithelia. PMID:23028911
Zinc finger binding motifs do not explain recombination rate variation within or between species of Drosophila. PMID:23028758
The RNA polymerase II CTD coordinates transcription and RNA processing. PMID:23028141
The search for genetic modifiers of disease severity in the β-hemoglobinopathies. PMID:23028136
Somatic Populations of PGT135-137 HIV-1-Neutralizing Antibodies Identified by 454 Pyrosequencing and Bioinformatics. PMID:23024643
Activity based protein profiling to detect serine hydrolase alterations in virus infected cells. PMID:23024641
Integrative genomics in cardiovascular medicine. PMID:23024270
Cell type-specific termination of transcription by transposable element sequences. PMID:23020800
Translating genomic information into clinical medicine: lung cancer as a paradigm. PMID:23019146
ncRNAclassifier: a tool for detection and classification of transposable element sequences in RNA hairpins. PMID:23009561
The minimal active human SVA retrotransposon requires only the 5'-hexamer and Alu-like domains. PMID:23007156
LINE1 family member is negative regulator of HLA-G expression. PMID:23002136
Identification and functional characterization of a novel UDP-glucuronosyltransferase 2A1 splice variant: potential importance in tobacco-related cancer susceptibility. PMID:22984225
Direct mapping of symbolic DNA sequence into frequency domain in global repeat map algorithm. PMID:22977183
Circular retrotransposition products generated by a LINE retrotransposon. PMID:22977178
Reconstructing the demographic history of the human lineage using whole-genome sequences from human and three great apes. PMID:22975719
RCDA: a highly sensitive and specific alternatively spliced transcript assembly tool featuring upstream consecutive exon structures. PMID:22971325
Whole genome sequencing of field isolates provides robust characterization of genetic diversity in Plasmodium vivax. PMID:22970335
A gene family derived from transposable elements during early angiosperm evolution has reproductive fitness benefits in Arabidopsis thaliana. PMID:22969437
c-fos and its Consequences in Pain. PMID:22969311
What are we learning from the cancer genome? PMID:22965149
Zinc and the modulation of redox homeostasis. PMID:22960578
No additional copies of HERV-Fc1 in the germ line of multiple sclerosis patients. PMID:22958517
Transposable elements in TDP-43-mediated neurodegenerative disorders. PMID:22957047
Coverage of genomic medicine: information gap between lay public and scientists. PMID:22956889
Evidence of abundant purifying selection in humans for recently acquired regulatory functions. PMID:22956687
Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome. PMID:22955982
Decoding the human genome. PMID:22955971
Cardiomyogenesis in the aging and failing human heart. PMID:22955965
Genomics: ENCODE explained. PMID:22955614
Effective gene trapping mediated by Sleeping Beauty transposon. PMID:22952894
Uncovering transcription factor modules using one- and three-dimensional analyses. PMID:22952238
Application of next generation sequencing in mammalian embryogenomics: lessons learned from endogenous betaretroviruses of sheep. PMID:22951118
Self-assembly of thin plates from micrococcal nuclease-digested chromatin of metaphase chromosomes. PMID:22947873
siSPOTR: a tool for designing highly specific and potent siRNAs for human and mouse. PMID:22941647
The roles played by highly truncated splice variants of G protein-coupled receptors. PMID:22938630
Chromatin and epigenetic regulation of pre-mRNA processing. PMID:22936691
Transcriptome sequencing in Sezary syndrome identifies Sezary cell and mycosis fungoides-associated lncRNAs and novel transcripts. PMID:22936659
The next generation of complex lung genetic studies. PMID:22936355
Coevolution between simple sequence repeats (SSRs) and virus genome size. PMID:22931422
Phylogenetic analysis of genome rearrangements among five mammalian orders. PMID:22929217
Genetics of asthma susceptibility and severity. PMID:22929093
The diversity of class II transposable elements in mammalian genomes has arisen from ancestral phylogenetic splits during ancient waves of proliferation through the genome. PMID:22923465
Challenges in medical applications of whole exome/genome sequencing discoveries. PMID:22921985
The rhizome of life: what about metazoa? PMID:22919641
SRSF2 mutations in 275 cases with chronic myelomonocytic leukemia (CMML). PMID:22919025
Molecular reconstruction of extinct LINE-1 elements and their interaction with nonautonomous elements. PMID:22918960
Opportunities and challenges associated with clinical diagnostic genome sequencing: a report of the Association for Molecular Pathology. PMID:22918138
The human transcriptome: an unfinished story. PMID:22916334
Eco-geographical diversification of bitter taste receptor genes (TAS2Rs) among subspecies of chimpanzees (Pan troglodytes). PMID:22916235
Genetics and regulatory impact of alternative polyadenylation in human B-lymphoblastoid cells. PMID:22916029
Single nucleotide polymorphisms can create alternative polyadenylation signals and affect gene expression through loss of microRNA-regulation. PMID:22915998
Retrotransposon long interspersed nucleotide element-1 (LINE-1) is activated during salamander limb regeneration. PMID:22913491
Rescuing Alu: recovery of new inserts shows LINE-1 preserves Alu activity through A-tail expansion. PMID:22912586
Rapid development of a potent photo-triggered inhibitor of the serine hydrolase RBBP9. PMID:22907802
Poly(A) binding protein C1 is essential for efficient L1 retrotransposition and affects L1 RNP formation. PMID:22907758
The mouse DXZ4 homolog retains Ctcf binding and proximity to Pls3 despite substantial organizational differences compared to the primate macrosatellite. PMID:22906166
ROS-activated anticancer prodrugs: a new strategy for tumor-specific damage. PMID:22900465
Polyploidy and the evolution of complex traits. PMID:22900230
Male-specific repeats in wild Bovidae. PMID:22895838
Franklin H. Epstein Lecture. Both ends of the leash--the human links to good dogs with bad genes. PMID:22894576
Human intron-encoded Alu RNAs are processed and packaged into Wdr79-associated nucleoplasmic box H/ACA RNPs. PMID:22892240
Bacterial tyrosine kinases: evolution, biological function and structural insights. PMID:22889913
Transposon Invasion of the Paramecium Germline Genome Countered by a Domesticated PiggyBac Transposase and the NHEJ Pathway. PMID:22888464
Stepping stones in DNA sequencing. PMID:22887891
A beginners guide to SNP calling from high-throughput DNA-sequencing data. PMID:22886560
Human endogenous retrovirus expression is inversely associated with chronic immune activation in HIV-1 infection. PMID:22879884
The mammalian PYHIN gene family: phylogeny, evolution and expression. PMID:22871040
Characterization of transposable elements in the ectomycorrhizal fungus Laccaria bicolor. PMID:22870194
ERK1/2 activation is a therapeutic target in age-related macular degeneration. PMID:22869729
Analysis of jaagsiekte sheep retrovirus (JSRV) envelope protein domains in transformation. PMID:22864547
Cell-type specificity of ChIP-predicted transcription factor binding sites. PMID:22863112
Exploring metazoan evolution through dynamic and holistic changes in protein families and domains. PMID:22862991
Human endogenous retrovirus K Gag coassembles with HIV-1 Gag and reduces the release efficiency and infectivity of HIV-1. PMID:22855497
Optofluidic detection for cellular phenotyping. PMID:22854915
Whole-genome and whole-exome sequencing in neurological diseases. PMID:22847385
Expression of endogenous retroviruses is negatively regulated by the pluripotency marker Rex1/Zfp42. PMID:22844087
Whole genome sequencing for lung cancer. PMID:22833821
Decoding plant and animal genome plasticity from differential paleo-evolutionary patterns and processes. PMID:22833223
High-resolution gene expression atlases for adult and developing mouse brain and spinal cord. PMID:22832508
Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress. PMID:22830651
DNA repair and crossing over favor similar chromosome regions as discovered in radiation hybrid of Triticum. PMID:22827734
Exploring predisposition and treatment response--the promise of genomics. PMID:22824110
FAST-SeqS: a simple and efficient method for the detection of aneuploidy by massively parallel sequencing. PMID:22815955
Alternative splicing: a potential source of functional innovation in the eukaryotic genome. PMID:22811948
Points of view: Representing the genome. PMID:22803197
The macrosatellite DXZ4 mediates CTCF-dependent long-range intrachromosomal interactions on the human inactive X chromosome. PMID:22791747
Splicing of internal large exons is defined by novel cis-acting sequence elements. PMID:22790982
Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells. PMID:22785314
Compressive genomics. PMID:22781691
Intron Retention and TE Exonization Events in ZRANB2. PMID:22778693
A high-resolution 15,000(Rad) radiation hybrid panel for the domestic cat. PMID:22777158
Retargeting sleeping beauty transposon insertions by engineered zinc finger DNA-binding domains. PMID:22776959
Genomics and bioinformatics of Parkinson's disease. PMID:22762024
HIV DNA integration. PMID:22762018
Microarray-based sketches of the HERV transcriptome landscape. PMID:22761958
Role of MHC-linked susceptibility genes in the pathogenesis of human and murine lupus. PMID:22761632
Mammalian NUMT insertion is non-random. PMID:22761406
Do human transposable element small RNAs serve primarily as genome defenders or genome regulators? PMID:22754749
REMiner-II: a tool for rapid identification and configuration of repetitive element arrays from large mammalian chromosomes as a single query. PMID:22750555
EWS/FLI-responsive GGAA microsatellites exhibit polymorphic differences between European and African populations. PMID:22749036
LINE-1 methylation in visceral adipose tissue of severely obese individuals is associated with metabolic syndrome status and related phenotypes. PMID:22748066
ALCAM regulates motility, invasiveness, and adherens junction formation in uveal melanoma cells. PMID:22745734
Genomic amplification of an endogenous retrovirus in zebrafish T-cell malignancies. PMID:22745640
Vaccination with cancer- and HIV infection-associated endogenous retrotransposable elements is safe and immunogenic. PMID:22745376
Why bioimage informatics matters. PMID:22743769
RNA-Seq and human complex diseases: recent accomplishments and future perspectives. PMID:22739340
Inverted Alu dsRNA structures do not affect localization but can alter translation efficiency of human mRNAs independent of RNA editing. PMID:22735697
RNAi in the regulation of mammalian viral infections. PMID:22734679
TOLKIN--Tree of Life Knowledge and Information Network: filling a gap for collaborative research in biological systematics. PMID:22724002
The unstable CCTG repeat responsible for myotonic dystrophy type 2 originates from an AluSx element insertion into an early primate genome. PMID:22723857
The bonobo genome compared with the chimpanzee and human genomes. PMID:22722832
Modeling neurodevelopmental disorders using human neurons. PMID:22717528
Alu expression in human cell lines and their retrotranspositional potential. PMID:22716230
Evolution of coding and non-coding genes in HOX clusters of a marsupial. PMID:22708672
Terminal 4q deletion syndrome. PMID:22707778
Long interspersed nuclear element-1 hypomethylation in cancer: biology and clinical applications. PMID:22704344
The genomic landscape shaped by selection on transposable elements across 18 mouse strains. PMID:22703977
The evolution of human genetic studies of cleft lip and cleft palate. PMID:22703175
Sequence-specific binding of recombinant Zbed4 to DNA: insights into Zbed4 participation in gene transcription and its association with other proteins. PMID:22693546
UniPrimer: A Web-Based Primer Design Tool for Comparative Analyses of Primate Genomes. PMID:22693428
Genome-wide genetic variations are highly correlated with proximal DNA methylation patterns. PMID:22689467
3'-UTR-located inverted Alu repeats facilitate mRNA translational repression and stress granule accumulation. PMID:22688648
An Alu-based phylogeny of gibbons (hylobatidae). PMID:22683814
Emerging view of the human virome. PMID:22683423
Reduced GNG2 expression levels in mouse malignant melanomas and human melanoma cell lines. PMID:22679562
Repetitive element DNA methylation levels in white blood cell DNA from sisters discordant for breast cancer from the New York site of the Breast Cancer Family Registry. PMID:22678115
Integration of maternal genome into the neonate genome through breast milk mRNA transcripts and reverse transcriptase. PMID:22676860
Next-generation sequencing and large genome assemblies. PMID:22676195
Infectious endogenous retroviruses in cats and emergence of recombinant viruses. PMID:22674983
Transcriptional networks driving enhancer function in the CFTR gene. PMID:22671145
Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score. PMID:22668792
Global hypomethylation in hepatocellular carcinoma and its relationship to aflatoxin B(1) exposure. PMID:22666524
Modes of retrotransposition of long interspersed element-1 by environmental factors. PMID:22666219
Human Genomic Deletions Generated by SVA-Associated Events. PMID:22666087
The hallmarks of cancer: a long non-coding RNA point of view. PMID:22664915
Patterns of cellular and HPV 16 methylation as biomarkers for cervical neoplasia. PMID:22664184
Genome regulation by long noncoding RNAs. PMID:22663078
IMGT-ONTOLOGY 2012. PMID:22654892
Biological roles and therapeutic potential of hydroxy-carboxylic Acid receptors. PMID:22654812
Genomes, populations and diseases: ethnic genomics and personalized medicine. PMID:22649660
Combining two technologies for full genome sequencing of human. PMID:22649622
Opportunities and challenges for nutritional proteomics in cancer prevention. PMID:22649262
Divergent dispersion behavior of ssDNA fragments during microchip electrophoresis in pDMA and LPA entangled polymer networks. PMID:22648809
High-throughput sequencing to decipher the genetic heterogeneity of deafness. PMID:22647651
Application of next-generation sequencing technologies in virology. PMID:22647373
Translational research in infectious disease: current paradigms and challenges ahead. PMID:22633095
C-GATE - catalogue of genes affected by transposable elements. PMID:22621612
Recombinant SINEs are formed at high frequency during induced retrotransposition in vivo. PMID:22617294
Long non-coding RNAs: versatile master regulators of gene expression and crucial players in cancer. PMID:22611467
Gene transfer to chicks using lentiviral vectors administered via the embryonic chorioallantoic membrane. PMID:22606269
The RGD finger of Del-1 is a unique structural feature critical for integrin binding. PMID:22601780
One community's effort to control genetic disease. PMID:22594747
Spectraplakins: master orchestrators of cytoskeletal dynamics. PMID:22584905
Comparative studies of glycosylphosphatidylinositol-anchored high-density lipoprotein-binding protein 1: evidence for a eutherian mammalian origin for the GPIHBP1 gene from an LY6-like gene. PMID:22582156
Human transposon tectonics. PMID:22579280
Silencing of endogenous envelope genes in human choriocarcinoma cells shows that envPb1 is involved in heterotypic cell fusions. PMID:22573740
Microarray analysis of LTR retrotransposon silencing identifies Hdac1 as a regulator of retrotransposon expression in mouse embryonic stem cells. PMID:22570599
Genetics: polymorphisms, epigenetics, and something in between. PMID:22567405
The impact of genomics on pediatric research and medicine. PMID:22566424
Studies of endogenous retroviruses reveal a continuing evolutionary saga. PMID:22565131
Genomic impact, chromosomal distribution and transcriptional regulation of HERV elements. PMID:22562360
Shape-based alignment of genomic landscapes in multi-scale resolution. PMID:22561376
Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication. PMID:22559943
Expansion of CORE-SINEs in the genome of the Tasmanian devil. PMID:22559330
Linking the epigenome to the genome: correlation of different features to DNA methylation of CpG islands. PMID:22558141
piRNA-mediated transgenerational inheritance of an acquired trait. PMID:22555593
Large-scale transcriptome sequencing and gene analyses in the crab-eating macaque (Macaca fascicularis) for biomedical research. PMID:22554259
Endogenous hepadnaviruses in the genome of the budgerigar (Melopsittacus undulatus) and the evolution of avian hepadnaviruses. PMID:22553337
The unconventional structure of centromeric nucleosomes. PMID:22552438
Current challenges in de novo plant genome sequencing and assembly. PMID:22546054
Is somatic retrotransposition a parasitic or symbiotic phenomenon? PMID:22545239
What Nematode genomes tell us about the importance of horizontal gene transfers in the evolutionary history of animals. PMID:22545237
Orangutan Alu quiescence reveals possible source element: support for ancient backseat drivers. PMID:22541534
DICER1 loss and Alu RNA induce age-related macular degeneration via the NLRP3 inflammasome and MyD88. PMID:22541070
Conserved Motifs and Prediction of Regulatory Modules in Caenorhabditis elegans. PMID:22540038
Accumulation and rapid decay of non-LTR retrotransposons in the genome of the three-spine stickleback. PMID:22534163
Different measures of "genome-wide" DNA methylation exhibit unique properties in placental and somatic tissues. PMID:22531475
The distribution of a germline methylation marker suggests a regional mechanism of LINE-1 silencing by the piRNA-PIWI system. PMID:22530917
Unique profile of ordered arrangements of repetitive elements in the C57BL/6J mouse genome implicating their functional roles. PMID:22529984
A selection index for gene expression evolution and its application to the divergence between humans and chimpanzees. PMID:22529958
Env-less endogenous retroviruses are genomic superspreaders. PMID:22529376
Identification of BC005512 as a DNA damage responsive murine endogenous retrovirus of GLN family involved in cell growth regulation. PMID:22514700
A beginner's guide to eukaryotic genome annotation. PMID:22510764
Sequence and expression analysis of gaps in human chromosome 20. PMID:22510267
Global DNA hypomethylation in peripheral blood leukocytes as a biomarker for cancer risk: a meta-analysis. PMID:22509334
Advances in BAC-based physical mapping and map integration strategies in plants. PMID:22500080
From genes to environment: using integrative genomics to build a "systems-level" understanding of autism spectrum disorders. PMID:22497667
Differential epigenetic regulation of TOX subfamily high mobility group box genes in lung and breast cancers. PMID:22496870
Harnessing genomics and genome biology to understand malaria biology. PMID:22495435
Multiple cellular mechanisms prevent chromosomal rearrangements involving repetitive DNA. PMID:22494239
Patterns and evolution of nucleotide landscapes in seed plants. PMID:22492812
Extensive terminal and asymmetric processing of small RNAs from rRNAs, snoRNAs, snRNAs, and tRNAs. PMID:22492706
Survey sequencing reveals elevated DNA transposon activity, novel elements, and variation in repetitive landscapes among vesper bats. PMID:22491057
Clinical software development for the Web: lessons learned from the BOADICEA project. PMID:22490389
Finding a place for genomics in health disparities research. PMID:22488458
The conserved Cockayne syndrome B-piggyBac fusion protein (CSB-PGBD3) affects DNA repair and induces both interferon-like and innate antiviral responses in CSB-null cells. PMID:22483866
Resolving the breakpoints of the 17q21.31 microdeletion syndrome with next-generation sequencing. PMID:22482802
Dynamics of gene duplication and transposons in microbial genomes following a sudden environmental change. PMID:22479691
Targeting novel sites: The N-terminal DNA binding domain of non-LTR retrotransposons is an adaptable module that is implicated in changing site specificities. PMID:22479684
Comparative omics-driven genome annotation refinement: application across Yersiniae. PMID:22479471
C. elegans germ cells show temperature and age-dependent expression of Cer1, a Gypsy/Ty3-related retrotransposon. PMID:22479180
Features of methylation and gene expression in the promoter-associated CpG islands using human methylome data. PMID:22474411
Primate genome gain and loss: a bone dysplasia, muscular dystrophy, and bone cancer syndrome resulting from mutated retroviral-derived MTAP transcripts. PMID:22464254
The concept of RNA-assisted protein folding: the role of tRNA. PMID:22462735
Pharmacogenetics: implementing personalized medicine. PMID:22461093
Exploring the cancer genome in the era of next-generation sequencing. PMID:22460448
Neuroinflammation in the aging down syndrome brain; lessons from Alzheimer's disease. PMID:22454637
The genetics of age-related health outcomes. PMID:22454370
A regulatory role for repeated decoy transcription factor binding sites in target gene expression. PMID:22453733
Annotation of primate miRNAs by high throughput sequencing of small RNA libraries. PMID:22453055
Analysis of chromatin dynamics during glucocorticoid receptor activation. PMID:22451486
The hypothalamic-neurohypophyseal system: from genome to physiology. PMID:22448850
Discovery of defense- and neuropeptides in social ants by genome-mining. PMID:22448224
Protective effect of human endogenous retrovirus K dUTPase variants on psoriasis susceptibility. PMID:22437317
Regular patterns for proteome-wide distribution of protein abundance across species. PMID:22427835
Molecular Genetics and Economics. PMID:22427719
Pharmacogenomics in early-phase oncology clinical trials: is there a sweet spot in phase II? PMID:22427349
Transcriptome analysis reveals the time of the fourth round of genome duplication in common carp (Cyprinus carpio). PMID:22424280
The structural biology of HIV-1: mechanistic and therapeutic insights. PMID:22421880
Aviram-Ratner rectifying mechanism for DNA base-pair sequencing through graphene nanogaps. PMID:22418779
Widespread recurrent evolution of genomic features. PMID:22417916
Vertebrate hepatic lipase genes and proteins: a review supported by bioinformatic studies. PMID:22408368
Active human retrotransposons: variation and disease. PMID:22406018
Hairless mutation: a driving force of humanization from a human-ape common ancestor by enforcing upright walking while holding a baby with both hands. PMID:22404045
AIM1 and LINE-1 epigenetic aberrations in tumor and serum relate to melanoma progression and disease outcome. PMID:22402438
High Levels of Sequence Diversity in the 5' UTRs of Human-Specific L1 Elements. PMID:22400009
The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. PMID:22398612
Modelling human regulatory variation in mouse: finding the function in genome-wide association studies and whole-genome sequencing. PMID:22396661
Functions of PIWI proteins in spermatogenesis. PMID:22384420
Assessment of metagenomic assembly using simulated next generation sequencing data. PMID:22384016
Genetic and epigenetic studies offer new therapeutic options for the treatment of T-cell acute lymphoblastic leukemia. PMID:22383740
Decoding the cardiac message: the 2011 Thomas W. Smith Memorial Lecture. PMID:22383710
Low-level environmental cadmium exposure is associated with DNA hypomethylation in Argentinean women. PMID:22382075
Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels. PMID:22373820
Detection of interacting transcription factors in human tissues using predicted DNA binding affinity. PMID:22369666
Translating the brain transcriptome in neuroAIDS: from non-human primates to humans. PMID:22367717
Orphan G protein-coupled receptors (GPCRs): biological functions and potential drug targets. PMID:22367282
A novel framework for the comparative analysis of biological networks. PMID:22363585
Male germline control of transposable elements. PMID:22357546
EZR1: a novel family of highly expressed retroelements induced by TCDD and regulated by a NF-κB-like factor in embryos of zebrafish (Danio rerio). PMID:22356696
DNA sequencing: clinical applications of new DNA sequencing technologies. PMID:22354974
Target selection for structural genomics based on combining fold recognition and crystallisation prediction methods: application to the human proteome. PMID:22354707
Exploring the implications of INDELs in neuropsychiatric genetics: challenges and perspectives. PMID:22350990
Non-coding RNAs as regulators of mammary development and breast cancer. PMID:22350981
Phosphoproteomic differences in major depressive disorder postmortem brains indicate effects on synaptic function. PMID:22350622
Immune cell activation by trophoblast-derived microvesicles is mediated by syncytin 1. PMID:22348442
Chemical approaches for structure and function of RNA in postgenomic era. PMID:22347623
A genomewide screen for suppressors of Alu-mediated rearrangements reveals a role for PIF1. PMID:22347400
Gene expression and stress response mediated by the epigenetic regulation of a transposable element small RNA. PMID:22346759
Rates and fitness consequences of new mutations in humans. PMID:22345605
Construction of BIBAC and BAC libraries from a variety of organisms for advanced genomics research. PMID:22343430
Preparation of megabase-sized DNA from a variety of organisms using the nuclei method for advanced genomics research. PMID:22343429
Retrotransposons at Drosophila telomeres: host domestication of a selfish element for the maintenance of genome integrity. PMID:22342531
Molecular methods for pathogen and microbial community detection and characterization: current and potential application in diagnostic microbiology. PMID:22342514
Gene therapy: implications for craniofacial regeneration. PMID:22337437
Rationally designed small molecules targeting the RNA that causes myotonic dystrophy type 1 are potently bioactive. PMID:22332923
DNA methylation in repetitive elements and post-traumatic stress disorder: a case-control study of US military service members. PMID:22332656
Germline pharmacogenomics in oncology: decoding the patient for targeting therapy. PMID:22321460
Feature-by-feature--evaluating de novo sequence assembly. PMID:22319599
Sequence-specific biosensors report drug-induced changes in epigenetic silencing in living cells. PMID:22313050
Retroviruses push the envelope for mammalian placentation. PMID:22308481
Detecting rare variants. PMID:22307713
DNA methylation: a timeline of methods and applications. PMID:22303369
Transcriptional regulation: a genomic overview. PMID:22303220
Mono-allelic retrotransposon insertion addresses epigenetic transcriptional repression in human genome. PMID:22300442
Detecting false-positive signals in exome sequencing. PMID:22294350
DNA methylome analysis using short bisulfite sequencing data. PMID:22290186
Genetics of Sjögren's syndrome in the genome-wide association era. PMID:22289719
Selective binding of anti-DNA antibodies to native dsDNA fragments of differing sequence. PMID:22285306
Argonaute and the nuclear RNAs: new pathways for RNA-mediated control of gene expression. PMID:22283730
Informatics technology mimics ecology: dense, mutualistic collaboration networks are associated with higher publication rates. PMID:22279593
Transcriptome analysis of silver carp (Hypophthalmichthys molitrix) by paired-end RNA sequencing. PMID:22279088
Sensitive quantitative analysis of murine LINE1 DNA methylation using high resolution melt analysis. PMID:22274612
Gene properties and chromatin state influence the accumulation of transposable elements in genes. PMID:22272293
Straightforward inference of ancestry and admixture proportions through ancestry-informative insertion deletion multiplexing. PMID:22272242
Applications of targeted gene capture and next-generation sequencing technologies in studies of human deafness and other genetic disabilities. PMID:22269275
The distribution of phosphorylated SR proteins and alternative splicing are regulated by RANBP2. PMID:22262462
A recurrent translocation is mediated by homologous recombination between HERV-H elements. PMID:22260357
ENU mutagenesis in mice identifies candidate genes for hypogonadism. PMID:22258617
GRK2 and β-arrestins in cardiovascular disease: Something old, something new. PMID:22254193
Long-range autocorrelations of CpG islands in the human genome. PMID:22253817
Genetic interactions between chromosomes 11 and 18 contribute to airway hyperresponsiveness in mice. PMID:22253740
Immunogenetics of spontaneous control of HIV. PMID:22248321
Human genome sequencing in health and disease. PMID:22248320
Immunotherapeutic potential of anti-human endogenous retrovirus-K envelope protein antibodies in targeting breast tumors. PMID:22247020
Reverse-engineering human regulatory networks. PMID:22246697
Molecular genetic studies of complex phenotypes. PMID:22243791
Expression patterns of non-coding spliced transcripts from human endogenous retrovirus HERV-H elements in colon cancer. PMID:22238681
A genome-wide association study of gestational diabetes mellitus in Korean women. PMID:22233651
Two Strains of Crocosphaera watsonii with Highly Conserved Genomes are Distinguished by Strain-Specific Features. PMID:22232617
Chk1 phosphorylation of Metnase enhances DNA repair but inhibits replication fork restart. PMID:22231448
Minimal absent words in four human genome assemblies. PMID:22220210
'Omic approaches to preventing or managing metastatic breast cancer. PMID:22216753
Reducing system noise in copy number data using principal components of self-self hybridizations. PMID:22207624
Alu elements: know the SINEs. PMID:22204421
Similarities and differences between "uncapped" telomeres and DNA double-strand breaks. PMID:22203190
L1 expression and regulation in humans and rodents. PMID:22202032
LINEs, SINEs and other retroelements: do birds of a feather flock together? PMID:22201808
Expressing genes do not forget their LINEs: transposable elements and gene expression. PMID:22201807
Genomic islands of divergence in hybridizing Heliconius butterflies identified by large-scale targeted sequencing. PMID:22201164
LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders. PMID:22200636
MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. PMID:22192575
Polymorphic integrations of an endogenous gammaretrovirus in the mule deer genome. PMID:22190723
A new 'Linc' between noncoding RNAs and blood development. PMID:22190456
Modulation of auxin-binding protein 1 gene expression in maize and the teosintes by transposon insertions in its promoter. PMID:22187004
Genetic and epigenetic variations contributed by Alu retrotransposition. PMID:22185517
Methods, challenges, and promise of next-generation sequencing in cancer biology. PMID:22180681
Performance comparison of whole-genome sequencing platforms. PMID:22178993
A mammalian conserved element derived from SINE displays enhancer properties recapitulating Satb2 expression in early-born callosal projection neurons. PMID:22174821
Mining the Gene Wiki for functional genomic knowledge. PMID:22165947
A novel human TPIP splice-variant (TPIP-C2) mRNA, expressed in human and mouse tissues, strongly inhibits cell growth in HeLa cells. PMID:22164291
Comparative Structures and Evolution of Vertebrate Carboxyl Ester Lipase (CEL) Genes and Proteins with a Major Role in Reverse Cholesterol Transport. PMID:22162806
Human genetics and genomics a decade after the release of the draft sequence of the human genome. PMID:22155605
Constraints on genes shape long-term conservation of macro-synteny in metazoan genomes. PMID:22151646
GAGE: A critical evaluation of genome assemblies and assembly algorithms. PMID:22147368
Identification of a genomic reservoir for new TRIM genes in primate genomes. PMID:22144910
Repetitive elements may comprise over two-thirds of the human genome. PMID:22144907
Genome-wide association studies of chronic kidney disease: what have we learned? PMID:22143329
Low-pass genome-wide sequencing and variant inference using identity-by-descent in an isolated human population. PMID:22135348
Dr.VIS: a database of human disease-related viral integration sites. PMID:22135288
T2DM: Why Epigenetics? PMID:22132323
Safe harbours for the integration of new DNA in the human genome. PMID:22129804
Sequence shortening in the rodent ancestor. PMID:22128134
Evolutionary history of novel genes on the tammar wallaby Y chromosome: Implications for sex chromosome evolution. PMID:22128133
The NF1 gene contains hotspots for L1 endonuclease-dependent de novo insertion. PMID:22125493
New Generations: Sequencing Machines and Their Computational Challenges. PMID:22121326
Next-generation sequencing technologies and applications for human genetic history and forensics. PMID:22115430
Heat shock factor binding in Alu repeats expands its involvement in stress through an antisense mechanism. PMID:22112862
Allele Frequencies of 10 Autosomal STR Loci from Chakma and Tripura Tribal Populations in Bangladesh. PMID:22110959
Adaptive evolution of the matrix extracellular phosphoglycoprotein in mammals. PMID:22103247
i-ADHoRe 3.0--fast and sensitive detection of genomic homology in extremely large data sets. PMID:22102584
Next steps in cardiovascular disease genomic research--sequencing, epigenetics, and transcriptomics. PMID:22100807
Perioperative genomics. PMID:22099920
The emergence of lncRNAs in cancer biology. PMID:22096659
Distribution of a marker of germline methylation differs between major families of transposon-derived repeats in the human genome. PMID:22093876
Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. PMID:22090374
Genetics and patient outcome after cardiac surgery: unravelling translational findings. PMID:22088869
AluScan: a method for genome-wide scanning of sequence and structure variations in the human genome. PMID:22087792
Next-generation sequencing of apoptotic DNA breakpoints reveals association with actively transcribed genes and gene translocations. PMID:22087219
Characterising chromosome rearrangements: recent technical advances in molecular cytogenetics. PMID:22086080
Nuclear receptor HNF4α binding sequences are widespread in Alu repeats. PMID:22085832
iDASH: integrating data for analysis, anonymization, and sharing. PMID:22081224
Neurodegeneration the RNA way. PMID:22079416
Assessing the role of tandem repeats in shaping the genomic architecture of great apes. PMID:22076140
Prediction of disease and phenotype associations from genome-wide association studies. PMID:22076134
The seven-transmembrane receptor Gpr1 governs processes relevant for the antagonistic interaction of Trichoderma atroviride with its host. PMID:22075023
Occupancy classification of position weight matrix-inferred transcription factor binding sites. PMID:22073148
Non-retroviral fossils in vertebrate genomes. PMID:22069518
How to apply de Bruijn graphs to genome assembly. PMID:22068540
Primate genomes for biomedicine. PMID:22068533
YY1 associates with the macrosatellite DXZ4 on the inactive X chromosome and binds with CTCF to a hypomethylated form in some male carcinomas. PMID:22064860
HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. PMID:22064851
Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. PMID:22056041
Expedited batch processing and analysis of transposon insertions. PMID:22054356
The non-autonomous retrotransposon SVA is trans-mobilized by the human LINE-1 protein machinery. PMID:22053090
Translesion DNA synthesis in the context of cancer research. PMID:22047021
A living fossil in the genome of a living fossil: Harbinger transposons in the coelacanth genome. PMID:22045999
Locus- and domain-dependent control of DNA methylation at mouse B1 retrotransposons during male germ cell development. PMID:22042642
A guided tour of large genome size in animals: what we know and where we are heading. PMID:22042526
Mutation bias is the driving force of codon usage in the Gallus gallus genome. PMID:22039174
Expression of glia maturation factor in neuropathological lesions of Alzheimer's disease. PMID:22035352
The search for allelic variants that cause monogenic disorders or predispose to common, complex polygenic phenotypes. PMID:22034389
Impact of the genome project on the identification of disease genes. PMID:22034246
Genetic variation and pharmacogenomics: concepts, facts, and challenges. PMID:22033504
Global mapping of cell type-specific open chromatin by FAIRE-seq reveals the regulatory role of the NFI family in adipocyte differentiation. PMID:22028663
Characterization and potential functional significance of human-chimpanzee large INDEL variation. PMID:22024410
Genotyping performance assessment of whole genome amplified DNA with respect to multiplexing level of assay and its period of storage. PMID:22022531
Intronic L1 retrotransposons and nested genes cause transcriptional interference by inducing intron retention, exonization and cryptic polyadenylation. PMID:22022525
Analysis of primary structure of chromatin with next-generation sequencing. PMID:22022339
Pack-MULEs: Recycling and reshaping genes through GC-biased acquisition. PMID:22016862
The transposable element profile of the anolis genome: How a lizard can provide insights into the evolution of vertebrate genome size and structure. PMID:22016857
Neisseria gonorrhoeae and humans perform an evolutionary LINE dance. PMID:22016852
Independently derived targeting of 28S rDNA by A- and D-clade R2 retrotransposons: Plasticity of integration mechanism. PMID:22016843
Smaller genetic risk in catabolic process explains lower energy expenditure, more athletic capability and higher prevalence of obesity in Africans. PMID:22016803
Towards in vitro molecular diagnostics using nanostructures. PMID:22009454
Genome analyses substantiate male mutation bias in many species. PMID:22006834
Paleovirology - ghosts and gifts of viruses past. PMID:22003379
Blinded study determination of high sensitivity and specificity microchip electrophoresis-SSCP/HA to detect mutations in the p53 gene. PMID:22002021
The genomics of autoimmune disease in the era of genome-wide association studies and beyond. PMID:22001415
Targeted protein-omic methods are bridging the gap between proteomic and hypothesis-driven protein analysis approaches. PMID:21999828
Meta-analysis and genome-wide interpretation of genetic susceptibility to drug addiction. PMID:21999673
The human genome: a multifractal analysis. PMID:21999602
Changes in population dynamics in mutualistic versus pathogenic viruses. PMID:21994724
Multitasking: Making the Most out of the Retroviral Envelope. PMID:21994694
Prenatal smoke exposure and genomic DNA methylation in a multiethnic birth cohort. PMID:21994404
A matter of life or death: how microsatellites emerge in and vanish from the human genome. PMID:21994250
A high-resolution map of human evolutionary constraint using 29 mammals. PMID:21993624
Reprogramming somatic cells into iPS cells activates LINE-1 retroelement mobility. PMID:21989055
Comparative analysis of neural transcriptomes and functional implication of unannotated intronic expression. PMID:21985610
Birthweight, maternal weight trajectories and global DNA methylation of LINE-1 repetitive elements. PMID:21980406
Isochores and the regulation of gene expression in the human genome. PMID:21979159
Pathogenic exon-trapping by SVA retrotransposon and rescue in Fukuyama muscular dystrophy. PMID:21979053
The DNA damage checkpoint allows recombination between divergent DNA sequences in budding yeast. PMID:21978436
Advancing neuroscience through epigenetics: molecular mechanisms of learning and memory. PMID:21978007
Methylation of L1Hs promoters is lower on the inactive X, has a tendency of being higher on autosomes in smaller genomes and shows inter-individual variability at some loci. PMID:21972244
Functions of noncoding RNAs in neural development and neurological diseases. PMID:21969146
Variation in the mutation rate across mammalian genomes. PMID:21969038
Empirical evaluation reveals best fit of a logistic mutation model for human Y-chromosomal microsatellites. PMID:21968190
MR molecular imaging of angiogenesis using targeted perfluorocarbon nanoparticles. PMID:21966025
Breakpoint characterization of a novel large intragenic deletion of MUTYH detected in a MAP patient: case report. PMID:21962078
Association of hypomethylation of LINE-1 repetitive element in blood leukocyte DNA with an increased risk of hepatocellular carcinoma. PMID:21960343
Comprehensive comparison of three commercial human whole-exome capture platforms. PMID:21955857
Developing and implementing an institute-wide data sharing policy. PMID:21955348
What are the determinants of gene expression levels and breadths in the human genome? PMID:21945885
Alu pair exclusions in the human genome. PMID:21943335
Retrotransposon activation contributes to fragile X premutation rCGG-mediated neurodegeneration. PMID:21940752
Short- and long-term evolutionary dynamics of bacterial insertion sequences: insights from Wolbachia endosymbionts. PMID:21940637
Similarities between long interspersed element-1 (LINE-1) reverse transcriptase and telomerase. PMID:21940498
RiDs db: Repeats in diseases database. PMID:21938212
Polymerization and nucleic acid-binding properties of human L1 ORF1 protein. PMID:21937507
Clinical implementation of comprehensive strategies to characterize cancer genomes: opportunities and challenges. PMID:21935500
Genetic effects at pleiotropic loci are context-dependent with consequences for the maintenance of genetic variation in populations. PMID:21931559
Metabolomics annotates ABHD3 as a physiologic regulator of medium-chain phospholipids. PMID:21926997
Assemblathon 1: a competitive assessment of de novo short read assembly methods. PMID:21926179
Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates. PMID:21925323
Haplotype phasing: existing methods and new developments. PMID:21921926
Skin cancer concerns and genetic risk information-seeking in primary care. PMID:21921576
Comparative analysis of teleost genome sequences reveals an ancient intron size expansion in the zebrafish lineage. PMID:21920901
Unlocking Mendelian disease using exome sequencing. PMID:21920049
Genetic causation of neointimal hyperplasia in hemodialysis vascular access dysfunction. PMID:21917012
Genomic relationship between SINE retrotransposons, Pol III-Pol II transcription, and chromatin organization: the journey from junk to jewel. PMID:21916613
Age-dependent recombination rates in human pedigrees. PMID:21912527
Characterizing genetic interactions in human disease association studies using statistical epistasis networks. PMID:21910885
Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. PMID:21909094
4040 SNPs for genomic analysis in the rhesus macaque (Macaca mulatta). PMID:21907785
diArk 2.0 provides detailed analyses of the ever increasing eukaryotic genome sequencing data. PMID:21906294
Remote homologue identification of Drosophila GAGA factor in mouse. PMID:21904435
An autosomal analysis gives no genetic evidence for complex speciation of humans and chimpanzees. PMID:21903679
Statistical Optimization of Pharmacogenomics Association Studies: Key Considerations from Study Design to Analysis. PMID:21887206
Moving towards high density clinical signature studies with a human proteome catalogue developing multiplexing mass spectrometry assay panels. PMID:21884626
Retrotransposon-centered analysis of piRNA targeting shows a shift from active to passive retrotransposon transcription in developing mouse testes. PMID:21884594
Transcription factor proteomics: identification by a novel gel mobility shift-three-dimensional electrophoresis method coupled with southwestern blot and high-performance liquid chromatography-electrospray-mass spectrometry analysis. PMID:21880322
Endogenous APOBEC3B restricts LINE-1 retrotransposition in transformed cells and human embryonic stem cells. PMID:21878639
Novel Alu retrotransposon insertion leading to Alström syndrome. PMID:21877133
Protein-binding microarray analysis of tumor suppressor AP2α target gene specificity. PMID:21876733
Context-dependent individualization of nucleotides and virtual genomic hybridization allow the precise location of human SNPs. PMID:21876154
Convergent evolution of two mammalian neuronal enhancers by sequential exaptation of unrelated retroposons. PMID:21876128
Gypsy and the birth of the SCAN domain. PMID:21865395
Placenta-specific expression of the interleukin-2 (IL-2) receptor β subunit from an endogenous retroviral promoter. PMID:21865161
Approaches for the study of cancer: towards the integration of genomics, proteomics and metabolomics. PMID:21865133
The roles and evolutionary patterns of intronless genes in deuterostomes. PMID:21860604
Evolutionary patterns of recently emerged animal duplogs. PMID:21859807
Genetics, genomics, and cancer risk assessment: State of the Art and Future Directions in the Era of Personalized Medicine. PMID:21858794
On the sequence-directed nature of human gene mutation: the role of genomic architecture and the local DNA sequence environment in mediating gene mutations underlying human inherited disease. PMID:21853507
Control of striatal signaling by g protein regulators. PMID:21852966
Co-evolution between transposable elements and their hosts: a major factor in genome size evolution? PMID:21850458
Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes. PMID:21850457
Dynamic interactions between transposable elements and their hosts. PMID:21850042
Augmented expression of glia maturation factor in Alzheimer's disease. PMID:21835226
Stable folding core in the folding transition state of an alpha-helical integral membrane protein. PMID:21831834
Genetic testing for early detection of individuals at risk of coronary heart disease and monitoring response to therapy: challenges and promises. PMID:21830102
Organization and molecular evolution of CENP-A--associated satellite DNA families in a basal primate genome. PMID:21828373
Trimeric structure and flexibility of the L1ORF1 protein in human L1 retrotransposition. PMID:21822284
tRNA genes protect a reporter gene from epigenetic silencing in mouse cells. PMID:21822054
Where splicing joins chromatin. PMID:21818411
A comprehensively molecular haplotype-resolved genome of a European individual. PMID:21813624
The Human Immunopeptidome Project, a suggestion for yet another postgenome next big thing. PMID:21813418
GFP-based evaluation system of recombinant expression through the secretory pathway in insect cells and its application to the extracellular domains of class C GPCRs. PMID:21805523
REMiner: a tool for unbiased mining and analysis of repetitive elements and their arrangement structures of large chromosomes. PMID:21803149
LINE-1 elements in structural variation and disease. PMID:21801021
The Anolis lizard genome: an amniote genome without isochores. PMID:21795750
The evolution of the search for novel genes in mammalian sex determination: from mice to men. PMID:21795084
Variables and strategies in development of therapeutic post-transcriptional gene silencing agents. PMID:21785698
Parasites or cohabitants: cruel omnipresent usurpers or creative "éminences grises"? PMID:21785696
Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly. PMID:21785424
Evolutionary patterns of RNA-based duplication in non-mammalian chordates. PMID:21779328
H3K9me3-binding proteins are dispensable for SETDB1/H3K9me3-dependent retroviral silencing. PMID:21774827
Rampant horizontal transfer of SPIN transposons in squamate reptiles. PMID:21771716
Bias detection and correction in RNA-Sequencing data. PMID:21771300
Exon 11 skipping of E-cadherin RNA downregulates its expression in head and neck cancer cells. PMID:21764905
Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutations. PMID:21764165
NCI, NHLBI first international consensus conference on late effects after pediatric hematopoietic cell transplantation: etiology and pathogenesis of late effects after HCT performed in childhood--methodologic challenges. PMID:21763253
Targeting epigenetics through histone deacetylase inhibitors in acute lymphoblastic leukemia. PMID:21762078
An Alu repeat-mediated genomic GCNT2 deletion underlies congenital cataracts and adult i blood group. PMID:21761136
Gene gain and loss during evolution of obligate parasitism in the white rust pathogen of Arabidopsis thaliana. PMID:21750662
Genetic evolution of pancreatic cancer: lessons learnt from the pancreatic cancer genome sequencing project. PMID:21749982
Key features of the two-intron Saccharomyces cerevisiae gene SUS1 contribute to its alternative splicing. PMID:21749978
The immunoglobulin super family protein RIG-3 prevents synaptic potentiation and regulates Wnt signaling. PMID:21745641
Construction of an American mink bacterial artificial chromosome (BAC) library and sequencing candidate genes important for the fur industry. PMID:21740547
Analysis of muscle and ovary transcriptome of Sus scrofa: assembly, annotation and marker discovery. PMID:21729922
Arterial thrombus formation in cardiovascular disease. PMID:21727917
Transcriptional variations mediated by an alternative promoter of the FPR3 gene. PMID:21717223
Developmental functions of piRNAs and transposable elements: a Drosophila point-of-view. PMID:21712652
Breakpoint characterization of large deletions in EXT1 or EXT2 in 10 multiple osteochondromas families. PMID:21703028
Sequencing technologies and genome sequencing. PMID:21698376
Positive selection shaped the convergent evolution of independently expanded kallikrein subfamilies expressed in mouse and rat saliva proteomes. PMID:21695125
Inferring causative variants in microRNA target sites. PMID:21693556
Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee. PMID:21685127
Contrasting 5' and 3' evolutionary histories and frequent evolutionary convergence in Meis/hth gene structures. PMID:21680890
Advantages of mRNA display selections over other selection techniques for investigation of protein-protein interactions. PMID:21679115
Current status of genome-wide association studies in cancer. PMID:21678065
SNPs occur in regions with less genomic sequence conservation. PMID:21674007
Origin and evolution of SINEs in eukaryotic genomes. PMID:21673742
Advances in epigenetics and epigenomics for neurodegenerative diseases. PMID:21671162
Three tiers of genome evolution in reptiles. PMID:21669810
Global methylation in exposure biology and translational medical science. PMID:21669556
TSIDER1, a short and non-autonomous Salivarian trypanosome-specific retroposon related to the ingi6 subclade. PMID:21664383
Alu-specific microhomology-mediated deletion of the final exon of SPAST in three unrelated subjects with hereditary spastic paraplegia. PMID:21659953
Targeting RAD51 phosphotyrosine-315 to prevent unfaithful recombination repair in BCR-ABL1 leukemia. PMID:21653319
Codon usage in vertebrates is associated with a low risk of acquiring nonsense mutations. PMID:21651781
Population biobanks and returning individual research results: mission impossible or new directions? PMID:21643981
A genetic and structural study of genome rearrangements mediated by high copy repeat Ty1 elements. PMID:21637792
Combining computational prediction of cis-regulatory elements with a new enhancer assay to efficiently label neuronal structures in the medaka fish. PMID:21637758
Mutations in retrotransposon AtCOPIA4 compromises resistance to Hyaloperonospora parasitica in Arabidopsis thaliana. PMID:21637617
Identification and detection of a novel human endogenous retrovirus-related gene, and structural characterization of its related elements. PMID:21637440
Effects of L1-ORF2 fragments on green fluorescent protein gene expression. PMID:21637438
Allele-specific, age-dependent and BMI-associated DNA methylation of human MCHR1. PMID:21637341
Identification of tammar wallaby SIRH12, derived from a marsupial-specific retrotransposition event. PMID:21636603
Comparative studies of de novo assembly tools for next-generation sequencing technologies. PMID:21636596
Retrotransposition of marked SVA elements by human L1s in cultured cells. PMID:21636526
Reading TE leaves: new approaches to the identification of transposable element insertions. PMID:21632748
A reduced representation approach to population genetic analyses and applications to human evolution. PMID:21628451
Identification and functional characterization in vivo of a novel splice variant of LDLR in rhesus macaques. PMID:21628398
Mobile DNA and the TE-Thrust hypothesis: supporting evidence from the primates. PMID:21627776
Coexistence of NtCENH3 and two retrotransposons in tobacco centromeres. PMID:21626175
Exploiting nucleotide composition to engineer promoters. PMID:21625601
The latrophilins, "split-personality" receptors. PMID:21618826
Human piRNAs are under selection in Africans and repress transposable elements. PMID:21613236
Landscape of next-generation sequencing technologies. PMID:21612267
Efficient fitting of conductance-based model neurons from somatic current clamp. PMID:21611777
An shRNA-based screen of splicing regulators identifies SFRS3 as a negative regulator of IL-1β secretion. PMID:21611201
Compensatory signals associated with the activation of human GC 5' splice sites. PMID:21609956
Novel transposable elements from Anopheles gambiae. PMID:21605407
Functional consequences of bidirectional promoters. PMID:21601935
Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project. PMID:21596777
Genomic medicine and neurological disease. PMID:21594611
Why is it crucial to reintegrate pathology into cancer research? PMID:21590787
The first sequenced carnivore genome shows complex host-endogenous retrovirus relationships. PMID:21589882
Identification of microRNA precursors based on random forest with network-level representation method of stem-loop structure. PMID:21575268
Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon. PMID:21575266
Distributions of transposable elements reveal hazardous zones in mammalian introns. PMID:21573203
Nanopore Sequencing: Electrical Measurements of the Code of Life. PMID:21572978
Evolutionary conservation of the functional modularity of primate and murine LINE-1 elements. PMID:21572950
Strategic approaches to unraveling genetic causes of cardiovascular diseases. PMID:21566222
ComB: SNP calling and mapping analysis for color and nucleotide space platforms. PMID:21563978
Comparative studies of vertebrate lipoprotein lipase: a key enzyme of very low density lipoprotein metabolism. PMID:21561822
L1 hybridization enrichment: a method for directly accessing de novo L1 insertions in the human germline. PMID:21560187
Comparing de novo genome assembly: the long and short of it. PMID:21559467
Discovering how environmental exposures alter genes could lead to new treatments for chronic illnesses. PMID:21555469
Effect of reverse transcriptase inhibitors on LINE-1 and Ty1 reverse transcriptase activities and on LINE-1 retrotransposition. PMID:21545744
Different transcription activity of HERV-K LTR-containing and LTR-lacking genes of the KIAA1245/NBPF gene subfamily. PMID:21544646
Variation in array size, monomer composition and expression of the macrosatellite DXZ4. PMID:21544201
A revised nomenclature for transcribed human endogenous retroviral loci. PMID:21542922
Mind the dbGAP: the application of data mining to identify biological mechanisms. PMID:21540468
RNAi: a potential new class of therapeutic for human genetic disease. PMID:21537948
Towards a more functional concept of causality in cancer research. PMID:21537385
An automated homology-based approach for identifying transposable elements. PMID:21535899
Chromatin immunoprecipitation to analyze DNA binding sites of HMGA2. PMID:21533145
Two-stepping through time: mammals and viruses. PMID:21531564
B7-h2 is a costimulatory ligand for CD28 in human. PMID:21530327
Strong human endogenous retrovirus-specific T cell responses are associated with control of HIV-1 in chronic infection. PMID:21525339
Profiling the proteome in renal transplantation. PMID:21520424
Precursor miR-886, a novel noncoding RNA repressed in cancer, associates with PKR and modulates its activity. PMID:21518807
Size matters: versatile use of PiggyBac transposons as a genetic manipulation tool. PMID:21516337
Cell surface signaling molecules in the control of immune responses: a tide model. PMID:21511182
Free-solution electrophoretic separations of DNA-drag-tag conjugates on glass microchips with no polymer network and no loss of resolution at increased electric field strength. PMID:21500207
Cell-based Models for Discovery of Pharmacogenomic Markers of Anticancer Agent Toxicity. PMID:21499559
Chromatin organization in sperm may be the major functional consequence of base composition variation in the human genome. PMID:21490963
Transcriptome sequencing demonstrates that human papillomavirus is not active in cutaneous squamous cell carcinoma. PMID:21490616
A comparison of genomic copy number calls by Partek Genomics Suite, Genotyping Console and Birdsuite algorithms to quantitative PCR. PMID:21489293
Alzheimer's genetics in the GWAS era: a continuing story of 'replications and refutations'. PMID:21487954
Production and partial purification of membrane proteins using a liposome-supplemented wheat cell-free translation system. PMID:21481249
The impact of next-generation sequencing on genomics. PMID:21477781
Engineering scalable biological systems. PMID:21468204
Natural genetic variation caused by small insertions and deletions in the human genome. PMID:21460062
Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome. PMID:21460061
A genome-wide analysis of FRT-like sequences in the human genome. PMID:21448289
XIST RNA and architecture of the inactive X chromosome: implications for the repeat genome. PMID:21447818
Both size and GC-content of minimal introns are selected in human populations. PMID:21437290
Macoilin, a conserved nervous system-specific ER membrane protein that regulates neuronal excitability. PMID:21437263
MicroRNA genes derived from repetitive elements and expanded by segmental duplication events in mammalian genomes. PMID:21436881
Toward a better understanding of ADHD: LPHN3 gene variants and the susceptibility to develop ADHD. PMID:21432600
Overview of the development of personalized genomic medicine and surgery. PMID:21424870
HIV integration targeting: a pathway involving Transportin-3 and the nuclear pore protein RanBP2. PMID:21423673
Hypomethylation of intragenic LINE-1 represses transcription in cancer cells through AGO2. PMID:21423624
The human microbiome and surgical disease. PMID:21422915
Medical DNA sequencing. PMID:21415728
Homolog-specific PCR primer design for profiling splice variants. PMID:21415011
Interactome networks and human disease. PMID:21414488
The struggle for life of the genome's selfish architects. PMID:21414203
Chromosome conformation capture uncovers potential genome-wide interactions between human conserved non-coding sequences. PMID:21408183
Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PMID:21408061
Genome-virome interactions: examining the role of common viral infections in complex disease. PMID:21407242
Making sense of cancer genomic data. PMID:21406553
Ocular proteomics with emphasis on two-dimensional gel electrophoresis and mass spectrometry. PMID:21406065
Intrinsic restriction activity by apolipoprotein B mRNA editing enzyme APOBEC1 against the mobility of autonomous retrotransposons. PMID:21398638
Improved integration time estimation of endogenous retroviruses with phylogenetic data. PMID:21394200
Molecular evolution of immunoglobulin superfamily genes in primates. PMID:21390552
Recent amplification of the kangaroo endogenous retrovirus, KERV, limited to the centromere. PMID:21389136
InTRONs in biotech. PMID:21387124
Minimal absent words in prokaryotic and eukaryotic genomes. PMID:21386877
DNABIT Compress - Genome compression algorithm. PMID:21383923
Identification of a unique library of complex, but ordered, arrays of repetitive elements in the human genome and implication of their potential involvement in pathobiology. PMID:21376035
Phylogenetic and functional characterization of the hAT transposon superfamily. PMID:21368277
Comprehensive analysis of alternative splicing and functionality in neuronal differentiation of P19 cells. PMID:21365003
Effect of the transposable element environment of human genes on gene length and expression. PMID:21362639
Identification of CD44 as a surface biomarker for drug resistance by surface proteome signature technology. PMID:21357442
Integrative genomic analysis of human ribosomal DNA. PMID:21355038
Double-strand breaks in heterochromatin move outside of a dynamic HP1a domain to complete recombinational repair. PMID:21353298
Polygenic modeling of genome-wide association studies: an application to prostate and breast cancer. PMID:21348634
A Comparative Study of Metabolic Network Topology between a Pathogenic and a Non-Pathogenic Bacterium for Potential Drug Target Identification. PMID:21347179
Nonsynonymous substitution rate (Ka) is a relatively consistent parameter for defining fast-evolving and slow-evolving protein-coding genes. PMID:21342519
Substitution patterns are under different influences in primates and rodents. PMID:21339508
Horizontal gene transfer between bacteria and animals. PMID:21334091
Genomics for disease treatment and prevention. PMID:21333845
Systems biology: the next frontier for bioinformatics. PMID:21331364
Illuminating transcription pathways using fluorescent reporter genes and yeast functional genomics. PMID:21326895
ZBED6: The birth of a new transcription factor in the common ancestor of placental mammals. PMID:21326889
Advances of genomic science and systems biology in renal transplantation: a review. PMID:21318414
Methylation at global LINE-1 repeats in human blood are affected by gender but not by age or natural hormone cycles. PMID:21311577
Restless genomes humans as a model organism for understanding host-retrotransposable element dynamics. PMID:21310298
Charting a course for genomic medicine from base pairs to bedside. PMID:21307933
A decade's perspective on DNA sequencing technology. PMID:21307932
Initial impact of the sequencing of the human genome. PMID:21307931
Structural properties of the Caenorhabditis elegans neuronal network. PMID:21304930
The sociobiology of molecular systems. PMID:21301472
Cocaine dynamically regulates heterochromatin and repetitive element unsilencing in nucleus accumbens. PMID:21300862
A detailed comparative analysis on the overall codon usage patterns in hepatitis A virus. PMID:21296111
Fluoride-cleavable, fluorescently labelled reversible terminators: synthesis and use in primer extension. PMID:21294195
Functional relevance of CpG island length for regulation of gene expression. PMID:21288871
Genome-wide association studies of sleep disorders. PMID:21285061
Comparative and demographic analysis of orang-utan genomes. PMID:21270892
Vertebrate endothelial lipase: comparative studies of an ancient gene and protein in vertebrate evolution. PMID:21267636
Gene Expression Profiling via Multigene Concatemers. PMID:21267445
A novel compression tool for efficient storage of genome resequencing data. PMID:21266471
Cancer evolution and individual susceptibility. PMID:21264404
The in vivo kinetics of RNA polymerase II elongation during co-transcriptional splicing. PMID:21264352
Analysis of human P[4]G2 rotavirus strains isolated in Brazil reveals codon usage bias and strong compositional constraints. PMID:21255687
FUBP3 interacts with FGF9 3' microsatellite and positively regulates FGF9 translation. PMID:21252297
Cutting-edge issues in primary biliary cirrhosis. PMID:21243445
Chromosome size in diploid eukaryotic species centers on the average length with a conserved boundary. PMID:21239390
Transcriptional control of the human glucocorticoid receptor: identification and analysis of alternative promoter regions. PMID:21234764
Genomic fluidity: an integrative view of gene diversity within microbial populations. PMID:21232151
A systematic evaluation of expression of HERV-W elements; influence of genomic context, viral structure and orientation. PMID:21226900
Systematic evaluation of genome-wide methylated DNA enrichment using a CpG island array. PMID:21211017
SeqWare Query Engine: storing and searching sequence data in the cloud. PMID:21210981
Impact of Alu repeats on the evolution of human p53 binding sites. PMID:21208455
Gene inactivation and its implications for annotation in the era of personal genomics. PMID:21205862
From synthetic genome to creation of life. PMID:21204002
The good viruses: viral mutualistic symbioses. PMID:21200397
Pharmacogenetics of drug metabolizing enzymes and transporters: effects on pharmacokinetics and pharmacodynamics of anticancer agents. PMID:21194402
Systems approaches to molecular cancer diagnostics. PMID:21189224
Repetitive element hypomethylation in blood leukocyte DNA and cancer incidence, prevalence, and mortality in elderly individuals: the Normative Aging Study. PMID:21188491
Epigenomics in cancer management. PMID:21188117
Insertion sequence inversions mediated by ectopic recombination between terminal inverted repeats. PMID:21187977
The solute carrier families have a remarkably long evolutionary history with the majority of the human families present before divergence of Bilaterian species. PMID:21186191
RISCI--Repeat Induced Sequence Changes Identifier: a comprehensive, comparative genomics-based, in silico subtractive hybridization pipeline to identify repeat induced sequence changes in closely related genomes. PMID:21184688
Molecular characterization, genomic distribution and evolutionary dynamics of Short INterspersed Elements in the termite genome. PMID:21184097
Defining the transcriptome and proteome in three functionally different human cell lines. PMID:21179022
The making of a photosynthetic animal. PMID:21177950
T-lex: a program for fast and accurate assessment of transposable element presence using next-generation sequencing data. PMID:21177644
Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast. PMID:21177495
NF-κB addiction and its role in cancer: 'one size does not fit all'. PMID:21170083
Haplotype-resolved genome sequencing of a Gujarati Indian individual. PMID:21170042
Quantitative analysis of culture using millions of digitized books. PMID:21163965
Characterization of a Xenopus tropicalis endogenous retrovirus with developmental and stress-dependent expression. PMID:21159866
Nanotribology results show that DNA forms a mechanically resistant 2D network in metaphase chromatin plates. PMID:21156137
Next generation sequencing and analysis of a conserved transcriptome of New Zealand's kiwi. PMID:21156082
The effect of next-generation sequencing technology on complex trait research. PMID:21155765
The reverse transcription inhibitor abacavir shows anticancer activity in prostate cancer cell lines. PMID:21151977
Mugsy: fast multiple alignment of closely related whole genomes. PMID:21148543
Genetic cardiovascular risk prediction: will we get there? PMID:21147729
Dissecting DNA hypermethylation in cancer. PMID:21146531
Application of Wavelet Packet Transform to detect genetic polymorphisms by the analysis of inter-Alu PCR patterns. PMID:21143911
The interplay between evolution, regulation and tissue specificity in the Human Hereditary Diseasome. PMID:21143807
Comparative genetic approaches to the evolution of human brain and behavior. PMID:21140466
Characterizations and validations of novel antibodies toward translational research. PMID:21137080
Applications of protein microarrays for biomarker discovery. PMID:21136793
Mutation type is not clinically useful in predicting prognosis in hypertrophic cardiomyopathy. PMID:21135372
Quantum steps to better sequencing. PMID:21131989
Alu repeat discovery and characterization within human genomes. PMID:21131385
AID: a riddle wrapped in a mystery inside an enigma. PMID:21128007
The evolution and diversity of DNA transposons in the genome of the Lizard Anolis carolinensis. PMID:21127169
A novel web-based TinT application and the chronology of the Primate Alu retroposon activity. PMID:21126360
Endogenous viral elements in animal genomes. PMID:21124940
Deciphering the code for retroviral integration target site selection. PMID:21124862
The reference human genome demonstrates high risk of type 1 diabetes and other disorders. PMID:21121051
Coordinated genome-wide modifications within proximal promoter cis-regulatory elements during vertebrate evolution. PMID:21118975
LTC: a novel algorithm to improve the efficiency of contig assembly for physical mapping in complex genomes. PMID:21118513
Novel intron markers to study the phylogeny of closely related mammalian species. PMID:21118501
Progress and promise of genome-wide association studies for human complex trait genetics. PMID:21115973
Evolution of an antifreeze protein by neofunctionalization under escape from adaptive conflict. PMID:21115821
Universal platform for quantitative analysis of DNA transposition. PMID:21110848
Unraveling the genetics of otitis media: from mouse to human and back again. PMID:21107580
Protection of HIV neutralizing aptamers against rectal and vaginal nucleases: implications for RNA-based therapeutics. PMID:21106536
Limitations of next-generation genome sequence assembly. PMID:21102452
Biguanide metformin acts on tau phosphorylation via mTOR/protein phosphatase 2A (PP2A) signaling. PMID:21098287
Sharing clinical research data in the United States under the Health Insurance Portability and Accountability Act and the Privacy Rule. PMID:21092099
The genetics of type 2 diabetes: what have we learned from GWAS? PMID:21091714
Systematic analysis of gene expression level with tissue-specificity, function and protein subcellular localization in human transcriptome. PMID:21088908
CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins. PMID:21087992
The DNA methylome of human peripheral blood mononuclear cells. PMID:21085693
Genome-wide analysis of copy number variation in type 1 diabetes. PMID:21085585
L1 retrotransposition in neurons is modulated by MeCP2. PMID:21085180
Identification of novel endogenous betaretroviruses which are transcribed in the bovine placenta. PMID:21084469
Patient profiling for treatment toxicity: potential use of clinical and genomic factors. PMID:21080116
Grand challenge commentary: The chemistry of a dynamic genome. PMID:21079591
Grand challenge commentary: Informative diagnostics for personalized medicine. PMID:21079587
International Union of Basic and Clinical Pharmacology. LXXIX. Cannabinoid receptors and their ligands: beyond CB₁ and CB₂. PMID:21079038
Targeting of highly conserved Dengue virus sequences with anti-Dengue virus trans-splicing group I introns. PMID:21078188
Expression, tandem repeat copy number variation and stability of four macrosatellite arrays in the human genome. PMID:21078170
Linkage disequilibrium reveals different demographic history in egg laying chickens. PMID:21078133
Pseudokinases-remnants of evolution or key allosteric regulators? PMID:21074407
Characterization of L1 retrotransposition with high-throughput dual-luciferase assays. PMID:21071410
Evolution of CD33-related siglecs: regulating host immune functions and escaping pathogen exploitation? PMID:21070233
Analysis of in situ pre-mRNA targets of human splicing factor SF1 reveals a function in alternative splicing. PMID:21062807
Stress-induced activation of heterochromatic transcription. PMID:21060865
How many antiviral small interfering RNAs may be encoded by the mammalian genomes? PMID:21059241
Translating genomics into improved healthcare. PMID:21056961
The molecular biology, biochemistry, and physiology of human steroidogenesis and its disorders. PMID:21051590
Nucleic acid chaperone properties of ORF1p from the non-LTR retrotransposon, LINE-1. PMID:21045547
Whole transcriptome analysis of the fasting and fed Burmese python heart: insights into extreme physiological cardiac adaptation. PMID:21045117
Assessment of genetic variation for the LINE-1 retrotransposon from next generation sequence data. PMID:21044359
Epigenetic control of retrotransposon expression in human embryonic stem cells. PMID:21041477
RBPDB: a database of RNA-binding specificities. PMID:21036867
Discovery-driven research and bioinformatics in nuclear receptor and coregulator signaling. PMID:21029773
Genomics: In search of rare human variants. PMID:20981085
Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans. PMID:20980553
Feedback inhibition of L1 and alu retrotransposition through altered double strand break repair kinetics. PMID:20979631
Genome-wide comparative gene family classification. PMID:20976221
RNA processing and export. PMID:20961978
A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1. PMID:20959003
Human brain evolution: harnessing the genomics (r)evolution to link genes, cognition, and behavior. PMID:20955931
An Sp185/333 gene cluster from the purple sea urchin and putative microsatellite-mediated gene diversification. PMID:20955585
Genetics in schizophrenia: where are we and what next? PMID:20954426
Targeting energy expenditure via fuel switching and beyond. PMID:20953861
Marine genomics: at the interface of marine microbial ecology and biodiscovery. PMID:20953417
Characterization of LINE-1 ribonucleoprotein particles. PMID:20949108
Association of nuclear localization of a long interspersed nuclear element-1 protein in breast tumors with poor prognostic outcomes. PMID:20948976
Data structures and compression algorithms for high-throughput sequencing technologies. PMID:20946637
Epigenetic modifications in pluripotent and differentiated cells. PMID:20944600
Discovery and characterization of mammalian endogenous parvoviruses. PMID:20943964
Technological innovation revisited. PMID:20943599
Pharmacogenetics of Anti-Diabetes Drugs. PMID:20936101
The evolution and expression of the snaR family of small non-coding RNAs. PMID:20935053
Diagnosis and monitoring of abdominal aortic aneurysm: current status and future prospects. PMID:20932435
Mapping genes that predict treatment outcome in admixed populations. PMID:20921971
The redox basis of epigenetic modifications: from mechanisms to functional consequences. PMID:20919933
Global methylation profiles in DNA from different blood cell types. PMID:20890131
Rat traps: filling the toolbox for manipulating the rat genome. PMID:20887642
Post-genomics and skin inflammation. PMID:20886018
DNA transposons: nature and applications in genomics. PMID:20885819
Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PMID:20885785
U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation. PMID:20881964
MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences. PMID:20880995
GeneWaltz--A new method for reducing the false positives of gene finding. PMID:20875138
CAGE: Combinatorial Analysis of Gene-cluster Evolution. PMID:20874406
Relating underrepresented genomic DNA patterns and tiRNAs: the rule behind the observation and beyond. PMID:20860791
At the edge of translation - materials to program cells for directed differentiation. PMID:20860763
MetMap enables genome-scale Methyltyping for determining methylation states in populations. PMID:20856582
SeqAnt: a web service to rapidly identify and annotate DNA sequence variations. PMID:20854673
Predictors of global methylation levels in blood DNA of healthy subjects: a combined analysis. PMID:20846947
Genome-scale approaches to investigate oxidative DNA damage. PMID:20838563
In silico models of cancer. PMID:20836040
RNA Genes: Retroelements and Virally Retroposable microRNAs in Human Embryonic Stem Cells. PMID:20835360
Defining genetic risk for graft-versus-host disease and mortality following allogeneic hematopoietic stem cell transplantation. PMID:20827186
Automated construction and analysis of the design space for biochemical systems. PMID:20823298
Sequencing and analysis of an Irish human genome. PMID:20822512
Ten years of genetics and genomics: what have we achieved and where are we heading? PMID:20820184
Plasmodium immunomics. PMID:20816843
Prediction of alternatively spliced exons using support vector machines. PMID:20815140
Epigenetic regulatory mechanisms associated with infertility. PMID:20814440
Quality, quantity and harmony: the DataSHaPER approach to integrating data across bioclinical studies. PMID:20813861
Towards a complete resolution of the genetic architecture of disease. PMID:20813421
Phenylbutyric acid suppresses protein accumulation-mediated ER stress in retrovirus-infected astrocytes and delays onset of paralysis in infected mice. PMID:20813146
Mobilizing diversity: transposable element insertions in genetic variation and disease. PMID:20813032
Integrating common and rare genetic variation in diverse human populations. PMID:20811451
Reference-unbiased copy number variant analysis using CGH microarrays. PMID:20802225
Genes devoid of full-length transposable element insertions are involved in development and in the regulation of transcription in human and closely related species. PMID:20798934
Current concepts of follicle-stimulating hormone receptor gene regulation. PMID:20739665
Individualized medicine 2010. PMID:20731747
The Nobel Prize as a Reward Mechanism in the Genomics Era: Anonymous Researchers, Visible Managers and the Ethics of Excellence. PMID:20730106
A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease risk. PMID:20729854
Visualization and genetic analysis of alternative splicing regulation in vivo using fluorescence reporters in transgenic Caenorhabditis elegans. PMID:20725066
Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE. PMID:20724440
Use of chromosome walking in discovery of single-nucleotide polymorphism in noncoding regions of a candidate actin gene in Pinus radiata. PMID:20720301
Recent expansion of a new Ingi-related clade of Vingi non-LTR retrotransposons in hedgehogs. PMID:20716533
Distinguishing between cancer driver and passenger gene alteration candidates via cross-species comparison: a pilot study. PMID:20707908
Human endogenous retroviruses and multiple sclerosis: innocent bystanders or disease determinants? PMID:20696240
Slingshot: a PiggyBac based transposon system for tamoxifen-inducible 'self-inactivating' insertional mutagenesis. PMID:20688953
Epigenetic silencing of engineered L1 retrotransposition events in human embryonic carcinoma cells. PMID:20686575
Genomic signatures of germline gene expression. PMID:20686123
Chromosomal integration of adenoviral vector DNA in vivo. PMID:20686029
Genome-wide detection and characterization of endogenous retroviruses in Bos taurus. PMID:20686017
Crystal structure of chiral gammaPNA with complementary DNA strand: insights into the stability and specificity of recognition and conformational preorganization. PMID:20681704
hHSS1: a novel secreted factor and suppressor of glioma growth located at chromosome 19q13.33. PMID:20680400
A new framework for studying the isochore evolution: estimation of the equilibrium GC content based on the temporal mutation rate model. PMID:20675617
Variable histone modifications at the A(vy) metastable epiallele. PMID:20671424
Inhibition of superinfection and the evolution of viral latency. PMID:20660193
Elucidating the higher-order structure of biopolymers by structural probing and mass spectrometry: MS3D. PMID:20648672
Divergence, demography and gene loss along the human lineage. PMID:20643734
Tissue-specific regulatory regions of the PTH gene localized by novel chromosome 11 rearrangement breakpoints in a parathyroid adenoma. PMID:20641034
Epigenetic effects of shiftwork on blood DNA methylation. PMID:20636218
Annotating non-coding regions of the genome. PMID:20628352
Choosing a genome browser for a Model Organism Database: surveying the maize community. PMID:20627860
Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. PMID:20626842
PiggyBac-ing on a primate genome: novel elements, recent activity and horizontal transfer. PMID:20624734
Mining non-model genomic libraries for microsatellites: BAC versus EST libraries and the generation of allelic richness. PMID:20624300
Breakpoint determination of 15 large deletions in Peutz-Jeghers subjects. PMID:20623358
Advances in Bioconjugation. PMID:20622973
Integrating Epigenomics into Pharmacogenomic Studies. PMID:20622972
Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition. PMID:20622855
Proteogenomics to discover the full coding content of genomes: a computational perspective. PMID:20620248
Demethylation by 5-aza-2'-deoxycytidine in colorectal cancer cells targets genomic DNA whilst promoter CpG island methylation persists. PMID:20618997
LTR retroelements in the genome of Daphnia pulex. PMID:20618961
Circulation Research and human genetic studies. PMID:20616334
Long-range function of an intergenic retrotransposon. PMID:20615953
Different integration site structures between L1 protein-mediated retrotransposition in cis and retrotransposition in trans. PMID:20615209
The impact of CpG island on defining transcriptional activation of the mouse L1 retrotransposable elements. PMID:20613872
Accidental amplification and inactivation of a methyltransferase gene eliminates cytosine methylation in Mycosphaerella graminicola. PMID:20610411
Miniature inverted-repeat transposable elements of Stowaway are active in potato. PMID:20610409
Probing the probes: fitness factors for small molecule tools. PMID:20609406
The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. PMID:20609256
Gene therapy in glaucoma-part I: Basic mechanisms and molecular genetics. PMID:20606864
Genetic variation of copia suppression in Drosophila melanogaster. PMID:20606692
Gene transfer efficiency and genome-wide integration profiling of Sleeping Beauty, Tol2, and piggyBac transposons in human primary T cells. PMID:20606646
Natural mutagenesis of human genomes by endogenous retrotransposons. PMID:20603005
Mobile interspersed repeats are major structural variants in the human genome. PMID:20602999
LINE-1 retrotransposition activity in human genomes. PMID:20602998
All y'all need to know 'bout retroelements in cancer. PMID:20600922
Origin and evolution of LINE-1 derived "half-L1" retrotransposons (HAL1). PMID:20600705
Comparative studies of mammalian acid lipases: Evidence for a new gene family in mouse and rat (Lipo). PMID:20598663
Hydrophobic Fractionation Enhances Novel Protein Detection by Mass Spectrometry in Triple Negative Breast Cancer. PMID:20596302
Mammalian evolution may not be strictly bifurcating. PMID:20591845
Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. PMID:20591532
Mobile element scanning (ME-Scan) by targeted high-throughput sequencing. PMID:20591181
Patents in genomics and human genetics. PMID:20590431
Five classic articles in genetic epidemiology. PMID:20589189
Long-term stability of demethylation after transient exposure to 5-aza-2'-deoxycytidine correlates with sustained RNA polymerase II occupancy. PMID:20587535
Estimating enrichment of repetitive elements from high-throughput sequence data. PMID:20584328
Detection and analysis of alternative splicing in Yarrowia lipolytica reveal structural constraints facilitating nonsense-mediated decay of intron-retaining transcripts. PMID:20573210
Identifying compositionally homogeneous and nonhomogeneous domains within the human genome using a novel segmentation algorithm. PMID:20571085
The role of proteomics in the diagnosis of chorioamnionitis and early-onset neonatal sepsis. PMID:20569812
Molecular diagnostics for personal medicine using a nanopore. PMID:20564464
Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology. PMID:20562415
A new era in clinical genetic testing for hypertrophic cardiomyopathy. PMID:20559996
Pharmacogenetics of heart failure: evidence, opportunities, and challenges for cardiovascular pharmacogenomics. PMID:20559955
Imaging and modeling of myocardial metabolism. PMID:20559785
CLIA-tested genetic variants on commercial SNP arrays: potential for incidental findings in genome-wide association studies. PMID:20556870
Gene polymorphisms and their role in epilepsy treatment and prognosis. PMID:20556360
A novel FcεRIβ-chain truncation regulates human mast cell proliferation and survival. PMID:20554927
Large-scale analysis of orthologs and paralogs under covarion-like and constant-but-different models of amino acid evolution. PMID:20551039
Arabidopsis thaliana chromosome 4 replicates in two phases that correlate with chromatin state. PMID:20548960
Shotgun proteomics identifies proteins specific for acute renal transplant rejection. PMID:20543976
Organization of Biomedical Data for Collaborative Scientific Research: A Research Information Management System. PMID:20543892
Architecture of the Tn7 posttransposition complex: an elaborate nucleoprotein structure. PMID:20538004
Characteristics of transposable element exonization within human and mouse. PMID:20532223
Activity-based protein profiling identifies a host enzyme, carboxylesterase 1, which is differentially active during hepatitis C virus replication. PMID:20530478
Contrasting GC-content dynamics across 33 mammalian genomes: relationship with life-history traits and chromosome sizes. PMID:20530252
SeLOX--a locus of recombination site search tool for the detection and directed evolution of site-specific recombination systems. PMID:20529878
Endogenous retroviruses in trophoblast differentiation and placental development. PMID:20528833
The role of transposable elements in the evolution of non-mammalian vertebrates and invertebrates. PMID:20525173
Leveraging human genetics to develop future therapeutic strategies in rheumatoid arthritis. PMID:20510233
Assembly of large genomes using second-generation sequencing. PMID:20508146
A single amino acid substitution confers enhanced methylation activity of mammalian Dnmt3b on chromatin DNA. PMID:20507910
Utility of sequenced genomes for microsatellite marker development in non-model organisms: a case study of functionally important genes in nine-spined sticklebacks (Pungitius pungitius). PMID:20507571
ALDH1L2 is the mitochondrial homolog of 10-formyltetrahydrofolate dehydrogenase. PMID:20498374
The mutational spectrum of non-CpG DNA varies with CpG content. PMID:20498119
Mechanisms for nonrecurrent genomic rearrangements associated with CMT1A or HNPP: rare CNVs as a cause for missing heritability. PMID:20493460
High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes. PMID:20488934
Bs1, a new chimeric gene formed by retrotransposon-mediated exon shuffling in maize. PMID:20488894
Genomics and genetics of gonadotropin beta-subunit genes: Unique FSHB and duplicated LHB/CGB loci. PMID:20488225
Cost-effective sequencing of full-length cDNA clones powered by a de novo-reference hybrid assembly. PMID:20479877
Effects of Alu elements on global nucleosome positioning in the human genome. PMID:20478020
LINE-1 retrotransposons: mediators of somatic variation in neuronal genomes? PMID:20471112
Biophysical characterization of recombinant proteins: a key to higher structural genomics success. PMID:20466062
Non-long terminal repeat (non-LTR) retrotransposons: mechanisms, recent developments, and unanswered questions. PMID:20462415
A total of 220 patients with autosomal dominant spastic paraplegia do not display mutations in the SLC33A1 gene (SPG42). PMID:20461110
Colloquium paper: in the light of evolution IV: the human condition. PMID:20460311
Modeling non-uniformity in short-read rates in RNA-Seq data. PMID:20459815
A database and API for variation, dense genotyping and resequencing data. PMID:20459810
Recombination-associated sequence homogenization of neighboring Alu elements: signature of nonallelic gene conversion. PMID:20453015
The enemy within: dormant retroviruses awaken. PMID:20448571
Colloquium paper: footprints of nonsentient design inside the human genome. PMID:20445101
A study of alternative splicing in the pig. PMID:20444244
Epigenetic regulation of a murine retrotransposon by a dual histone modification mark. PMID:20442873
Between a chicken and a grape: estimating the number of human genes. PMID:20441615
Computational challenges in the analysis of ancient DNA. PMID:20441577
Using genetics to deliver personalized SLE therapy-a realistic prospect? PMID:20440286
From IMGT-ONTOLOGY to IMGT/LIGMotif: the IMGT standardized approach for immunoglobulin and T cell receptor gene identification and description in large genomic sequences. PMID:20433708
The genome of the Western clawed frog Xenopus tropicalis. PMID:20431018
The Rhox genes. PMID:20430877
Beyond desensitization: physiological relevance of arrestin-dependent signaling. PMID:20427692
Genome-wide association studies: contribution of genomics to understanding blood pressure and essential hypertension. PMID:20425154
Curve-based multivariate distance matrix regression analysis: application to genetic association analyses involving repeated measures. PMID:20423962
Mammalian carboxylesterase 3: comparative genomics and proteomics. PMID:20422440
Universal global imprints of genome growth and evolution--equivalent length and cumulative mutation density. PMID:20418954
Candidate gene association studies: successes and failures. PMID:20417090
SVA retrotransposons: Evolution and genetic instability. PMID:20416380
The application of mass-spectrometry-based protein biomarker discovery to theragnostics. PMID:20406221
Testicular postgenomics: targeting the regulation of spermatogenesis. PMID:20403865
Comparative gene expression in toxic versus non-toxic strains of the marine dinoflagellate Alexandrium minutum. PMID:20403159
Analysis of SRrp86-regulated alternative splicing: control of c-Jun and IκBβ activity. PMID:20400856
Genome-wide analysis of transposable elements and tandem repeats in the compact placozoan genome. PMID:20398319
Mendelian disorders and multifactorial traits: the big divide or one for all? PMID:20395971
A complex task? Direct modulation of transcription factors with small molecules. PMID:20395165
The transcript repeat element: the human Alu sequence as a component of gene networks influencing cancer. PMID:20393868
Sequence composition similarities with the 7SL RNA are highly predictive of functional genomic features. PMID:20392819
Unconstrained mining of transcript data reveals increased alternative splicing complexity in the human transcriptome. PMID:20385588
A splicing-independent function of SF2/ASF in microRNA processing. PMID:20385090
A human-specific de novo protein-coding gene associated with human brain functions. PMID:20376170
Alternative splicing and evolution: diversification, exon definition and function. PMID:20376054
De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis. PMID:20375099
The past, present, and future of direct-to-consumer genetic tests. PMID:20373667
Personal genomes in progress: from the human genome project to the personal genome project. PMID:20373666
Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers. PMID:20363979
Multiple personal genomes await. PMID:20360717
Human genome at ten: The sequence explosion. PMID:20360711
Transcription of mouse Sp2 yields alternatively spliced and sub-genomic mRNAs in a tissue- and cell-type-specific fashion. PMID:20353838
A clustered set of three Sp-family genes is ancestral in the Metazoa: evidence from sequence analysis, protein domain structure, developmental expression patterns and chromosomal location. PMID:20353601
Assessment of collaboration and interoperability in an information management system to support bioscience research. PMID:20351900
A general framework for studying genetic effects and gene-environment interactions with missing data. PMID:20348396
A LINE-1 component to human aging: do LINE elements exact a longevity cost for evolutionary advantage? PMID:20346965
A role for human endogenous retrovirus-K (HML-2) in rheumatoid arthritis: investigating mechanisms of pathogenesis. PMID:20345981
Protogenin defines a transition stage during embryonic neurogenesis and prevents precocious neuronal differentiation. PMID:20335479
Conservation of human microsatellites across 450 million years of evolution. PMID:20333231
Population genomics of intron splicing in 38 Saccharomyces cerevisiae genome sequences. PMID:20333215
Exploring repetitive DNA landscapes using REPCLASS, a tool that automates the classification of transposable elements in eukaryotic genomes. PMID:20333191
On the origin and evolution of vertebrate olfactory receptor genes: comparative genome analysis among 23 chordate species. PMID:20333175
Independent mammalian genome contractions following the KT boundary. PMID:20333172
Metnase/SETMAR: a domesticated primate transposase that enhances DNA repair, replication, and decatenation. PMID:20309721
What can we learn about the distribution of fitness effects of new mutations from DNA sequence data? PMID:20308093
A mobile threat to genome stability: The impact of non-LTR retrotransposons upon the human genome. PMID:20307669
Genome organization of major tandem repeats in the hard tick, Ixodes scapularis. PMID:20306126
Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multibody docking server. PMID:20305088
Engineering of single Ig superfamily domain of intercellular adhesion molecule 1 (ICAM-1) for native fold and function. PMID:20304924
Laboratory methods for the analysis of primate mobile elements. PMID:20238081
Computational methods for the analysis of primate mobile elements. PMID:20238080
Genome-wide association studies and beyond. PMID:20235850
Serum DNA motifs predict disease and clinical status in multiple sclerosis. PMID:20228264
Heads or tails: L1 insertion-associated 5' homopolymeric sequences. PMID:20226075
Mobile DNA and evolution in the 21st century. PMID:20226073
Epigenetic histone modifications of human transposable elements: genome defense versus exaptation. PMID:20226072
An algorithm for the reconstruction of consensus sequences of ancient segmental duplications and transposon copies in eukaryotic genomes. PMID:20223737
The (r)evolution of SINE versus LINE distributions in primate genomes: sex chromosomes are important. PMID:20219940
Involvement of transposon-like elements in penicillin gene cluster regulation. PMID:20219692
Somatic expression of LINE-1 elements in human tissues. PMID:20215437
Transposases are the most abundant, most ubiquitous genes in nature. PMID:20215432
Redefining CpG islands using hidden Markov models. PMID:20212320
RNA dust: where are the genes? PMID:20211845
Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates. PMID:20210993
A Study of the Distribution of Phylogenetically Conserved Blocks within Clusters of Mammalian Homeobox Genes. PMID:20209015
Using the DFCI gene index databases for biological discovery. PMID:20205187
A time for atlases and atlases for time. PMID:20204142
Visualizing genomes: techniques and challenges. PMID:20195257
An effective model for natural selection in promoters. PMID:20194951
Personal genome sequencing: current approaches and challenges. PMID:20194435
Pharmacogenetics and personal genomes. PMID:20190862
Imaging of Abdominal Aortic Aneurysm: the present and the future. PMID:20180767
Genomic gems: SINE RNAs regulate mRNA production. PMID:20176473
Genome-wide identification of susceptibility alleles for viral infections through a population genetics approach. PMID:20174570
A new model system swims into focus: using the zebrafish to visualize intestinal metabolism in vivo. PMID:20174460
Codon usage biases of transposable elements and host nuclear genes in Arabidopsis thaliana and Oryza sativa. PMID:20172490
Inheritance of DNA transferred from American trypanosomes to human hosts. PMID:20169193
Genome destabilization by homologous recombination in the germ line. PMID:20164840
Methylation status of individual CpG sites within Alu elements in the human genome and Alu hypomethylation in gastric carcinomas. PMID:20163738
Isolation and characterization of a novel zinc finger gene, ZNFD, activating AP1(PMA) transcriptional activities. PMID:20162441
Acceleration of Ungapped Extension in Mercury BLAST. PMID:20160873
Genetics of psychiatric disorders methods: molecular approaches. PMID:20159337
Modeling neutral evolution of Alu elements using a branching process. PMID:20158868
Transposon identification using profile HMMs. PMID:20158867
Chromatin modifications: the driving force of senescence and aging? PMID:20157508
Structure of avian thymic hormone, a high-affinity avian beta-parvalbumin, in the Ca2+-free and Ca2+-bound states. PMID:20156445
Kinetic and structural analysis of substrate specificity in two copper amine oxidases from Hansenula polymorpha. PMID:20155950
Beyond the HapMap Genotypic Data: Prospects of Deep Resequencing Projects. PMID:20151045
Evolutionary biology: Face of the past reconstructed. PMID:20148020
Discrete subcellular partitioning of human retrotransposon RNAs despite a common mechanism of genome insertion. PMID:20147320
2x genomes--depth does matter. PMID:20144222
Child and adolescent psychiatric genetics. PMID:20140632
CpG methylation of a silent controlling element in the murine Avy allele is incomplete and unresponsive to methyl donor supplementation. PMID:20140227
Mutations in Grxcr1 are the basis for inner ear dysfunction in the pirouette mouse. PMID:20137774
Generation of expression vectors for high-throughput functional analysis of target genes in Schizosaccharomyces pombe. PMID:20127475
U87MG decoded: the genomic sequence of a cytogenetically aberrant human cancer cell line. PMID:20126413
A gene-centric human proteome project: HUPO--the Human Proteome organization. PMID:20124355
One Decade Later: What has Gene Expression Profiling Told us About Neuronal Cell Types, Brain Function and Disease? PMID:20119529
Construction of gene/transcription regulatory networks. PMID:20118125
How far can we go with structural mass spectrometry of protein complexes? PMID:20116283
Overlapping splicing regulatory motifs--combinatorial effects on splicing. PMID:20110253
Integrating the multiple dimensions of genomic and epigenomic landscapes of cancer. PMID:20108112
The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing. PMID:20105308
A transposon and transposase system for human application. PMID:20104209
Implication of the env gene of the human endogenous retrovirus W family in the expression of BDNF and DRD3 and development of recent-onset schizophrenia. PMID:20100784
Selection and mutation in the "new" genetics: an emerging hypothesis. PMID:20099069
Translation efficiency in humans: tissue specificity, global optimization and differences between developmental stages. PMID:20097653
Identical repeated backbone of the human genome. PMID:20096123
Dermatology: the last 30 years--a rollercoaster ride. PMID:20095306
A comparative approach for the investigation of biological information processing: an examination of the structure and function of computer hard drives and DNA. PMID:20092652
Identification and characterization of microRNAs and endogenous siRNAs in Schistosoma japonicum. PMID:20092619
Genetics: Decoding a national treasure. PMID:20090741
Metabolic syndrome components in murine models. PMID:20088816
Highly punctuated patterns of population structure on the X chromosome and implications for African evolutionary history. PMID:20085712
Intergenic, gene terminal, and intragenic CpG islands in the human genome. PMID:20085634
Exploring prion protein biology in flies: genetics and beyond. PMID:20083902
Human Rad52 binds and wraps single-stranded DNA and mediates annealing via two hRad52-ssDNA complexes. PMID:20081207
Bifurcation and enhancement of autonomous-nonautonomous retrotransposon partnership through LTR Swapping in soybean. PMID:20081112
Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life. PMID:20080632
The imprinted retrotransposon-like gene PEG11 (RTL1) is expressed as a full-length protein in skeletal muscle from Callipyge sheep. PMID:20072617
Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes. PMID:20067941
Biomarkers of lead exposure and DNA methylation within retrotransposons. PMID:20064768
Effort required to finish shotgun-generated genome sequences differs significantly among vertebrates. PMID:20064230
Endogenous non-retroviral RNA virus elements in mammalian genomes. PMID:20054395
Custom human endogenous retroviruses dedicated microarray identifies self-induced HERV-W family elements reactivated in testicular cancer upon methylation control. PMID:20053729
Chaperone requirements for biosynthesis of the trypanosome variant surface glycoprotein. PMID:20052285
Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. PMID:20051556
Finding Occurrences of Relevant Functional Elements in Genomic Signatures. PMID:20046539
Improving the efficiency of genomic loci capture using oligonucleotide arrays for high throughput resequencing. PMID:20043857
Elucidating novel mechanisms of brain injury following subarachnoid hemorrhage: an emerging role for neuroproteomics. PMID:20043714
High-throughput sequencing of retrotransposon integration provides a saturated profile of target activity in Schizosaccharomyces pombe. PMID:20040583
Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. PMID:20037582
Development of a Pharmacogenetic Predictive Test in asthma: proof of concept. PMID:20032818
Next-generation sequencing. PMID:20030863
Potential impact of stress activated retrotransposons on genome evolution in a marine diatom. PMID:20028555
Functional diversity of human protein kinase splice variants marks significant expansion of human kinome. PMID:20028505
From race to repositories: bioethics in a genomics age. PMID:20027284
Copy number variations in East-Asian population and their evolutionary and functional implications. PMID:20026555
De novo assembly of human genomes with massively parallel short read sequencing. PMID:20019144
ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth. PMID:20016685
Human genomics: The genome finishers. PMID:20016572
Sequence determinants of human microsatellite variability. PMID:20015383
Exome sequencing of a multigenerational human pedigree. PMID:20011588
Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PMID:20011109
The CRF system, stress, depression and anxiety-insights from human genetic studies. PMID:20010888
Synthetic viruses: a new opportunity to understand and prevent viral disease. PMID:20010599
A first look at entire human methylomes. PMID:20010593
Alcohol exposure alters DNA methylation profiles in mouse embryos at early neurulation. PMID:20009564
Alpha3, a transposable element that promotes host sexual reproduction. PMID:20008928
Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements. PMID:20008508
Genome-wide scans for footprints of natural selection. PMID:20008396
Deciphering the transcriptional circuitry of microRNA genes expressed during human monocytic differentiation. PMID:20003307
Pharmacogenomics: a new paradigm to personalize treatments in nephrology patients. PMID:19968662
Stretching chromatin through confinement. PMID:19967112
Comprehensive genomic access to vector integration in clinical gene therapy. PMID:19966782
Understanding genetic epidemiologic association studies Part 1: fundamentals. PMID:19962167
Mechanisms of copy number variation and hybrid gene formation in the KIR immune gene complex. PMID:19959527
GWAS or Gee Whiz, PSAS or Pshaw: elucidating the biologic and clinical significance of genetic variation in cardiovascular disease. PMID:19959124
Proteomic identification of multitasking proteins in unexpected locations complicates drug targeting. PMID:19949400
Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila. PMID:19948818
Pharmacogenetics in heart failure: how it will shape the future. PMID:19945055
High-throughput single nucleotide polymorphism genotyping using nanofluidic Dynamic Arrays. PMID:19943955
Application of OMICS technologies in occupational and environmental health research; current status and projections. PMID:19933307
Use of cell lines in the investigation of pharmacogenetic loci. PMID:19925429
CG dinucleotide periodicities recognized by the Dnmt3a-Dnmt3L complex are distinctive at retroelements and imprinted domains. PMID:19921333
Expression profiling of repetitive elements by melting temperature analysis: variation in HERV-W gag expression across human individuals and tissues. PMID:19919688
Discovery and annotation of functional chromatin signatures in the human genome. PMID:19918365
Alu repeats increase local recombination rates. PMID:19917129
Discovery of regulatory elements is improved by a discriminatory approach. PMID:19911049
The pivotal roles of TIA proteins in 5' splice-site selection of alu exons and across evolution. PMID:19911040
Correlation of microsynteny conservation and disease gene distribution in mammalian genomes. PMID:19909546
Genome-wide association studies in cancer--current and future directions. PMID:19906782
Talua SINE biology in the genome of the Reticulitermes subterranean termites (Isoptera, Rhinotermitidae). PMID:19904483
A role for the MS analysis of nucleic acids in the post-genomics age. PMID:19897384
Genome sequence, comparative analysis, and population genetics of the domestic horse. PMID:19892987
Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. PMID:19892720
Identification and functional analyses of 11,769 full-length human cDNAs focused on alternative splicing. PMID:19880432
Environmental stresses inhibit splicing in the aquatic fungus Blastocladiella emersonii. PMID:19874600
A novel mouse HSF3 has the potential to activate nonclassical heat-shock genes during heat shock. PMID:19864465
LINE dancing in the human genome: transposable elements and disease. PMID:19863772
Conceptualizing child health disparities: a role for developmental neurogenomics. PMID:19861470
An exon-based comparative variant analysis pipeline to study the scale and role of frameshift and nonsense mutation in the human-chimpanzee divergence. PMID:19859573
Can an infectious disease genomics project predict and prevent the next pandemic? PMID:19855828
Finding distal regulatory elements in the human genome. PMID:19854636
APOBEC3 proteins inhibit LINE-1 retrotransposition in the absence of ORF1p binding. PMID:19845642
Friendly viruses: the special relationship between endogenous retroviruses and their host. PMID:19845636
Next-generation gap. PMID:19844227
Large introns in relation to alternative splicing and gene evolution: a case study of Drosophila bruno-3. PMID:19840385
Chronic health conditions in childhood cancer survivors: is it all treatment-related--or do genetics play a role? PMID:19838838
Reading between the LINEs to see into the past. PMID:19837475
Regulated expression of a transgene introduced on an oriP/EBNA-1 PAC shuttle vector into human cells. PMID:19835613
Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity. PMID:19835609
Requirements for recruitment of a G protein-coupled receptor to clathrin-coated pits in budding yeast. PMID:19828733
Analysis of transposons and repeat composition of the sunflower (Helianthus annuus L.) genome. PMID:19826774
Oncogene mutations, copy number gains and mutant allele specific imbalance (MASI) frequently occur together in tumor cells. PMID:19826477
Transposable elements in disease-associated cryptic exons. PMID:19823873
The NIH Human Microbiome Project. PMID:19819907
Emergence of single-molecule sequencing and potential for molecular diagnostic applications. PMID:19817551
Social and ethical checkpoints for bottom-up synthetic biology, or protocells. PMID:19816801
Insights into the nature and consequences of our variable genome. PMID:19808931
Predictive chromatin signatures in the mammalian genome. PMID:19808796
Beyond society: the evolution of organismality. PMID:19805423
Triplet repeat length bias and variation in the human transcriptome. PMID:19805156
High resolution analysis of the human transcriptome: detection of extensive alternative splicing independent of transcriptional activity. PMID:19804644
The origins and impact of primate segmental duplications. PMID:19796838
Recent advances of genetic ancestry testing in biomedical research and direct to consumer testing. PMID:19793051
Identification of copy number variants defining genomic differences among major human groups. PMID:19789632
Regulation of the epithelial sodium channel [ENaC] in kidneys of salt-sensitive Dahl rats: insights on alternative splicing. PMID:19785774
Common variants in polygenic schizophrenia. PMID:19785721
tRNA over-expression in breast cancer and functional consequences. PMID:19783824
Long-term consequences of hematopoietic stem cell transplantation: current state of the science. PMID:19782145
High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans. PMID:19778439
Assessment of Population Structure and Its Effects on Genome-Wide Association Studies. PMID:19777146
An Alu-derived intronic splicing enhancer facilitates intronic processing and modulates aberrant splicing in ATM. PMID:19773425
Rheumatoid arthritis genetics: 2009 update. PMID:19772830
Many LINE1 elements contribute to the transcriptome of human somatic cells. PMID:19772661
Environmental influence on L1 retrotransposons in the adult hippocampus. PMID:19771587
High-throughput SNP genotyping: combining tag SNPs and molecular beacons. PMID:19768600
The completion of the Mammalian Gene Collection (MGC). PMID:19767417
Light-mediated remote control of signaling pathways. PMID:19765679
A c-Myc regulatory subnetwork from human transposable element sequences. PMID:19763338
Human miRNA precursors with box H/ACA snoRNA features. PMID:19763159
The impact of retrotransposons on human genome evolution. PMID:19763152
MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes. PMID:19762481
Prediction of antibody response using recombinant human protein fragments as antigen. PMID:19760667
Insights into electron tunneling across hydrogen-bonded base-pairs in complete molecular circuits for single-stranded DNA sequencing. PMID:19759919
An evolutionary perspective of animal microRNAs and their targets. PMID:19759918
Two-parameter characterization of chromosome-scale recombination rate. PMID:19752285
Genome-wide association studies for atherosclerotic vascular disease and its risk factors. PMID:19750184
Splice site strength-dependent activity and genetic buffering by poly-G runs. PMID:19749754
Prepublication data sharing. PMID:19741685
Human endogenous retroviral long terminal repeat sequences as cell type-specific promoters in retroviral vectors. PMID:19741000
Evidence for large diversity in the human transcriptome created by Alu RNA editing. PMID:19740767
Genetics and the general physician: insights, applications and future challenges. PMID:19737788
Update on genomics in veterinary oncology. PMID:19732729
Spatial organization of genes as a component of regulated expression. PMID:19727792
Non-B DNA structure-induced genetic instability and evolution. PMID:19727556
The B6 database: a tool for the description and classification of vitamin B6-dependent enzymatic activities and of the corresponding protein families. PMID:19723314
Systematic identification and characterization of chicken (Gallus gallus) ncRNAs. PMID:19720738
p53 responsive elements in human retrotransposons. PMID:19718052
Computational reasoning across multiple models. PMID:19717801
Global microsatellite content distinguishes humans, primates, animals, and plants. PMID:19717526
Genotype imputation. PMID:19715440
CDT retroelement: The stratagem to survive extreme vegetative dehydration. PMID:19704456
Detection of genomic variation by selection of a 9 mb DNA region and high throughput sequencing. PMID:19684856
Computational analyses of mammalian lactate dehydrogenases: human, mouse, opossum and platypus LDHs. PMID:19679512
Mapping the human membrane proteome: a majority of the human membrane proteins can be classified according to function and evolutionary origin. PMID:19678920
Metalloproteins and metal sensing. PMID:19675642
Computational finishing of large sequence contigs reveals interspersed nested repeats and gene islands in the rf1-associated region of maize. PMID:19675151
The role of LINEs and CpG islands in dosage compensation on the chicken Z chromosome. PMID:19672682
Insights from genomic profiling of transcription factors. PMID:19668247
Single-molecule sequencing of an individual human genome. PMID:19668243
Cooperative-binding and splicing-repressive properties of hnRNP A1. PMID:19667073
Cross-sectional dating of novel haplotypes of HERV-K 113 and HERV-K 115 indicate these proviruses originated in Africa before Homo sapiens. PMID:19666991
Trypanosomatid genomes contain several subfamilies of ingi-related retroposons. PMID:19666780
Transposable elements and factors influencing their success in eukaryotes. PMID:19666747
Group I introns and inteins: disparate origins but convergent parasitic strategies. PMID:19666710
Doubts about complex speciation between humans and chimpanzees. PMID:19664844
The molecular characterization and clinical management of multiple myeloma in the post-genome era. PMID:19657360
Statistical aspects of discerning indel-type structural variation via DNA sequence alignment. PMID:19656394
Establishing a population-based cancer registry DNA biorepository: the Hawai'i Tumor Registry's Sharing Ohana project. PMID:19653421
5'-Transducing SVA retrotransposon groups spread efficiently throughout the human genome. PMID:19652014
Establishment of Hox vertebral identities in the embryonic spine precursors. PMID:19651306
Retroelements and their impact on genome evolution and functioning. PMID:19649766
Evolutionary history reconstruction for Mammalian complex gene clusters. PMID:19645598
Genomic mutation rates: what high-throughput methods can tell us. PMID:19644920
Bipartite functions of the CREB co-activators selectively direct alternative splicing or transcriptional activation. PMID:19644446
Evolutionary and expression signatures of pseudogenes in Arabidopsis and rice. PMID:19641029
Genetic and pharmacologic alteration of cathepsin expression influences reovirus pathogenesis. PMID:19640986
Exon-trapping mediated by the human retrotransposon SVA. PMID:19635844
Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation. PMID:19630943
Sequencing primate genomes: what have we learned? PMID:19630567
Alternative splicing of G protein-coupled receptors: physiology and pathophysiology. PMID:19629391
Coevolution of interacting fertilization proteins. PMID:19629160
Publish together or perish: the increasing number of authors per article in academic journals is the consequence of a changing scientific culture. Some researchers define authorship quite loosely. PMID:19626176
Characterization and distribution of retrotransposons and simple sequence repeats in the bovine genome. PMID:19625614
The evolutionary dynamics of the Helena retrotransposon revealed by sequenced Drosophila genomes. PMID:19624823
InvAluable junk: the cellular impact and function of Alu and B2 RNAs. PMID:19621349
Alternative splicing of transcription factors' genes: beyond the increase of proteome diversity. PMID:19609452
LEDGF/p75 proteins with alternative chromatin tethers are functional HIV-1 cofactors. PMID:19609362
Exaptation of an ancient Alu short interspersed element provides a highly conserved vitamin D-mediated innate immune response in humans and primates. PMID:19607716
A method for identifying alternative or cryptic donor splice sites within gene and mRNA sequences. Comparisons among sequences from vertebrates, echinoderms and other groups. PMID:19607703
A compartmentalized approach to the assembly of physical maps. PMID:19604400
The ClinSeq Project: piloting large-scale genome sequencing for research in genomic medicine. PMID:19602640
Every genome sequence needs a good map. PMID:19596977
Genome-wide prediction of cis-acting RNA elements regulating tissue-specific pre-mRNA alternative splicing. PMID:19594881
Modeling the repertoire of true tumor-specific MHC I epitopes in a human tumor. PMID:19593447
Transposons that clean up after themselves. PMID:19589181
A highly annotated whole-genome sequence of a Korean individual. PMID:19587683
Evolutionary flexibility of protein complexes. PMID:19583842
OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif. PMID:19583839
DNA migration mechanism analyses for applications in capillary and microchip electrophoresis. PMID:19582705
Transcriptional and post-transcriptional profile of human chromosome 21. PMID:19581486
Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation. PMID:19578405
Genome-wide association studies and the genetic dissection of complex traits. PMID:19569043
Genome desertification in eutherians: can gene deserts explain the uneven distribution of genes in placental mammalian genomes? PMID:19568804
Translational bioinformatics applications in genome medicine. PMID:19566916
Genomics of type 2 diabetes mellitus: implications for the clinician. PMID:19564886
More than 9,000,000 unique genes in human gut bacterial community: estimating gene numbers inside a human body. PMID:19562079
Comparative methylation of ERVWE1/syncytin-1 and other human endogenous retrovirus LTRs in placenta tissues. PMID:19561344
Allelic polymorphism within the TAS1R3 promoter is associated with human taste sensitivity to sucrose. PMID:19559618
Rational design of ligands targeting triplet repeating transcripts that cause RNA dominant disease: application to myotonic muscular dystrophy type 1 and spinocerebellar ataxia type 3. PMID:19552411
Synergies and distinctions between computational disciplines in biomedical research: perspective from the Clinical andTranslational Science Award programs. PMID:19550198
Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. PMID:19546169
Stochastic noise in splicing machinery. PMID:19546110
High G+C Content of Herpes Simplex Virus DNA: Proposed Role in Protection Against Retrotransposon Insertion. PMID:19543363
Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly. PMID:19542148
Challenges, current status and future perspectives of proteomics in improving understanding, diagnosis and treatment of vascular disease. PMID:19541510
Dynamics of transposable elements: towards a community ecology of the genome. PMID:19540613
7TMRmine: a Web server for hierarchical mining of 7TMR proteins. PMID:19538753
Patterns of oligonucleotide sequences in viral and host cell RNA identify mediators of the host innate immune system. PMID:19536338
Identification, characterization and expression of novel Sex Hormone Binding Globulin alternative first exons in the human prostate. PMID:19534810
Annotation and visualization of endogenous retroviral sequences using the Distributed Annotation System (DAS) and eBioX. PMID:19534743
Transcripts of unknown function in multiple-signaling pathways involved in human stem cell differentiation. PMID:19531736
Differential radio-sensitivities of human chromosomes 1 and 2 in one donor in interphase- and metaphase-spreads after 60Co gamma-irradiation. PMID:19531236
Apprehending multicellularity: regulatory networks, genomics, and evolution. PMID:19530132
Using RNA interference to identify specific modifiers of a temperature-sensitive, embryonic-lethal mutation in the Caenorhabditis elegans ubiquitin-like Nedd8 protein modification pathway E1-activating gene rfl-1. PMID:19528325
Structural implication of splicing stochastics. PMID:19528068
The European renal genome project: an integrated approach towards understanding the genetics of kidney development and disease. PMID:19521566
The 1001 genomes project for Arabidopsis thaliana. PMID:19519932
Chromodomains and LTR retrotransposons in plants. PMID:19513271
Tracking the past: interspersed repeats in an extinct Afrotherian mammal, Mammuthus primigenius. PMID:19508981
The repertoire of G-protein-coupled receptors in Xenopus tropicalis. PMID:19508718
Stepwise evolution of two giant composite LTR-retrotransposon-like elements DA and Xiao. PMID:19500371
Phylogeny of the macaques (Cercopithecidae: Macaca) based on Alu elements. PMID:19497354
A novel protein isoform of the multicopy human NAIP gene derives from intragenic Alu SINE promoters. PMID:19488400
L1 retrotransposition occurs mainly in embryogenesis and creates somatic mosaicism. PMID:19487571
Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships. PMID:19483094
Transposon-mediated genome manipulation in vertebrates. PMID:19478801
A comparative approach shows differences in patterns of numt insertion during hominoid evolution. PMID:19471988
The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. PMID:19470904
A transcript profiling approach reveals the zinc finger transcription factor ZNF191 is a pleiotropic factor. PMID:19463170
Next-generation sequencing of vertebrate experimental organisms. PMID:19452216
SEPT9 gene sequencing analysis reveals recurrent mutations in hereditary neuralgic amyotrophy. PMID:19451530
Gene organization and sequence analyses of transfer RNA genes in Trypanosomatid parasites. PMID:19450263
A novel L1 retrotransposon marker for HeLa cell line identification. PMID:19450234
A HUPO test sample study reveals common problems in mass spectrometry-based proteomics. PMID:19448641
A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide. PMID:19447786
Source gene composition and gene conversion of the AluYh and AluYi lineages of retrotransposons. PMID:19442302
Noisy splicing, more than expression regulation, explains why some exons are subject to nonsense-mediated mRNA decay. PMID:19442261
Mobile elements create structural variation: analysis of a complete human genome. PMID:19439515
Genomic disorders ten years on. PMID:19439022
Changes in DNA methylation of tandem DNA repeats are different from interspersed repeats in cancer. PMID:19437537
TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences. PMID:19429695
Repair-mediated duplication by capture of proximal chromosomal DNA has shaped vertebrate genome evolution. PMID:19424419
Widespread genomic signatures of natural selection in hominid evolution. PMID:19424416
Minireview: Evolution of NURSA, the Nuclear Receptor Signaling Atlas. PMID:19423650
Predicting potential miRNA target sites within gene promoters. PMID:19423343
LINE-1 methylation in plasma DNA as a biomarker of activity of DNA methylation inhibitors in patients with solid tumors. PMID:19421002
SNP detection for massively parallel whole-genome resequencing. PMID:19420381
Remarkable evolutionary conservation of SOX14 orthologues. PMID:19417540
Phylogenetic analysis, structural evolution and functional divergence of the 12-oxo-phytodienoate acid reductase gene family in plants. PMID:19416520
The GNAS Locus: Quintessential Complex Gene Encoding Gsalpha, XLalphas, and other Imprinted Transcripts. PMID:19412439
Characteristics of human and mouse orthologous protein-coding nucleotide sequences with large g+c content variations. PMID:19412417
Comparative analysis of Alu repeats in primate genomes. PMID:19411604
Evolutionary descent of a human chromosome 6 neocentromere: a jump back to 17 million years ago. PMID:19411601
Constructing genomic maps of positive selection in humans: where do we go from here? PMID:19411596
Automated FingerPrint Background removal: FPB. PMID:19405935
Comparative component analysis of exons with different splicing frequencies. PMID:19404386
Personalized medicine: a transformative approach is needed. PMID:19398733
Tumor-directed gene therapy in mice using a composite nonviral gene delivery system consisting of the piggyBac transposon and polyethylenimine. PMID:19397814
Repetitive DNA elements, nucleosome binding and human gene expression. PMID:19393174
Analysis of the complement and molecular evolution of tRNA genes in cow. PMID:19393063
Bos taurus genome assembly. PMID:19393050
The RNA polymerase dictates ORF1 requirement and timing of LINE and SINE retrotransposition. PMID:19390602
Repertoire of microRNAs in epithelial ovarian cancer as determined by next generation sequencing of small RNA cDNA libraries. PMID:19390579
Marker selection for genetic case-control association studies. PMID:19390530
LC-MS/MS-based proteome profiling in Daphnia pulex and Daphnia longicephala: the Daphnia pulex genome database as a key for high throughput proteomics in Daphnia. PMID:19383153
Old can be new again: HAPPY whole genome sequencing, mapping and assembly. PMID:19381348
Estimating the age of retrotransposon subfamilies using maximum likelihood. PMID:19379804
Promoter analysis: gene regulatory motif identification with A-GLAM. PMID:19378149
Genomewide association studies and human disease. PMID:19369657
Structural determinants of protein folding. PMID:19367367
Intelligently deciphering unintelligible designs: algorithmic algebraic model checking in systems biology. PMID:19364723
Advances in systems biology are enhancing our understanding of disease and moving us closer to novel disease treatments. PMID:19363597
An indel in transmembrane helix 2 helps to trace the molecular evolution of class A G-protein-coupled receptors. PMID:19357801
Race and ancestry in biomedical research: exploring the challenges. PMID:19348695
Balanced translocations in mental retardation. PMID:19347365
DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources. PMID:19344873
A theoretical model for template-free synthesis of long DNA sequence. PMID:19343541
Perdeuteration, purification, crystallization and preliminary neutron diffraction of an ocean pout type III antifreeze protein. PMID:19342793
Applications of metabolomics and proteomics to the mdx mouse model of Duchenne muscular dystrophy: lessons from downstream of the transcriptome. PMID:19341503
The cycle of genome-directed medicine. PMID:19341487
Fascin-1 promoter activity is regulated by CREB and the aryl hydrocarbon receptor in human carcinoma cells. PMID:19340314
Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. PMID:19339662
Genomewide association studies: history, rationale, and prospects for psychiatric disorders. PMID:19339359
Human-specific modulation of transcriptional activity provided by endogenous retroviral insertions. PMID:19339349
Drosophila melanogaster as a model organism of brain diseases. PMID:19333415
Comparative genomic study reveals a transition from TA richness in invertebrates to GC richness in vertebrates at CpG flanking sites: an indication for context-dependent mutagenicity of methylated CpG sites. PMID:19329065
Identification of conserved regulatory elements in mammalian promoter regions: a case study using the PCK1 promoter. PMID:19329064
A robust linkage map of the porcine autosomes based on gene-associated SNPs. PMID:19327136
Heterochromatic genome stability requires regulators of histone H3 K9 methylation. PMID:19325889
The ubiquitylation machinery of the endoplasmic reticulum. PMID:19325625
Large-scale analysis of exonized mammalian-wide interspersed repeats in primate genomes. PMID:19324900
Harnessing nature's toolbox: regulatory elements for synthetic biology. PMID:19324675
Planning the human variome project: the Spain report. PMID:19306394
CpG islands: algorithms and applications in methylation studies. PMID:19302978
The apolipoprotein L family of programmed cell death and immunity genes rapidly evolved in primates at discrete sites of host-pathogen interactions. PMID:19299565
HLA-A allele associations with viral MER9-LTR nucleotide sequences at two distinct loci within the MHC alpha block. PMID:19294374
Genome-wide hypomethylation in head and neck cancer is more pronounced in HPV-negative tumors and is associated with genomic instability. PMID:19293934
Human genetic variation and its contribution to complex traits. PMID:19293820
Human genes involved in copy number variation: mechanisms of origin, functional effects and implications for disease. PMID:19287135
Cancer gene discovery in mouse and man. PMID:19285540
Missing call bias in high-throughput genotyping. PMID:19284636
TFCat: the curated catalog of mouse and human transcription factors. PMID:19284633
Topological and organizational properties of the products of house-keeping and tissue-specific genes in protein-protein interaction networks. PMID:19284572
Using biological networks to search for interacting loci in genome-wide association studies. PMID:19277065
A census of human transcription factors: function, expression and evolution. PMID:19274049
Finding the fifth base: genome-wide sequencing of cytosine methylation. PMID:19273618
Diverse cis factors controlling Alu retrotransposition: what causes Alu elements to die? PMID:19273617
Integration target site selection by a resurrected human endogenous retrovirus. PMID:19270161
Gene targeting in mouse embryonic stem cells. PMID:19266325
A functional and regulatory network associated with PIP expression in human breast cancer. PMID:19262752
Odor coding by a Mammalian receptor repertoire. PMID:19261596
A tale of tails: insights into the coordination of 3' end processing during homologous recombination. PMID:19260026
Duplication count distributions in DNA sequences. PMID:19256873
ChIP-based methods for the identification of long-range chromatin interactions. PMID:19247990
Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes. PMID:19246569
Methods to determine DNA structural alterations and genetic instability. PMID:19245837
Genomics and identity: the bioinformatisation of human life. PMID:19242821
A survey of available tools and web servers for analysis of protein-protein interactions and interfaces. PMID:19240123
A framework for evolutionary systems biology. PMID:19239699
Molecular evolution of the antiretroviral TRIM5 gene. PMID:19238338
Beyond chemotherapy: targeted therapies in ovarian cancer. PMID:19238149
Guinea pig ID-like families of SINEs. PMID:19232383
Protein evolution on a human signaling network. PMID:19226461
Identifying protein-coding genes in genomic sequences. PMID:19226436
Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation. PMID:19224649
Genomic profiling of mesenchymal stem cells. PMID:19224407
Predicting human height by Victorian and genomic methods. PMID:19223933
The position of repetitive DNA sequence in the southern cattle tick genome permits chromosome identification. PMID:19221885
Ectodermal dysplasia-cutaneous syndactyly syndrome maps to chromosome 7p21.1-p14.3. PMID:19221800
Microsatellites are molecular clocks that support accurate inferences about history. PMID:19221007
Evolutionary history of Na,K-ATPases and their osmoregulatory role. PMID:19214758
Experimental animal model and RNA interference: a promising association for bladder cancer research. PMID:19214530
ChIP-seq accurately predicts tissue-specific activity of enhancers. PMID:19212405
Structural determinants involved in the formation and activation of G protein betagamma dimers. PMID:19212142
Partial correlation analysis indicates causal relationships between GC-content, exon density and recombination rate in the human genome. PMID:19208170
Alternative pre-mRNA splicing switches modulate gene expression in late erythropoiesis. PMID:19196664
Revisiting the missing protein-coding gene catalog of the domestic dog. PMID:19193219
Cryptic variation in the human mutation rate. PMID:19192947
Dense chromatin plates in metaphase chromosomes. PMID:19189102
AID can restrict L1 retrotransposition suggesting a dual role in innate and adaptive immunity. PMID:19188259
Site-specific integration of retroviral DNA in human cells using fusion proteins consisting of human immunodeficiency virus type 1 integrase and the designed polydactyl zinc-finger protein E2C. PMID:19186211
Quantitative variation of LINE-1 sequences in five species and three subspecies of the subgenus Mus and in five Robertsonian races of Mus musculus domesticus. PMID:19184476
The effect of transposable element insertions on gene expression evolution in rodents. PMID:19183808
Integrating sequence with FPC fingerprint maps. PMID:19181701
Reduced neutrophil count in people of African descent is due to a regulatory variant in the Duffy antigen receptor for chemokines gene. PMID:19180233
LINE retrotransposon RNA is an essential structural and functional epigenetic component of a core neocentromeric chromatin. PMID:19180186
A new link between epigenetic progenitor lesions in cancer and the dynamics of signal transduction. PMID:19177016
Bioinformatic flowchart and database to investigate the origins and diversity of clan AA peptidases. PMID:19173708
Orientation, distance, regulation and function of neighbouring genes. PMID:19164091
What are microarrays teaching us about sleep? PMID:19162550
Characterization of taxonomically restricted genes in a phylum-restricted cell type. PMID:19161630
Minisatellite MS32 alleles show population specificity among Thai, Chinese, and Japanese. PMID:19159965
Decline in genomic DNA methylation through aging in a cohort of elderly subjects. PMID:19150625
De novo induction of genetically engineered brain tumors in mice using plasmid DNA. PMID:19147555
Genomic and proteomic analysis of allogeneic hematopoietic cell transplant outcome. Seeking greater understanding the pathogenesis of GVHD and mortality. PMID:19147066
Non-LTR retrotransposons encode noncanonical RRM domains in their first open reading frame. PMID:19139409
Duplication within the SEPT9 gene associated with a founder effect in North American families with hereditary neuralgic amyotrophy. PMID:19139049
Human ribonuclease 9, a member of ribonuclease A superfamily, specifically expressed in epididymis, is a novel sperm-binding protein. PMID:19137000
Passport, a native Tc1 transposon from flatfish, is functionally active in vertebrate cells. PMID:19136468
Structural alphabets for protein structure classification: a comparison study. PMID:19135454
Evolutionary sequence modeling for discovery of peptide hormones. PMID:19132080
Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes. PMID:19123937
Adaptive evolution in zinc finger transcription factors. PMID:19119423
Mobilization of endogenous retroviruses in mice after infection with an exogenous retrovirus. PMID:19116259
Genomic organization of repetitive DNAs in the cichlid fish Astronotus ocellatus. PMID:19112556
Chromosomal inversions between human and chimpanzee lineages caused by retrotransposons. PMID:19112500
The GC-heterogeneity of teleost fishes. PMID:19108743
Isolation and characterization of post-splicing lariat-intron complexes. PMID:19103666
A proviral puzzle with a prosimian twist. PMID:19091949
Evolutionary-new centromeres preferentially emerge within gene deserts. PMID:19087244
A global network for investigating the genomic epidemiology of malaria. PMID:19079050
Brain tumor susceptibility: the role of genetic factors and uses of mouse models to unravel risk. PMID:19076777
The YH database: the first Asian diploid genome database. PMID:19073702
Genome-wide association studies in the genetics of asthma. PMID:19063818
Introduction to the special issue: psychological aspects of genomics and child health. PMID:19060299
The human genome in the LINE of fire. PMID:19057007
SNUGB: a versatile genome browser supporting comparative and functional fungal genomics. PMID:19055845
Gene flow and genetic structure in the Galician population (NW Spain) according to Alu insertions. PMID:19055739
DNA sequencing by microchip electrophoresis using mixtures of high- and low-molar mass poly(N,N-dimethylacrylamide) matrices. PMID:19053157
Polymer systems designed specifically for DNA sequencing by microchip electrophoresis: a comparison with commercially available materials. PMID:19053156
Thermoresponsive N-alkoxyalkylacrylamide polymers as a sieving matrix for high-resolution DNA separations on a microfluidic chip. PMID:19053065
Identification of common genetic variants that account for transcript isoform variation between human populations. PMID:19052777
Comparative genomics and molecular dynamics of DNA repeats in eukaryotes. PMID:19052325
A satellite-like sequence, representing a "clone gap" in the human genome, was likely involved in the seeding of a novel centromere in macaque. PMID:19048265
Chromosome 12p deletions in TEL-AML1 childhood acute lymphoblastic leukemia are associated with retrotransposon elements and occur postnatally. PMID:19047175
An ancient duplication of exon 5 in the Snap25 gene is required for complex neuronal development/function. PMID:19043548
A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes. PMID:19043541
Methods for integration site distribution analyses in animal cell genomes. PMID:19038346
Genome Environment Browser (GEB): a dynamic browser for visualising high-throughput experimental data in the context of genome features. PMID:19038045
L1 recombination-associated deletions generate human genomic variation. PMID:19036926
SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry. PMID:19036792
The HuRef Browser: a web resource for individual human genomics. PMID:19036787
Estimating translational selection in eukaryotic genomes. PMID:19033257
Genetic signature for human risk assessment: lessons from trichloroethylene. PMID:19031419
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. PMID:19029536
Mapping key features of transcriptional regulatory circuitry in embryonic stem cells. PMID:19022761
Prediction of alternatively skipped exons and splicing enhancers from exon junction arrays. PMID:19021909
Genome and proteome annotation: organization, interpretation and integration. PMID:19019817
Does selection against transcriptional interference shape retroelement-free regions in mammalian genomes? PMID:19018283
Exon definition as a potential negative force against intron losses in evolution. PMID:19014515
Identification of the HERV-K gag antigen in prostate cancer by SEREX using autologous patient serum and its immunogenicity. PMID:19006261
A single amino acid substitution in a segment of the CA protein within Gag that has similarity to human immunodeficiency virus type 1 blocks infectivity of a human endogenous retrovirus K provirus in the human genome. PMID:19004950
Chemical genomics: massively parallel technologies for rapid lead identification and target validation. PMID:19003080
Toward genomic cell culture engineering. PMID:19003075
Alternative splicing and disease. PMID:18992329
Two-dimensional combinatorial screening identifies specific 6'-acylated kanamycin A- and 6'-acylated neamine-RNA hairpin interactions. PMID:18991404
The diploid genome sequence of an Asian individual. PMID:18987735
Epigenetic mechanisms in mammals. PMID:18985277
Alternative isoform regulation in human tissue transcriptomes. PMID:18978772
Width of gene expression profile drives alternative splicing. PMID:18974852
Expression patterns of protein kinases correlate with gene architecture and evolutionary rates. PMID:18974838
DNA hypomethylation arises later in prostate cancer progression than CpG island hypermethylation and contributes to metastatic tumor heterogeneity. PMID:18974140
Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples. PMID:18973670
LINE-like retrotransposition in Saccharomyces cerevisiae. PMID:18957700
Comparative sequence analyses reveal sites of ancestral chromosomal fusions in the Indian muntjac genome. PMID:18957082
Nutritional genomics, polyphenols, diets, and their impact on dietetics. PMID:18954579
Complex organisation and structure of the ghrelin antisense strand gene GHRLOS, a candidate non-coding RNA gene. PMID:18954468
Bacteriophage Mu integration in yeast and mammalian genomes. PMID:18953026
Determining the impact of alternative splicing events on transcriptome dynamics. PMID:18950505
Proteomics: applications in transfusion medicine. PMID:18946951
Topology of class A G protein-coupled receptors: insights gained from crystal structures of rhodopsins, adrenergic and adenosine receptors. PMID:18945819
Autoreactive B cells discriminate CpG-rich and CpG-poor DNA and this response is modulated by IFN-alpha. PMID:18941176
Prevalence in the United States of selected candidate gene variants: Third National Health and Nutrition Examination Survey, 1991-1994. PMID:18936436
Long-range chromosomal interactions and gene regulation. PMID:18931780
A 4,103 marker integrated physical and comparative map of the horse genome. PMID:18931483
Applications of emerging molecular technologies in glioblastoma multiforme. PMID:18928343
DDBJ dealing with mass data produced by the second generation sequencer. PMID:18927114
Parallel analysis of tetramerization domain mutants of the human p53 protein using PCR colonies. PMID:18923936
Mechanism of Alu integration into the human genome. PMID:18923924
Genomic medicine: a new frontier of medicine in the twenty first century. PMID:18923923
Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences. PMID:18852105
Harnessing Nutrigenomics: Development of web-based communication, databases, resources, and tools. PMID:18850216
What would you do if you could sequence everything? PMID:18846086
Solution conformation and thermodynamic characteristics of RNA binding by the splicing factor U2AF65. PMID:18842594
Retrocopy contributions to the evolution of the human genome. PMID:18842134
Relationships of gag-pol diversity between Ty3/Gypsy and Retroviridae LTR retroelements and the three kings hypothesis. PMID:18842133
Refinement of macaque synteny arrangement with respect to the official rheMac2 macaque sequence assembly. PMID:18841486
Diverse splicing patterns of exonized Alu elements in human tissues. PMID:18841251
STIF: Identification of stress-upregulated transcription factor binding sites in Arabidopsis thaliana. PMID:18841238
Genome-wide studies highlight indirect links between human replication origins and gene regulation. PMID:18838675
Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood. PMID:18838674
GenBlastA: enabling BLAST to identify homologous gene sequences. PMID:18838612
Retroelements (LINEs and SINEs) in vole genomes: differential distribution in the constitutive heterochromatin. PMID:18836842
Trichoderma G protein-coupled receptors: functional characterisation of a cAMP receptor-like protein from Trichoderma atroviride. PMID:18836726
Active Alu retrotransposons in the human genome. PMID:18836035
Impact of non-homologous end-joining deficiency on random and targeted DNA integration: implications for gene targeting. PMID:18835848
Splice-mediated Variants of Proteins (SpliVaP) - data and characterization of changes in signatures among protein isoforms due to alternative splicing. PMID:18831736
Evolution of the aging brain transcriptome and synaptic regulation. PMID:18830410
Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools. PMID:18828907
Sole copy of Z2-type human cytidine deaminase APOBEC3H has inhibitory activity against retrotransposons and HIV-1. PMID:18827027
GDF3 is a BMP inhibitor that can activate Nodal signaling only at very high doses. PMID:18823971
Androgen synthesis in adrenarche. PMID:18821018
Murine endogenous retroviruses. PMID:18818872
Ultraconserved coding regions outside the homeobox of mammalian Hox genes. PMID:18816392
Comparative analysis of distinct non-coding characteristics potentially contributing to the divergence of human tissue-specific genes. PMID:18815892
Analysis and synthesis of high-amplitude Cis-elements in the mammalian circadian clock. PMID:18815372
The updated concept of genome and its implications in biotechnological research and molecular diagnostics. PMID:18802794
Transposition of a 600 thousand-year-old LTR retrotransposon in the model legume Lotus japonicus. PMID:18802778
Deletion of the pluripotency-associated Tex19.1 gene causes activation of endogenous retroviruses and defective spermatogenesis in mice. PMID:18802469
Ome sweet ome: what can the genome tell us about the connectome? PMID:18801435
A probabilistic framework to predict protein function from interaction data integrated with semantic knowledge. PMID:18801191
Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2. PMID:18794351
Exhaustive prediction of disease susceptibility to coding base changes in the human genome. PMID:18793467
The SET and transposase domain protein Metnase enhances chromosome decatenation: regulation by automethylation. PMID:18790802
Short tandem repeats in human exons: a target for disease mutations. PMID:18789129
Clinical review: the genetics of type 2 diabetes: a realistic appraisal in 2008. PMID:18782870
ReRep: computational detection of repetitive sequences in genome survey sequences (GSS). PMID:18782453
Metabolic innovations towards the human lineage. PMID:18782449
The short-sequence designs of isochores from the human genome. PMID:18780784
Dynamics and differential proliferation of transposable elements during the evolution of the B and A genomes of wheat. PMID:18780739
Antiretroelement activity of APOBEC3H was lost twice in recent human evolution. PMID:18779051
Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival. PMID:18778477
LINE-1 methylation patterns of different loci in normal and cancerous cells. PMID:18776216
The human set and transposase domain protein Metnase interacts with DNA Ligase IV and enhances the efficiency and accuracy of non-homologous end-joining. PMID:18773976
Isolated populations and complex disease gene identification. PMID:18771588
Analysis of transposon interruptions suggests selection for L1 elements on the X chromosome. PMID:18769724
Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3'-end of genes. PMID:18757892
Advances in chemical carcinogenesis: a historical review and prospective. PMID:18757397
Identification and correction of abnormal, incomplete and mispredicted proteins in public databases. PMID:18752676
Molecular evolution of the keratin associated protein gene family in mammals, role in the evolution of mammalian hair. PMID:18721477
A novel computational and structural analysis of nsSNPs in CFTR gene. PMID:18716917
Current developments in the genetics of autism: from phenome to genome. PMID:18716561
A resource for transcriptomic analysis in the mouse brain. PMID:18714383
VisualRepbase: an interface for the study of occurrences of transposable element families. PMID:18710569
MarkerSet: a marker selection tool based on markers location and informativity in experimental designs. PMID:18710478
Genetic variation in an individual human exome. PMID:18704161
Distribution of the transposable elements bilbo and gypsy in original and colonizing populations of Drosophila subobscura. PMID:18702820
Restriction by APOBEC3 proteins of endogenous retroviruses with an extracellular life cycle: ex vivo effects and in vivo "traces" on the murine IAPE and human HERV-K elements. PMID:18702815
Mouse maelstrom, a component of nuage, is essential for spermatogenesis and transposon repression in meiosis. PMID:18694567
Orientation-dependent regulation of integrated HIV-1 expression by host gene transcriptional readthrough. PMID:18692773
Determining significance of pairwise co-occurrences of events in bursty sequences. PMID:18691400
A novel missense mutation in the EDA gene associated with X-linked recessive isolated hypodontia. PMID:18688569
A general definition and nomenclature for alternative splicing events. PMID:18688268
Reduced purifying selection prevails over positive selection in human copy number variant evolution. PMID:18687881
Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties. PMID:18687880
Impacts of protein-protein interaction domains on organism and network complexity. PMID:18687879
A novel mode of enhancer evolution: the Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity. PMID:18687876
Integration site preference of xenotropic murine leukemia virus-related virus, a new human retrovirus associated with prostate cancer. PMID:18684813
Evolution of the mammalian transcription factor binding repertoire via transposable elements. PMID:18682548
The take and give between retrotransposable elements and their hosts. PMID:18680436
Identification and characterization of novel human tissue-specific RFX transcription factors. PMID:18673564
The agouti mouse model: an epigenetic biosensor for nutritional and environmental alterations on the fetal epigenome. PMID:18673496
Patterns of positive selection in six Mammalian genomes. PMID:18670650
Rise of the machines. PMID:18670625
Maps of cis-Regulatory Nodes in Megabase Long Genome Segments are an Inevitable Intermediate Step Toward Whole Genome Functional Mapping. PMID:18660850
Recent computational approaches to understand gene regulation: mining gene regulation in silico. PMID:18660846
Fine mapping of the GLC1K juvenile primary open-angle glaucoma locus and exclusion of candidate genes. PMID:18648523
Induction of chromosomal translocations in mouse and human cells using site-specific endonucleases. PMID:18647997
Integrated one- and two-photon imaging platform reveals clonal expansion as a major driver of mutation load. PMID:18647827
Increased cell motility and invasion upon knockdown of lipolysis stimulated lipoprotein receptor (LSR) in SW780 bladder cancer cells. PMID:18647386
SpliceCenter: a suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies. PMID:18638396
Human endogenous retrovirus K (HML-2) elements in the plasma of people with lymphoma and breast cancer. PMID:18632860
Human endogenous retrovirus K triggers an antigen-specific immune response in breast cancer patients. PMID:18632641
Sequences, annotation and single nucleotide polymorphism of the major histocompatibility complex in the domestic cat. PMID:18629345
SSRD: simple sequence repeats database of the human genome. PMID:18629286
ORF organization and gene recognition in the yeast genome. PMID:18629282
Endogenous retroviruses and human evolution. PMID:18629260
Identification and comparative analysis of the peptidyl-prolyl cis/trans isomerase repertoires of H. sapiens, D. melanogaster, C. elegans, S. cerevisiae and Sz. pombe. PMID:18629211
A 4 Mb high resolution BAC contig on bovine chromosome 1q12 and comparative analysis with human chromosome 21q22. PMID:18629192
A computational strategy for protein function assignment which addresses the multidomain problem. PMID:18629055
11th Intelligent Systems for Molecular Biology 2003 (ISMB 2003). PMID:18629025
The characteristics of human genes: analysis of human chromosome 22. PMID:18629020
Definition of the gene content of the human genome: the need for deep experimental verification. PMID:18628909
Upstream - news in genomics. PMID:18628853
Circulating tumor cells in breast cancer: methodology and clinical repercussions. PMID:18628068
A race through the maze of genomic evidence. PMID:18613945
Sequence information encoded in DNA that may influence long-range chromatin structure correlates with human chromosome functions. PMID:18612465
The biological effects of simple tandem repeats: lessons from the repeat expansion diseases. PMID:18593815
Four-color DNA sequencing with 3'-O-modified nucleotide reversible terminators and chemically cleavable fluorescent dideoxynucleotides. PMID:18591653
Clinical, agricultural, and evolutionary biology of myostatin: a comparative review. PMID:18591260
Genetic polymorphisms and endometrial cancer risk. PMID:18588460
Creating and evaluating genetic tests predictive of drug response. PMID:18587383
A robust framework for detecting structural variations in a genome. PMID:18586745
Identifying gene-disease associations using centrality on a literature mined gene-interaction network. PMID:18586725
A model of higher accuracy for the individual haplotyping problem based on weighted SNP fragments and genotype with errors. PMID:18586702
MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries. PMID:18583537
Diverse molecular functions of Hu proteins. PMID:18581050
A physical map of human Alu repeats cleavage by restriction endonucleases. PMID:18578890
Regulation of ABCG2 expression at the 3' untranslated region of its mRNA through modulation of transcript stability and protein translation by a putative microRNA in the S1 colon cancer cell line. PMID:18573883
The principle of recursive genome function. PMID:18566877
Discovery and verification of functional single nucleotide polymorphisms in regulatory genomic regions: current and developing technologies. PMID:18565787
The amphioxus genome illuminates vertebrate origins and cephalochordate biology. PMID:18562680
Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes. PMID:18562677
Meiotic recombination at the ends of chromosomes in Saccharomyces cerevisiae. PMID:18562657
Comparative analyses of human single- and multilocus tandem repeats. PMID:18562644
Conserved footprints of APOBEC3G on Hypermutated human immunodeficiency virus type 1 and human endogenous retrovirus HERV-K(HML2) sequences. PMID:18562517
Evolution of C2H2-zinc finger genes and subfamilies in mammals: species-specific duplication and loss of clusters, genes and effector domains. PMID:18559114
Mitochondria as chi. PMID:18558648
Towards liquid chromatography time-scale peptide sequencing and characterization of post-translational modifications in the negative-ion mode using electron detachment dissociation tandem mass spectrometry. PMID:18555696
L1 mobile element expression causes multiple types of toxicity. PMID:18555620
Molecular cloning and characterization of a novel transcript variant of Mtsarg1 gene. PMID:18551385
Evolution of the hyaluronic acid synthesis (has) operon in Streptococcus zooepidemicus and other pathogenic streptococci. PMID:18551332
CpG dinucleotides and the mutation rate of non-CpG DNA. PMID:18550801
Genomic sequencing of single microbial cells from environmental samples. PMID:18550420
Genomic research and incidental findings. PMID:18547197
Structural basis for the regulation mechanism of the tyrosine kinase CapB from Staphylococcus aureus. PMID:18547145
Hierarchy of nonhomologous end-joining, single-strand annealing and gene conversion at site-directed DNA double-strand breaks. PMID:18539610
Patterns of evolution and host gene mimicry in influenza and other RNA viruses. PMID:18535658
LINE-1 ORF1 protein enhances Alu SINE retrotransposition. PMID:18534786
The Gordon Wilson Lecture: neurohormonal signaling pathways that link cardiac growth and death. PMID:18528498
Dunning rat prostate adenocarcinomas and alternative splicing reporters: powerful tools to study epithelial plasticity in prostate tumors in vivo. PMID:18523850
To gate or not to gate: are the delta subunits in the glutamate receptor family functional ion channels? PMID:18521762
Trans-regulation of the expression of the transcription factor MtHAP2-1 by a uORF controls root nodule development. PMID:18519645
Genome size of termites (Insecta, Dictyoptera, Isoptera) and wood roaches (Insecta, Dictyoptera, Cryptocercidae). PMID:18516576
Human endogenous retrovirus (HERV-K) reverse transcriptase as a breast cancer prognostic marker. PMID:18516289
Uprobe 2008: an online resource for universal overgo hybridization-based probe retrieval and design. PMID:18515352
The current excitement about copy-number variation: how it relates to gene duplications and protein families. PMID:18511261
Genetic susceptibility to cancer: the role of polymorphisms in candidate genes. PMID:18505952
Identification of mutations in Caenorhabditis elegans that cause resistance to high levels of dietary zinc and analysis using a genomewide map of single nucleotide polymorphisms scored by pyrosequencing. PMID:18505880
In silico promoters: modelling of cis-regulatory context facilitates target predictio. PMID:18505473
Mouse segmental duplication and copy number variation. PMID:18500340
Recombinant adeno-associated virus transduction and integration. PMID:18500252
Alu element-mediated gene silencing. PMID:18497743
Targeting the human cancer pathway protein interaction network by structural genomics. PMID:18487680
DiRE: identifying distant regulatory elements of co-expressed genes. PMID:18487623
Fine expression profiling of full-length transcripts using a size-unbiased cDNA library prepared with the vector-capping method. PMID:18487259
Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA. PMID:18485226
Aspects of coverage in medical DNA sequencing. PMID:18485222
Comparative analysis of CpG islands in four fish genomes. PMID:18483567
Loss of genes implicated in gastric function during platypus evolution. PMID:18482448
CpG island density and its correlations with genomic features in mammalian genomes. PMID:18477403
Finishing the finished human chromosome 22 sequence. PMID:18477386
Estimating the size of the human interactome. PMID:18474861
LINE-1 methylation status of endogenous DNA double-strand breaks. PMID:18474527
Discovery and assembly of repeat family pseudomolecules from sparse genomic sequence data using the Assisted Automated Assembler of Repeat Families (AAARF) algorithm. PMID:18474116
The evolution of alternative splicing in the Pax family: the view from the Basal chordate amphioxus. PMID:18473110
A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. PMID:18469162
Bioinformatic analyses of mammalian 5'-UTR sequence properties of mRNAs predicts alternative translation initiation sites. PMID:18466625
Ancestry-related differences in gene expression: findings may enhance understanding of health disparities between populations. PMID:18466094
The impact of recombination on nucleotide substitutions in the human genome. PMID:18464896
Understanding the development of human bladder cancer by using a whole-organ genomic mapping strategy. PMID:18458673
Cis- and trans-splicing of mRNAs mediated by tRNA sequences in eukaryotic cells. PMID:18458335
DXZ4 chromatin adopts an opposing conformation to that of the surrounding chromosome and acquires a novel inactive X-specific role involving CTCF and antisense transcripts. PMID:18456864
Confirming the phylogeny of mammals by use of large comparative sequence data sets. PMID:18453548
Clinical uses of microarrays in cancer research. PMID:18453086
Ethical and social implications of genetic testing for communication disorders. PMID:18452941
A HapMap harvest of insights into the genetics of common disease. PMID:18451988
Personalized genomic medicine with a patchwork, partially owned genome. PMID:18449389
Gene-environment interactions in the development of complex disease phenotypes. PMID:18441400
Genetic determinants of phenotypic diversity in humans. PMID:18439327
Revisiting Wilson and Jungner in the genomic age: a review of screening criteria over the past 40 years. PMID:18438522
Bioinformatics in China: a personal perspective. PMID:18437216
UniPrime: a workflow-based platform for improved universal primer design. PMID:18424794
The family history: reemergence of an established tool. PMID:18424345
Analysis of chimpanzee history based on genome sequence alignments. PMID:18421364
The evolutionary history and tissue mapping of amino acid transporters belonging to solute carrier families SLC32, SLC36, and SLC38. PMID:18418736
Of impact, metrics and ethics. PMID:18414852
A primer on ankyrin repeat function in TRP channels and beyond. PMID:18414734
A scaffold analysis tool using mate-pair information in genome sequencing. PMID:18414585
Selective binding of sterol regulatory element-binding protein isoforms and co-regulatory proteins to promoters for lipid metabolic genes in liver. PMID:18413311
The human ABC transporter pseudogene family: Evidence for transcription and gene-pseudogene interference. PMID:18405356
RNA landscape of evolution for optimal exon and intron discrimination. PMID:18391195
Biogenesis of short intronic repeat 27-nucleotide small RNA from endothelial nitric-oxide synthase gene. PMID:18390539
Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs. PMID:18384671
Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition. PMID:18381897
DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testes. PMID:18381894
Reconstructing phylogenies and phenotypes: a molecular view of human evolution. PMID:18380860
Complex alternative splicing. PMID:18380340
The functional impact of structural variation in humans. PMID:18378036
Losing helena: the extinction of a drosophila line-like element. PMID:18377637
Improved detection of global copy number variation using high density, non-polymorphic oligonucleotide probes. PMID:18373861
Epigenetic regulation of heterochromatic DNA stability. PMID:18372168
Snagger: a user-friendly program for incorporating additional information for tagSNP selection. PMID:18371222
Both selective and neutral processes drive GC content evolution in the human genome. PMID:18371205
Transcriptional profiling uncovers a network of cholesterol-responsive atherosclerosis target genes. PMID:18369455
An abundant evolutionarily conserved CSB-PiggyBac fusion protein expressed in Cockayne syndrome. PMID:18369450
Transposable elements and the evolution of regulatory networks. PMID:18368054
Analysis of repetitive DNA distribution patterns in the Tribolium castaneum genome. PMID:18366801
Alternative splicing of the G protein-coupled receptor superfamily in human airway smooth muscle diversifies the complement of receptors. PMID:18362331
Endogenous retroviruses of the chicken genome. PMID:18361801
Tissue-specific differences in the accumulation of sequence rearrangements with age. PMID:18358792
Integrating global gene expression analysis and genetics. PMID:18358333
Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias. PMID:18356314
Structures, folding patterns, and functions of intramolecular DNA G-quadruplexes found in eukaryotic promoter regions. PMID:18355457
Velvet: algorithms for de novo short read assembly using de Bruijn graphs. PMID:18349386
Genetics and genomics for clinicians. PMID:18349101
An optimized nested polymerase chain reaction (PCR) approach allows detection and characterization of human immunodeficiency virus type 1 (HIV-1) env and gag genes from clinical samples. PMID:18348315
PCR-based detection of Pol III-transcribed transposons and its application to the rodent model of ultraviolet response. PMID:18347948
Comparing whole genomes using DNA microarrays. PMID:18347592
The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates. PMID:18346970
Identification of putative endogenous retroviruses actively transcribed in the brain. PMID:18343986
Genome assembly forensics: finding the elusive mis-assembly. PMID:18341692
Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus. PMID:18340040
Transposition of a reconstructed Harbinger element in human cells and functional homology with two transposon-derived cellular genes. PMID:18339812
Expression of human nPTB is limited by extreme suboptimal codon content. PMID:18335065
Possible involvement of SINEs in mammalian-specific brain formation. PMID:18334644
Multifactorial interplay controls the splicing profile of Alu-derived exons. PMID:18332115
Physiogenomic analysis of localized FMRI brain activity in schizophrenia. PMID:18330705
Mapping of a new autosomal recessive non-syndromic hearing impairment locus (DFNB45) to chromosome 1q43-q44. PMID:18325041
A survey on haplotyping algorithms for tightly linked markers. PMID:18324755
Cross-kingdom patterns of alternative splicing and splice recognition. PMID:18321378
Show me the data. PMID:18320078
RetroPred: A tool for prediction, classification and extraction of non-LTR retrotransposons (LINEs & SINEs) from the genome by integrating PALS, PILER, MEME and ANN. PMID:18317579
A cryptic unstable transcript mediates transcriptional trans-silencing of the Ty1 retrotransposon in S. cerevisiae. PMID:18316478
SPACE: an algorithm to predict and quantify alternatively spliced isoforms using microarrays. PMID:18312629
Term-tissue specific models for prediction of gene ontology biological processes using transcriptional profiles of aging in drosophila melanogaster. PMID:18307794
Distinct genomic signatures of adaptation in pre- and postnatal environments during human evolution. PMID:18305157
The pharmacogenomic era: promise for personalizing attention deficit hyperactivity disorder therapy. PMID:18295157
Transposable elements as drivers of genomic and biological diversity in vertebrates. PMID:18293113
Evolutionarily conserved cytogenetic changes in hematological malignancies of dogs and humans--man and his best friend share more than companionship. PMID:18293109
Recent advances in cotton genomics. PMID:18288253
The progress on genetic analysis of nasopharyngeal carcinoma. PMID:18288251
Deletion of many yeast introns reveals a minority of genes that require splicing for function. PMID:18287520
The use of multiple displacement amplification to amplify complex DNA libraries. PMID:18285362
Conserved themes in small-RNA-mediated transposon control. PMID:18282709
Genomic identification of regulatory elements by evolutionary sequence comparison and functional analysis. PMID:18282510
Alternative splicing of Alu exons--two arms are better than one. PMID:18276646
Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PMID:18271625
Integrase, LEDGF/p75 and HIV replication. PMID:18264802
Human Pso4 is a metnase (SETMAR)-binding partner that regulates metnase function in DNA repair. PMID:18263876
The impact of multiple splice sites in human L1 elements. PMID:18261861
The diversity of retrotransposons and the properties of their reverse transcriptases. PMID:18261821
Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: a somatic view of the germline. PMID:18256234
Nucleoside analogue reverse transcriptase inhibitors differentially inhibit human LINE-1 retrotransposition. PMID:18253495
Mechanisms and consequences of small supernumerary marker chromosomes: from Barbara McClintock to modern genetic-counseling issues. PMID:18252220
Gross deletions involving IGHM, BTK, or Artemis: a model for genomic lesions mediated by transposable elements. PMID:18252213
Clinical pharmacology--providing tools and expertise for translational medicine. PMID:18251756
Molecular imaging in oncology. PMID:18250026
Mechanism of IS200/IS605 family DNA transposases: activation and transposon-directed target site selection. PMID:18243097
Progress in unraveling the genetics of coronary artery disease and myocardial infarction. PMID:18241611
Do Alu repeats drive the evolution of the primate transcriptome? PMID:18241332
Reviews in molecular biology and biotechnology: transmembrane signaling by G protein-coupled receptors. PMID:18240029
E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI). PMID:18230160
High frequency of microsatellites in S. cerevisiae meiotic recombination hotspots. PMID:18226240
Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events. PMID:18225947
Meta-analysis of 23 type 2 diabetes linkage studies from the International Type 2 Diabetes Linkage Analysis Consortium. PMID:18223311
Surprises of the genome and "personalized" medicine. PMID:18222356
Primary T-lymphocytes rescue the replication of HIV-1 DIS RNA mutants in part by facilitating reverse transcription. PMID:18216043
A genome-wide screen for noncoding elements important in primate evolution. PMID:18215302
Human endogenous retrovirus-FRD envelope protein (syncytin 2) expression in normal and trisomy 21-affected placenta. PMID:18215254
LINE-1 family member GCRG123 gene is up-regulated in human gastric signet-ring cell carcinoma. PMID:18205268
BEN: a novel domain in chromatin factors and DNA viral proteins. PMID:18203771
Inherent size constraints on prokaryote gene networks due to "accelerating" growth. PMID:18202872
Loss of LINE-1 activity in the megabats. PMID:18202382
Viruses associated with human cancer. PMID:18201576
LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. PMID:18194517
Suggestive evidence for linkage for restless legs syndrome on chromosome 19p13. PMID:18193462
The Environmental Polymorphisms Registry: a DNA resource to study genetic susceptibility loci. PMID:18193459
The animal in the genome: comparative genomics and evolution. PMID:18192189
Site-specific gene transfer with high efficiency onto a carbon nanotube-loaded electrode. PMID:18192165
Gene Ontology annotation quality analysis in model eukaryotes. PMID:18187504
Genome-wide expression profiles of endogenous retroviruses in lymphoid tissues and their biological properties. PMID:18187179
Core-SINE blocks comprise a large fraction of monotreme genomes; implications for vertebrate chromosome evolution. PMID:18185983
Ultrafast DNA sequencing on a microchip by a hybrid separation mechanism that gives 600 bases in 6.5 minutes. PMID:18184818
Effects of template sequence and secondary structure on DNA-templated reactivity. PMID:18179216
Assessment of programs for ligand binding affinity prediction. PMID:18172838
Show me the data. PMID:18166622
High-resolution mapping of DNA hypermethylation and hypomethylation in lung cancer. PMID:18162535
Discordant evolution of the adjacent antiretroviral genes TRIM22 and TRIM5 in mammals. PMID:18159944
Sources for comparative studies of placentation. II. Genomic resources. PMID:18155141
Alternative approach to a heavy weight problem. PMID:18096750
Maintenance of transposon-free regions throughout vertebrate evolution. PMID:18093339
Literature Lab: a method of automated literature interrogation to infer biology from microarray analysis. PMID:18088408
Gene and genon concept: coding versus regulation. A conceptual and information-theoretic analysis of genetic storage and expression in the light of modern molecular biology. PMID:18087760
Show me the data. PMID:18086910
Show me the data. PMID:18086866
Genome wide screens in yeast to identify potential binding sites and target genes of DNA-binding proteins. PMID:18086703
Virtual screening for the discovery of bioactive natural products. PMID:18084917
ZNF418, a novel human KRAB/C2H2 zinc finger protein, suppresses MAPK signaling pathway. PMID:18084723
Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells. PMID:18084025
Gene number expansion and contraction in vertebrate genomes with respect to invertebrate genomes. PMID:18083775
DA and Xiao-two giant and composite LTR-retrotransposon-like elements identified in the human genome. PMID:18083327
Variable transcriptional activity of endogenous retroviruses in human breast cancer. PMID:18077721
Genomic drift and copy number variation of sensory receptor genes in humans. PMID:18077390
Placental syncytins: Genetic disjunction between the fusogenic and immunosuppressive activity of retroviral envelope proteins. PMID:18077339
DNA transposons and the evolution of eukaryotic genomes. PMID:18076328
Functional endogenous LINE-1 retrotransposons are expressed and mobilized in rat chloroleukemia cells. PMID:18073200
Penalized likelihood for sparse contingency tables with an application to full-length cDNA libraries. PMID:18072965
A syndromic form of autosomal recessive congenital microcephaly (Jawad syndrome) maps to chromosome 18p11.22-q11.2. PMID:18071751
Prediction of protein function improving sequence remote alignment search by a fuzzy logic algorithm. PMID:18066655
Urinary biomarkers in the early diagnosis of acute kidney injury. PMID:18059454
Glia maturation factor overexpression in neuroblastoma cells activates glycogen synthase kinase-3beta and caspase-3. PMID:18054898
The haplo-spliceo-transcriptome: common variations in alternative splicing in the human population. PMID:18054116
Insertional mutagenesis strategies in zebrafish. PMID:18047701
Transposable elements and the dynamic somatic genome. PMID:18047697
Biased exonization of transposed elements in duplicated genes: A lesson from the TIF-IA gene. PMID:18047649
Resolving the fast kinetics of cooperative binding: Ca2+ buffering by calretinin. PMID:18044987
An intronic signal for alternative splicing in the human genome. PMID:18043753
Identification of DNA basepairing via tunnel-current decay. PMID:18041859
Evaluating the protein coding potential of exonized transposable element sequences. PMID:18036258
TEnest: automated chronological annotation and visualization of nested plant transposable elements. PMID:18032588
Impact of genomics on animal agriculture and opportunities for animal health. PMID:18022262
Pre-mRNA secondary structures influence exon recognition. PMID:18020710
The challenges of developing novel antiparasitic drugs. PMID:18004600
Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. PMID:18003932
Ensembl 2008. PMID:18000006
A genomewide association study of skin pigmentation in a South Asian population. PMID:17999355
A paradigm for virus-host coevolution: sequential counter-adaptations between endogenous and exogenous retroviruses. PMID:17997604
T cell responses to human endogenous retroviruses in HIV-1 infection. PMID:17997601
Inferring genome-scale rearrangement phylogeny and ancestral gene order: a Drosophila case study. PMID:17996033
Targeted discovery of novel human exons by comparative genomics. PMID:17989246
TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates. PMID:17986453
SERpredict: detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements. PMID:17986331
Initial sequence and comparative analysis of the cat genome. PMID:17975172
Differential distribution and association of repeat DNA sequences in the lateral element of the synaptonemal complex in rat spermatocytes. PMID:17968579
Role of APOBEC3 in genetic diversity among endogenous murine leukemia viruses. PMID:17967065
Exonization of active mouse L1s: a driver of transcriptome evolution? PMID:17963496
Classification and nomenclature of all human homeobox genes. PMID:17963489
Human PAML browser: a database of positive selection on human genes using phylogenetic methods. PMID:17962310
Copy number variants and common disorders: filling the gaps and exploring complexity in genome-wide association studies. PMID:17953491
Alu recombination-mediated structural deletions in the chimpanzee genome. PMID:17953488
Biased distributions and decay of long interspersed nuclear elements in the chicken genome. PMID:17947446
CFGP: a web-based, comparative fungal genomics platform. PMID:17947331
Short sequence motifs, overrepresented in mammalian conserved non-coding sequences. PMID:17945028
Systematic analysis of alternative first exons in plant genomes. PMID:17941993
A macaque's-eye view of human insertions and deletions: differences in mechanisms. PMID:17941704
Postintegrative gene silencing within the Sleeping Beauty transposition system. PMID:17938204
ADAM15 gene structure and differential alternative exon use in human tissues. PMID:17937806
Unique retrotransposon LINE-1 distribution at the Prader-Willi Angelman syndrome locus. PMID:17932619
Demographic histories of ERV-K in humans, chimpanzees and rhesus monkeys. PMID:17925874
Tripartite chimeric pseudogene from the genome of rice blast fungus Magnaporthe grisea suggests double template jumps during long interspersed nuclear element (LINE) reverse transcription. PMID:17922896
Family expansion and gene rearrangements contributed to the functional specialization of PRDM genes in vertebrates. PMID:17916234
Gel-forming mucins appeared early in metazoan evolution. PMID:17911254
Members of a large retroposon family are determinants of post-transcriptional gene expression in Leishmania. PMID:17907803
Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data. PMID:17907796
Design and implementation of a generalized laboratory data model. PMID:17897463
Dyneins across eukaryotes: a comparative genomic analysis. PMID:17897317
The PDZ domain as a complex adaptive system. PMID:17895993
Information capture using SNPs from HapMap and whole-genome chips differs in a sample of inflammatory and cardiovascular gene-centric regions from genome-wide estimates. PMID:17895426
Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21. PMID:17895424
Reverse polarization in amino acid and nucleotide substitution patterns between human-mouse orthologs of two compositional extrema. PMID:17895298
The Gypsy Database (GyDB) of mobile genetic elements. PMID:17895280
The G protein-coupled receptor subset of the rat genome. PMID:17892602
SAGETTARIUS: a program to reduce the number of tags mapped to multiple transcripts and to plan SAGE sequencing stages. PMID:17884916
Telomeric co-localization of the modified base J and contingency genes in the protozoan parasite Trypanosoma cruzi. PMID:17881368
Sequencing and analyzing the t(1;7) reciprocal translocation breakpoints associated with a case of childhood-onset schizophrenia/autistic disorder. PMID:17879154
Structural parameterization and functional prediction of antigenic polypeptome sequences with biological activity through quantitative sequence-activity models (QSAM) by molecular electronegativity edge-distance vector (VMED). PMID:17879071
Osteopenia in Sparc (osteonectin)-deficient mice: characterization of phenotypic determinants of femoral strength and changes in gene expression. PMID:17878319
OCPAT: an online codon-preserved alignment tool for evolutionary genomic analysis of protein coding sequences. PMID:17877817
Biochemical characterization of a SET and transposase fusion protein, Metnase: its DNA binding and DNA cleavage activity. PMID:17877369
Genetics and genomics: a call for papers. PMID:17875835
Identification of novel candidate genes associated with cleft lip and palate using array comparative genomic hybridisation. PMID:17873121
DNA sequencing: bench to bedside and beyond. PMID:17855400
The random versus fragile breakage models of chromosome evolution: a matter of resolution. PMID:17851692
Dual-specificity splice sites function alternatively as 5' and 3' splice sites. PMID:17848517
End-sequencing and characterization of silkworm (Bombyx mori) bacterial artificial chromosome libraries. PMID:17822570
Regulation of transcription of the RNA splicing factor hSlu7 by Elk-1 and Sp1 affects alternative splicing. PMID:17804646
The diploid genome sequence of an individual human. PMID:17803354
Recognition of HIV-1 peptides by host CTL is related to HIV-1 similarity to human proteins. PMID:17786195
Previously described sequence variant in CDK5RAP2 gene in a Pakistani family with autosomal recessive primary microcephaly. PMID:17764569
Apollo2Go: a web service adapter for the Apollo genome viewer to enable distributed genome annotation. PMID:17760972
Genomics, biogeography, and the diversification of placental mammals. PMID:17728403
Design and evaluation of Actichip, a thematic microarray for the study of the actin cytoskeleton. PMID:17727702
A model of segmental duplication formation in Drosophila melanogaster. PMID:17726166
Tissue-dependent paired expression of miRNAs. PMID:17726050
siRNA-dependent and -independent post-transcriptional cosuppression of the LTR-retrotransposon MAGGY in the phytopathogenic fungus Magnaporthe oryzae. PMID:17726046
Exonization of the LTR transposable elements in human genome. PMID:17725822
Patterns of damage in genomic DNA sequences from a Neandertal. PMID:17715061
Tailor-made zinc-finger transcription factors activate FLO11 gene expression with phenotypic consequences in the yeast Saccharomyces cerevisiae. PMID:17710146
The birth of new exons: mechanisms and evolutionary consequences. PMID:17709368
Assessing the social meaning, value and implications of research in genomics. PMID:17699526
Methods for identifying novel integrin ligands. PMID:17697887
A physical map of the bovine genome. PMID:17697342
SREBP controls oxygen-dependent mobilization of retrotransposons in fission yeast. PMID:17696611
A yeast model for target-primed (non-LTR) retrotransposition. PMID:17683538
Crossregulation and functional redundancy between the splicing regulator PTB and its paralogs nPTB and ROD1. PMID:17679092
Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution. PMID:17675364
Human gene organization driven by the coordination of replication and transcription. PMID:17675363
A periodic pattern of SNPs in the human genome. PMID:17673700
Alternative polyadenylation produces two major transcripts of Alix. PMID:17673164
Genomic biology: the epigenomic era opens. PMID:17671496
Heritability of alternative splicing in the human genome. PMID:17671095
Bird and mammal sex-chromosome orthologs map to the same autosomal region in a salamander (ambystoma). PMID:17660573
Genetic susceptibility to peripheral arterial disease: a dark corner in vascular biology. PMID:17656669
Automated recognition of retroviral sequences in genomic data--RetroTector. PMID:17636050
Effects of recombination rate on human endogenous retrovirus fixation and persistence. PMID:17634225
Evolutionary history of mammalian transposons determined by genome-wide defragmentation. PMID:17630829
A correlation with exon expression approach to identify cis-regulatory elements for tissue-specific alternative splicing. PMID:17626050
Functional persistence of exonized mammalian-wide interspersed repeat elements (MIRs). PMID:17623809
LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss. PMID:17617907
Conservation of transcriptional sensing systems in prokaryotes: a perspective from Escherichia coli. PMID:17617412
Online genetic databases informing human genome epidemiology. PMID:17610726
Analysis of the features and source gene composition of the AluYg6 subfamily of human retrotransposons. PMID:17603915
The potential of high-content high-throughput microscopy in drug discovery. PMID:17603554
Genetics of gestational diabetes mellitus and type 2 diabetes. PMID:17596461
Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome. PMID:17594509
Real-time definition of non-randomness in the distribution of genomic events. PMID:17593969
Rate of recombinational deletion among human endogenous retroviruses. PMID:17581995
A brief review of short tandem repeat mutation. PMID:17572359
Identification of common genetic variation that modulates alternative splicing. PMID:17571926
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. PMID:17571346
The Release 5.1 annotation of Drosophila melanogaster heterochromatin. PMID:17569856
Detection of DNA structural motifs in functional genomic elements. PMID:17568009
Identification of higher-order functional domains in the human ENCODE regions. PMID:17568007
Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas. PMID:17568004
Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. PMID:17568002
Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. PMID:17567994
Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi. PMID:17567986
The human phylome. PMID:17567924
LINE-1 ORF1 protein localizes in stress granules with other RNA-binding proteins, including components of RNA interference RNA-induced silencing complex. PMID:17562864
The Tol1 transposable element of the medaka fish moves in human and mouse cells. PMID:17554475
Glia maturation factor regulation of STAT expression: a novel mechanism in experimental autoimmune encephalomyelitis. PMID:17551829
RTAnalyzer: a web application for finding new retrotransposons and detecting L1 retrotransposition signatures. PMID:17545202
Unravelling the world of cis-regulatory elements. PMID:17541666
High-density single nucleotide polymorphism array analysis in patients with germline deletions of 22q11.2 and malignant rhabdoid tumor. PMID:17541642
The selection of acceptable protein mutations. PMID:17540730
Proteomic analysis of in vivo-assembled pre-mRNA splicing complexes expands the catalog of participating factors. PMID:17537823
Characterization of the sequence specificity of the R1Bm endonuclease domain by structural and biochemical studies. PMID:17537809
Identifying pattern-defined regulatory islands in mammalian genomes. PMID:17535887
Whole-genome sequencing and assembly with high-throughput, short-read technologies. PMID:17534434
Chemogenomic approaches to rational drug design. PMID:17533416
The emergence of alternative 3' and 5' splice site exons from constitutive exons. PMID:17530917
Establishment of high-resolution FISH mapping system and its application for molecular cytogenetic characterization of chromosomes in newt, Cynops pyrrhogaster (Urodela, Amphibia). PMID:17525830
Computational and biological inference of gene regulatory networks of the LINE-1 retrotransposon. PMID:17521869
Comparing segmentations by applying randomization techniques. PMID:17521423
A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database. PMID:17521420
Virtual Northern analysis of the human genome. PMID:17520019
Reducing uncertainty in health-care resource allocation. PMID:17519908
CAG-encoded polyglutamine length polymorphism in the human genome. PMID:17519034
Endonuclease-independent insertion provides an alternative pathway for L1 retrotransposition in the human genome. PMID:17517773
Interchromosomal crossover in human cells is associated with long gene conversion tracts. PMID:17515608
Germline methylation patterns inferred from local nucleotide frequency of repetitive sequences in the human genome. PMID:17514347
Sequencing and association analysis of the type 1 diabetes-linked region on chromosome 10p12-q11. PMID:17509149
Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome. PMID:17506886
Rapid birth-death evolution specific to xenobiotic cytochrome P450 genes in vertebrates. PMID:17500592
In search of polymorphic Alu insertions with restricted geographic distributions. PMID:17498924
Mechanisms controlling production of membrane and secreted immunoglobulin during B cell development. PMID:17496345
Completing the map of human genetic variation. PMID:17495918
Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica. PMID:17495012
An analysis of the gene complement of a marsupial, Monodelphis domestica: evolution of lineage-specific genes and giant chromosomes. PMID:17495010
Symbiosis as an adaptive process and source of phenotypic complexity. PMID:17494762
The neoselectionist theory of genome evolution. PMID:17494746
Methods for estimating human endogenous retrovirus activities from EST databases. PMID:17493249
LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. PMID:17485477
A search engine to identify pathway genes from expression data on multiple organisms. PMID:17477880
A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array. PMID:17477871
Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. PMID:17463089
Mapping of a gene for alopecia with mental retardation syndrome (APMR3) on chromosome 18q11.2-q12.2. PMID:17451405
Regulatory circuit of human microRNA biogenesis. PMID:17447837
Algebraic correction methods for computational assessment of clone overlaps in DNA fingerprint mapping. PMID:17442113
Detecting microsatellites within genomes: significant variation among algorithms. PMID:17442102
All APOBEC3 family proteins differentially inhibit LINE-1 retrotransposition. PMID:17439959
Origin and evolution of human microRNAs from transposable elements. PMID:17435244
A recombineering based approach for high-throughput conditional knockout targeting vector construction. PMID:17426124
A kingdom-specific protein domain HMM library for improved annotation of fungal genomes. PMID:17425790
Gene expression profiles differentiate between sterile SIRS and early sepsis. PMID:17414611
From genes to functional classes in the study of biological systems. PMID:17407596
A new platform linking chromosomal and sequence information. PMID:17406992
Recent integrations of mammalian Hmg retropseudogenes. PMID:17406091
Ancient lentiviruses leave their mark. PMID:17404211
The ancient mariner sails again: transposition of the human Hsmar1 element by a reconstructed transposase and activities of the SETMAR protein on transposon ends. PMID:17403897
Online resources for SNP analysis: a review and route map. PMID:17401150
Impact of pharmacogenomics on clinical practice in oncology. PMID:17397243
Recurrent DNA inversion rearrangements in the human genome. PMID:17389356
Transcript specificity in yeast pre-mRNA splicing revealed by mutations in core spliceosomal components. PMID:17388687
Genetic resources, genome mapping and evolutionary genomics of the pig (Sus scrofa). PMID:17384734
Discovery and analysis of the first endogenous lentivirus. PMID:17384150
Hyperconserved CpG domains underlie Polycomb-binding sites. PMID:17376869
Non-random genomic divergence in repetitive sequences of human and chimpanzee in genes of different functional categories. PMID:17375324
Natural epigenetic protection against the I-factor, a Drosophila LINE retrotransposon, by remnants of ancestral invasions. PMID:17375190
Nonnatural protein-protein interaction-pair design by key residues grafting. PMID:17372228
Non-coding sequence retrieval system for comparative genomic analysis of gene regulatory elements. PMID:17362514
Physical and functional interactions of human endogenous retrovirus proteins Np9 and rec with the promyelocytic leukemia zinc finger protein. PMID:17360752
A comparative genomics approach to identifying the plasticity transcriptome. PMID:17355637
Genome-wide identification of spliced introns using a tiling microarray. PMID:17351133
Hawkeye: an interactive visual analytics tool for genome assemblies. PMID:17349036
A summer program designed to educate college students for careers in bioinformatics. PMID:17339396
The evolutionary history of human DNA transposons: evidence for intense activity in the primate lineage. PMID:17339369
A mutation in the lipase H (LIPH) gene underlie autosomal recessive hypotrichosis. PMID:17333281
A comprehensive crop genome research project: the Superhybrid Rice Genome Project in China. PMID:17331896
Life sciences and biotechnology in China. PMID:17331895
Analysis of phenotype-genotype connection: the story of dissecting disease pathogenesis in genomic era in China, and beyond. PMID:17327209
RNA-editing-mediated exon evolution. PMID:17326827
Conserved and novel Wnt clusters in the basal eumetazoan Nematostella vectensis. PMID:17310352
Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome. PMID:17307883
Molecular evolution of the ependymin protein family: a necessary update. PMID:17302986
In silico identification of NF-kappaB-regulated genes in pancreatic beta-cells. PMID:17302974
A family of human microRNA genes from miniature inverted-repeat transposable elements. PMID:17301878
Copy-number variations add a new layer of complexity in the human genome. PMID:17296953
Mapping of transcription start sites of human retina expressed genes. PMID:17286855
Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization. PMID:17284678
Expression and phylogenetic analyses of human endogenous retrovirus HC2 belonging to the HERV-T family in human tissues and cancer cells. PMID:17277898
The flamenco locus controls the gypsy and ZAM retroviruses and is required for Drosophila oogenesis. PMID:17277359
Enhancer identification through comparative genomics. PMID:17276707
Genome re-annotation: a wiki solution? PMID:17274839
Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans. PMID:17274809
Transition-transversion bias is not universal: a counter example from grasshopper pseudogenes. PMID:17274688
Large-scale identification of novel transcripts in the human genome. PMID:17267814
A mobile element-based evolutionary history of guenons (tribe Cercopithecini). PMID:17266768
Considerations in the identification of functional RNA structural elements in genomic alignments. PMID:17263882
Massive amplification of rolling-circle transposons in the lineage of the bat Myotis lucifugus. PMID:17261799
Reconstitution of an infectious human endogenous retrovirus. PMID:17257061
Splice site identification using probabilistic parameters and SVM classification. PMID:17254299
Haploinsufficiency of the SERPINA6 gene is associated with severe muscle fatigue: A de novo mutation in corticosteroid-binding globulin deficiency. PMID:17245537
Evolutionary history of LINE-1 in the major clades of placental mammals. PMID:17225861
Repeated recruitment of LTR retrotransposons as promoters by the anti-apoptotic locus NAIP during mammalian evolution. PMID:17222062
Retrotransposons and tandem repeat sequences in the nuclear genomes of cryptomonad algae. PMID:17211547
Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. PMID:17210932
A tale of two templates: automatically resolving double traces has many applications, including efficient PCR-based elucidation of alternative splices. PMID:17210930
Biomphalaria glabrata transcriptome: identification of cell-signalling, transcriptional control and immune-related genes from open reading frame expressed sequence tags (ORESTES). PMID:17208299
hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. PMID:17207965
Frequent but borderline methylation of p16 (INK4a) and TIMP3 in medulloblastoma and sPNET revealed by quantitative analyses. PMID:17206475
Genetic diversity of 10 X chromosome STRs in northern Portugal. PMID:17206433
Intron dynamics in ribosomal protein genes. PMID:17206276
SNPSTR: a database of compound microsatellite-SNP markers. PMID:17202172
New developments in the InterPro database. PMID:17202162
The prokineticins: a novel pair of regulatory peptides. PMID:17200460
Comparative genomic analysis of prion genes. PMID:17199895
Tissue-specific differences in human transfer RNA expression. PMID:17194224
Assignment of the gene locus for severe congenital neutropenia to chromosome 1q22 in the original Kostmann family from Northern Sweden. PMID:17188649
High performance computing in biology: multimillion atom simulations of nanoscale systems. PMID:17187988
How repetitive are genomes? PMID:17187668
Evidence for large inversion polymorphisms in the human genome from HapMap data. PMID:17185644
Gene function and expression level influence the insertion/fixation dynamics of distinct transposon families in mammalian introns. PMID:17181857
Analyzing the cardiac muscle proteome by liquid chromatography-mass spectrometry-based expression proteomics. PMID:17172675
DNA cleavage and Trp53 differentially affect SINE transcription. PMID:17171681
Noncoding RNAs database (ncRNAdb). PMID:17169980
Directionality of point mutation and 5-methylcytosine deamination rates in the chimpanzee genome. PMID:17166280
Evolution of secretin family GPCR members in the metazoa. PMID:17166275
Genomic selective constraints in murid noncoding DNA. PMID:17166057
Selection of target sites for mobile DNA integration in the human genome. PMID:17166054
Searching for sequence directed mutagenesis in eukaryotes. PMID:17160648
Different levels of alternative splicing among eukaryotes. PMID:17158149
Inviting instability: Transposable elements, double-strand breaks, and the maintenance of genome integrity. PMID:17157332
Mammalian small nucleolar RNAs are mobile genetic elements. PMID:17154719
Murine MusD retrotransposon: structure and molecular evolution of an "intracellularized" retrovirus. PMID:17151128
Variation resources at UC Santa Cruz. PMID:17151077
PReMod: a database of genome-wide mammalian cis-regulatory module predictions. PMID:17148480
HIGM syndrome caused by insertion of an AluYb8 element in exon 1 of the CD40LG gene. PMID:17146684
Transgenic analysis of Dlx regulation in fish tooth development reveals evolutionary retention of enhancer function despite organ loss. PMID:17146045
Cell divisions are required for L1 retrotransposition. PMID:17145770
Selection and cloning of poly(rC)-binding protein 2 and Raf kinase inhibitor protein RNA activators of 2',5'-oligoadenylate synthetase from prostate cancer cells. PMID:17145707
Repetitive sequence environment distinguishes housekeeping genes. PMID:17141428
Novel porcine repetitive elements. PMID:17140439
[Schizophrenia, human genetics and genetic counselling. Human genetic counselling as part of the psychiatric/psychotherapeutic treatment concept]. PMID:17139521
Improved repeat identification and masking in Dipterans. PMID:17137733
Characterization of the short RNAs bound by the P19 suppressor of RNA silencing in mouse embryonic stem cells. PMID:17135486
Characteristics, causes and evolutionary consequences of male-biased mutation. PMID:17134994
What makes us human: revisiting an age-old question in the genomic era. PMID:17134487
Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome. PMID:17134480
Pharmacogenetics and diseases of the colon. PMID:17133087
Both sense and antisense strands of the LTR of the Schistosoma mansoni Pao-like retrotransposon Sinbad drive luciferase expression. PMID:17131159
The human SETMAR protein preserves most of the activities of the ancestral Hsmar1 transposase. PMID:17130240
VISTA Enhancer Browser--a database of tissue-specific human enhancers. PMID:17130149
Animal models for the study of tendinopathy. PMID:17127722
Phylogenetic analysis of RhoGAP domain-containing proteins. PMID:17127216
Active retrotransposition by a synthetic L1 element in mice. PMID:17124176
Display technologies: application for the discovery of drug and gene delivery agents. PMID:17123658
Accurate and reliable high-throughput detection of copy number variation in the human genome. PMID:17122085
Koala retrovirus: a genome invasion in real time. PMID:17118218
Genome assembly comparison identifies structural variants in the human genome. PMID:17115057
miRGen: a database for the study of animal microRNA genomic organization and function. PMID:17108354
Ectodermal dysplasia of hair and nail type: mapping of a novel locus to chromosome 17p12-q21.2. PMID:17107387
RNA from the 5' end of the R2 retrotransposon controls R2 protein binding to and cleavage of its DNA target site. PMID:17105809
Emergence of primate genes by retrotransposon-mediated sequence transduction. PMID:17101974
Transposon insertion site profiling chip (TIP-chip). PMID:17101968
BAC clones generated from sheared DNA. PMID:17098394
Asymptotically increasing compliance of genomes with Chargaff's second parity rules through inversions and inverted transpositions. PMID:17093051
The frequency of eubacterium-to-eukaryote lateral gene transfers shows significant cross-taxa variation within amoebozoa. PMID:17086451
Induction of antioxidant and detoxification response by oxidants in cardiomyocytes: evidence from gene expression profiling and activation of Nrf2 transcription factor. PMID:17081560
Selective inhibition of Alu retrotransposition by APOBEC3G. PMID:17079095
DNA methylation profiling of human chromosomes 6, 20 and 22. PMID:17072317
Functional characterization of the promoter for the mouse SPTLC2 gene, which encodes subunit 2 of serine palmitoyltransferase. PMID:17070807
Similar compositional biases are caused by very different mutational effects. PMID:17068325
Characterization of pre-insertion loci of de novo L1 insertions. PMID:17067767
Amplification of histone genes by circular chromosome formation in Saccharomyces cerevisiae. PMID:17066037
Assessing the number of ancestral alternatively spliced exons in the human genome. PMID:17062157
Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation. PMID:17059607
The rate, not the spectrum, of base pair substitutions changes at a GC-content transition in the human NF1 gene region: implications for the evolution of the mammalian genome structure. PMID:17057231
Different evolutionary fates of recently integrated human and chimpanzee LINE-1 retrotransposons. PMID:17055192
The influence of recombination on human genetic diversity. PMID:17044736
At least 50% of human-specific HERV-K (HML-2) long terminal repeats serve in vivo as active promoters for host nonrepetitive DNA transcription. PMID:17041225
Identification of insertion hot spots for non-LTR retrotransposons: computational and biochemical application to Entamoeba histolytica. PMID:17040894
Molecular characterization and genomic distribution of Isis: a new retrotransposon of Drosophila buzzatii. PMID:17039376
Human heterochromatin proteins form large domains containing KRAB-ZNF genes. PMID:17038565
ATM and ATR pathways signal alternative splicing of Drosophila TAF1 pre-mRNA in response to DNA damage. PMID:17030624
Design factors that influence PCR amplification success of cross-species primers among 1147 mammalian primer pairs. PMID:17029642
Heterogeneous genomic molecular clocks in primates. PMID:17029560
Testing chromosomal phylogenies and inversion breakpoint reuse in Drosophila. PMID:17028333
The transposable element landscape of the model legume Lotus japonicus. PMID:17028332
Alu elements as regulators of gene expression. PMID:17020921
The piggyBac transposon holds promise for human gene therapy. PMID:17015820
Generation Scotland: the Scottish Family Health Study; a new resource for researching genes and heritability. PMID:17014726
Gene mutations and genomic rearrangements in the mouse as a result of transposon mobilization from chromosomal concatemers. PMID:17009875
Phylogenetic reconstruction of orthology, paralogy, and conserved synteny for dog and human. PMID:17009864
piggyBac is a flexible and highly active transposon as compared to sleeping beauty, Tol2, and Mos1 in mammalian cells. PMID:17005721
Multiple effects govern endogenous retrovirus survival patterns in human gene introns. PMID:17005047
Comparative sequence analysis reveals an intricate network among REST, CREB and miRNA in mediating neuronal gene expression. PMID:17002790
Current concepts in neuroendocrine cancer metabolism. PMID:17001465
Solution structure and functional importance of a conserved RNA hairpin of eel LINE UnaL2. PMID:17000640
A path or a new road in laboratory diagnostics? Biological mass spectrometry: facts and perspectives. PMID:16998599
Reconstructing contiguous regions of an ancestral genome. PMID:16983148
Spatial organization of transcription by RNA polymerase III. PMID:16971453
A high-throughput method for cloning and sequencing human immunodeficiency virus type 1 integration sites. PMID:16971446
Large-scale intron conservation and order-of-magnitude variation in intron loss/gain rates in apicomplexan evolution. PMID:16963708
Molecular approaches in the diagnosis of primary immunodeficiency diseases. PMID:16960849
The distribution of L1 and Alu retroelements in relation to GC content on human sex chromosomes is consistent with the ectopic recombination model. PMID:16955238
The KAP1 corepressor functions to coordinate the assembly of de novo HP1-demarcated microenvironments of heterochromatin required for KRAB zinc finger protein-mediated transcriptional repression. PMID:16954381
Isochores exhibit evidence of genes interacting with the large-scale genomic environment. PMID:16951086
Systematic identification of pseudogenes through whole genome expression evidence profiling. PMID:16945953
Detection of a gypsy-like sequence in the genome of the cat flea Ctenocephalides felis (Bouché 1835). PMID:16941190
RNA editing level in the mouse is determined by the genomic repeat repertoire. PMID:16940548
In vivo requirement of the small subunit of U2AF for recognition of a weak 3' splice site. PMID:16940179
Gene order data from a model amphibian (Ambystoma): new perspectives on vertebrate genome structure and evolution. PMID:16939647
Comparison of multiple vertebrate genomes reveals the birth and evolution of human exons. PMID:16938881
Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA. PMID:16938852
Genetics and proteomics: deciphering gene association studies in critical illness. PMID:16934133
EGASP: the human ENCODE Genome Annotation Assessment Project. PMID:16925836
A novel locus for alopecia with mental retardation syndrome (APMR2) maps to chromosome 3q26.2-q26.31. PMID:16922726
Complex minisatellite rearrangements generated in the total or partial absence of Rad27/hFEN1 activity occur in a single generation and are Rad51 and Rad52 dependent. PMID:16914748
Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs. PMID:16914452
Comprehensive splice-site analysis using comparative genomics. PMID:16914448
Gene function correlates with potential for G4 DNA formation in the human genome. PMID:16914419
Conservative repair of a chromosomal double-strand break by single-strand DNA through two steps of annealing. PMID:16908537
Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication. PMID:16899447
Radiation hybrid map of the porcine genome comprising 2035 EST loci. PMID:16897346
Matrix-assisted laser desorption/ionisation, time-of-flight mass spectrometry in genomics research. PMID:16895448
Population genetics models of competition between transposable element subfamilies. PMID:16888345
Single nucleotide polymorphisms and breast cancer: not yet a success story. PMID:16887007
High-resolution comparative mapping among man, cattle and mouse suggests a role for repeat sequences in mammalian genome evolution. PMID:16882342
L1 retrotransposons in human cancers. PMID:16877821
The genomic distribution of L1 elements: the role of insertion bias and natural selection. PMID:16877820
L1 antisense promoter drives tissue-specific transcription of human genes. PMID:16877819
LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease: mutation detection bias and multiple mechanisms of target gene disruption. PMID:16877817
The potential regulation of L1 mobility by RNA interference. PMID:16877813
Links between repeated sequences. PMID:16877810
Obesity and its therapy: from genes to community action. PMID:16873005
Ubl4b, an X-derived retrogene, is specifically expressed in post-meiotic germ cells in mammals. PMID:16872915
PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs. PMID:16872538
A critical beta6-beta7 loop in the pleckstrin homology domain of ceramide kinase. PMID:16872273
MicroRNA and 3T3-L1 pre-adipocyte differentiation. PMID:16870994
Phylogenetically widespread alternative splicing at unusual GYNGYN donors. PMID:16869967
The cnidarian-bilaterian ancestor possessed at least 56 homeoboxes: evidence from the starlet sea anemone, Nematostella vectensis. PMID:16867185
From functional genomics to functional immunomics: new challenges, old problems, big rewards. PMID:16863395
Free-energy distribution of binary protein-protein binding suggests cross-species interactome differences. PMID:16861299
The complexity of the mammalian transcriptome. PMID:16857706
Transposable element derived DNaseI-hypersensitive sites in the human genome. PMID:16857058
Computational identification of transcriptional regulatory elements in DNA sequence. PMID:16855295
AUG sequences are required to sustain nonsense-codon-mediated suppression of splicing. PMID:16855285
Strategies for the detection of copy number and other structural variants in the human genome. PMID:16848978
Neuropeptide B and W: neurotransmitters in an emerging G-protein-coupled receptor system. PMID:16847439
Identification and analysis of genes and pseudogenes within duplicated regions in the human and mouse genomes. PMID:16846249
Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information. PMID:16845118
Integration of human immunodeficiency virus type 1 in untreated infection occurs preferentially within genes. PMID:16840357
Genomic sites of human immunodeficiency virus type 2 (HIV-2) integration: similarities to HIV-1 in vitro and possible differences in vivo. PMID:16840312
Structure function analysis of SH2D2A isoforms expressed in T cells reveals a crucial role for the proline rich region encoded by SH2D2A exon 7. PMID:16839418
Systematic analysis of head-to-head gene organization: evolutionary conservation and potential biological relevance. PMID:16839196
Curation of complex, context-dependent immunological data. PMID:16836764
U1-like snRNAs lacking complementarity to canonical 5' splice sites. PMID:16829670
Analysing the developing brain transcriptome with the GenePaint platform. PMID:16825306
The L1 retrotranspositional stimulation by particulate and soluble cadmium exposure is independent of the generation of DNA breaks. PMID:16823085
Epigenetic regulation of the rice retrotransposon Tos17. PMID:16821043
Array-CGH and breast cancer. PMID:16817944
Introns regulate RNA and protein abundance in yeast. PMID:16816425
Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses. PMID:16805923
Comparative genomic analysis links karyotypic evolution with genomic evolution in the Indian muntjac (Muntiacus muntjak vaginalis). PMID:16791631
The evolution of mobile DNAs: when will transposons create phylogenies that look as if there is a master gene? PMID:16790583
Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions. PMID:16785431
Essential domains for ribonucleoprotein complex formation required for retrotransposition of telomere-specific non-long terminal repeat retrotransposon SART1. PMID:16782900
Activation of the nonreceptor protein tyrosine kinase Ack by multiple extracellular stimuli. PMID:16777958
Effects of random mutations in the human immunodeficiency virus type 1 transcriptional promoter on viral fitness in different host cell environments. PMID:16775355
Intra- and interindividual epigenetic variation in human germ cells. PMID:16773567
Human genomic deletions mediated by recombination between Alu elements. PMID:16773564
Evidence for variation in abundance of antisense transcripts between multicellular animals but no relationship between antisense transcriptionand organismic complexity. PMID:16769979
Fitness cost of LINE-1 (L1) activity in humans. PMID:16766655
Impact of diets and nutrients/drugs on early epigenetic programming. PMID:16763902
Amphioxus: a peaceful anchovy fillet to illuminate Chordate Evolution (II). PMID:16763667
MCALIGN2: faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution. PMID:16762073
Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences. PMID:16759380
GMF-knockout mice are unable to induce brain-derived neurotrophic factor after exercise. PMID:16758368
Remarkably high activities of testicular cytochrome c in destroying reactive oxygen species and in triggering apoptosis. PMID:16757556
LINE FUSION GENES: a database of LINE expression in human genes. PMID:16756682
The GC content of primates and rodents genomes is not at equilibrium: a reply to Antezana. PMID:16752218
GC content evolution of the human and mouse genomes: insights from the study of processed pseudogenes in regions of different recombination rates. PMID:16752212
Apical sodium dependent bile acid transporter (ASBT, SLC10A2): a potential prodrug target. PMID:16749855
The G protein-coupled receptor subset of the chicken genome. PMID:16741557
Physical map-assisted whole-genome shotgun sequence assemblies. PMID:16741162
Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes. PMID:16740159
Pathogenesis and vertical transmission of a transplacental rat cytomegalovirus. PMID:16737550
The jewels of our genome: the search for the genomic changes underlying the evolutionarily unique capacities of the human brain. PMID:16733552
Protein family expansions and biological complexity. PMID:16733546
Identification and characterisation of five novel miniature inverted-repeat transposable elements (MITEs) in amphioxus (Branchiostoma floridae). PMID:16733534
Getting closer to a pre-vertebrate genome: the non-LTR retrotransposons of Branchiostoma floridae. PMID:16733533
Synthetic protein-protein interaction domains created by shuffling Cys2His2 zinc-fingers. PMID:16732192
Cellular inhibitors of long interspersed element 1 and Alu retrotransposition. PMID:16728505
HapMap, pharmacogenomics, and the goal of personalized prescribing. PMID:16722846
Imaging biomarkers as surrogate endpoints for drug development. PMID:16721568
Zinc binding to a regulatory zinc-sensing domain monitored in vivo by using FRET. PMID:16720702
Phenotypic characterization of DFNA24: prelingual progressive sensorineural hearing impairment. PMID:16717440
Functional noncoding sequences derived from SINEs in the mammalian genome. PMID:16717141
Evolution of small nucleolar RNAs in nematodes. PMID:16714446
Evolutionary tinkering with transposable elements. PMID:16705033
DFNB68, a novel autosomal recessive non-syndromic hearing impairment locus at chromosomal region 19p13.2. PMID:16703383
GREM, a technique for genome-wide isolation and quantitative analysis of promoter active repeats. PMID:16698959
Overview of the structure of all-AT oligonucleotides: organization in helices and packing interactions. PMID:16698788
Saccharomyces cerevisiae: a useful model host to study fundamental biology of viral replication. PMID:16698107
Identification and characterization of piggyBac-like elements in the genome of domesticated silkworm, Bombyx mori. PMID:16685528
Genome Network and FANTOM3: assessing the complexity of the transcriptome. PMID:16683037
A simple physical model predicts small exon length variations. PMID:16683028
Heterotachy in mammalian promoter evolution. PMID:16683025
Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome. PMID:16683019
ASEtrap: a biological method for speeding up the exploration of spliceomes. PMID:16682744
Alu RNP and Alu RNA regulate translation initiation in vitro. PMID:16682445
Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing. PMID:16682442
Birth of a chimeric primate gene by capture of the transposase gene from a mobile element. PMID:16672366
New strategies in drug discovery. PMID:16671397
Human LINE-1 retrotransposon induces DNA damage and apoptosis in cancer cells. PMID:16670018
The mapping of DFNB62, a new locus for autosomal recessive non-syndromic hearing impairment, to chromosome 12p13.2-p11.23. PMID:16650082
Microfabricated bioprocessor for integrated nanoliter-scale Sanger DNA sequencing. PMID:16648246
Genomic platforms for cancer research: potential diagnostic and prognostic applications in clinical oncology. PMID:16648115
Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data. PMID:16643658
Weak selection and recent mutational changes influence polymorphic synonymous mutations in humans. PMID:16632609
Comparative genomics of the syndecans defines an ancestral genomic context associated with matrilins in vertebrates. PMID:16620374
Archaeology and evolution of transfer RNA genes in the Escherichia coli genome. PMID:16618964
Extensive individual variation in L1 retrotransposition capability contributes to human genetic diversity. PMID:16618923
Molecular evolution of the periphilin gene in relation to human endogenous retrovirus m element. PMID:16612547
Newly identified families of human endogenous retroviruses. PMID:16611924
Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. PMID:16606704
A comprehensive catalog of human KRAB-associated zinc finger genes: insights into the evolutionary history of a large family of transcriptional repressors. PMID:16606702
An isochore map of human chromosomes. PMID:16597586
Localization of a novel autosomal recessive nonsyndromic hearing impairment locus DFNB65 to chromosome 20q13.2-q13.32. PMID:16596430
Locked nucleic acid: high-affinity targeting of complementary RNA for RNomics. PMID:16594628
Genetic factors in the predisposition to drug-induced hypersensitivity reactions. PMID:16584129
The effects of mismatch repair and RAD1 genes on interchromosomal crossover recombination in Saccharomyces cerevisiae. PMID:16582436
The independence of our genome assemblies. PMID:16576752
Extensive adenosine-to-inosine editing detected in Alu repeats of antisense RNAs reveals scarcity of sense-antisense duplex formation. PMID:16574103
Protein secondary structure prediction for a single-sequence using hidden semi-Markov models. PMID:16571137
The enigmatic nature of apocrine breast lesions. PMID:16570182
Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions. PMID:16566817
Evolutionary basis of codon usage and nucleotide composition bias in vertebrate DNA viruses. PMID:16557338
LINE-1 RNA splicing and influences on mammalian gene expression. PMID:16554555
Multiplex degenerate PCR coupled with an oligo sorbent array for human endogenous retrovirus expression profiling. PMID:16554552
Detection of 100% of mutations in 124 individuals using a standard UV/Vis microplate reader: a novel concept for mutation scanning. PMID:16554551
The temporal program of DNA replication: new insights into old questions. PMID:16552593
Multiple lineage specific expansions within the guanylyl cyclase gene family. PMID:16549024
Development of an unbiased statistical method for the analysis of unigenic evolution. PMID:16545116
cDNA-based gene mapping and GC3 profiling in the soft-shelled turtle suggest a chromosomal size-dependent GC bias shared by sauropsids. PMID:16544192
Distribution of L1-retroposons on the giant sex chromosomes of Microtus cabrerae (Arvicolidae, Rodentia): functional and evolutionary implications. PMID:16544191
A third approach to gene prediction suggests thousands of additional human transcribed regions. PMID:16543943
The 3of5 web application for complex and comprehensive pattern matching in protein sequences. PMID:16542452
Identification and characterization of the CDK12/cyclin L1 complex involved in alternative splicing regulation. PMID:16537916
Cotranscriptional recognition of human intronic box H/ACA snoRNAs occurs in a splicing-independent manner. PMID:16537900
Dual inhibitory effects of APOBEC family proteins on retrotransposition of mammalian endogenous retroviruses. PMID:16537839
Modulation of poliovirus replicative fitness in HeLa cells by deoptimization of synonymous codon usage in the capsid region. PMID:16537593
Identification of a genetic cluster influencing memory performance and hippocampal activity in humans. PMID:16537520
Identification of proangiogenic genes and pathways by high-throughput functional genomics: TBK1 and the IRF3 pathway. PMID:16537515
Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat. PMID:16536879
Word frequency analysis reveals enrichment of dinucleotide repeats on the human X chromosome and [GATA]n in the X escape region. PMID:16533911
Recently mobilized transposons in the human and chimpanzee genomes. PMID:16532396
Biases and reconciliation in estimates of linkage disequilibrium in the human genome. PMID:16532390
A mutation in the hair matrix and cuticle keratin KRTHB5 gene causes ectodermal dysplasia of hair and nail type. PMID:16525032
Mutations of the Drosophila zinc finger-encoding gene vielfältig impair mitotic cell divisions and cause improper chromosome segregation. PMID:16525017
From genomes to systems: the path with yeast. PMID:16524836
Crystal structure of Homo sapiens PTD012 reveals a zinc-containing hydrolase fold. PMID:16522806
CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure. PMID:16520826
Large-scale mutagenesis and phenotypic screens for the nervous system and behavior in mice. PMID:16519954
Modification of the Creator recombination system for proteomics applications--improved expression by addition of splice sites. PMID:16519801
Genome size and metabolic intensity in tetrapods: a tale of two lines. PMID:16519230
Ancient retroviral insertions among human populations. PMID:16518567
Large-scale trends in the evolution of gene structures within 11 animal genomes. PMID:16518452
An isoform of ZBP-89 predisposes the colon to colitis. PMID:16517939
Multistep microsatellite mutation in the maternally transmitted locus D13S317: a case of maternal allele mismatch in the child. PMID:16514543
Breakpoint Associated with a novel 2.3 Mb deletion in the VCFS region of 22q11 and the role of Alu (SINE) in recurring microdeletions. PMID:16512914
dbRIP: a highly integrated database of retrotransposon insertion polymorphisms in humans. PMID:16511833
The expanding transcriptome: the genome as the 'Book of Sand'. PMID:16511566
A reliable method to display authentic DNase I hypersensitive sites at long-ranges in single-copy genes from large genomes. PMID:16510851
SinicView: a visualization environment for comparisons of multiple nucleotide sequence alignment tools. PMID:16509994
Gamma radiation increases endonuclease-dependent L1 retrotransposition in a cultured cell assay. PMID:16507671
Methylation-free site patterns along a 1-Mb locus on Chr19 in cancerous and normal cells are similar. A new fast approach for analyzing unmethylated CCGG sites distribution. PMID:16501994
The fragile breakage versus random breakage models of chromosome evolution. PMID:16501665
The role of inflammation in the pathogenesis of age-related macular degeneration. PMID:16500214
Mutational analysis of human eIF4AIII identifies regions necessary for exon junction complex formation and nonsense-mediated mRNA decay. PMID:16495234
The human LINE-1 retrotransposon creates DNA double-strand breaks. PMID:16490214
High-throughput isolation of ultra-pure plasmid DNA by a robotic system. PMID:16483377
Bias of selection on human copy-number variants. PMID:16482228
A "holistic" kinesin phylogeny reveals new kinesin families and predicts protein functions. PMID:16481395
Permissive transcriptional activity at the centromere through pockets of DNA hypomethylation. PMID:16477312
A large family of ancient repeat elements in the human genome is under strong selection. PMID:16477033
Gene losses during human origins. PMID:16464126
Features of Arabidopsis genes and genome discovered using full-length cDNAs. PMID:16463100
Decoding the fine-scale structure of a breast cancer genome and transcriptome. PMID:16461635
Immunogenomics: molecular hide and seek. PMID:16460649
Mobilization of RAG-generated signal ends by transposition and insertion in vivo. PMID:16449665
Transposable elements have contributed to thousands of human proteins. PMID:16443682
Retroviral elements and their hosts: insertional mutagenesis in the mouse germ line. PMID:16440055
Human immunodeficiency virus type 1 incorporated with fusion proteins consisting of integrase and the designed polydactyl zinc finger protein E2C can bias integration of viral DNA into a predetermined chromosomal region in human cells. PMID:16439549
Genomic fossils as a snapshot of the human transcriptome. PMID:16432206
A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. PMID:16432200
Teaching an old dog new tricks: SINEs of canine genomic diversity. PMID:16432182
Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration. PMID:16426464
Distribution of human SNPs and its effect on high-throughput genotyping. PMID:16425292
Unconventional translation of mammalian LINE-1 retrotransposons. PMID:16418485
Genome-scale identification of membrane-associated human mRNAs. PMID:16415983
Divergent patterns of recent retroviral integrations in the human and chimpanzee genomes: probable transmissions between other primates and chimpanzees. PMID:16415014
The Epc-N domain: a predicted protein-protein interaction domain found in select chromatin associated proteins. PMID:16412250
The mariner transposons belonging to the irritans subfamily were maintained in chordate genomes by vertical transmission. PMID:16408242
The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA. PMID:16407334
Intronic binding sites for hnRNP A/B and hnRNP F/H proteins stimulate pre-mRNA splicing. PMID:16396608
Differential exoprotease activities confer tumor-specific serum peptidome patterns. PMID:16395409
Genomewide comparative analysis of the highly abundant transposable element DINE-1 suggests a recent transpositional burst in Drosophila yakuba. PMID:16387876
MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data. PMID:16381984
HOLLYWOOD: a comparative relational database of alternative splicing. PMID:16381932
Recombination, rearrangement, reshuffling, and divergence in a centromeric region of rice. PMID:16381819
Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms. PMID:16376498
A computational screen for mammalian pseudouridylation guide H/ACA RNAs. PMID:16373490
Transposon-free regions in mammalian genomes. PMID:16365385
L1 integration in a transgenic mouse model. PMID:16365384
Large-scale structure of genomic methylation patterns. PMID:16365381
A genome-wide study of dual coding regions in human alternatively spliced genes. PMID:16365380
A novel method distinguishes between mutation rates and fixation biases in patterns of single-nucleotide substitution. PMID:16362483
Selective constraint on noncoding regions of hominid genomes. PMID:16362073
Splicing regulators: targets and drugs. PMID:16356274
Transcription-mediated gene fusion in the human genome. PMID:16344562
Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. PMID:16344560
Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates. PMID:16344559
A high-resolution whole-genome cattle-human comparative map reveals details of mammalian chromosome evolution. PMID:16339895
Structure and architecture of the maize genome. PMID:16339807
Short interspersed elements (SINEs) are a major source of canine genomic diversity. PMID:16339378
Hotspots of mutation and breakage in dog and human chromosomes. PMID:16339377
SNP-VISTA: an interactive SNP visualization tool. PMID:16336665
Engineered human dicentric chromosomes show centromere plasticity. PMID:16331407
Divergent non-LTR retrotransposon lineages from the genomes of scorpions (Arachnida: Scorpiones). PMID:16328371
Analysis of repetitive element DNA methylation by MethyLight. PMID:16326863
The "impact factor" revisited. PMID:16324222
Canine genomics and genetics: running with the pack. PMID:16311623
Analysis of vertebrate genomes suggests a new model for clade B serpin evolution. PMID:16305753
Clinical analysis by microchip capillary electrophoresis. PMID:16299048
Principal component analysis for predicting transcription-factor binding motifs from array-derived data. PMID:16297243
Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. PMID:16284200
Paucity of chimeric gene-transposable element transcripts in the Drosophila melanogaster genome. PMID:16283942
MysTR: an endogenous retrovirus family in mammals that is undergoing recent amplifications to unprecedented copy numbers. PMID:16282470
Expression analysis of candidate breast tumour suppressor genes on chromosome 16q. PMID:16280054
Alternative splicing and protein function. PMID:16274476
Aging syndrome genes and premature coronary artery disease. PMID:16262891
A novel autosomal recessive non-syndromic hearing impairment locus (DFNB47) maps to chromosome 2p25.1-p24.3. PMID:16261342
Gain-of-function screen for genes that affect Drosophila muscle pattern formation. PMID:16254604
Transcriptional regulation of early transposon elements, an active family of mouse long terminal repeat retrotransposons. PMID:16254322
Large-scale recombination rate patterns are conserved among human populations. PMID:16251464
Characteristics and regulatory elements defining constitutive splicing and different modes of alternative splicing in human and mouse. PMID:16251388
MAASE: an alternative splicing database designed for supporting splicing microarray applications. PMID:16251387
Nickel stimulates L1 retrotransposition by a post-transcriptional mechanism. PMID:16249005
Analysis of the Xenopus Werner syndrome protein in DNA double-strand break repair. PMID:16247024
Evidence for maternally transmitted small interfering RNA in the repression of transposition in Drosophila virilis. PMID:16247000
Positive selection of Iris, a retroviral envelope-derived host gene in Drosophila melanogaster. PMID:16244705
A method of precise mRNA/DNA homology-based gene structure prediction. PMID:16242044
A genome-wide survey demonstrates widespread non-linear mRNA in expressed sequences from multiple species. PMID:16237125
Structural elements of bulk chromatin within metaphase chromosomes. PMID:16235122
Multi-alignment of orthologous genome regions in five species provides new insights into the evolutionary make-up of mammalian genomes. PMID:16235120
On the possibility of origin of a short element of Drosophila (suffix) from a related long retroelement (F element). PMID:16229149
Distinct enzyme combinations in AKAP signalling complexes permit functional diversity. PMID:16228013
Nitric oxide and zinc homeostasis in acute lung injury. PMID:16222044
Protein molecular function prediction by Bayesian phylogenomics. PMID:16217548
Regulation of plant defense responses in Arabidopsis by EDR2, a PH and START domain-containing protein. PMID:16212604
Haplotype analysis of the human endogenous retrovirus locus HERV-K(HML-2.HOM) and its evolutionary implications. PMID:16211423
Tracking Alu evolution in New World primates. PMID:16209711
ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences. PMID:16207377
The function and expansion of the Patched- and Hedgehog-related homologs in C. elegans. PMID:16204193
In silico characterization of the family of PARP-like poly(ADP-ribosyl)transferases (pARTs). PMID:16202152
Emergence of young human genes after a burst of retroposition in primates. PMID:16201836
Modeling the amplification dynamics of human Alu retrotransposons. PMID:16201008
How homologous recombination generates a mutable genome. PMID:16197735
Uncertainty principle of genetic information in a living cell. PMID:16197549
Sequence and comparative genomic analysis of actin-related proteins. PMID:16195354
Roles of organic anion transporters (OATs) and a urate transporter (URAT1) in the pathophysiology of human disease. PMID:16189627
ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun. PMID:16184192
Diversification of stem cell molecular repertoire by alternative splicing. PMID:16183747
Gene therapy imaging in patients for oncological applications. PMID:16180032
The use of racial, ethnic, and ancestral categories in human genetics research. PMID:16175499
Fine mapping and physical characterization of two linked quantitative trait loci affecting milk fat yield in dairy cattle on BTA26. PMID:16172504
A linear memory algorithm for Baum-Welch training. PMID:16171529
A genome-wide survey of structural variation between human and chimpanzee. PMID:16169929
Differential gene expression in anatomical compartments of the human eye. PMID:16168081
Genomewide screening reveals high levels of insertional polymorphism in the human endogenous retrovirus family HERV-K(HML2): implications for present-day activity. PMID:16160178
Comparison of transcript profiling on Arabidopsis microarray platform technologies. PMID:16158238
Human endogenous retroviral elements as indicators of ectopic recombination events in the primate genome. PMID:16157677
A small family of sushi-class retrotransposon-derived genes in mammals and their relation to genomic imprinting. PMID:16155747
Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes. PMID:16150157
Capture of extranuclear DNA at fission yeast double-strand breaks. PMID:16143617
Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates. PMID:16140992
Evolutionary mechanisms shaping the genomic structure of the Williams-Beuren syndrome chromosomal region at human 7q11.23. PMID:16140988
Integration targeting by avian sarcoma-leukosis virus and human immunodeficiency virus in the chicken genome. PMID:16140779
Letter from the editor: Adenosine-to-inosine RNA editing in Alu repeats in the human genome. PMID:16138094
Specificity and versatility of SH3 and other proline-recognition domains: structural basis and implications for cellular signal transduction. PMID:16134966
Meprin beta metalloprotease gene polymorphisms associated with diabetic nephropathy in the Pima Indians. PMID:16133184
Human subtelomere structure and variation. PMID:16132815
Two rounds of whole genome duplication in the ancestral vertebrate. PMID:16128622
Combined evidence annotation of transposable elements in genome sequences. PMID:16110336
The zebrafish gene map defines ancestral vertebrate chromosomes. PMID:16109975
Origin and evolution of new exons in rodents. PMID:16109974
Multiple fates of L1 retrotransposition intermediates in cultured human cells. PMID:16107723
A human-curated annotation of the Candida albicans genome. PMID:16103911
Large-scale analysis of adeno-associated virus vector integration sites in normal human cells. PMID:16103194
Human endogenous retrovirus expression profiles in samples from brains of patients with schizophrenia and bipolar disorders. PMID:16103141
Identification of RNA editing sites in the SNP database. PMID:16100382
Localization of a novel autosomal recessive non-syndromic hearing impairment locus DFNB55 to chromosome 4q12-q13.2. PMID:16098016
Genomic medicine: genetic variation and its impact on the future of health care. PMID:16096102
The role of mutation accumulation in HIV progression. PMID:16096099
Transposable elements donate lineage-specific regulatory sequences to host genomes. PMID:16093685
Use of endogenous retroviral sequences (ERVs) and structural markers for retroviral phylogenetic inference and taxonomy. PMID:16092962
Using progenitor strain information to identify quantitative trait nucleotides in outbred mice. PMID:16085706
A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription. PMID:16083503
A comprehensive expressed sequence tag linkage map for tiger salamander and Mexican axolotl: enabling gene mapping and comparative genomics in Ambystoma. PMID:16079226
Estimating the tempo and mode of gene family evolution from comparative genomic data. PMID:16077014
Construction of a cytogenetically anchored microsatellite map in rabbit. PMID:16075371
Transcription factor binding sites in the pol gene intragenic regulatory region of HIV-1 are important for virus infectivity. PMID:16061936
FAST DB: a website resource for the study of the expression regulation of human gene products. PMID:16052034
Preferential binding of a G-quadruplex ligand to human chromosome ends. PMID:16052031
Application of Affymetrix array and Massively Parallel Signature Sequencing for identification of genes involved in prostate cancer progression. PMID:16042785
The Alu insertion in the CLCN5 gene of a patient with Dent's disease leads to exon 11 skipping. PMID:16041495
Mouse behavioural analysis in systems biology. PMID:16035954
Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages. PMID:16034026
Progressive proximal expansion of the primate X chromosome centromere. PMID:16030148
Bioinformatics approaches for cross-species liver cancer analysis based on microarray gene expression profiling. PMID:16026603
The scale of mutational variation in the murid genome. PMID:16024822
Identification of novel mammalian growth regulatory factors by genome-scale quantitative image analysis. PMID:16024821
Gene-breaking: a new paradigm for human retrotransposon-mediated gene evolution. PMID:16024818
Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences. PMID:16024817
Ten novel mutations in the molybdenum cofactor genes MOCS1 and MOCS2 and in vitro characterization of a MOCS2 mutation that abolishes the binding ability of molybdopterin synthase. PMID:16021469
Diverse spatial, temporal, and sexual expression of recently duplicated androgen-binding protein genes in Mus musculus. PMID:16018816
MPrime: efficient large scale multiple primer and oligonucleotide design for customized gene microarrays. PMID:16014168
The genomics of probiotic intestinal microorganisms. PMID:15998456
Conservation anchors in the vertebrate genome. PMID:15998454
Two high throughput technologies to detect segmental aneuploidies identify new Williams-Beuren syndrome patients with atypical deletions. PMID:15994861
Enhanced microarray performance using low complexity representations of the transcriptome. PMID:15987785
Replication-associated strand asymmetries in mammalian genomes: toward detection of replication origins. PMID:15985556
BoS: a large and diverse family of short interspersed elements (SINEs) in Brassica oleracea. PMID:15983875
Horizontal transfer of two operons coding for hydrogenases between bacteria and archaea. PMID:15983865
A systematic analysis of LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease. PMID:15983781
The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. PMID:15980563
AntiHunter 2.0: increased speed and sensitivity in searching BLAST output for EST antisense transcripts. PMID:15980558
ARGO: a web system for the detection of degenerate motifs and large-scale recognition of eukaryotic promoters. PMID:15980502
Distribution of immunodeficiency fact files with XML--from Web to WAP. PMID:15978138
The element(s) at the nontranscribed Xist locus of the active X chromosome controls chromosomal replication timing in the mouse. PMID:15972460
Genomic evolution of MHC class I region in primates. PMID:15967992
Punctuated duplication seeding events during the evolution of human chromosome 2p11. PMID:15965031
Guanosine triphosphate acts as a cofactor to promote assembly of initial P-element transposase-DNA synaptic complexes. PMID:15964992
A subset of nuclear receptor coregulators act as coupling proteins during synthesis and maturation of RNA transcripts. PMID:15964789
Substantial regional variation in substitution rates in the human genome: importance of GC content, gene density, and telomere-specific effects. PMID:15959677
Exploring hepatic hormone actions using a compilation of gene expression profiles. PMID:15953391
Satellog: a database for the identification and prioritization of satellite repeats in disease association studies. PMID:15949044
A complementation method for functional analysis of mammalian genes. PMID:15944448
Evolutionary diversity and potential recombinogenic role of integration targets of Non-LTR retrotransposons. PMID:15944437
Intra- and inter-specific variations in the copy number of two types of retrotransposons from the ectomycorrhizal basidiomycete Tricholoma matsutake. PMID:15940467
Genetic variations in the gene encoding TFAP2B are associated with type 2 diabetes mellitus. PMID:15940393
(TG/CA)n repeats in human gene families: abundance and selective patterns of distribution according to function and gene length. PMID:15935094
Factors affecting statistical power in the detection of genetic association. PMID:15931375
Analysis of 5' junctions of human LINE-1 and Alu retrotransposons suggests an alternative model for 5'-end attachment requiring microhomology-mediated end-joining. PMID:15930490
Dichotomous splicing signals in exon flanks. PMID:15930489
Positive selection for indel substitutions in the rodent sperm protein catsper1. PMID:15930155
Gene finding in the chicken genome. PMID:15924626
Kinetic analysis of the role of the tyrosine 13, phenylalanine 56 and glutamine 54 network in the U1A/U1 hairpin II interaction. PMID:15914668
A novel transgenic chimaeric mouse system for the rapid functional evaluation of genes encoding secreted proteins. PMID:15914664
Genome comparison without alignment using shortest unique substrings. PMID:15910684
Targeting alternatively spliced sequence features for cancer diagnosis and therapeutics. PMID:15902958
Genome-scale evidence of the nematode-arthropod clade. PMID:15892869
Paleogenomic record of the extinction of human endogenous retrovirus ERV9. PMID:15890939
Size of the protein-coding genome and rate of molecular evolution. PMID:15883855
The genome of the social amoeba Dictyostelium discoideum. PMID:15875012
The biased distribution of Alus in human isochores might be driven by recombination. PMID:15871047
Why are young and old repetitive elements distributed differently in the human genome? PMID:15871040
Toward predictive models of mammalian cells. PMID:15869393
Chemical synthesis of proteins. PMID:15869385
Under the genomic radar: the stealth model of Alu amplification. PMID:15867427
Fishing for answers with transposons. PMID:15864468
A novel algorithm for finding interspersed repeat regions. PMID:15862119
Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability. PMID:15860774
Amplification of whole tumor genomes and gene-by-gene mapping of genomic aberrations from limited sources of fresh-frozen and paraffin-embedded DNA. PMID:15858140
Evolution and distribution of class II-related endogenous retroviruses. PMID:15858031
Functional constraint and divergence in the G protein family in Caenorhabditis elegans and Caenorhabditis briggsae. PMID:15856303
A newly discovered human alpha-globin gene. PMID:15855277
Polygalacturonase from Sitophilus oryzae: possible horizontal transfer of a pectinase gene from fungi to weevils. PMID:15841240
SINEs point to abundant editing in the human genome. PMID:15833131
Gene regulation in planta by plant-derived engineered zinc finger protein transcription factors. PMID:15830130
Design and synthesis of a 3'-O-allyl photocleavable fluorescent nucleotide as a reversible terminator for DNA sequencing by synthesis. PMID:15829589
A combinatorial code for splicing silencing: UAGG and GGGG motifs. PMID:15828859
Genotype, phenotype and cancer: role of low penetrance genes and environment in tumour susceptibility. PMID:15824445
A hybrid neural network system for prediction and recognition of promoter regions in human genome. PMID:15822155
A novel class of Helitron-related transposable elements in maize contain portions of multiple pseudogenes. PMID:15821872
Retropseudogenes derived from the human Ro/SS-A autoantigen-associated hY RNAs. PMID:15817567
Functional roles of 3'-terminal structures of template RNA during in vivo retrotransposition of non-LTR retrotransposon, R1Bm. PMID:15814816
A comprehensive literature review of haplotyping software and methods for use with unrelated individuals. PMID:15814067
Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana. PMID:15805491
Multiple mechanisms are implicated in the generation of 5q35 microdeletions in Sotos syndrome. PMID:15805156
Practical lessons from protein structure prediction. PMID:15805122
Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus. PMID:15804358
Chromosome sorting in tetraploid wheat and its potential for genome analysis. PMID:15802508
The majority of human genes have regions repeated in other human genes. PMID:15802472
Symmetrical base preferences surrounding HIV-1, avian sarcoma/leukosis virus, and murine leukemia virus integration sites. PMID:15802467
The genetics of depression and related traits. PMID:15802088
Precise identification of endogenous proviruses of NFS/N mice participating in recombination with moloney ecotropic murine leukemia virus (MuLV) to generate polytropic MuLVs. PMID:15795252
Evolutionary cores of domain co-occurrence networks. PMID:15788102
Localized transfection on arrays of magnetic beads coated with PCR products. PMID:15782208
Novel G-protein-coupled receptor-like proteins in the plant pathogenic fungus Magnaporthe grisea. PMID:15774025
The DNA sequence of the human X chromosome. PMID:15772651
Evolutionary sequence analysis of complete eukaryote genomes. PMID:15762985
A microarray configuration to quantify expression levels and relative abundance of splice variants. PMID:15760843
Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example. PMID:15752422
CD14-dependent modulation of transcriptional activities of endogenous retroviruses in the lung after injury. PMID:15744557
Database of mRNA gene expression profiles of multiple human organs. PMID:15741514
novoSNP, a novel computational tool for sequence variation discovery. PMID:15741513
Quantifying the mechanisms for segmental duplications in mammalian genomes by statistical analysis and modeling. PMID:15741274
Leaky ribosomal scanning in mammalian genomes: significance of histone H4 alternative translation in vivo. PMID:15741183
Krüppel-like factors 4 and 5: the yin and yang regulators of cellular proliferation. PMID:15740636
Function and regulation of Tumbleweed (RacGAP50C) in neuroblast proliferation and neuronal morphogenesis. PMID:15738386
Lineage-specific expansions of retroviral insertions within the genomes of African great apes but not humans and orangutans. PMID:15737067
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. PMID:15735639
DNA coiled coils. PMID:15728387
The mouse RNase 4 and RNase 5/ang 1 locus utilizes dual promoters for tissue-specific expression. PMID:15722482
Discovery of active proteins directly from combinatorial randomized protein libraries without display, purification or sequencing: identification of novel zinc finger proteins. PMID:15722478
Comparative sequencing provides insights about the structure and conservation of marsupial and monotreme genomes. PMID:15718282
Blood-brain barrier genomics, proteomics, and new transporter discovery. PMID:15717066
Protein coding potential of retroviruses and other transposable elements in vertebrate genomes. PMID:15716312
Naturally occurring antisense: transcriptional leakage or real overlap? PMID:15710751
Human endogenous retrovirus HERV-K14 families: status, variants, evolution, and mobilization of other cellular sequences. PMID:15709013
Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. PMID:15706033
The rice nuclear genome continuously integrates, shuffles, and eliminates the chloroplast genome to cause chloroplast-nuclear DNA flux. PMID:15705954
Integrating alternative splicing detection into gene prediction. PMID:15705189
LINE-1 amplification accompanies explosive genome repatterning in rodents. PMID:15702417
Vertebrate-like betagamma-crystallins in the ocular lenses of a copepod. PMID:15702356
Linking disease-associated genes to regulatory networks via promoter organization. PMID:15701758
A potential role for RNA interference in controlling the activity of the human LINE-1 retrotransposon. PMID:15701756
Smoking-gene interaction and disease development: relevance to pancreatic cancer and atherosclerosis. PMID:15696395
Molecular characterization and chromosomal distribution of Galileo, Kepler and Newton, three foldback transposable elements of the Drosophila buzzatii species complex. PMID:15695364
Insights into vertebrate evolution from the chicken genome sequence. PMID:15693954
Isolation, characterization, and evolutionary divergence of mouse RNase 6: evidence for unusual evolution in rodents. PMID:15693621
Allelic variation of HERV-K(HML-2) endogenous retroviral elements in human populations. PMID:15693620
Haldane and the first estimates of the human mutation rate. PMID:15689624
Automated genomic sequence analysis of the three collagen VI genes: applications to Ullrich congenital muscular dystrophy and Bethlem myopathy. PMID:15689448
Pooled genomic indexing of rhesus macaque. PMID:15687293
A genotyping system capable of simultaneously analyzing >1000 single nucleotide polymorphisms in a haploid genome. PMID:15687291
Activation of pre-mRNA splicing by human RNPS1 is regulated by CK2 phosphorylation. PMID:15684395
Pharmacogenetic approaches in the treatment of asthma. PMID:15683609
Evidence for widespread degradation of gene control regions in hominid genomes. PMID:15678168
The profile of repeat-associated histone lysine methylation states in the mouse epigenome. PMID:15678104
FAM20: an evolutionarily conserved family of secreted proteins expressed in hematopoietic cells. PMID:15676076
Noncoding DNA, isochores and gene expression: nucleosome formation potential. PMID:15673716
Murine endogenous retroviruses and their transcriptional potentials. PMID:15672595
Fast and reliable prediction of noncoding RNAs. PMID:15665081
Sorghum genome sequencing by methylation filtration. PMID:15660154
Evolution of DNA sequence nonhomologies among maize inbreds. PMID:15659640
Identification of putative new splicing targets for ETR-3 using sequences identified by systematic evolution of ligands by exponential enrichment. PMID:15657417
Conserved transcription factor binding sites of cancer markers derived from primary lung adenocarcinoma microarrays. PMID:15653641
Stratification of acute myeloid leukemia based on gene expression profiles. PMID:15646648
Syncytin-A and syncytin-B, two fusogenic placenta-specific murine envelope genes of retroviral origin conserved in Muridae. PMID:15644441
Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. PMID:15642101
Microarray-based resequencing of multiple Bacillus anthracis isolates. PMID:15642093
A novel autosomal recessive nonsyndromic hearing impairment locus (DFNB42) maps to chromosome 3q13.31-q22.3. PMID:15641023
Estimation of the extent of synteny between Tetraodon nigroviridis and Homo sapiens genomes. PMID:15638467
Mapping of a novel autosomal recessive nonsyndromic deafness locus (DFNB46) to chromosome 18p11.32-p11.31. PMID:15637723
Gene and alternative splicing annotation with AIR. PMID:15632090
Highly conserved non-coding sequences are associated with vertebrate development. PMID:15630479
Analysis on frequency and density of microsatellites in coding sequences of several eukaryotic genomes. PMID:15629040
Hereditary persistence of alpha-fetoprotein and H19 expression in liver of BALB/cJ mice is due to a retrovirus insertion in the Zhx2 gene. PMID:15626755
Plant MITEs: useful tools for plant genetics and genomics. PMID:15626339
A statistical approach designed for finding mathematically defined repeats in shotgun data and determining the length distribution of clone-inserts. PMID:15626332
Azolla--a model organism for plant genomic studies. PMID:15626330
Spatially and temporally controlled gene transfer by electroporation into adherent cells on plasmid DNA-loaded electrodes. PMID:15613595
Global analysis of gene expression in mammalian kidney. PMID:15611884
All systems GO for understanding mouse gene function. PMID:15610553
Generation and analysis of expressed sequence tags from the salt-tolerant mangrove species Avicennia marina (Forsk) Vierh. PMID:15609053
Alu and L1 retroelements are correlated with the tissue extent and peak rate of gene expression, respectively. PMID:15608386
HOPPSIGEN: a database of human and mouse processed pseudogenes. PMID:15608268
DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes. PMID:15608249
The Vertebrate Genome Annotation (Vega) database. PMID:15608237
The UCSC Proteome Browser. PMID:15608236
Ensembl 2005. PMID:15608235
DDBJ in collaboration with mass-sequencing teams on annotation. PMID:15608189
TPMD: a database and resources of microsatellite marker genotyped in Taiwanese populations. PMID:15608171
Rfam: annotating non-coding RNAs in complete genomes. PMID:15608160
Emerging strategies and applications of pharmacogenomics. PMID:15606999
MARA: a novel approach for highly multiplexed locus-specific SNP genotyping using high-density DNA oligonucleotide arrays. PMID:15601992
Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics. PMID:15601538
Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps. PMID:15601531
Shedding genomic ballast: extensive parallel loss of ancestral gene families in animals. PMID:15599514
Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. PMID:15598822
Comprehensive analysis of human endogenous retrovirus transcriptional activity in human tissues with a retrovirus-specific microarray. PMID:15596828
The C-value enigma in plants and animals: a review of parallels and an appeal for partnership. PMID:15596463
Detection of aneuploidies by paralogous sequence quantification. PMID:15591276
Comparison of splice sites in mammals and chicken. PMID:15590946
Uprobe: a genome-wide universal probe resource for comparative physical mapping in vertebrates. PMID:15590945
Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes. PMID:15590944
Evolution and functional classification of vertebrate gene deserts. PMID:15590943
Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. PMID:15590940
A genome-wide survey of segmental duplications that mediate common human genetic variation of chromosomal architecture. PMID:15588494
DFNB44, a novel autosomal recessive non-syndromic hearing impairment locus, maps to chromosome 7p14.1-q11.22. PMID:15583425
Increased noncanonical splicing of autoantigen transcripts provides the structural basis for expression of untolerized epitopes. PMID:15577853
The mouse genome: experimental examination of gene predictions and transcriptional start sites. PMID:15574821
Reconstructing large regions of an ancestral mammalian genome in silico. PMID:15574820
Highly conserved upstream sequences for transcription factor genes and implications for the regulatory network. PMID:15572454
Preferential accessibility to specific genomic loci for the repair of double-strand breaks in human cells. PMID:15562005
Protein-mediated error correction for de novo DNA synthesis. PMID:15561997
Distinct genomic integration of MLV and SIV vectors in primate hematopoietic stem and progenitor cells. PMID:15550989
CLOE: identification of putative functional relationships among genes by comparison of expression profiles between two species. PMID:15550177
Cell migration and metastasis as targets of small RNA-based molecular genetic analyses. PMID:15548858
Coding sequences of functioning human genes derived entirely from mobile element sequences. PMID:15546984
Sequence and comparative analysis of the maize NB mitochondrial genome. PMID:15542500
Assembly and characterization of heterochromatin and euchromatin on human artificial chromosomes. PMID:15535865
Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome. PMID:15534692
Parametric inference for biological sequence analysis. PMID:15534223
Identification and characterization of a novel form of the human L-dopa decarboxylase mRNA. PMID:15532536
Genetic predictors of the clinical response to opioid analgesics: clinical utility and future perspectives. PMID:15530129
Non-recurrent 17p11.2 deletions are generated by homologous and non-homologous mechanisms. PMID:15526218
The human L1 promoter: variable transcription initiation sites and a major impact of upstream flanking sequence on promoter activity. PMID:15520289
Whole-genome analysis of Alu repeat elements reveals complex evolutionary history. PMID:15520288
Serial segmental duplications during primate evolution result in complex human genome architecture. PMID:15520286
Open reading frame sequencing and structure-based alignment of polypeptides encoded by RT1-Bb, RT1-Ba, RT1-Db, and RT1-Da alleles. PMID:15517241
Natural genetic variation caused by transposable elements in humans. PMID:15514065
Variation in sequence and organization of splicing regulatory elements in vertebrate genes. PMID:15505203
Large-scale cDNA transfection screening for genes related to cancer development and progression. PMID:15498874
Specific pattern of ionic channel gene expression associated with pacemaker activity in the mouse heart. PMID:15498808
From ORFeome to biology: a functional genomics pipeline. PMID:15489336
Human ORFeome version 1.1: a platform for reverse proteomics. PMID:15489335
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). PMID:15489334
A gateway-compatible yeast one-hybrid system. PMID:15489331
Analysis of small human proteins reveals the translation of upstream open reading frames of mRNAs. PMID:15489325
An ORFeome-based analysis of human transcription factor genes and the construction of a microarray to interrogate their expression. PMID:15489324
Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing. PMID:15489323
Isochore structures in the genome of the plant Arabidopsis thaliana. PMID:15486696
Genetic steps of mammalian homologous repair with distinct mutagenic consequences. PMID:15485900
Mammalian circadian biology: elucidating genome-wide levels of temporal organization. PMID:15485355
An active murine transposon family pair: retrotransposition of "master" MusD copies and ETn trans-mobilization. PMID:15479948
An intermediate grade of finished genomic sequence suitable for comparative analyses. PMID:15479945
Genome-wide analyses of avian sarcoma virus integration sites. PMID:15479807
Pyrosequencing: sequence typing at the speed of light. PMID:15477652
Identification of endogenous retroviral reading frames in the human genome. PMID:15476554
Extending the mutual information measure to rank inferred literature relationships. PMID:15471547
Introns and splicing elements of five diverse fungi. PMID:15470237
High-level beta-globin expression and preferred intragenic integration after lentiviral transduction of human cord blood stem cells. PMID:15467834
Retrotransposition-Competent Human LINE-1 Induces Apoptosis in Cancer Cells With Intact p53. PMID:15467158
Inverted repeat structure of the human genome: the X-chromosome contains a preponderance of large, highly homologous inverted repeats that contain testes genes. PMID:15466286
Evolution and distribution of RNA polymerase II regulatory sites from RNA polymerase III dependant mobile Alu elements. PMID:15461819
A comprehensive transcript index of the human genome generated using microarrays and computational approaches. PMID:15461792
The decline of isochores in mammals: an assessment of the GC content variation along the mammalian phylogeny. PMID:15461422
PhyloGenie: automated phylome generation and analysis. PMID:15459293
Distinct PAR/IQGAP expression patterns during murine development: implications for thrombin-associated cytoskeletal reorganization. PMID:15457341
PHR1, a PH domain-containing protein expressed in primary sensory neurons. PMID:15456885
Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome. PMID:15454550
Duplicative and conservative transpositions of larval serum protein 1 genes in the genus Drosophila. PMID:15454541
Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences. PMID:15452276
High-resolution comparative mapping of pig Chromosome 4, emphasizing the FAT1 region. PMID:15389320
Sequence composition and genome organization of maize. PMID:15388850
Transcription-coupled and splicing-coupled strand asymmetries in eukaryotic genomes. PMID:15388799
Clustering of genes coding for DNA binding proteins in a region of atypical evolution of the human genome. PMID:15383909
Human endogenous retroviruses: transposable elements with potential? PMID:15373898
Improving specificity of DNA hybridization-based methods. PMID:15371554
What can we learn from noncoding regions of similarity between genomes? PMID:15369604
Np9 protein of human endogenous retrovirus K interacts with ligand of numb protein X. PMID:15367597
Organization and evolution of a gene-rich region of the mouse genome: a 12.7-Mb region deleted in the Del(13)Svea36H mouse. PMID:15364904
Human, mouse, and rat genome large-scale rearrangements: stability versus speciation. PMID:15364903
A novel class of mammalian-specific tailless retropseudogenes. PMID:15364902
Pattern of sequence variation across 213 environmental response genes. PMID:15364900
Continued colonization of the human genome by mitochondrial DNA. PMID:15361937
Gene family evolution: an in-depth theoretical and simulation analysis of non-linear birth-death-innovation models. PMID:15357876
Over 20% of human transcripts might form sense-antisense pairs. PMID:15356298
Effects of length and location on the cellular response to double-stranded RNA. PMID:15353564
Enhancer trapping in zebrafish using the Sleeping Beauty transposon. PMID:15347431
Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. PMID:15345045
EGPred: prediction of eukaryotic genes using ab initio methods after combining with sequence similarity approaches. PMID:15342559
Widespread RNA editing of embedded alu elements in the human transcriptome. PMID:15342557
Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions. PMID:15342556
Comparative analysis of apicomplexa and genomic diversity in eukaryotes. PMID:15342554
Expansion and contraction of the DUP240 multigene family in Saccharomyces cerevisiae populations. PMID:15342502
The knockout mouse project. PMID:15340423
Essential motifs in the 3' untranslated region required for retrotransposition and the precise start of reverse transcription in non-long-terminal-repeat retrotransposon SART1. PMID:15340053
LINE-1 distribution in Afrotheria and Xenarthra: implications for understanding the evolution of LINE-1 in eutherian genomes. PMID:15338236
XHM: a system for detection of potential cross hybridizations in DNA microarrays. PMID:15333145
Large-scale sequencing of the CD33-related Siglec gene cluster in five mammalian species reveals rapid evolution by multiple mechanisms. PMID:15331780
Probing the active site of YjeE: a vital Escherichia coli protein of unknown function. PMID:15324301
Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences. PMID:15314653
Retroelements and the human genome: new perspectives on an old relation. PMID:15310846
Preference of DNA methyltransferases for CpG islands in mouse embryonic stem cells. PMID:15310660
Detection of retroviral antisense transcripts and promoter activity of the HERV-K(C4) insertion in the MHC class III region. PMID:15309346
Tissue microarrays for high-throughput molecular pathology. PMID:15307452
In vivo transcriptional profiling of Plasmodium falciparum. PMID:15296511
Regeneration and the need for simpler model organisms. PMID:15293803
The mouse kinome: discovery and comparative genomics of all mouse protein kinases. PMID:15289607
A non-EST-based method for exon-skipping prediction. PMID:15289480
The complete genome and proteome of Mycoplasma mobile. PMID:15289470
Origins of chromosomal rearrangement hotspots in the human genome: evidence from the AZFa deletion hotspots. PMID:15287977
Phylogenetic profiling of the Arabidopsis thaliana proteome: what proteins distinguish plants from other organisms? PMID:15287975
Detecting single DNA copy number variations in complex genomes using one nanogram of starting DNA and BAC-array CGH. PMID:15284333
The Retinome - defining a reference transcriptome of the adult mammalian retina/retinal pigment epithelium. PMID:15283859
Human endogenous retrovirus family HERV-K(HML-5): status, evolution, and reconstruction of an ancient betaretrovirus in the human genome. PMID:15280487
Integrated self-inactivating lentiviral vectors produce full-length genomic transcripts competent for encapsidation and integration. PMID:15280451
Selective and mutational patterns associated with gene expression in humans: influences on synonymous composition and intron presence. PMID:15280243
Comparative genomics: methods and applications. PMID:15278216
Solution structure of an RNA stem-loop derived from the 3' conserved region of eel LINE UnaL2. PMID:15273327
Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization. PMID:15272118
A YY1-binding site is required for accurate human LINE-1 transcription initiation. PMID:15272086
5' Long serial analysis of gene expression (LongSAGE) and 3' LongSAGE for transcriptome characterization and genome annotation. PMID:15272081
Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G. PMID:15269786
Synaptotagmins are trafficked to distinct subcellular domains including the postsynaptic compartment. PMID:15263020
Comparative genomic analysis identifies an ADP-ribosylation factor-like gene as the cause of Bardet-Biedl syndrome (BBS3). PMID:15258860
Novel conserved domains in proteins with predicted roles in eukaryotic cell-cycle regulation, decapping and RNA stability. PMID:15257761
Identification of 315 genes essential for early zebrafish development. PMID:15256591
Clustering of DNA sequences in human promoters. PMID:15256515
Comparative genomics of transcriptional control in the human malaria parasite Plasmodium falciparum. PMID:15256513
The repetitive landscape of the chicken genome. PMID:15256510
Comparative evolutionary genomics of androgen-binding protein genes. PMID:15256509
Preparation of DNA-modified nanoparticles and preliminary study for colorimetric SNP analysis using their selective aggregations. PMID:15254253
A set of BAC clones spanning the human genome. PMID:15247347
Generation of longer 3' cDNA fragments from massively parallel signature sequencing tags. PMID:15247327
Pharmacogenetics of antipsychotic-induced weight gain. PMID:15243737
Development of a macroarray to specifically analyze immunological gene expression in swine. PMID:15242943
Structural and functional analysis of rice genome. PMID:15240912
Distribution of short paired duplications in mammalian genomes. PMID:15240876
Demarcating the gene-rich regions of the wheat genome. PMID:15240829
Sequence-based prediction of protein domains. PMID:15240828
Evolutionary conservation and selection of human disease gene orthologs in the rat and mouse genomes. PMID:15239832
Analysis of alternative splicing with microarrays: successes and challenges. PMID:15239822
After 'completion': the changing face of human chromosomes 21 and 22. PMID:15239819
Evidence for multiple cycles of strand invasion during repair of double-strand gaps in Drosophila. PMID:15238522
The prevalence of MADH4 and BMPR1A mutations in juvenile polyposis and absence of BMPR2, BMPR1B, and ACVR1 mutations. PMID:15235019
Post-translational generation of constitutively active cores from larger phosphatases in the malaria parasite, Plasmodium falciparum: implications for proteomics. PMID:15230980
Low number of mitochondrial pseudogenes in the chicken (Gallus gallus) nuclear genome: implications for molecular inference of population history and phylogenetics. PMID:15219233
The Iccare web server: an attempt to merge sequence and mapping information for plant and animal species. PMID:15215424
IsoFinder: computational prediction of isochores in genome sequences. PMID:15215396
PromoSer: improvements to the algorithm, visualization and accessibility. PMID:15215378
A web server for performing electronic PCR. PMID:15215361
Microarray analysis of transposition targets in Escherichia coli: the impact of transcription. PMID:15210965
Molecular and functional characterization of novel CRFR1 isoforms from the skin. PMID:15206947
Localization of a novel locus for hereditary nail dysplasia to chromosome 17q25.1-17q25.3. PMID:15200512
A high proportion of chromosome 21 promoter polymorphisms influence transcriptional activity. PMID:15200235
Extensive expansion of the claudin gene family in the teleost fish, Fugu rubripes. PMID:15197168
The insertional history of an active family of L1 retrotransposons in humans. PMID:15197167
A transcript finishing initiative for closing gaps in the human transcriptome. PMID:15197164
Retrotransposon-derived elements in the mammalian genome: a potential source of disease. PMID:15190191
After the genome--the phenome? PMID:15190190
Bacterial alpha2-macroglobulins: colonization factors acquired by horizontal gene transfer from the metazoan genome? PMID:15186489
Interplay between Drosophila Bloom's syndrome helicase and Ku autoantigen during nonhomologous end joining repair of P element-induced DNA breaks. PMID:15184650
Candidate gene studies of antipsychotic drug efficacy and drug-induced weight gain. PMID:15184105
Genome-wide identification of genes likely to be involved in human genetic disease. PMID:15181176
Detection of chromosomal regions showing differential gene expression in human skeletal muscle and in alveolar rhabdomyosarcoma. PMID:15176974
High-resolution proteomic mapping in the vertebrate central nervous system: close proximity of connexin35 to NMDA glutamate receptor clusters and co-localization of connexin36 with immunoreactivity for zonula occludens protein-1 (ZO-1). PMID:15173637
Evidence for interaction between the TCO and NMTC1 loci in familial non-medullary thyroid cancer. PMID:15173224
Differential alu mobilization and polymorphism among the human and chimpanzee lineages. PMID:15173113
The small chromosomes of Trypanosoma brucei involved in antigenic variation are constructed around repetitive palindromes. PMID:15173109
Three ATP-binding cassette transporter genes, Abca14, Abca15, and Abca16, form a cluster on mouse Chromosome 7F3. PMID:15170222
Nizp1, a novel multitype zinc finger protein that interacts with the NSD1 histone lysine methyltransferase through a unique C2HR motif. PMID:15169884
Genome annotation of a 1.5 Mb region of human chromosome 6q23 encompassing a quantitative trait locus for fetal hemoglobin expression in adults. PMID:15169551
The Ro 60 kDa autoantigen: insights into cellular function and role in autoimmunity. PMID:15168680
Human genome research in China. PMID:15168679
Nucleotide variation at Msn and Alas2, two genes flanking the centromere of the X chromosome in humans. PMID:15166166
In vivo analysis of synaptonemal complex formation during yeast meiosis. PMID:15166136
Construction and characterization of a soybean bacterial artificial chromosome library and use of multiple complementary libraries for genome physical mapping. PMID:15164176
Resting CD4+ T cells from human immunodeficiency virus type 1 (HIV-1)-infected individuals carry integrated HIV-1 genomes within actively transcribed host genes. PMID:15163705
Activation of cryptic 3' splice sites within introns of cellular genes following gene entrapment. PMID:15155860
Microfluidic device reads up to four consecutive base pairs in DNA sequencing-by-synthesis. PMID:15155856
Multi-species sequence comparison reveals dynamic evolution of the elastin gene that has involved purifying selection and lineage-specific insertions/deletions. PMID:15149554
Linkage disequilibrium mapping via cladistic analysis of single-nucleotide polymorphism haplotypes. PMID:15148658
A new role for expressed pseudogenes as ncRNA: regulation of mRNA stability of its homologous coding gene. PMID:15148580
An approach to large scale identification of non-obvious structural similarities between proteins. PMID:15147578
Secondary structure models of the 3' untranslated regions of diverse R2 RNAs. PMID:15146081
Multiple groups of endogenous betaretroviruses in mice, rats, and other mammals. PMID:15140976
Large-scale integration of human genetic and physical maps. PMID:15140834
A neutral model of transcriptome evolution. PMID:15138501
Crystal structures of a DNA octaplex with I-motif of G-quartets and its splitting into two quadruplexes suggest a folding mechanism of eight tandem repeats. PMID:15133122
Genomic biodiversity, phylogenetics and coevolution in proteins. PMID:15130847
ELXR: a resource for rapid exon-directed sequence analysis. PMID:15128450
Maize DNA-sequencing strategies and genome organization. PMID:15128439
Construction, characterization and chromosomal mapping of bacterial artificial chromosome (BAC) library of Yunnan snub-nosed monkey (Rhinopithecus bieti). PMID:15125639
GeneWise and Genomewise. PMID:15123596
ESTGenes: alternative splicing from ESTs in Ensembl. PMID:15123595
The otter annotation system. PMID:15123593
The Ensembl automatic gene annotation system. PMID:15123590
The functional genomic distribution of protein divergence in two animal phyla: coevolution, genomic conflict, and constraint. PMID:15123580
Analysis of segmental duplications and genome assembly in the mouse. PMID:15123579
Identification of "pathologs" (disease-related genes) from the RIKEN mouse cDNA dataset using human curation plus FACTS, a new biological information extraction system. PMID:15115540
[Necessity and usefulness of bioinformatic methods for microarray data analysis]. PMID:15112041
Physicians, genetics and life insurance. PMID:15111477
L1 and HERV-W retrotransposons are hypomethylated in human ovarian carcinomas. PMID:15109395
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PMID:15103394
Detection and evaluation of intron retention events in the human transcriptome. PMID:15100430
No statistical support for correlation between the positions of protein interaction sites and alternatively spliced regions. PMID:15096275
Evidence that RNA editing modulates splice site selection in the 5-HT2C receptor gene. PMID:15087490
Differential evolution of the Saccharomyces cerevisiae DUP240 paralogs and implication of recombination in phylogeny. PMID:15087486
Periodic explosive expansion of human retroelements associated with the evolution of the hominoid primate. PMID:15082888
Evidence for a piwi-dependent RNA silencing of the gypsy endogenous retrovirus by the Drosophila melanogaster flamenco gene. PMID:15082550
Comparison of human chromosome 21 conserved nongenic sequences (CNGs) with the mouse and dog genomes shows that their selective constraint is independent of their genic environment. PMID:15078857
The genetic architecture of selection at the human dopamine receptor D4 (DRD4) gene locus. PMID:15077199
A gene atlas of the mouse and human protein-encoding transcriptomes. PMID:15075390
Inhibition of glutamate receptor 2 translation by a polymorphic repeat sequence in the 5'-untranslated leaders. PMID:15071096
Genome-wide identification of DNaseI hypersensitive sites using active chromatin sequence libraries. PMID:15070753
Regulation of alternative RNA splicing by exon definition and exon sequences in viral and mammalian gene expression. PMID:15067211
Structural features of the rice chromosome 4 centromere. PMID:15064362
FB elements can promote exon shuffling: a promoter-less white allele can be reactivated by FB mediated transposition in Drosophila melanogaster. PMID:15060822
Repression of PML nuclear body-associated transcription by oxidative stress-activated Bach2. PMID:15060166
BAC resources for the rat genome project. PMID:15060022
Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome. PMID:15060021
Integration of the rat recombination and EST maps in the rat genomic sequence and comparative mapping analysis with the mouse genome. PMID:15060020
The Atlas genome assembly system. PMID:15060016
Aligning multiple genomic sequences with the threaded blockset aligner. PMID:15060014
Dynamic building of a BAC clone tiling path for the Rat Genome Sequencing Project. PMID:15060010
Insertions and deletions are male biased too: a whole-genome analysis in rodents. PMID:15059997
Occurrence and consequences of coding sequence insertions and deletions in Mammalian genomes. PMID:15059996
Comparative recombination rates in the rat, mouse, and human genomes. PMID:15059993
Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes. PMID:15059992
Recent segmental duplications in the working draft assembly of the brown Norway rat. PMID:15059990
Hotspots of mammalian chromosomal evolution. PMID:15059256
The mammalian transcriptome and the function of non-coding DNA sequences. PMID:15059247
Organization and expression of the SLC36 cluster of amino acid transporter genes. PMID:15058382
The DNA sequence and analysis of human chromosome 13. PMID:15057823
Regulation of the MID1 protein function is fine-tuned by a complex pattern of alternative splicing. PMID:15057556
Proteomics for nasal secretion analysis. PMID:15056405
Comparison of computational methods for identifying translation initiation sites in EST data. PMID:15053846
Monosomy 1p36 breakpoints indicate repetitive DNA sequence elements may be involved in generating and/or stabilizing some terminal deletions. PMID:15053483
Genetics, individuality, and medicine in the 21st century. PMID:15053009
Long live structural biology. PMID:15048098
Applicability of tandem mass spectrometry to the automated comparative sequencing of long-chain oligonucleotides. PMID:15047056
Long-term reinfection of the human genome by endogenous retroviruses. PMID:15044706
[Molecular-genetic mechanisms of developing the brain based on an embryonic Xenopus model]. PMID:15042834
Phylogenetic analysis of Ciona intestinalis gene superfamilies supports the hypothesis of successive gene expansions. PMID:15042337
Membrane model for the G-protein-coupled receptor rhodopsin: hydrophobic interface and dynamical structure. PMID:15041649
A scale invariant clustering of genes on human chromosome 7. PMID:15040817
Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals. PMID:15031317
Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. PMID:15024419
Evaluation of monocot and eudicot divergence using the sugarcane transcriptome. PMID:15020759
Bioinformatical assay of human gene morbidity. PMID:15020709
A bacterial genetic screen identifies functional coding sequences of the insect mariner transposable element Famar1 amplified from the genome of the earwig, Forficula auricularia. PMID:15020471
The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations. PMID:15020430
Velvet, a dominant Egfr mutation that causes wavy hair and defective eyelid development in mice. PMID:15020428
Human immunodeficiency virus type 1 subtypes have a distinct long terminal repeat that determines the replication rate in a host-cell-specific manner. PMID:15016888
Fine mapping a gene for pediatric gastroesophageal reflux on human chromosome 13q14. PMID:15014979
Tempo and mode of evolution of a primate-specific retrotransposon belonging to the LINE 1 family. PMID:15008424
Standardized phylogenetic tree: a reference to discover functional evolution. PMID:15008414
Detection of new transposable element families in Drosophila melanogaster and Anopheles gambiae genomes. PMID:15008403
Novel microsatellite markers and single nucleotide polymorphisms refine the tylosis with oesophageal cancer (TOC) minimal region on 17q25 to 42.5 kb: sequencing does not identify the causative gene. PMID:15007728
Evolutionary implication of human endogenous retrovirus HERV-H family. PMID:15007706
Long terminal repeat retrotransposons of Mus musculus. PMID:15003117
[The human genome and advances in medicine: limits and future prospects]. PMID:14998477
Getting into position: the catalytic mechanisms of protein ubiquitylation. PMID:14998368
Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. PMID:14993201
Rapid isolation of viral integration site reveals frequent integration of HTLV-1 into expressed loci. PMID:14991527
The human olfactory receptor gene family. PMID:14983052
Differential recruitment of nuclear receptor coactivators may determine alternative RNA splice site choice in target genes. PMID:14982999
Evidence for a subpopulation of conserved alternative splicing events under selection pressure for protein reading frame preservation. PMID:14982953
Prospects of a computational origin of life endeavor. PMID:14979655
Identification of novel virulence-associated genes via genome analysis of hypothetical genes. PMID:14977936
Unlocking hidden genomic sequence. PMID:14973330
Large-scale determination of the methylation status of retrotransposons in different tissues using a methylation tags approach. PMID:14973327
ETR-3 and CELF4 protein domains required for RNA binding and splicing activity in vivo. PMID:14973222
Finding and interpreting genetic variations that are important to ophthalmologists. PMID:14971589
SNPs in cancer research and treatment. PMID:14970847
Functional bias and spatial organization of genes in mutational hot and cold regions in the human genome. PMID:14966531
DNA methylation may restrict but does not determine differential gene expression at the Sgy/Tead2 locus during mouse development. PMID:14966277
An intronic enhancer regulates splicing of the twintron of Drosophila melanogaster prospero pre-mRNA by two different spliceosomes. PMID:14966268
Statistical analysis of over-represented words in human promoter sequences. PMID:14963262
Numerous novel annotations of the human genome sequence supported by a 5'-end-enriched cDNA collection. PMID:14962985
The multiassembly problem: reconstructing multiple transcript isoforms from EST fragment mixtures. PMID:14962984
Whole-genome shotgun assembly and comparison of human genome assemblies. PMID:14769938
Gene structure conservation aids similarity based gene prediction. PMID:14764925
Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila. PMID:14762063
An unappreciated role for RNA surveillance. PMID:14759258
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. PMID:14759257
Human endogenous retrovirus K solo-LTR formation and insertional polymorphisms: implications for human and viral evolution. PMID:14757818
Solution structure and backbone dynamics of the pleckstrin homology domain of the human protein kinase B (PKB/Akt). Interaction with inositol phosphates. PMID:14755158
Dnmt1 expression in pre- and postimplantation embryogenesis and the maintenance of IAP silencing. PMID:14749379
Presence of dUTPase in the various human endogenous retrovirus K (HERV-K) families. PMID:14745533
Method for analyzing signaling networks in complex cellular systems. PMID:14745015
Design and synthesis of a photocleavable biotinylated nucleotide for DNA analysis by mass spectrometry. PMID:14744978
Different rates of LINE-1 (L1) retrotransposon amplification and evolution in New World monkeys. PMID:14743320
Phylogenetic analysis of Sec7-domain-containing Arf nucleotide exchangers. PMID:14742722
More active human L1 retrotransposons produce longer insertions. PMID:14742665
Both rare and common polymorphisms contribute functional variation at CHGA, a regulator of catecholamine physiology. PMID:14740315
3' rapid amplification of cDNA ends (RACE) walking for rapid structural analysis of large transcripts. PMID:14740256
Duplication, coclustering, and selection of human Alu retrotransposons. PMID:14736919
Packaging and reverse transcription of snRNAs by retroviruses may generate pseudogenes. PMID:14730028
Human RNPS1 and its associated factors: a versatile alternative pre-mRNA splicing regulator in vivo. PMID:14729963
A mutation in PCSK9 causing autosomal-dominant hypercholesterolemia in a Utah pedigree. PMID:14727179
Protocadherin X ( PCDHX) and Y ( PCDHY) genes; multiple mRNA isoforms encoding variant signal peptides and cytoplasmic domains. PMID:14727141
A novel Krüppel-Associated Box identified in a panel of mammalian zinc finger proteins. PMID:14727140
An enhancer-trap LacZ transgene reveals a distinct expression pattern of Kinesin family 26B in mouse embryos. PMID:14727108
Triplex-forming oligonucleotide target sequences in the human genome. PMID:14726484
Secreted protein prediction system combining CJ-SPHMM, TMHMM, and PSORT. PMID:14724739
The LTR enhancer of ERV-9 human endogenous retrovirus is active in oocytes and progenitor cells in transgenic zebrafish and humans. PMID:14718667
Analysis of multiple genomic sequence alignments: a web resource, online tools, and lessons learned from analysis of mammalian SCL loci. PMID:14718377
A BAC- and BIBAC-based physical map of the soybean genome. PMID:14718376
Identification of androgen-coregulated protein networks from the microsomes of human prostate cancer cells. PMID:14709176
Analysis of sequence variations in several human genes using phosphoramidite bond DNA fragmentation and chip-based MALDI-TOF. PMID:14707175
Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis. PMID:14707168
Mapping and initial analysis of human subtelomeric sequence assemblies. PMID:14707167
Benzimidazole derivatives. 4. The recognition of the voluminous substituent attached to the basic amino group of 5-HT4 receptor antagonists. PMID:14703122
A comprehensive radiation hybrid map of bovine Chromosome 26 (BTA26): comparative chromosomal organization between HSA10q and BTA26 and BTA28. PMID:14694908
Comparative sequence analysis of a single-gene conserved segment in mouse and human. PMID:14694903
Identification of an envelope protein from the FRD family of human endogenous retroviruses (HERV-FRD) conferring infectivity and functional conservation among simians. PMID:14694139
Genome structure and thymic expression of an endogenous retrovirus in zebrafish. PMID:14694121
Predictive medicine in non-malignant urological disorders. PMID:14689222
DNA-methyltransferase 1 mRNA is selectively overexpressed in telencephalic GABAergic interneurons of schizophrenia brains. PMID:14684836
Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. PMID:14681826
GenePaint.org: an atlas of gene expression patterns in the mouse embryo. PMID:14681479
LIFEdb: a database for functional genomics experiments integrating information from external sources, and serving as a sample tracking system. PMID:14681468
HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE. PMID:14681467
Human protein reference database as a discovery resource for proteomics. PMID:14681466
AluGene: a database of Alu elements incorporated within protein-coding genes. PMID:14681464
FREP: a database of functional repeats in mouse cDNAs. PMID:14681460
ASD: the Alternative Splicing Database. PMID:14681360
DDBJ in the stream of various biological data. PMID:14681352
Functional genomics in rodent models of hypertension. PMID:14678491
Application of chromosomal substitution techniques in gene-function discovery. PMID:14678490
Identifying genes and genetic variation underlying human diseases and complex phenotypes via recombination mapping. PMID:14678489
Comparative genomic analysis as a tool for biological discovery. PMID:14678488
Genomic characterization of a repetitive motif strongly associated with developmental genes in Drosophila. PMID:14675495
Evolving strategies for the incorporation of bioinformatics within the undergraduate cell biology curriculum. PMID:14673489
CoAA, a nuclear receptor coactivator protein at the interface of transcriptional coactivation and RNA splicing. PMID:14673176
Targeted nuclear import of open reading frame 1 protein is required for in vivo retrotransposition of a telomere-specific non-long terminal repeat retrotransposon, SART1. PMID:14673147
Multiple variable first exons: a mechanism for cell- and tissue-specific gene regulation. PMID:14672974
Advances in pharmacogenomic research and development. PMID:14668540
Phylogenomic identification of five new human homologs of the DNA repair enzyme AlkB. PMID:14667252
Role of viruses in human evolution. PMID:14666532
The breakpoint region of the most common isochromosome, i(17q), in human neoplasia is characterized by a complex genomic architecture with large, palindromic, low-copy repeats. PMID:14666446
Comparison of the canine and human olfactory receptor gene repertoires. PMID:14659017
Clone-based systematic haplotyping (CSH): a procedure for physical haplotyping of whole genomes. PMID:14656974
Analysis of the gene-dense major histocompatibility complex class III region and its comparison to mouse. PMID:14656967
A genome-wide survey of human pseudogenes. PMID:14656963
Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. PMID:14656962
Shuffling of genes within low-copy repeats on 22q11 (LCR22) by Alu-mediated recombination events during evolution. PMID:14656960
Identification and characterization of multi-species conserved sequences. PMID:14656959
A PCR primer bank for quantitative gene expression analysis. PMID:14654707
Gene structure prediction in syntenic DNA segments. PMID:14654703
Secure web book to store structural genomics research data. PMID:14649296
Establishing the yeast Saccharomyces cerevisiae as a system for expression of human proteins on a proteome-scale. PMID:14649293
The German cDNA network: cDNAs, functional genomics and proteomics. PMID:14649292
The EGF-TM7 family: a postgenomic view. PMID:14647991
The nature and identification of quantitative trait loci: a community's view. PMID:14634638
Fragile site orthologs FHIT/FRA3B and Fhit/Fra14A2: evolutionarily conserved but highly recombinogenic. PMID:14630947
Rates of DNA duplication and mitochondrial DNA insertion in the human genome. PMID:14629044
Strand compositional asymmetries of nuclear DNA in eukaryotes. PMID:14629042
SVA elements are nonautonomous retrotransposons that cause disease in humans. PMID:14628287
The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PMID:14624247
Genomics, proteomics and bioinformatics of human heart failure. PMID:14620738
The dual nature of human extracellular superoxide dismutase: one sequence and two structures. PMID:14615576
A combinatorial network of evolutionarily conserved myelin basic protein regulatory sequences confers distinct glial-specific phenotypes. PMID:14614079
Characterizing embryonic gene expression patterns in the mouse using nonredundant sequence-based selection. PMID:14613977
Nucleotide frequency variation across human genes. PMID:14613976
POCUS: mining genomic sequence annotation to predict disease genes. PMID:14611661
Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates. PMID:14611660
Allelic heterogeneity in LINE-1 retrotransposition activity. PMID:14610717
Wnk1 kinase deficiency lowers blood pressure in mice: a gene-trap screen to identify potential targets for therapeutic intervention. PMID:14610273
The history of Pediatric Infectious Diseases. PMID:14605240
Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents. PMID:14597721
A panoramic view of gene expression in the human kidney. PMID:14595018
The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags. PMID:14593198
Splice site prediction with quadratic discriminant analysis using diversity measure. PMID:14576308
Genomic organization and linkage via a bidirectional promoter of the AP-3 (adaptor protein-3) mu3A and AK (adenosine kinase) genes: deletion mutants of AK in Chinese hamster cells extend into the AP-3 mu3A gene. PMID:14575525
De novo insertion of an Alu sequence in the coding region of the CLCN5 gene results in Dent's disease. PMID:14569459
The IDDM-associated solitary retroviral promoters DQ-LTR3 and DQ-LTR13 have a distinct impact on the expression of selected DQB1 genes in different cell lines in vitro. PMID:14566435
Human endogenous retroviruses with transcriptional potential in the brain. PMID:14564540
Adaptative value of a PKC-PKI55 feedback loop of inhibition that prevents the kinase's deregulation. PMID:14562957
Regulation of alternative splicing by SRrp86 and its interacting proteins. PMID:14559993
Genomewide screening for fusogenic human endogenous retrovirus envelopes identifies syncytin 2, a gene conserved on primate evolution. PMID:14557543
Hypomethylation of L1 retrotransposons in colorectal cancer and adjacent normal tissue. PMID:14534800
An endogenous retroviral long terminal repeat is the dominant promoter for human beta1,3-galactosyltransferase 5 in the colon. PMID:14534330
Genetic analysis of NF-kappaB/Rel transcription factors defines functional specificities. PMID:14532125
Transcriptional regulation of the human LINE-1 retrotransposon L1.2B. PMID:14530963
Development of human protein reference database as an initial platform for approaching systems biology in humans. PMID:14525934
Two distinct modes of microsatellite mutation processes: evidence from the complete genomic sequences of nine species. PMID:14525926
Positive selection on protein-length in the evolution of a primate sperm ion channel. PMID:14523237
Predicting aberrant CpG island methylation. PMID:14519846
Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing. PMID:14519201
Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina. PMID:14519200
Zinc fingers can act as Zn2+ sensors to regulate transcriptional activation domain function. PMID:14517251
Genome-scale functional profiling of the mammalian AP-1 signaling pathway. PMID:14514886
DFNB39, a recessive form of sensorineural hearing impairment, maps to chromosome 7q11.22-q21.12. PMID:14512973
Functional intergenic transcription: a case study of the X-inactivation centre. PMID:14511490
Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. PMID:14508680
Evolution of olfactory receptor genes in the human genome. PMID:14507991
Identification of a family of cAMP response element-binding protein coactivators by genome-scale functional analysis in mammalian cells. PMID:14506290
An Alu transposition model for the origin and expansion of human segmental duplications. PMID:14505274
Probe selection for high-density oligonucleotide arrays. PMID:14500916
Discovery of novel splice forms and functional analysis of cancer-specific alternative splicing in human expressed sequences. PMID:14500827
Structures of trinucleotide repeats in human transcripts and their functional implications. PMID:14500808
Heparan sulfate 2-O-sulfotransferase (Hs2st) and mouse development. PMID:12975615
Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. PMID:12975311
Parallel analysis of transcript and metabolic profiles: a new approach in systems biology. PMID:12973302
Transcription factories: quantitative studies of nanostructures in the mammalian nucleus. PMID:12971722
Survey of human genes of retroviral origin: identification and transcriptome of the genes with coding capacity for complete envelope proteins. PMID:12970426
The COG database: an updated version includes eukaryotes. PMID:12969510
Repetitive elements in genomes of parasitic protozoa. PMID:12966140
cDNA2Genome: a tool for mapping and annotating cDNAs. PMID:12964951
Molecular evolutionary analysis of the widespread piggyBac transposon family and related "domesticated" sequences. PMID:12955498
RNA interference: from an ancient mechanism to a state of the art therapeutic application? PMID:12955224
Conversion of sub-megasized DNA to desired structures using a novel Bacillus subtilis genome vector. PMID:12954788
Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. PMID:12954770
GANESH: software for customized annotation of genome regions. PMID:12952886
PANTHER: a library of protein families and subfamilies indexed by function. PMID:12952881
Assessment of genome-wide protein function classification for Drosophila melanogaster. PMID:12952880
Haplotype information and linkage disequilibrium mapping for single nucleotide polymorphisms. PMID:12952879
Retrotransposons and their recognition of pol II promoters: a comprehensive survey of the transposable elements from the complete genome sequence of Schizosaccharomyces pombe. PMID:12952871
The organization and evolution of the human Y chromosome. PMID:12952526
Prospects of genetic epidemiology in the 21st century. PMID:12952133
Comparative analysis of the base biases at the gene terminal portions in seven eukaryote genomes. PMID:12930971
Insights from human/mouse genome comparisons. PMID:12925891
EST-based gene discovery in pig: virtual expression patterns and comparative mapping to human. PMID:12925889
Messenger RNA reprogramming by spliceosome-mediated RNA trans-splicing. PMID:12925685
Bioinformatics and medical informatics: collaborations on the road to genomic medicine? PMID:12925552
ISSOL '02. Abstracts of the 13th International Conference on the Origin of Life. Oaxaca, Mexico, June 30-July 5, 2002. PMID:12924381
Identification of a DNA-binding site and transcriptional target for the EWS-WT1(+KTS) oncoprotein. PMID:12923058
U1 snRNP-dependent function of TIAR in the regulation of alternative RNA processing of the human calcitonin/CGRP pre-mRNA. PMID:12917321
The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes. PMID:12915492
Neocentromeres in 15q24-26 map to duplicons which flanked an ancestral centromere in 15q25. PMID:12915487
Locating sequence on FPC maps and selecting a minimal tiling path. PMID:12915486
Application of comparative genomics in the identification and analysis of novel families of membrane-associated receptors in bacteria. PMID:12914674
THoR: a tool for domain discovery and curation of multiple alignments. PMID:12914660
Refinement of a chimpanzee pericentric inversion breakpoint to a segmental duplication cluster. PMID:12914658
Recent segmental and gene duplications in the mouse genome. PMID:12914656
Potential for retroposition by old Alu subfamilies. PMID:12911029
Atypical expansion in mice of the sensory neuron-specific Mrg G protein-coupled receptor family. PMID:12909716
An important role for RUNX3 in human L1 transcription and retrotransposition. PMID:12907736
Horizontal gene transfer: a critical view. PMID:12902542
A cattle-human comparative map built with cattle BAC-ends and human genome sequence. PMID:12902387
Effects of recombination rate and gene density on transposable element distributions in Arabidopsis thaliana. PMID:12902382
A gene recommender algorithm to identify coexpressed genes in C. elegans. PMID:12902378
Cotranscriptional recruitment of the U1 snRNP to intron-containing genes in yeast. PMID:12897147
The Drosophila dysfusion basic helix-loop-helix (bHLH)-PAS gene controls tracheal fusion and levels of the trachealess bHLH-PAS protein. PMID:12897136
Localization of a novel autosomal recessive non-syndromic hearing impairment locus (DFNB38) to 6q26-q27 in a consanguineous kindred from Pakistan. PMID:12890929
Mass spectrometric analysis of glycans in elucidating the pathogenesis of CDG type IIx. PMID:12889655
Parallel competition analysis of Saccharomyces cerevisiae strains differing by a single base using polymerase colonies. PMID:12888536
The ERV-9 LTR enhancer is not blocked by the HS5 insulator and synthesizes through the HS5 site non-coding, long RNAs that regulate LTR enhancer function. PMID:12888519
Patterns of sequence conservation at termini of long terminal repeat (LTR) retrotransposons and DNA transposons in the human genome: lessons from phage Mu. PMID:12888514
The human genome contains many types of chimeric retrogenes generated through in vivo RNA recombination. PMID:12888497
Intracellular mRNA cleavage by 3' tRNase under the direction of 2'-O-methyl RNA heptamers. PMID:12888494
Identification of Plasmodium falciparum antigens by antigenic analysis of genomic and proteomic data. PMID:12886016
Determination of molecular alignment tensors without backbone resonance assignment: Aid to rapid analysis of protein-protein interactions. PMID:12878840
The evolution, distribution and diversity of endogenous retroviruses. PMID:12876457
Effects of the interaction between genotype and environment. Research into the genetic epidemiology of alcohol dependence. PMID:12875047
Genomic approaches to the genetics of alcoholism. PMID:12875046
Nonparametric disequilibrium mapping of functional sites using haplotypes of multiple tightly linked single-nucleotide polymorphism markers. PMID:12871923
Novel functional role of CA repeats and hnRNP L in RNA stability. PMID:12869704
Dragon gene start finder: an advanced system for finding approximate locations of the start of gene transcriptional units. PMID:12869582
Sequence divergence within transposable element families in the Drosophila melanogaster genome. PMID:12869581
The origin of human chromosome 1 and its homologs in placental mammals. PMID:12869576
Gene transfer from organelles to the nucleus: frequent and in big chunks. PMID:12861078
A two-locus gene conversion model with selection and its application to the human RHCE and RHD genes. PMID:12857961
Computational approaches to identify promoters and cis-regulatory elements in plant genomes. PMID:12857799
Revamp a model-status and prospects of the Dictyostelium genome project. PMID:12856150
On the number of protein-protein interactions in the yeast proteome. PMID:12853633
The first completed genome sequence from a teleost fish (Fugu rubripes) adds significant diversity to the nuclear receptor superfamily. PMID:12853622
Bacteria-host communication: the language of hormones. PMID:12847292
Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii. PMID:12844361
A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening set. PMID:12844283
Intronic sequences flanking alternatively spliced exons are conserved between human and mouse. PMID:12840041
HPr kinase/phosphorylase, the sensor enzyme of catabolite repression in Gram-positive bacteria: structural aspects of the enzyme and the complex with its protein substrate. PMID:12837773
The cadherin superfamily database. PMID:12836704
Introns in, introns out in plant gene families: a genomic approach of the dynamics of gene structure. PMID:12836690
The 2R hypothesis and the human genome sequence. PMID:12836689
2R or not 2R: testing hypotheses of genome duplication in early vertebrates. PMID:12836688
More genes in vertebrates? PMID:12836687
Major transitions in evolution by genome fusions: from prokaryotes to eukaryotes, metazoans, bilaterians and vertebrates. PMID:12836681
Gene duplication and other evolutionary strategies: from the RNA world to the future. PMID:12836680
Mapping of 19032 mouse cDNAs on mouse chromosomes. PMID:12836671
A transcription map of the 6p22.3 reading disability locus identifying candidate genes. PMID:12834540
Novel types of mutation in the choroideremia ( CHM) gene: a full-length L1 insertion and an intronic mutation activating a cryptic exon. PMID:12827496
Divergence of the genes on human chromosome 21 between human and other hominoids and variation of substitution rates among transcription units. PMID:12826612
The role of genetic polymorphisms in environmental health. PMID:12826477
Automated Gene Ontology annotation for anonymous sequence data. PMID:12824400
Dragon Gene Start Finder identifies approximate locations of the 5' ends of genes. PMID:12824365
PromoSer: A large-scale mammalian promoter and transcription start site identification service. PMID:12824364
MGAlignIt: A web service for the alignment of mRNA/EST and genomic sequences. PMID:12824360
The mammalian protein-protein interaction database and its viewing system that is linked to the main FANTOM2 viewer. PMID:12819152
Connecting sequence and biology in the laboratory mouse. PMID:12819150
DNA book. PMID:12819147
G protein-coupled receptor genes in the FANTOM2 database. PMID:12819145
Kinesin superfamily proteins (KIFs) in the mouse transcriptome. PMID:12819144
Phosphoregulators: protein kinases and protein phosphatases of mouse. PMID:12819143
Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome. PMID:12819142
Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage. PMID:12819134
The mouse secretome: functional classification of the proteins secreted into the extracellular environment. PMID:12819133
Antisense transcripts with FANTOM2 clone set and their implications for gene regulation. PMID:12819130
Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome. PMID:12819126
Of mice and men: phylogenetic footprinting aids the discovery of regulatory elements. PMID:12814519
TMC and EVER genes belong to a larger novel family, the TMC gene family encoding transmembrane proteins. PMID:12812529
Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution. PMID:12810957
Expansion of the receptor-like kinase/Pelle gene family and receptor-like proteins in Arabidopsis. PMID:12805585
Functional analysis of the endogenous retroviral promoter of the human endothelin B receptor gene. PMID:12805445
Genetic variation among world populations: inferences from 100 Alu insertion polymorphisms. PMID:12805277
An active non-LTR retrotransposon with tandem structure in the compact genome of the pufferfish Tetraodon nigroviridis. PMID:12805276
Identification of promoter regions in the human genome by using a retroviral plasmid library-based functional reporter gene assay. PMID:12805274
A method to assess compositional bias in biological sequences and its application to prion-like glutamine/asparagine-rich domains in eukaryotic proteomes. PMID:12801414
Horizontally transferred genes in plant-parasitic nematodes: a high-throughput genomic approach. PMID:12801413
What makes a mitochondrion? PMID:12801406
Comparative sequencing of human and chimpanzee MHC class I regions unveils insertions/deletions as the major path to genomic divergence. PMID:12799463
Nuclear matrix association of the human beta-globin locus utilizing a novel approach to quantitative real-time PCR. PMID:12799453
Computational discovery of internal micro-exons. PMID:12799353
New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes. PMID:12799346
End-sequence profiling: sequence-based analysis of aberrant genomes. PMID:12788976
Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs. PMID:12783626
Construction and utility of 10-kb libraries for efficient clone-gap closure for rice genome sequencing. PMID:12783166
Characterization, expression and phylogenetic study of R2R3-MYB genes in orchid. PMID:12777054
Faithful expression of a tagged Fugu WT1 protein from a genomic transgene in zebrafish: efficient splicing of pufferfish genes in zebrafish but not mice. PMID:12771206
Identification of conserved regulatory elements by comparative genome analysis. PMID:12760745
The effect of nonsense codons on splicing: a genomic analysis. PMID:12756320
Continuous exchange of sequence information between dispersed Tc1 transposons in the Caenorhabditis elegans genome. PMID:12750326
Genome informatics: current status and future prospects. PMID:12750305
A high resolution physical and RH map of pig chromosome 6q1.2 and comparative analysis with human chromosome 19q13.1. PMID:12744726
Human-mouse gene identification by comparative evidence integration and evolutionary analysis. PMID:12743024
Assessment of SAGE in transcript identification. PMID:12743019
A genomewide survey of developmentally relevant genes in Ciona intestinalis. IX. Genes for muscle structural proteins. PMID:12740698
Coincidence of synteny breakpoints with malignancy-related deletions on human chromosome 3. PMID:12738884
A genomewide survey of developmentally relevant genes in Ciona intestinalis. II. Genes for homeobox transcription factors. PMID:12736825
Real-time PCR-based method for the estimation of genome sizes. PMID:12736322
Conservation of human alternative splice events in mouse. PMID:12736303
Translational control of Scamper expression via a cell-specific internal ribosome entry site. PMID:12736299
Identifying related L1 retrotransposons by analyzing 3' transduced sequences. PMID:12734010
Analysis of 5'-end sequences of chimpanzee cDNAs. PMID:12727913
Selecting open reading frames from DNA. PMID:12727911
Selection on human genes as revealed by comparisons to chimpanzee cDNA. PMID:12727903
Genome size evolution in pufferfish: a comparative analysis of diodontid and tetraodontid pufferfish genomes. PMID:12727902
Retroposed copies of the HMG genes: a window to genome dynamics. PMID:12727900
Complex evolution of 7E olfactory receptor genes in segmental duplications. PMID:12727898
Comparative analysis of vertebrate dystrophin loci indicate intron gigantism as a common feature. PMID:12727896
Functional aspects of protein mono-ADP-ribosylation. PMID:12727863
Crawling into a new era-the Dictyostelium genome project. PMID:12727861
Survival of Tdc transposable elements of the En/Spm superfamily in the carrot genome. PMID:12715153
A semiautomated approach to gene discovery through expressed sequence tag data mining: discovery of new human transporter genes. PMID:12713273
A method for the assessment of disease associations with single-nucleotide polymorphism haplotypes and environmental variables in case-control studies. PMID:12704570
Dispersal of NK homeobox gene clusters in amphioxus and humans. PMID:12704239
Mapping by sequencing the Pneumocystis genome using the ordering DNA sequences V3 tool. PMID:12702676
MatchMiner: a tool for batch navigation among gene and gene product identifiers. PMID:12702208
Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence. PMID:12702206
Comparative genomic tools and databases: providing insights into the human genome. PMID:12697725
Refined physical map of the human PAX2/HOX11/NFKB2 cancer gene region at 10q24 and relocalization of the HPV6AI1 viral integration site to 14q13.3-q21.1. PMID:12697057
The genomification of medicine. PMID:12695360
Human chromosome 7: DNA sequence and biology. PMID:12690205
Connexin 26 35delG does not represent a mutational hotspot. PMID:12684873
Interaction of CA repeat polymorphism of the endothelial nitric oxide synthase and hyperhomocysteinemia in acute coronary syndromes: evidence of gender-specific differences. PMID:12684755
Using analytical ultracentrifugation to study compositional variation in vertebrate genomes. PMID:12684711
Transcript identification by analysis of short sequence tags--influence of tag length, restriction site and transcript database. PMID:12682372
Hot L1s account for the bulk of retrotransposition in the human population. PMID:12682288
The G protein-coupled receptor repertoires of human and mouse. PMID:12679517
An occupational reproductive research agenda for the third millennium. PMID:12676620
The microRNAs of Caenorhabditis elegans. PMID:12672692
High-density map of short tandem repeats across the human major histocompatibility complex. PMID:12671742
GALA, a database for genomic sequence alignments and annotations. PMID:12671007
Nonrandom tripeptide sequence distributions at protein carboxyl termini. PMID:12671002
Classification of race and ethnicity: implications for public health. PMID:12668755
Overexpressed nuclear factor-kappaB can participate in endogenous C-reactive protein induction, and enhances the effects of C/EBPbeta and signal transducer and activator of transcription-3. PMID:12667216
Roles of hnRNP A1, SR proteins, and p68 helicase in c-H-ras alternative splicing regulation. PMID:12665590
DNA helix: the importance of being GC-rich. PMID:12654999
Computationally identifying novel NF-kappa B-regulated immune genes in the human genome. PMID:12654722
Efficient high-throughput resequencing of genomic DNA. PMID:12654721
Sequence information can be obtained from single DNA molecules. PMID:12651960
Irruption of genomics in the search for disease related genes. PMID:12651875
Genome architecture catalyzes nonrecurrent chromosomal rearrangements. PMID:12649807
High-resolution imaging of normal anatomy, and neural and adrenal malformations in mouse embryos using magnetic resonance microscopy. PMID:12647873
Mineralized tissue and vertebrate evolution: the secretory calcium-binding phosphoprotein gene cluster. PMID:12646701
Bioinformatic analysis of the human mu opioid receptor (OPRM1) splice and polymorphic variants. PMID:12645995
Examination of sequence homology between human chromosome 20 and the mouse genome: intense conservation of many genomic elements. PMID:12644935
Mice lacking the 68-amino-acid, mammal-specific N-terminal extension of WT1 develop normally and are fertile. PMID:12640141
Combined analysis of genome scans of dutch and finnish families reveals a susceptibility locus for high-density lipoprotein cholesterol on chromosome 16q. PMID:12638083
ATLAS: a system to selectively identify human-specific L1 insertions. PMID:12632328
Rapid direct sequence analysis of the dystrophin gene. PMID:12632325
More on the sequencing of the human genome. PMID:12631699
Revisiting the independence of the publicly and privately funded drafts of the human genome. PMID:12631691
Compounds isolated at the Institute of Microbiology in 1989-2001 and future trends. PMID:12630311
Sequence analyses of G-protein-coupled receptors: similarities to rhodopsin. PMID:12627940
A high-throughput gene expression analysis technique using competitive PCR and matrix-assisted laser desorption ionization time-of-flight MS. PMID:12624187
The spatial targeting and nuclear matrix binding domains of SRm160. PMID:12624182
Genome-wide analysis of microsatellite repeats in humans: their abundance and density in specific genomic regions. PMID:12620123
Positional clustering of differentially expressed genes on human chromosomes 20, 21 and 22. PMID:12620117
Schizosaccharomyces pombe essential genes: a pilot study. PMID:12618370
Segmental duplications in euchromatic regions of human chromosome 5: a source of evolutionary instability and transcriptional innovation. PMID:12618367
Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome. PMID:12618366
Role of pharmacogenomics in individualising treatment with SSRIs. PMID:12617694
Molecular classification of familial non-BRCA1/BRCA2 breast cancer. PMID:12610208
Target discovery and validation in the post-genomic era. PMID:12608710
The Tre2 (USP6) oncogene is a hominoid-specific gene. PMID:12604796
Genome-wide targeted search for human specific and polymorphic L1 integrations. PMID:12601470
Transgenerational inheritance of epigenetic states at the murine Axin(Fu) allele occurs after maternal and paternal transmission. PMID:12601169
The transcriptional activity of human Chromosome 22. PMID:12600945
Relevance of sequence and structure elements for deletion events in the dystrophin gene major hot-spot. PMID:12596052
Pyruvate carboxylase is an essential protein in the assembly of yeast peroxisomal oligomeric alcohol oxidase. PMID:12589070
A P-element insertion screen identified mutations in 455 novel essential genes in Drosophila. PMID:12586707
Detection and analysis of spliced chimeric mRNAs in sequence databanks. PMID:12582262
Influences of chromosome size, gene density and nuclear position on the frequency of constitutional translocations in the human population. PMID:12575798
Large differences between LINE-1 amplification rates in the human and chimpanzee lineages. PMID:12574987
A vertebrate RNA-binding protein Fox-1 regulates tissue-specific splicing via the pentanucleotide GCAUG. PMID:12574126
Tracking an embryonic L1 retrotransposition event. PMID:12569170
A new twist on transposons: the maize genome harbors helitron insertion. PMID:12566572
A complexity reduction algorithm for analysis and annotation of large genomic sequences. PMID:12566410
Sequence analysis of a functional Drosophila centromere. PMID:12566396
Genomic sequence and transcriptional profile of the boundary between pericentromeric satellites and genes on human chromosome arm 10p. PMID:12566394
A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. PMID:12566392
A novel algorithm for computational identification of contaminated EST libraries. PMID:12560505
Demystified. Human endogenous retroviruses. PMID:12560456
Of urchins and men: evolution of an alternative splicing unit in fibroblast growth factor receptor genes. PMID:12554864
Future directions in protein function prediction. PMID:12549818
Chromatin insulation by a transcriptional activator. PMID:12547916
The refined crystal structure of an eel pout type III antifreeze protein RD1 at 0.62-A resolution reveals structural microheterogeneity of protein and solvation. PMID:12547803
Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome. PMID:12537575
Whole-genome analysis of animal A- and B-type cyclins. PMID:12537559
The repertoire of protein kinases encoded in the draft version of the human genome: atypical variations and uncommon domain combinations. PMID:12537555
Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level. PMID:12537549
Computational comparison of two mouse draft genomes and the human golden path. PMID:12537546
Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics. PMID:12529507
The comprehensive mouse radiation hybrid map densely cross-referenced to the recombination map: a tool to support the sequence assemblies. PMID:12529315
Strategies and tools for whole-genome alignments. PMID:12529308
Distinguishing regulatory DNA from neutral sites. PMID:12529307
Pericentromeric duplications in the laboratory mouse. PMID:12529306
Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. PMID:12529304
Reevaluating human gene annotation: a second-generation analysis of chromosome 22. PMID:12529303
Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. PMID:12529302
Cross-species sequence comparisons: a review of methods and available resources. PMID:12529301
The phylogenetic diversity of eukaryotic transcription. PMID:12527774
Nucleotide variability at G6pd and the signature of malarial selection in humans. PMID:12524354
Vanishing GC-rich isochores in mammalian genomes. PMID:12524353
The evolution of isochores: evidence from SNP frequency distributions. PMID:12524350
Telomeric P elements associated with cytotype regulation of the P transposon family in Drosophila melanogaster. PMID:12524339
Application of DNA microarrays in pharmacogenomics and toxicogenomics. PMID:12523654
Enlarged FAMSBASE: protein 3D structure models of genome sequences for 41 species. PMID:12520053
The InterPro Database, 2003 brings increased coverage and new features. PMID:12520011
ASAP: the Alternative Splicing Annotation Project. PMID:12519958
ParaDB: a tool for paralogy mapping in vertebrate genomes. PMID:12519948
The UCSC Genome Browser Database. PMID:12519945
The esterase and PHD domains in CR1-like non-LTR retrotransposons. PMID:12519904
A second kindred linked to DFNA20 (17q25.3) reduces the genetic interval. PMID:12519370
Sequence variations in the public human genome data reflect a bottlenecked population history. PMID:12502794
Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. PMID:12502788
Cynomolgus monkey testicular cDNAs for discovery of novel human genes in the human genome sequence. PMID:12498619
Isolation and biochemical characterization of LEAP-2, a novel blood peptide expressed in the liver. PMID:12493837
Functional second genes generated by retrotransposition of the X-linked ribosomal protein genes. PMID:12490704
Common variations in noncoding regions of the human natriuretic peptide receptor A gene have quantitative effects. PMID:12483301
Dasheng and RIRE2. A nonautonomous long terminal repeat element and its putative autonomous partner in the rice genome. PMID:12481052
An ensemble method for identifying regulatory circuits with special reference to the qa gene cluster of Neurospora crassa. PMID:12477937
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. PMID:12477932
POTE, a highly homologous gene family located on numerous chromosomes and expressed in prostate, ovary, testis, placenta, and prostate cancer. PMID:12475935
The transcription cycle of RNA polymerase II in living cells. PMID:12473686
HapScope: a software system for automated and visual analysis of functionally annotated haplotypes. PMID:12466546
Highly efficient modification of bacterial artificial chromosomes (BACs) using novel shuttle vectors containing the R6Kgamma origin of replication. PMID:12466304
A scalable high-throughput chemical synthesizer. PMID:12466300
Generalized gap model for bacterial artificial chromosome clone fingerprint mapping and shotgun sequencing. PMID:12466299
Retroposed new genes out of the X in Drosophila. PMID:12466289
Selecting for functional alternative splices in ESTs. PMID:12466287
Distribution and characterization of regulatory elements in the human genome. PMID:12466286
Evidence for a fast, intrachromosomal conversion mechanism from mapping of nucleotide variants within a homogeneous alpha-satellite DNA array. PMID:12466285
A common mechanism for mitotic inactivation of C2H2 zinc finger DNA-binding domains. PMID:12464629
Accessing genomic data through XML-based remote procedure calls. PMID:12463907
Delivering bioinformatics training: bridging the gaps between computer science and biomedicine. PMID:12463819
Optimizing gene expression analysis in archival brain tissue. PMID:12462400
A long terminal repeat retrotransposon of fission yeast has strong preferences for specific sites of insertion. PMID:12455970
Evidence for lateral transfer of genes encoding ferredoxins, nitroreductases, NADH oxidase, and alcohol dehydrogenase 3 from anaerobic prokaryotes to Giardia lamblia and Entamoeba histolytica. PMID:12455953
Highly condensed potato pericentromeric heterochromatin contains rDNA-related tandem repeats. PMID:12454086
Identification of genes that are downregulated in the absence of the POU domain transcription factor pou3f1 (Oct-6, Tst-1, SCIP) in sciatic nerve. PMID:12451123
Map error reduction: using genetic and sequence-based physical maps to order closely linked markers. PMID:12446985
Genomic expansion and clustering of ZAD-containing C2H2 zinc-finger genes in Drosophila. PMID:12446571
Total sequence decomposition distinguishes functional modules, "molegos" in apurinic/apyrimidinic endonucleases. PMID:12445335
Extension of a local backbone description using a structural alphabet: a new approach to the sequence-structure relationship. PMID:12441385
SNP genotyping on a genome-wide amplified DOP-PCR template. PMID:12434007
Comparison of whole genome assemblies of the human genome. PMID:12434005
Finding signals that regulate alternative splicing in the post-genomic era. PMID:12429065
Decrease in hnRNP A/B expression during erythropoiesis mediates a pre-mRNA splicing switch. PMID:12426391
Protein-protein interactions between large proteins: two-hybrid screening using a functionally classified library composed of long cDNAs. PMID:12421765
Identification of new herpesvirus gene homologs in the human genome. PMID:12421761
Identification of candidate genes regulating HDL cholesterol using a chromosomal region expression array. PMID:12421756
Segmental polymorphisms in the proterminal regions of a subset of human chromosomes. PMID:12421753
Signatures of domain shuffling in the human genome. PMID:12421750
Structural characterization of the human proteome. PMID:12421749
Promoter proximal splice sites enhance transcription. PMID:12414732
Gene expression studies on soft tissue tumors. PMID:12414500
Human L1 element target-primed reverse transcription in vitro. PMID:12411507
EZ-Retrieve: a web-server for batch retrieval of coordinate-specified human DNA sequences and underscoring putative transcription factor-binding sites. PMID:12409480
tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features. PMID:12403461
Protein kinase CK2: structure, regulation and role in cellular decisions of life and death. PMID:12396231
Comparative proteome analysis of human temporal cortex lobes by two-dimensional electrophoresis and identification of selected common proteins. PMID:12396097
Receptor pharmacogenetics: relevance to CNS syndromes. PMID:12392580
A computational/functional genomics approach for the enrichment of the retinal transcriptome and the identification of positional candidate retinopathy genes. PMID:12391299
Interphase chromosomes in Arabidopsis are organized as well defined chromocenters from which euchromatin loops emanate. PMID:12384572
Birth and death of protein domains: a simple model of evolution explains power law behavior. PMID:12379152
Histidine protein kinases: key signal transducers outside the animal kingdom. PMID:12372152
Variations in abundance: genome-wide responses to genetic variation and vice versa. PMID:12372150
Molecular archeology of L1 insertions in the human genome. PMID:12372140
On the importance of being finished. PMID:12372139
Computer assisted cloning of human neutral alpha-glucosidase C (GANC): a new paralog in the glycosyl hydrolase gene family 31. PMID:12370436
Remarkable compartmentalization of transposable elements and pseudogenes in the heterochromatin of the Tetraodon nigroviridis genome. PMID:12368471
Retroelement distributions in the human genome: variations associated with age and proximity to genes. PMID:12368240
Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. PMID:12368239
Current methods of gene prediction, their strengths and weaknesses. PMID:12364589
Genetic and physiological data implicating the new human gene G72 and the gene for D-amino acid oxidase in schizophrenia. PMID:12364586
Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. PMID:12297621
Genetics of schizophrenia: from animal models to clinical studies. PMID:12271789
The SPOT technique as a tool for studying protein tyrosine phosphatase substrate specificities. PMID:12237455
Autism: in search of susceptibility genes. PMID:12230302
Sushi gets serious: the draft genome sequence of the pufferfish Fugu rubripes. PMID:12225591
Military research needs in biomedical informatics. PMID:12223503
Cures for the Third World's problems: the application of genomics to the diseases plaguing the developing world may have huge medical and economic benefits for those countries and might even prevent armed conflict. PMID:12223456
The functional importance of disease-associated mutation. PMID:12220483
Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags. PMID:12213963
Deterministic mutation rate variation in the human genome. PMID:12213772
Active Alu element "A-tails": size does matter. PMID:12213770
Comparative genomic sequence analysis of the human chromosome 21 Down syndrome critical region. PMID:12213769
A new method for large scale isolation of kidney glomeruli from mice. PMID:12213707
Human diallelic insertion/deletion polymorphisms. PMID:12205564
Dictionary-driven protein annotation. PMID:12202776
Genome-wide detection of tissue-specific alternative splicing in the human transcriptome. PMID:12202761
Synthesis and polymerase incorporation of 5'-amino-2',5'-dideoxy-5'-N-triphosphate nucleotides. PMID:12202759
Inactivation of CMP-N-acetylneuraminic acid hydroxylase occurred prior to brain expansion during human evolution. PMID:12192086
Classification of human B-ZIP proteins based on dimerization properties. PMID:12192032
Genetic linkage of attention-deficit/hyperactivity disorder on chromosome 16p13, in a region implicated in autism. PMID:12187510
A nonsense mutation in the gene encoding 2'-5'-oligoadenylate synthetase/L1 isoform is associated with West Nile virus susceptibility in laboratory mice. PMID:12186974
Transcriptome analysis of the retina. PMID:12186651
The SWIRM domain: a conserved module found in chromosomal proteins points to novel chromatin-modifying activities. PMID:12186646
The DNA-binding region of RAG 1 is not a homeodomain. PMID:12186638
Interactions between two fission yeast serine/arginine-rich proteins and their modulation by phosphorylation. PMID:12186627
The very youngest science. PMID:12186170
Promising deliveries, delivering promises. PMID:12186158
Application of physiological genomics to the study of hearing disorders. PMID:12181277
DNA probes on beads arrayed in a capillary, 'Bead-array', exhibited high hybridization performance. PMID:12177315
A functional gene discovery in the Fas-mediated pathway to apoptosis by analysis of transiently expressed randomized hybrid-ribozyme libraries. PMID:12177303
Parallel construction of orthologous sequence-ready clone contig maps in multiple species. PMID:12176935
Automated de novo identification of repeat sequence families in sequenced genomes. PMID:12176934
Functional cloning, sorting, and expression profiling of nucleic acid-binding proteins. PMID:12176925
Predicting protein cellular localization using a domain projection method. PMID:12176924
Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. PMID:12172016
Conversion of nucleotides sequences into genomic signals. PMID:12169214
Enzyme activity profiles of the secreted and membrane proteome that depict cancer cell invasiveness. PMID:12149457
Visualizing the genome: techniques for presenting human genome data and annotations. PMID:12149135
Binding of FGF-1 variants to protein kinase CK2 correlates with mitogenicity. PMID:12145206
Mutations in the DNAH11 (axonemal heavy chain dynein type 11) gene cause one form of situs inversus totalis and most likely primary ciliary dyskinesia. PMID:12142464
Single nucleotide polymorphism seeking long term association with complex disease. PMID:12140314
Tracing the LINEs of human evolution. PMID:12138175
Does hereditary metabolic disease modulate senescence and ageing? PMID:12137233
New names for old disciplines. PMID:12137224
Genome-wide comparison of differences in the integration sites of interspersed repeats between closely related genomes. PMID:12136119
Multiplex SNP genotyping in pooled DNA samples by a four-colour microarray system. PMID:12136118
Selective stimulation of translational expression by Alu RNA. PMID:12136107
Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences. PMID:12136103
NotI flanking sequences: a tool for gene discovery and verification of the human genome. PMID:12136098
General statistics of stochastic process of gene expression in eukaryotic cells. PMID:12136033
Dasheng: a recently amplified nonautonomous long terminal repeat element that is a major component of pericentromeric regions in rice. PMID:12136031
Chromosomal elements evolve at different rates in the Drosophila genome. PMID:12136017
Bench-to-bedside review: fulfilling promises of the Human Genome Project. PMID:12133180
Ischemia induces a translocation of the splicing factor tra2-beta 1 and changes alternative splicing patterns in the brain. PMID:12122051
Deductions about the number, organization, and evolution of genes in the tomato genome based on analysis of a large expressed sequence tag collection and selective genomic sequencing. PMID:12119366
Hint, Fhit, and GalT: function, structure, evolution, and mechanism of three branches of the histidine triad superfamily of nucleotide hydrolases and transferases. PMID:12119013
E. coli chromosomal DNA in a transgene locus created by microprojectile bombardment in tobacco. PMID:12113463
Simultaneous sequencing of multiple polymerase chain reaction products and combined polymerase chain reaction with cycle sequencing in single reactions. PMID:12107086
Expression and genomic analysis of midasin, a novel and highly conserved AAA protein distantly related to dynein. PMID:12102729
TAPP1 and TAPP2 are targets of phosphatidylinositol 3-kinase signaling in B cells: sustained plasma membrane recruitment triggered by the B-cell antigen receptor. PMID:12101241
Finding the needle in the haystack: why high-throughput screening is good for your health. PMID:12100740
GFScan: a gene family search tool at genomic DNA level. PMID:12097353
Validation of DNA sequences using mass spectrometry coupled with nucleoside mass tagging. PMID:12097352
Single nucleotide polymorphism mapping using genome-wide unique sequences. PMID:12097348
Alu-containing exons are alternatively spliced. PMID:12097342
The role of lineage-specific gene family expansion in the evolution of eukaryotes. PMID:12097341
A deletion-generator compound element allows deletion saturation analysis for genomewide phenotypic annotation. PMID:12096187
Evidence consistent with human L1 retrotransposition in maternal meiosis I. PMID:12094329
Full-length messenger RNA sequences greatly improve genome annotation. PMID:12093376
Estimation of genetic distances from human and mouse introns. PMID:12093375
ORMDL proteins are a conserved new family of endoplasmic reticulum membrane proteins. PMID:12093374
Parameter optimized surfaces (POPS): analysis of key interactions and conformational changes in the ribosome. PMID:12087181
The chAB4 and NF1-related long-range multisequence DNA families are contiguous in the centromeric heterochromatin of several human chromosomes. PMID:12087175
Obtaining reliable information from minute amounts of RNA using cDNA microarrays. PMID:12086591
Reduced risk of synovial sarcoma in females: X-chromosome inactivation? PMID:12085251
SKIP is an indispensable factor for Caenorhabditis elegans development. PMID:12084813
Genetics and social class. PMID:12080161
Maternal transmission of P element transposase activity in Drosophila melanogaster depends on the last P intron. PMID:12077325
Novel endogenous retrovirus in rabbits previously reported as human retrovirus 5. PMID:12072509
A comprehensive analysis of recently integrated human Ta L1 elements. PMID:12070800
Microsatellite evolution inferred from human-chimpanzee genomic sequence alignments. PMID:12070344
The family of toxin-related ecto-ADP-ribosyltransferases in humans and the mouse. PMID:12070318
Nutritional genomics. PMID:12065270
An electrochemical detection scheme for identification of single nucleotide polymorphisms using hairpin-forming probes. PMID:12060693
Evolution of gene fusions: horizontal transfer versus independent events. PMID:12049665
Murine NFX.1: isolation and characterization of its messenger RNA, mapping of its chromosomal location and assessment of its developmental expression. PMID:12047746
Role of synaptotagmin in Ca2+-triggered exocytosis. PMID:12047220
The human genome browser at UCSC. PMID:12045153
Tandem repeats in protein coding regions of primate genes. PMID:12045144
Comparative sequence analysis of the X-inactivation center region in mouse, human, and bovine. PMID:12045143
Pattern of organization of human mitochondrial pseudogenes in the nuclear genome. PMID:12045142
Spinocerebellar degenerations: an update. PMID:12044253
Systematic sequencing of cDNA clones using the transposon Tn5. PMID:12034835
Dissection of a complex enhancer element: maintenance of keratinocyte specificity but loss of differentiation specificity. PMID:12024040
SRp30c is a repressor of 3' splice site utilization. PMID:12024014
Efficient recovery of centric heterochromatin P-element insertions in Drosophila melanogaster. PMID:12019236
Intron-size constraint as a mutational mechanism in Rothmund-Thomson syndrome. PMID:12016592
Genome-wide identification of tissue-specific enhancers in the Ciona tadpole. PMID:12011440
Genetics in rheumatoid arthritis. PMID:12010603
An element in the 3' untranslated region of human LINE-1 retrotransposon mRNA binds NXF1(TAP) and can function as a nuclear export element. PMID:12003494
A high-density cytogenetic map of the Aegilops tauschii genome incorporating retrotransposons and defense-related genes: insights into cereal chromosome structure and function. PMID:11999849
A novel interferon regulatory factor (IRF), IRF-10, has a unique role in immune defense and is induced by the v-Rel oncoprotein. PMID:11997525
CFTR is a pattern recognition molecule that extracts Pseudomonas aeruginosa LPS from the outer membrane into epithelial cells and activates NF-kappa B translocation. PMID:11997458
RePS: a sequence assembler that masks exact repeats identified from the shotgun data. PMID:11997349
Large-scale protein annotation through gene ontology. PMID:11997345
Structure and evolution of the Smith-Magenis syndrome repeat gene clusters, SMS-REPs. PMID:11997339
Genes in a refined Smith-Magenis syndrome critical deletion interval on chromosome 17p11.2 and the syntenic region of the mouse. PMID:11997338
Systematic evaluation of map quality: human chromosome 22. PMID:11992248
Is 'big biology' a commercial enterprise? PMID:11983050
Science, medicine, and the future: Bioinformatics. PMID:11976246
Genomics and proteomics of allergic disease. PMID:11972626
Oligo(dT) primer generates a high frequency of truncated cDNAs through internal poly(A) priming during reverse transcription. PMID:11972056
Evolution of the RNA polymerase II C-terminal domain. PMID:11972039
Effective generation of transgenic pigs and mice by linker based sperm-mediated gene transfer. PMID:11964188
A major predisposition locus for severe obesity, at 4p15-p14. PMID:11957135
Analysis of a human brain transcriptome map. PMID:11955288
Revised 14.7-cM locus for the hyperparathyroidism-jaw tumor syndrome gene, HRPT2. PMID:11951180
Haemophilia A and haemophilia B: molecular insights. PMID:11950963
Genes on human chromosome 19 show extreme divergence from the mouse orthologs and a high GC content. PMID:11937628
BLAT--the BLAST-like alignment tool. PMID:11932250
Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates. PMID:11930003
Evolution of viruses by acquisition of genes that control nuclear functions in infected cells--an introduction. PMID:11928989
Common deletion of SMAD4 in juvenile polyposis is a mutational hotspot. PMID:11920286
An efficient algorithm for large-scale detection of protein families. PMID:11917018
Comparative genomics and evolution of proteins involved in RNA metabolism. PMID:11917006
An integrated physical and genetic map of the rice genome. PMID:11910002
On the sequencing and assembly of the human genome. PMID:11904395
Whole-genome disassembly. PMID:11904394
Large-scale analysis of the human and mouse transcriptomes. PMID:11904358
Telomeric and rDNA silencing in Saccharomyces cerevisiae are dependent on a nuclear NAD(+) salvage pathway. PMID:11901108
Untranslated regions of mRNAs. PMID:11897027
Linkage disequilibrium between the beta frequency of the human EEG and a GABAA receptor gene locus. PMID:11891318
mRNA expression profiling of laser microbeam microdissected cells from slender embryonic structures. PMID:11891179
Effects of glia maturation factor overexpression in primary astrocytes on MAP kinase activation, transcription factor activation, and neurotrophin secretion. PMID:11885780
Genome complexity reduction for SNP genotyping analysis. PMID:11880640
On the sequencing of the human genome. PMID:11880605
Molecular biologist's guide to proteomics. PMID:11875127
Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA). PMID:11875039
Novel fluorescence labeling and high-throughput assay technologies for in vitro analysis of protein interactions. PMID:11875038
Consensus promoter identification in the human genome utilizing expressed gene markers and gene modeling. PMID:11875035
Computational comparison of human genomic sequence assemblies for a region of chromosome 4. PMID:11875030
Processed pseudogenes of human endogenous retroviruses generated by LINEs: their integration, stability, and distribution. PMID:11875026
The human ribosomal protein genes: sequencing and comparative analysis of 73 genes. PMID:11875025
RNA-protein interactions that regulate pre-mRNA splicing. PMID:11868989
Prevalence of somatic alterations in the colorectal cancer cell genome. PMID:11867767
Genes, pseudogenes, and Alu sequence organization across human chromosomes 21 and 22. PMID:11867739
Critical residues within the BTB domain of PLZF and Bcl-6 modulate interaction with corepressors. PMID:11865059
Selection in the evolution of gene duplications. PMID:11864370
RNase 8, a novel RNase A superfamily ribonuclease expressed uniquely in placenta. PMID:11861908
A question of size: the eukaryotic proteome and the problems in defining it. PMID:11861898
Comparative analysis of the human dystrophin and utrophin gene structures. PMID:11861579
A microsatellite-based multilocus screen for the identification of local selective sweeps. PMID:11861576
Through a genome, darkly: comparative analysis of plant chromosomal DNA. PMID:11860213
Discovery of five conserved beta -defensin gene clusters using a computational search strategy. PMID:11854508
Short-chain dehydrogenase/reductase (SDR) relationships: a large family with eight clusters common to human, animal, and plant genomes. PMID:11847285
The first linkage disequilibrium (LD) maps: delineation of hot and cold blocks by diplotype analysis. PMID:11842208
Complex regulation of the human gene for the Z-DNA binding protein DLM-1. PMID:11842111
Genetic mapping of Y-chromosomal DNA markers in Pacific salmon. PMID:11841186
Classical and molecular cytogenetics of the zebrafish, Danio rerio (Cyprinidae, Cypriniformes): an overview. PMID:11841183
Gene mapping in fishes: a means to an end. PMID:11841175
Mammalian selenoprotein in which selenocysteine (Sec) incorporation is supported by a new form of Sec insertion sequence element. PMID:11839807
Fine-scale mapping of disease loci via shattered coalescent modeling of genealogies. PMID:11836651
Haemophilia A and haemophilia B: molecular insights. PMID:11836440
High-throughput selection of retrovirus producer cell lines leads to markedly improved efficiency of germ line-transmissible insertions in zebra fish. PMID:11836396
Current status of human chromosome 14. PMID:11836355
Match-only integral distribution (MOID) algorithm for high-density oligonucleotide array analysis. PMID:11835687
NIST physical standards for DNA-based medical testing. PMID:11835524
Proteomic approaches to characterize protein modifications: new tools to study the effects of environmental exposures. PMID:11834459
Localization of a susceptibility gene for common forms of stroke to 5q12. PMID:11833004
V-SINEs: a new superfamily of vertebrate SINEs that are widespread in vertebrate genomes and retain a strongly conserved segment within each repetitive unit. PMID:11827951
Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. PMID:11827946
A web-based tool to retrieve human genome polymorphisms from public databases. PMID:11825250
A model for data integration systems of biomedical data applied to online genetic databases. PMID:11825233
Transplantation of target site specificity by swapping the endonuclease domains of two LINEs. PMID:11823433
Limb-girdle muscular dystrophy type 2H associated with mutation in TRIM32, a putative E3-ubiquitin-ligase gene. PMID:11822024
Identification and characterization of subfamily-specific signatures in a large protein superfamily by a hidden Markov model approach. PMID:11818024
Bypass of heterology during strand transfer by Saccharomyces cerevisiae Rad51 protein. PMID:11812836
Gene expression in the developing mouse retina by EST sequencing and microarray analysis. PMID:11812828
Pharmacogenetics, pharmacogenomics and airway disease. PMID:11806845
Prediction of unidentified human genes on the basis of sequence similarity to novel cDNAs from cynomolgus monkey brain. PMID:11806829
C2A activates a cryptic Ca(2+)-triggered membrane penetration activity within the C2B domain of synaptotagmin I. PMID:11805296
In silico chromosome staining: reconstruction of Giemsa bands from the whole human genome sequence. PMID:11792839
High throughput DNA sequencing with a microfabricated 96-lane capillary array electrophoresis bioprocessor. PMID:11792836
Score tests for association between traits and haplotypes when linkage phase is ambiguous. PMID:11791212
A new approach to genome mapping and sequencing: slalom libraries. PMID:11788732
Loss of N-glycolylneuraminic acid in humans: Mechanisms, consequences, and implications for hominid evolution. PMID:11786991
2001 ASHG Presidential Address. On black boxes and storytellers: lessons learned in human genetics. PMID:11781874
The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study. PMID:11779845
Linker-mediated recombinational subcloning of large DNA fragments using yeast. PMID:11779844
ARACHNE: a whole-genome shotgun assembler. PMID:11779843
Genomic analysis of the olfactory receptor region of the mouse and human T-cell receptor alpha/delta loci. PMID:11779833
Human paralogs of KIAA0187 were created through independent pericentromeric-directed and chromosome-specific duplication mechanisms. PMID:11779832
A comparative genomic analysis of two distant diptera, the fruit fly, Drosophila melanogaster, and the malaria mosquito, Anopheles gambiae. PMID:11779831
Systematic identification of novel protein domain families associated with nuclear functions. PMID:11779830
Genome-scale evolution: reconstructing gene orders in the ancestral species. PMID:11779828
Generation and comparative analysis of approximately 3.3 Mb of mouse genomic sequence orthologous to the region of human chromosome 7q11.23 implicated in Williams syndrome. PMID:11779826
A 117-kb microdeletion removing HOXD9-HOXD13 and EVX2 causes synpolydactyly. PMID:11778160
Genetic, physical, and comparative map of the subtelomeric region of mouse Chromosome 4. PMID:11773963
Pharmacogenetic tactics and strategies: implications for paediatrics. PMID:11772149
Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome. PMID:11756672
Evidence of positive selection acting at the human dopamine receptor D4 gene locus. PMID:11756666
Jerky, a protein deficient in a mouse epilepsy model, is associated with translationally inactive mRNA in neurons. PMID:11756500
Evidence for linkage of stature to chromosome 3p26 in a large U.K. Family data set ascertained for type 2 diabetes. PMID:11753821
Molecular characteristics of non-small cell lung cancer. PMID:11752463
Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo. PMID:11752406
Olfactory Receptor Database: a metadata-driven automated population from sources of gene and protein sequences. PMID:11752336
DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs. PMID:11752328
SYSTERS, GeneNest, SpliceNest: exploring sequence space from genome to protein. PMID:11752319
The Pfam protein families database. PMID:11752314
Recent improvements to the SMART domain-based sequence annotation resource. PMID:11752305
The Gene Resource Locator: gene locus maps for transcriptome analysis. PMID:11752299
HERVd: database of human endogenous retroviruses. PMID:11752294
HUGE: a database for human large proteins identified in the Kazusa cDNA sequencing project. PMID:11752282
euGenes: a eukaryote genome information system. PMID:11752277
Annotating the human proteome: the Human Proteome Survey Database (HumanPSD) and an in-depth target database for G protein-coupled receptors (GPCR-PD) from Incyte Genomics. PMID:11752275
The Ensembl genome database project. PMID:11752248
DNA Data Bank of Japan (DDBJ) for genome scale research in life science. PMID:11752245
The EMBL Nucleotide Sequence Database. PMID:11752244
The Molecular Biology Database Collection: 2002 update. PMID:11752241
Genetic counseling for congenital heart disease: new approaches for a new decade. PMID:11743925
The SCAN domain of ZNF174 is a dimer. PMID:11741982
Genetic variations in human G protein-coupled receptors: implications for drug therapy. PMID:11741273
What use is the human genome for understanding the mouse? PMID:11737939
What does a worm want with 20,000 genes? PMID:11737938
Delivery of neurotrophic factors to the central nervous system: pharmacokinetic considerations. PMID:11735609
Human-specific duplication and mosaic transcripts: the recent paralogous structure of chromosome 22. PMID:11731936
GeneLynx: a gene-centric portal to the human genome. PMID:11731507
Twin priming: a proposed mechanism for the creation of inversions in L1 retrotransposition. PMID:11731496
Genomic characterization of recent human LINE-1 insertions: evidence supporting random insertion. PMID:11731495
Identification of disease-specific genes in chronic pancreatitis using DNA array technology. PMID:11729383
Codon usage bias covaries with expression breadth and the rate of synonymous evolution in humans, but this is not evidence for selection. PMID:11729162
Evidence for new alleles in the protein kinase adenosine monophosphate-activated gamma(3)-subunit gene associated with low glycogen content in pig skeletal muscle and improved meat quality. PMID:11729159
DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. PMID:11726688
Evolutionary perspective on innate immune recognition. PMID:11724812
Arrangements of macro- and microchromosomes in chicken cells. PMID:11721954
Non-random radial higher-order chromatin arrangements in nuclei of diploid human cells. PMID:11721953
Terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes. PMID:11717436
Association between divergence and interspersed repeats in mammalian noncoding genomic DNA. PMID:11717405
Establishment of a high throughput EST sequencing system using poly(A) tail-removed cDNA libraries and determination of 36,000 bovine ESTs. PMID:11713328
REPuter: the manifold applications of repeat analysis on a genomic scale. PMID:11713313
Non-coding RNAs: the architects of eukaryotic complexity. PMID:11713189
The map problem: a comparison of genetic and sequence-based physical maps. PMID:11706388
Methyl-CpG-binding protein 2 represses LINE-1 expression and retrotransposition but not Alu transcription. PMID:11691937
Hypermutability at a poly(A/T) tract in the human germline. PMID:11691928
GST-PRIME: a genome-wide primer design software for the generation of gene sequence tags. PMID:11691924
Spidey: a tool for mRNA-to-genomic alignments. PMID:11691860
Automated construction of high-density comparative maps between rat, human, and mouse. PMID:11691858
High-throughput variation detection and genotyping using microarrays. PMID:11691856
A streamlined process to phenotypically profile heterologous cDNAs in parallel using yeast cell-based assays. PMID:11691855
Determinants of CpG islands: expression in early embryo and isochore structure. PMID:11691850
The contribution of exon-skipping events on chromosome 22 to protein coding diversity. PMID:11691849
Pattern and timing of gene duplication in animal genomes. PMID:11691848
Comparing vertebrate whole-genome shotgun reads to the human genome. PMID:11691844
Methylation-mediated proviral silencing is associated with MeCP2 recruitment and localized histone H3 deacetylation. PMID:11689684
Genetically increased angiotensin I-converting enzyme level and renal complications in the diabetic mouse. PMID:11687636
Pharmacogenetics and pharmacogenomics. PMID:11678777
A human nuclease specific for G4 DNA. PMID:11675489
Open-system approaches to gene expression in the CNS. PMID:11606615
Consequences of recombination rate variation on quantitative trait locus mapping studies. Simulations based on the Drosophila melanogaster genome. PMID:11606535
Direct estimate of the mutation rate and the distribution of fitness effects in the yeast Saccharomyces cerevisiae. PMID:11606524
Adaptins: the final recount. PMID:11598180
The olfactory receptor family album. PMID:11597337
Genomics analysis of genes expressed in maize endosperm identifies novel seed proteins and clarifies patterns of zein gene expression. PMID:11595803
The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome. PMID:11593022
Navigating the human transcriptome. PMID:11592992
Protein-protein interaction panel using mouse full-length cDNAs. PMID:11591653
High-resolution BAC-based map of the central portion of mouse chromosome 5. PMID:11591652
Mouse BAC ends quality assessment and sequence analyses. PMID:11591651
SSAHA: a fast search method for large DNA databases. PMID:11591649
A comparative molecular analysis of developing mouse forelimbs and hindlimbs using serial analysis of gene expression (SAGE). PMID:11591645
Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. PMID:11591643
FOUNTAIN: a JAVA open-source package to assist large sequencing projects. PMID:11591214
Molecular indexing of human genomic DNA. PMID:11574697
A computational scan for U12-dependent introns in the human genome sequence. PMID:11574683
Exon structure conservation despite low sequence similarity: a relic of dramatic events in evolution? PMID:11574467
The trappist's approach to pathfinding: elucidating brain wiring using secretory-trap mutagenesis. PMID:11574063
Abundant protein domains occur in proportion to proteome size. PMID:11574058
A computational analysis of sequence features involved in recognition of short introns. PMID:11572975
Global methylation profiling of lung cancer identifies novel methylated genes. PMID:11571631
Comparing function and structure between entire proteomes. PMID:11567088
Alu-mediated inactivation of the human CMP- N-acetylneuraminic acid hydroxylase gene. PMID:11562455
Alu insertion polymorphisms for the study of human genomic diversity. PMID:11560904
Genetic analysis of endocytosis in Caenorhabditis elegans: coelomocyte uptake defective mutants. PMID:11560892
Dynamic modules and heterogeneity of function: a lesson from tyrosine kinase receptors in endothelial cells. PMID:11559587
Impact of molecular medicine on neuropsychiatry: the clinician's perspective. PMID:11559470
Matrix-induced fragmentation of P3'-N5' phosphoramidate-containing DNA: high-throughput MALDI-TOF analysis of genomic sequence polymorphisms. PMID:11557819
DNA microarrays in medical practice. PMID:11557712
Chemosensitivity prediction by transcriptional profiling. PMID:11553813
Use of gene markers to guide antihypertensive therapy. PMID:11551376
Assembly of the working draft of the human genome with GigAssembler. PMID:11544197
Identification of alternate polyadenylation sites and analysis of their tissue distribution using EST data. PMID:11544195
Cloning and characterization of a histone deacetylase, HDAC9. PMID:11535832
HERV-K(OLD): ancestor sequences of the human endogenous retrovirus family HERV-K(HML-2). PMID:11533155
The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay. PMID:11532962
Mutation in Brca2 stimulates error-prone homology-directed repair of DNA double-strand breaks occurring between repeated sequences. PMID:11532935
Nucleomorph genomes: much ado about practically nothing. PMID:11532218
An immune defect causing dominant chronic mucocutaneous candidiasis and thyroid disease maps to chromosome 2p in a single family. PMID:11517424
The interplay of biology and technology. PMID:11517346
A draft annotation and overview of the human genome. PMID:11516338
An Eulerian path approach to DNA fragment assembly. PMID:11504945
Multiplex polymerase chain reaction (PCR) with color-tagged module-shuffling primers for comparing gene expression levels in various cells. PMID:11504892
A genomewide scan for loci predisposing to type 2 diabetes in a U.K. population (the Diabetes UK Warren 2 Repository): analysis of 573 pedigrees provides independent replication of a susceptibility locus on chromosome 1q. PMID:11484155
Gene expression profiling in human fetal liver and identification of tissue- and developmental-stage-specific genes through compiled expression profiles and efficient cloning of full-length cDNAs. PMID:11483580
Sequence variation within the fragile X locus. PMID:11483579
Molecular characterization of two natural hotspots in the Drosophila buzzatii genome induced by transposon insertions. PMID:11483576
Treasures in the attic: rolling circle transposons discovered in eukaryotic genomes. PMID:11481459
A statistical view of genome transcription? PMID:11479687
Lower-than-expected linkage disequilibrium between tightly linked markers in humans suggests a role for gene conversion. PMID:11473344
Supersensitivity to anandamide and enhanced endogenous cannabinoid signaling in mice lacking fatty acid amide hydrolase. PMID:11470906
Molecular evolution of the homeodomain family of transcription factors. PMID:11470884
Molecular characterization and gene content of breakpoint boundaries in patients with neurofibromatosis type 1 with 17q11.2 microdeletions. PMID:11468690
Structure and evolution of the hAT transposon superfamily. PMID:11454746
Species-specific organization of CpG island promoters at mammalian homologous genes. PMID:11454739
Estrogen receptor interaction with estrogen response elements. PMID:11452016
Obscurin, a giant sarcomeric Rho guanine nucleotide exchange factor protein involved in sarcomere assembly. PMID:11448995
A sequence-based integrated map of chromosome 22. PMID:11435412
Predicting splice variant from DNA chip expression data. PMID:11435406
Estimating the efficacy and efficiency of cascade genetic screening. PMID:11431707
Bases and spaces: resources on the web for accessing the draft human genome - II - after publication of the draft. PMID:11423014
Endogenous retroviruses in the human genome sequence. PMID:11423012
Evolution of mammalian genome organization inferred from comparative gene mapping. PMID:11423011
The human olfactory receptor repertoire. PMID:11423007
Siglecs in the immune system. PMID:11412300
High-resolution multipoint linkage-disequilibrium mapping in the context of a human genome sequence. PMID:11410841
Identification and prevention of a GC content bias in SAGE libraries. PMID:11410683
Conserved vertebrate chromosome segments in the large salamander genome. PMID:11404337
The arabidopsis serrate gene encodes a zinc-finger protein required for normal shoot development. PMID:11402159
Mutations of the protocadherin gene PCDH15 cause Usher syndrome type 1F. PMID:11398101
Towards a complete sequence of the human Y chromosome. PMID:11387042
Characterizing glycosylation pathways. PMID:11387039
Regulated transposition of a fish transposon in the mouse germ line. PMID:11381141
The 1.4-Mb CMT1A duplication/HNPP deletion genomic region reveals unique genome architectural features and provides insights into the recent evolution of new genes. PMID:11381029
Segmental duplications: organization and impact within the current human genome project assembly. PMID:11381028
Mitochondria and the quality of human gametes. PMID:11359216
Computational inference of homologous gene structures in the human genome. PMID:11337476
Science, medicine, and the future: Postgenomic technologies: hunting the genes for common disorders. PMID:11325769
Goodbye to 'one by one' genetics. PMID:11305933
Networking proteins in yeast. PMID:11296274
Gene-diet interaction and plasma lipid response to dietary intervention. PMID:11286641
Genome-scale compositional comparisons in eukaryotes. PMID:11282969
Twin peaks: the draft human genome sequence. PMID:11276423
Integration of cytogenetic landmarks into the draft sequence of the human genome. PMID:11237021
Mining the draft human genome. PMID:11236999 -
The human genome browser at UCSC
PubMed citations: 4596.
4596 articles citing: The human genome browser at UCSC
Gene Promoter-Methylation Signature as Biomarker to Predict Cisplatin-Radiotherapy Sensitivity in Locally Advanced Cervical Cancer. PMID:35359376
Nuclear microRNA-466c regulates Vegfa expression in response to hypoxia. PMID:35358280
Alkaline nucleoplasm facilitates contractile gene expression in the mammalian heart. PMID:35357563
Exosomal DEK removes chemoradiotherapy resistance by triggering quiescence exit of breast cancer stem cells. PMID:35351996
Nasal airway transcriptome-wide association study of asthma reveals genetically driven mucus pathobiology. PMID:35347136
Epigenome-wide DNA methylation profiling of conditioned pain modulation in individuals with non-specific chronic low back pain. PMID:35346352
DNA methylation-based age acceleration observed in IDH wild-type glioblastoma is associated with better outcome-including in elderly patients. PMID:35331339
Methylation of Subtelomeric Chromatin Modifies the Expression of the lncRNA TERRA, Disturbing Telomere Homeostasis. PMID:35328692
Decrease in RNase HII and Accumulation of lncRNAs/DNA Hybrids: A Causal Implication in Psoriasis? PMID:35327560
Pervasive occurrence of splice-site-creating mutations and their possible involvement in genetic disorders. PMID:35304488
A pan-cancer analysis on the carcinogenic effect of human adenomatous polyposis coli. PMID:35303016
Oncogenic gene expression and epigenetic remodeling of cis-regulatory elements in ASXL1-mutant chronic myelomonocytic leukemia. PMID:35301312
scREMOTE: Using multimodal single cell data to predict regulatory gene relationships and to build a computational cell reprogramming model. PMID:35300460
Rapid DNA visual detection of polymicrobial bloodstream infection using filter paper. PMID:35296724
Methylation pattern of polymorphically imprinted nc886 is not conserved across mammalia. PMID:35294436
Cytogenetic and molecular analyses of 291 gastrointestinal stromal tumors: site-specific cytogenetic evolution as evidence of pathogenetic heterogeneity. PMID:35284037
Common Variation in EDN1 Regulatory Regions Highlights the Role of PPARγ as a Key Regulator of Endothelin in vitro. PMID:35282351
Transcriptional, epigenetic and metabolic signatures in cardiometabolic syndrome defined by extreme phenotypes. PMID:35279219
Secondary structure prediction for RNA sequences including N6-methyladenosine. PMID:35277476
Transcriptomic characterization of tissues from patients and subsequent pathway analyses reveal biological pathways that are implicated in spastic ataxia. PMID:35277195
Targeting HIF-2α in the Tumor Microenvironment: Redefining the Role of HIF-2α for Solid Cancer Therapy. PMID:35267567
Assessment of linkage disequilibrium patterns between structural variants and single nucleotide polymorphisms in three commercial chicken populations. PMID:35264116
TET2 Regulates 5-Hydroxymethylcytosine Signature and CD4+ T-Cell Balance in Allergic Rhinitis. PMID:35255541
CNViz: An R/Shiny Application for Interactive Copy Number Variant Visualization in Cancer. PMID:35251754
Landscape of adenosine-to-inosine RNA recoding across human tissues. PMID:35246538
Changes in DNA methylation hallmark alterations in chromatin accessibility and gene expression for eye lens differentiation. PMID:35246225
A Comprehensive Analysis of Fibrillar Collagens in Lamprey Suggests a Conserved Role in Vertebrate Musculoskeletal Evolution. PMID:35242758
TADA-a machine learning tool for functional annotation-based prioritisation of pathogenic CNVs. PMID:35232478
Robust and annotation-free analysis of alternative splicing across diverse cell types in mice. PMID:35229721
Conservation of chromatin conformation in carnivores. PMID:35217621
Evolutionarily conserved inhibitory uORFs sensitize Hox mRNA translation to start codon selection stringency. PMID:35217614
A Novel, Apparently Silent Variant in MFSD8 Causes Neuronal Ceroid Lipofuscinosis with Marked Intrafamilial Variability. PMID:35216386
ITK independent development of Th17 responses during hypersensitivity pneumonitis driven lung inflammation. PMID:35210549
Low Mutational Burden of Extranodal Marginal Zone Lymphoma of Mucosa-Associated Lymphoid Tissue in Patients with Primary Sjogren's Syndrome. PMID:35205758
TDP-43 represses cryptic exon inclusion in the FTD-ALS gene UNC13A. PMID:35197626
Functional noncoding SNPs in human endothelial cells fine-map vascular trait associations. PMID:35193936
Background splicing as a predictor of aberrant splicing in genetic disease. PMID:35188075
Mosaic cis-regulatory evolution drives transcriptional partitioning of HERVH endogenous retrovirus in the human embryo. PMID:35179489
Evolutionary History of TOPIIA Topoisomerases in Animals. PMID:35165762
Epigenomic and Transcriptomic Prioritization of Candidate Obesity-Risk Regulatory GWAS SNPs. PMID:35163195
Syntenin Regulated by miR-216b Promotes Cancer Progression in Pancreatic Cancer. PMID:35155233
Differences in nanoscale organization of regulatory active and inactive human chromatin. PMID:35150617
A genetic screen in C. elegans reveals roles for KIN17 and PRCC in maintaining 5' splice site identity. PMID:35143478
Analysis of Pathogenic Pseudoexons Reveals Novel Mechanisms Driving Cryptic Splicing. PMID:35140743
Plotgardener: Cultivating precise multi-panel figures in R. PMID:35134826
Clinical validation of genomic functional screen data: Analysis of observed BRCA1 variants in an unselected population cohort. PMID:35128484
Long Non-coding RNA MALAT1 Is Depleted With Age in Skeletal Muscle in vivo and MALAT1 Silencing Increases Expression of TGF-β1 in vitro. PMID:35126169
Mouse genomic and cellular annotations. PMID:35124726
Multi-omic analysis reveals significantly mutated genes and DDX3X as a sex-specific tumor suppressor in cutaneous melanoma. PMID:35121978
Deletion of the homeodomain gene Six3 from kisspeptin neurons causes subfertility in female mice. PMID:35121076
Improving the efficiency of single-cell genome sequencing based on overlapping pooling strategy and CNV analysis. PMID:35116153
Identification of potential functional variants and genes at 18q21.1 associated with the carcinogenesis of colorectal cancer. PMID:35108261
Prdm6 controls heart development by regulating neural crest cell differentiation and migration. PMID:35108221
DROSHA but not DICER is required for human haematopoietic stem cell function. PMID:35106155
Analysis of epigenetic features characteristic of L1 loci expressed in human cells. PMID:35100410
Genomic patterns of transcription-replication interactions in mouse primary B cells. PMID:35100392
The Clock:Cycle complex is a major transcriptional regulator of Drosophila photoreceptors that protects the eye from retinal degeneration and oxidative stress. PMID:35100266
Novel Classes and Evolutionary Turnover of Histone H2B Variants in the Mammalian Germline. PMID:35099534
Evaluating the relevance of sequence conservation in the prediction of pathogenic missense variants. PMID:35098354
N 6-methyladenosine enhances post-transcriptional gene regulation by microRNAs. PMID:35098135
Role of IGF2 in the Study of Development and Evolution of Prostate Cancer. PMID:35095996
Caenorhabditis elegans transposable elements harbor diverse transcription factor DNA-binding sites. PMID:35088854
Dual RNA-Seq analysis of SARS-CoV-2 correlates specific human transcriptional response pathways directly to viral expression. PMID:35079083
Human reproduction is regulated by retrotransposons derived from ancient Hominidae-specific viral infections. PMID:35075135
Evolution of a New Testis-Specific Functional Promoter Within the Highly Conserved Map2k7 Gene of the Mouse. PMID:35069705
Cost-Efficiency Optimization Serves as a Conserved Mechanism that Promotes Osteosarcoma in Mammals. PMID:35061072
An evolutionarily conserved mechanism that amplifies the effect of deleterious mutations in osteosarcoma. PMID:35061070
Correction of a Factor VIII genomic inversion with designer-recombinases. PMID:35058465
Clin.iobio: A Collaborative Diagnostic Workflow to Enable Team-Based Precision Genomics. PMID:35055388
Structural and Functional Characterization of Four Novel Fibrinogen Mutations in FGB Causing Congenital Fibrinogen Disorder. PMID:35054908
Thirteen Independent Genetic Loci Associated with Preserved Processing Speed in a Study of Cognitive Resilience in 330,097 Individuals in the UK Biobank. PMID:35052462
Capturing SNP Association across the NK Receptor and HLA Gene Regions in Multiple Sclerosis by Targeted Penalised Regression Models. PMID:35052430
Virtual Gene Concept and a Corresponding Pragmatic Research Program in Genetical Data Science. PMID:35052043
Transmural pressure signals through retinoic acid to regulate lung branching. PMID:35051272
Genome-wide analysis of copy number variants and normal facial variation in a large cohort of Bantu Africans. PMID:35047866
Methyl-lysine readers PHF20 and PHF20L1 define two distinct gene expression-regulating NSL complexes. PMID:35033534
StrVCTVRE: A supervised learning method to predict the pathogenicity of human genome structural variants. PMID:35032432
Amelioration of a neurodevelopmental disorder by carbamazepine in a case having a gain-of-function GRIA3 variant. PMID:35031858
Zinc finger protein 384 enhances colorectal cancer metastasis by upregulating MMP2. PMID:35029289
DREAM, a possible answer to the estrogen paradox of the Women's Health Initiative Trial. PMID:35028452
Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction. PMID:35021193
Interaction sites of the Epstein-Barr virus Zta transcription factor with the host genome in epithelial cells. PMID:35018326
Host genetic factors of COVID-19 susceptibility and disease severity in a Thai population. PMID:35013560
Long read sequencing reveals novel isoforms and insights into splicing regulation during cell state changes. PMID:35012468
Epigenetic Regulation of F2RL3 Associates With Myocardial Infarction and Platelet Function. PMID:35012325
Validation and genetic heritability estimation of known type 2 diabetes related variants in the Korean population. PMID:35012284
Altered White Matter and microRNA Expression in a Murine Model Related to Williams Syndrome Suggests That miR-34b/c Affects Brain Development via Ptpru and Dcx Modulation. PMID:35011720
Enhancer RNA Expression in Response to Glucocorticoid Treatment in Murine Macrophages. PMID:35011590
Meta-Analysis and Bioinformatics Detection of Susceptibility Genes in Diabetic Nephropathy. PMID:35008447
The 3p21.31 genetic locus promotes progression to type 1 diabetes through the CCR2/CCL2 pathway. PMID:35005592
CRISPRi links COVID-19 GWAS loci to LZTFL1 and RAVER1. PMID:34998241
Mutation of Hashimoto's Thyroiditis and Papillary Thyroid Carcinoma Related Genes and the Screening of Candidate Genes. PMID:34993154
Universal annotation of the human genome through integration of over a thousand epigenomic datasets. PMID:34991667
YAP1 and PRDM14 converge to promote cell survival and tumorigenesis. PMID:34990589
SUMOylation inhibition enhances dexamethasone sensitivity in multiple myeloma. PMID:34983615
Common Genomic Aberrations in Mouse and Human Breast Cancers with Concurrent P53 Deficiency and Activated PTEN-PI3K-AKT Pathway. PMID:34975329
Antibody-free profiling of transcription factor occupancy during early embryogenesis by FitCUT&RUN. PMID:34965941
Combining Human Genetics of Multiple Sclerosis with Oxidative Stress Phenotype for Drug Repositioning. PMID:34959343
LINC00467, Driven by Copy Number Amplification and DNA Demethylation, Is Associated with Oxidative Lipid Metabolism and Immune Infiltration in Breast Cancer. PMID:34956437
9-ING-41, a Small Molecule Inhibitor of GSK-3β, Potentiates the Effects of Chemotherapy on Colorectal Cancer Cells. PMID:34955846
Overcoming constraints on the detection of recessive selection in human genes from population frequency data. PMID:34951958
The HDAC Inhibitor Butyrate Impairs β Cell Function and Activates the Disallowed Gene Hexokinase I. PMID:34948127
Autism-Related Transcription Factors Underlying the Sex-Specific Effects of Prenatal Bisphenol A Exposure on Transcriptome-Interactome Profiles in the Offspring Prefrontal Cortex. PMID:34947998
DNA Methylation of PI3K/AKT Pathway-Related Genes Predicts Outcome in Patients with Pancreatic Cancer: A Comprehensive Bioinformatics-Based Study. PMID:34944974
A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data. PMID:34944901
Inflammatory activation of surface molecule shedding by upregulation of the pseudoprotease iRhom2 in colon epithelial cells. PMID:34930929
Long-range promoter-enhancer contacts are conserved during evolution and contribute to gene expression robustness. PMID:34930799
CCR5 and Biological Complexity: The Need for Data Integration and Educational Materials to Address Genetic/Biological Reductionism at the Interface of Ethical, Legal, and Social Implications. PMID:34925370
Prioritising positively selected variants in whole-genome sequencing data using FineMAV. PMID:34922440
A Functional SNP in the Promoter of LBX1 Is Associated With the Development of Adolescent Idiopathic Scoliosis Through Involvement in the Myogenesis of Paraspinal Muscles. PMID:34917617
Reactivation of transposable elements following hybridization in fission yeast. PMID:34907076
A cis-regulatory-directed pipeline for the identification of genes involved in cardiac development and disease. PMID:34906219
IRAK1-regulated IFN-γ signaling induces MDSC to facilitate immune evasion in FGFR1-driven hematological malignancies. PMID:34906138
Histone Chaperone Nucleophosmin Regulates Transcription of Key Genes Involved in Oral Tumorigenesis. PMID:34898280
MYC assembles and stimulates topoisomerases 1 and 2 in a "topoisome". PMID:34890565
A Novel SPINK5 Gene Mutation Associated with Netherton Syndrome in an Omani Patient. PMID:34888090
Cell-type-specific chromatin occupancy by the pioneer factor Zelda drives key developmental transitions in Drosophila. PMID:34887421
Epigenetic Dysregulation of KCNK9 Imprinting and Triple-Negative Breast Cancer. PMID:34885139
Regulation of Gene Expression by Telomere Position Effect. PMID:34884608
Natural SINEUP RNAs in Autism Spectrum Disorders: RAB11B-AS1 Dysregulation in a Neuronal CHD8 Suppression Model Leads to RAB11B Protein Increase. PMID:34880900
A predominant enhancer co-amplified with the SOX2 oncogene is necessary and sufficient for its expression in squamous cancer. PMID:34880227
Landscape of the oncogenic role of fatty acid synthase in human tumors. PMID:34879004
DPPA2 and DPPA4 are dispensable for mouse zygotic genome activation and pre-implantation development. PMID:34878123
A Model of Minor Histocompatibility Antigens in Allogeneic Hematopoietic Cell Transplantation. PMID:34868058
The high methylation level of a novel 151-bp CpG island in the ESR1 gene promoter is associated with a poor breast cancer prognosis. PMID:34863151
Signature selection analysis reveals candidate genes associated with production traits in Iranian sheep breeds. PMID:34861880
RNA-Scoop: interactive visualization of transcripts in single-cell transcriptomes. PMID:34859209
Reclassification of a TMC1 synonymous substitution as a variant disrupting splicing regulatory elements associated with recessive hearing loss. PMID:34857896
The circular RNA expression profile in ovarian serous cystadenocarcinoma reveals a complex circRNA-miRNA regulatory network. PMID:34857007
Rare and potentially pathogenic variants in hydroxycarboxylic acid receptor genes identified in breast cancer cases. PMID:34852802
The Drosophila HP1 family is associated with active gene expression across chromatin contexts. PMID:34849911
A reference genome for the nectar-robbing Black-throated Flowerpiercer (Diglossa brunneiventris). PMID:34849784
Inhibition of miR-155 Promotes TGF-β Mediated Suppression of HIV Release in the Cervical Epithelial Cells. PMID:34835072
POLRMT as a Novel Susceptibility Gene for Cardiotoxicity in Epirubicin Treatment of Breast Cancer Patients. PMID:34834357
Willin/FRMD6: A Multi-Functional Neuronal Protein Associated with Alzheimer's Disease. PMID:34831245
Genetic and Bioinformatic Strategies to Improve Diagnosis in Three Inherited Bleeding Disorders in Bogotá, Colombia. PMID:34828413
Beyond Trinucleotide Repeat Expansion in Fragile X Syndrome: Rare Coding and Noncoding Variants in FMR1 and Associated Phenotypes. PMID:34828275
Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer. PMID:34824214
Heterozygous missense variant of the proteasome subunit β-type 9 causes neonatal-onset autoinflammation and immunodeficiency. PMID:34819510
Cas9-specific immune responses compromise local and systemic AAV CRISPR therapy in multiple dystrophic canine models. PMID:34819506
Composition of nasal bacterial community and its seasonal variation in health care workers stationed in a clinical research laboratory. PMID:34818371
Identifying tumorigenic non-coding mutations through altered cis-regulation. PMID:34816127
Pan-cancer landscape of CD274 (PD-L1) rearrangements in 283,050 patient samples, its correlation with PD-L1 protein expression, and immunotherapy response. PMID:34815356
Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits. PMID:34815310
TSSr: an R package for comprehensive analyses of TSS sequencing data. PMID:34805991
Metformin Corrects Glucose Metabolism Reprogramming and NLRP3 Inflammasome-Induced Pyroptosis via Inhibiting the TLR4/NF-κB/PFKFB3 Signaling in Trophoblasts: Implication for a Potential Therapy of Preeclampsia. PMID:34804360
Machine learning of genomic features in organotropic metastases stratifies progression risk of primary tumors. PMID:34795255
R-loopBase: a knowledgebase for genome-wide R-loop formation and regulation. PMID:34792163
Leveraging Northern European population history: novel low-frequency variants for polycystic ovary syndrome. PMID:34791234
Risk of penile tumor development in Caucasian individuals is independent of the coding variant rs7208422 in the TMC8 (EVER2) gene. PMID:34790351
Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors. PMID:34789735
Drosophila yakuba - Tsc1. PMID:34786536
lncRNA DDGC participates in premature ovarian insufficiency through regulating RAD51 and WT1. PMID:34786213
Locus-specific expression of transposable elements in single cells with CELLO-seq. PMID:34782740
A single-cell atlas of chromatin accessibility in the human genome. PMID:34774128
PCR Primer Design for the Rapidly Evolving SARS-CoV-2 Genome. PMID:34773624
Archaeogenetic analysis of Neolithic sheep from Anatolia suggests a complex demographic history since domestication. PMID:34773064
Introns encode dsRNAs undetected by RIG-I/MDA5/interferons and sensed via RNase L. PMID:34772806
Profiling and Functional Analysis of microRNA Deregulation in Cancer-Associated Fibroblasts in Oral Squamous Cell Carcinoma Depicts an Anti-Invasive Role of microRNA-204 via Regulation of Their Motility. PMID:34769388
Modifier Role of Common RET Variants in Sporadic Medullary Thyroid Carcinoma. PMID:34769224
ATRX regulates glial identity and the tumor microenvironment in IDH-mutant glioma. PMID:34763709
Factorbook: an updated catalog of transcription factor motifs and candidate regulatory motif sites. PMID:34755879
Pol3Base: a resource for decoding the interactome, expression, evolution, epitranscriptome and disease variations of Pol III-transcribed ncRNAs. PMID:34747466
Conservation and divergence in gene regulation between mouse and human immune cells deserves equal emphasis. PMID:34740529
Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus. PMID:34737427
Integrative genome-wide analysis of dopaminergic neuron-specific PARIS expression in Drosophila dissects recognition of multiple PPAR-γ associated gene regulation. PMID:34728675
Chromosomal variants accumulate in genomes of the spontaneous aborted fetuses revealed by chromosomal microarray analysis. PMID:34727132
Timing RNA polymerase pausing with TV-PRO-seq. PMID:34723238
A novel protein truncating mutation in L2HGDH causes L-2-hydroxyglutaric aciduria in a consanguineous Pakistani family. PMID:34719772
Nanopore sequencing of SARS-CoV-2: Comparison of short and long PCR-tiling amplicon protocols. PMID:34714886
Using Genome Scale Mutant Libraries to Identify Essential Genes. PMID:34709619
A spotter's guide to SNPtic exons: The common splice variants underlying some SNP-phenotype correlations. PMID:34708937
Pan-cancer analysis combined with experiments predicts CTHRC1 as a therapeutic target for human cancers. PMID:34702252
Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci. PMID:34699533
Live imaging of retinotectal mapping reveals topographic map dynamics and a previously undescribed role for Contactin 2 in map sharpening. PMID:34698769
CRISPR/Cas9-mediated overexpression of long non-coding RNA SRY-box transcription factor 21 antisense divergent transcript 1 regulates the proliferation of osteosarcoma by increasing the expression of mechanistic target of rapamycin kinase and Kruppel-like factor 4. PMID:34696664
Identification of C3 and FN1 as potential biomarkers associated with progression and prognosis for clear cell renal cell carcinoma. PMID:34688260
Association between ADCY9 Gene Polymorphisms and Ritodrine Treatment Outcomes in Patients with Preterm Labor. PMID:34683946
Use of Average Mutual Information and Derived Measures to Find Coding Regions. PMID:34682048
Arcuate Nucleus Overexpression of NHLH2 Reduces Body Mass and Attenuates Obesity-Associated Anxiety/Depression-like Behavior. PMID:34675088
Alu RNA and their roles in human disease states. PMID:34672903
The translatome of neuronal cell bodies, dendrites, and axons. PMID:34670838
NRF3 upregulates gene expression in SREBP2-dependent mevalonate pathway with cholesterol uptake and lipogenesis inhibition. PMID:34667945
Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans. PMID:34667117
Transcription and splicing dynamics during early Drosophila development. PMID:34667107
Short single-stranded DNAs with putative non-canonical structures comprise a new class of plasma cell-free DNA. PMID:34649537
Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns. PMID:34648491
Gene.iobio: an interactive web tool for versatile, clinically-driven variant interrogation and prioritization. PMID:34645894
A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development. PMID:34644528
Insertional activation of STAT3 and LCK by HIV-1 proviruses in T cell lymphomas. PMID:34644108
Identification of Estrogen Signaling in a Prioritization Study of Intraocular Pressure-Associated Genes. PMID:34638643
A Novel Variant of ATP5MC3 Associated with Both Dystonia and Spastic Paraplegia. PMID:34636445
Coupling high-throughput mapping with proteomics analysis delineates cis-regulatory elements at high resolution. PMID:34634809
HOXC11 positively regulates the long non-coding RNA HOTAIR and is associated with poor prognosis in colon adenocarcinoma. PMID:34630664
Role of miR-2392 in driving SARS-CoV-2 infection. PMID:34624208
An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates. PMID:34621504
Bevacizumab-induced hypertension and proteinuria: a genome-wide study of more than 1000 patients. PMID:34616010
Upregulation of Human Endogenous Retroviruses in Bronchoalveolar Lavage Fluid of COVID-19 Patients. PMID:34612698
PRC1 drives Polycomb-mediated gene repression by controlling transcription initiation and burst frequency. PMID:34608337
Effective gene expression prediction from sequence by integrating long-range interactions. PMID:34608324
Seed sequence polymorphism rs2168518 and allele-specific target gene regulation of hsa-miR-4513. PMID:34605899
Myogenin controls via AKAP6 non-centrosomal microtubule-organizing center formation at the nuclear envelope. PMID:34605406
Characterization of METTL7B to Evaluate TME and Predict Prognosis by Integrative Analysis of Multi-Omics Data in Glioma. PMID:34604305
SamQL: a structured query language and filtering tool for the SAM/BAM file format. PMID:34600480
Hominini-specific regulation of CBLN2 increases prefrontal spinogenesis. PMID:34599306
Gosling: A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization. PMID:34596551
t(4;12)(q12;p13) ETV6-rearranged AML without eosinophilia does not involve PDGFRA: relevance for imatinib insensitivity. PMID:34587239
Conserved and species-specific chromatin remodeling and regulatory dynamics during mouse and chicken limb bud development. PMID:34584102
Patterns of Coevolutionary Adaptations across Time and Space in Mouse Gammaretroviruses and Three Restrictive Host Factors. PMID:34578445
CAMPAREE: a robust and configurable RNA expression simulator. PMID:34563123
Protein-coding repeat polymorphisms strongly shape diverse human phenotypes. PMID:34554798
Polymorphic estrogen receptor binding site causes Cd2-dependent sex bias in the susceptibility to autoimmune diseases. PMID:34552089
Admixture with indigenous people helps local adaptation: admixture-enabled selection in Polynesians. PMID:34551727
Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model. PMID:34548081
piRNA-independent transposon silencing by the Drosophila THO complex. PMID:34547226
Structural variants are a major source of gene expression differences in humans and often affect multiple nearby genes. PMID:34544830
An insertion variant of MGMT disrupts a STAT1 binding site and confers susceptibility to glioma. PMID:34544433
Using CRISPR-ERA Webserver for sgRNA Design. PMID:34541182
Profiling of 3D Genome Organization in Nasopharyngeal Cancer Needle Biopsy Patient Samples by a Modified Hi-C Approach. PMID:34539729
Assessment of HLA-B genetic variation with an HLA-B leader tool and implications in clinical transplantation. PMID:34529780
A novel duplication involving PRDM13 in a Turkish family supports its role in North Carolina macular dystrophy (NCMD/MCDR1). PMID:34526759
Multi-omics mapping of human papillomavirus integration sites illuminates novel cervical cancer target genes. PMID:34526665
Multi-platform profiling characterizes molecular subgroups and resistance networks in chronic lymphocytic leukemia. PMID:34518531
Cell-free DNA TAPS provides multimodal information for early cancer detection. PMID:34516908
A systems approach using Diversity Outbred mice distinguishes the cardiovascular effects and genetics of circulating GDF11 from those of its homolog, myostatin. PMID:34510201
Prioritization and functional analysis of GWAS risk loci for Barrett's esophagus and esophageal adenocarcinoma. PMID:34505128
Role of 53BP1 in end protection and DNA synthesis at DNA breaks. PMID:34503990
Gender-Dependent Deregulation of Linear and Circular RNA Variants of HOMER1 in the Entorhinal Cortex of Alzheimer's Disease. PMID:34502114
Epigenetics Is Implicated in the Basis of Gender Incongruence: An Epigenome-Wide Association Analysis. PMID:34489625
TGF-β/activin signaling promotes CDK7 inhibitor resistance in triple-negative breast cancer cells through upregulation of multidrug transporters. PMID:34481843
RDC complex executes a dynamic piRNA program during Drosophila spermatogenesis to safeguard male fertility. PMID:34473737
Chromatin and transcription factor profiling in rare stem cell populations using CUT&Tag. PMID:34467227
ASCL1, NKX2-1, and PROX1 co-regulate subtype-specific genes in small-cell lung cancer. PMID:34466783
SNP rs4971059 predisposes to breast carcinogenesis and chemoresistance via TRIM46-mediated HDAC1 degradation. PMID:34459501
Advances in Computational Methodologies for Classification and Sub-Cellular Locality Prediction of Non-Coding RNAs. PMID:34445436
YY1 Silencing Induces 5-Fluorouracil-Resistance and BCL2L15 Downregulation in Colorectal Cancer Cells: Diagnostic and Prognostic Relevance. PMID:34445183
Transcriptional Regulation of RUNX1: An Informatics Analysis. PMID:34440349
Multiple Acyl-CoA Dehydrogenase Deficiency with Variable Presentation Due to a Homozygous Mutation in a Bedouin Tribe. PMID:34440319
Post-Transcriptional Control of Mating-Type Gene Expression during Gametogenesis in Saccharomyces cerevisiae. PMID:34439889
Identification of Novel miRNAs in the F8 Gene Via Bioinformatics Tools. PMID:34435059
Sex dependent glial-specific changes in the chromatin accessibility landscape in late-onset Alzheimer's disease brains. PMID:34429139
Identifying Imaging Genetics Biomarkers of Alzheimer's Disease by Multi-Task Sparse Canonical Correlation Analysis and Regression. PMID:34422007
VDAC Genes Expression and Regulation in Mammals. PMID:34421651
NPAS4 regulates the transcriptional response of the suprachiasmatic nucleus to light and circadian behavior. PMID:34416169
Expression, Interaction, and Role of Pseudogene Adh6-ps1 in Cancer Phenotypes. PMID:34413637
Cadherin and Wnt signaling pathways as key regulators in diabetic nephropathy. PMID:34411124
Exploring the missing heritability in subjects with hearing loss, enlarged vestibular aqueducts, and a single or no pathogenic SLC26A4 variant. PMID:34410491
Transovarial transmission of a core virome in the Chagas disease vector Rhodnius prolixus. PMID:34407148
Deep Phenotyping and Genetic Characterization of a Cohort of 70 Individuals With 5p Minus Syndrome. PMID:34394178
Susceptibility loci and polygenic architecture highlight population specific and common genetic features in inguinal hernias: genetics in inguinal hernias. PMID:34392144
Corticosterone pattern-dependent glucocorticoid receptor binding and transcriptional regulation within the liver. PMID:34375333
The Landscape of Genetic Alterations Stratified Prognosis in Oriental Pancreatic Cancer Patients. PMID:34368001
Mutational patterns and clonal evolution from diagnosis to relapse in pediatric acute lymphoblastic leukemia. PMID:34362951
Comprehensive Evaluation of Differential Methylation Analysis Methods for Bisulfite Sequencing Data. PMID:34360271
Wnt target enhancer regulation by a CDX/TCF transcription factor collective and a novel DNA motif. PMID:34358319
Exome sequencing of child-parent trios with bladder exstrophy: Findings in 26 children. PMID:34355505
Pan-cancer chromatin analysis of the human vtRNA genes uncovers their association with cancer biology. PMID:34354812
GATA3 maintains the quiescent state of cochlear supporting cells by regulating p27kip1. PMID:34349220
Gene Body Methylation of the Lymphocyte-Specific Gene CARD11 Results in Its Overexpression and Regulates Cancer mTOR Signaling. PMID:34348992
MicroRNA-490-3p and -490-5p in carcinogenesis: Separate or the same goal? PMID:34345303
A UVB-responsive common variant at chromosome band 7p21.1 confers tanning response and melanoma risk via regulation of the aryl hydrocarbon receptor, AHR. PMID:34343493
GWAS Identifies a Region Containing the SALL1 Gene in Variation of Pigmentation Intensity Within the Chestnut Coat Color of Horses. PMID:34343312
The role of epigenetic modifications, long-range contacts, enhancers and topologically associating domains in the regulation of glioma grade-specific genes. PMID:34341417
Stage-specific transcriptomic changes in pancreatic α-cells after massive β-cell loss. PMID:34340653
Cytomegalovirus late transcription factor target sequence diversity orchestrates viral early to late transcription. PMID:34339482
InvertypeR: Bayesian inversion genotyping with Strand-seq data. PMID:34332539
Genome-wide association study of pancreatic fat: The Multiethnic Cohort Adiposity Phenotype Study. PMID:34329319
Comparative transcriptome analysis reveals regulatory network and regulators associated with proanthocyanidin accumulation in persimmon. PMID:34325657
Regulated control of gene therapies by drug-induced splicing. PMID:34321659
A comprehensive analysis of SNPs and CNVs identifies novel markers associated with disease outcomes in colorectal cancer. PMID:34309201
Bruton's Tyrosine Kinase and Its Isoforms in Cancer. PMID:34307353
A pH-eQTL Interaction at the RIT2-SYT4 Parkinson's Disease Risk Locus in the Substantia Nigra. PMID:34305570
Adenosine-to-inosine Alu RNA editing controls the stability of the pro-inflammatory long noncoding RNA NEAT1 in atherosclerotic cardiovascular disease. PMID:34302813
The clinical importance of tandem exon duplication-derived substitutions. PMID:34302486
Genomic signatures of the unjamming transition in compressed human bronchial epithelial cells. PMID:34301595
Web tools to perform long non-coding RNAs analysis in oncology research. PMID:34296748
Large palindromes on the primate X Chromosome are preserved by natural selection. PMID:34290043
A 12 kb multi-allelic copy number variation encompassing a GC gene enhancer is associated with mastitis resistance in dairy cattle. PMID:34288907
Early-life social experience affects offspring DNA methylation and later life stress phenotype. PMID:34285226
A plate-based single-cell ATAC-seq workflow for fast and robust profiling of chromatin accessibility. PMID:34282334
YB-1 Is Altered in Pregnancy-Associated Disorders and Affects Trophoblast in Vitro Properties via Alternation of Multiple Molecular Traits. PMID:34281280
The H3.3K27M oncohistone antagonizes reprogramming in Drosophila. PMID:34280185
Transcriptomes of an Array of Chicken Ovary, Intestinal, and Immune Cells and Tissues. PMID:34276773
Large parental differences in chromatin organization in pancreatic beta cell line explaining diabetes susceptibility effects. PMID:34267199
Prolyl-4-hydroxylase 3 maintains β cell glucose metabolism during fatty acid excess in mice. PMID:34264866
Analysis of the Prognostic Value and Gene Expression Mechanism of SHOX2 in Lung Adenocarcinoma. PMID:34262939
Haplotype-resolved germline and somatic alterations in renal medullary carcinomas. PMID:34261517
Meiotic recombination mirrors patterns of germline replication in mice and humans. PMID:34260899
Coding and noncoding variants in EBF3 are involved in HADDS and simplex autism. PMID:34256850
A direct capture method for purification and detection of viral nucleic acid enables epidemiological surveillance of SARS-CoV-2. PMID:34252764
Quantitative mapping of mRNA 3' ends in Pseudomonas aeruginosa reveals a pervasive role for premature 3' end formation in response to azithromycin. PMID:34252072
Novel PRMT7 mutation in a rare case of dysmorphism and intellectual disability. PMID:34244600
Characterizing nucleotide variation and expansion dynamics in human-specific variable number tandem repeats. PMID:34244228
Role of chromosome 1q copy number variation in hepatocellular carcinoma. PMID:34239701
Optimizing prediction of response to antidepressant medications using machine learning and integrated genetic, clinical, and demographic data. PMID:34238923
Joint disease-specificity at the regulatory base-pair level. PMID:34230488
Total Anomalous Pulmonary Venous Connection in Mother and Son with a Central 22q11.2 Microdeletion. PMID:34221520
Genetic determinants of multiple myeloma risk within the Wnt/beta-catenin signaling pathway. PMID:34216957
A functional map of genomic HIF1α-DNA complexes in the eye lens revealed through multiomics analysis. PMID:34215186
Genomic partitioning of inbreeding depression in humans. PMID:34214457
ATF3 Modulates the Resistance of Breast Cancer Cells to Tamoxifen through an N6-Methyladenosine-Based Epitranscriptomic Mechanism. PMID:34213887
VECTOR: An Integrated Correlation Network Database for the Identification of CeRNA Axes in Uveal Melanoma. PMID:34210067
Analysis of Genetic Variants Associated with Levels of Immune Modulating Proteins for Impact on Alzheimer's Disease Risk Reveal a Potential Role for SIGLEC14. PMID:34208838
mTOR Driven Gene Transcription Is Required for Cholesterol Production in Neurons of the Developing Cerebral Cortex. PMID:34204880
Tracking HIV-1-Infected Cell Clones Using Integration Site-Specific qPCR. PMID:34202310
Harnessing self-labeling enzymes for selective and concurrent A-to-I and C-to-U RNA base editing. PMID:34197596
JBrowseR: An R Interface to the JBrowse 2 Genome Browser. PMID:34196689
Protocol for using heterologous spike-ins to normalize for technical variation in chromatin immunoprecipitation. PMID:34189474
Drosophila yakuba - Tsc1. PMID:34189423
A novel frameshift mutation in the FGD1 gene causing Aarskog-Scott syndrome patient with hypogonadism: a case report. PMID:34189097
The zinc finger protein CLAMP promotes long-range chromatin interactions that mediate dosage compensation of the Drosophila male X-chromosome. PMID:34187599
Evolution of mouse circadian enhancers from transposable elements. PMID:34187518
Genetic load has potential in large populations but is realized in small inbred populations. PMID:34178103
UniBind: maps of high-confidence direct TF-DNA interactions across nine species. PMID:34174819
Whole-exome sequencing reveals a novel homozygous mutation in the COQ8B gene associated with nephrotic syndrome. PMID:34172776
Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples. PMID:34171993
Dysregulation of the secretory pathway connects Alzheimer's disease genetics to aggregate formation. PMID:34171228
Genetic risk for subjective reports of insomnia associates only weakly with polygraphic measures of insomnia in 2,770 adults. PMID:34170227
Genome-wide association study of body fat distribution traits in Hispanics/Latinos from the HCHS/SOL. PMID:34165540
Unraveling Genome Evolution Throughout Visual Analysis: The XCout Portal. PMID:34163150
Evolutionary and phylogenetic insights from a nuclear genome sequence of the extinct, giant, "subfossil" koala lemur Megaladapis edwardsi. PMID:34162703
LncRNAs and Available Databases. PMID:34160796
An enhancer screen identifies new suppressors of small-RNA-mediated epigenetic gene silencing. PMID:34157021
MetamORF: a repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses. PMID:34156446
Genome-enabled discovery of evolutionary divergence in brains and behavior. PMID:34155279
Deep sequencing of 1320 genes reveals the landscape of protein-truncating variants and their contribution to psoriasis in 19,973 Chinese individuals. PMID:34155038
Effect of the Expression of ELOVL5 and IGFBP6 Genes on the Metastatic Potential of Breast Cancer Cells. PMID:34149804
Gene Expression Modification by an Autosomal Inversion Associated With Three Male Mating Morphs. PMID:34149796
Initiation of Otx2 expression in the developing mouse retina requires a unique enhancer and either Ascl1 or Neurog2 activity. PMID:34143204
PHYTOCHROME-INTERACTING FACTORs trigger environmentally responsive chromatin dynamics in plants. PMID:34140685
A DNA methylation-based liquid biopsy for triple-negative breast cancer. PMID:34135468
CRISPR mediated targeting of DUX4 distal regulatory element represses DUX4 target genes dysregulated in Facioscapulohumeral muscular dystrophy. PMID:34131248
Copy number alterations identify a smoking-associated expression signature predictive of poor outcome in head and neck squamous cell carcinoma. PMID:34130230
Exome variant discrepancies due to reference-genome differences. PMID:34129815
TP73-AS1 is induced by YY1 during TMZ treatment and highly expressed in the aging brain. PMID:34115613
Using deep learning to identify bladder cancers with FGFR-activating mutations from histology images. PMID:34114376
Whole-Exome Sequencing Reveals a Rare Variant of OTOF Gene Causing Congenital Non-syndromic Hearing Loss Among Large Muslim Families Favoring Consanguinity. PMID:34113375
Mapping methylation quantitative trait loci in cardiac tissues nominates risk loci and biological pathways in congenital heart disease. PMID:34112112
Enhancing Gonadotrope Gene Expression Through Regulatory lncRNAs. PMID:34111287
Stable Epigenetic Programming of Effector and Central Memory CD4 T Cells Occurs Within 7 Days of Antigen Exposure In Vivo. PMID:34108962
The genetic architecture of age-related hearing impairment revealed by genome-wide association analysis. PMID:34108613
DNAscent v2: detecting replication forks in nanopore sequencing data with deep learning. PMID:34107894
The role of CTCF in the organization of the centromeric 11p15 imprinted domain interactome. PMID:34107024
Mapping genetic variability in mature miRNAs and miRNA binding sites in prostate cancer. PMID:34099864
Kiss1 is differentially regulated in male and female mice by the homeodomain transcription factor VAX1. PMID:34098016
One-step CRISPR-Cas9 protocol for the generation of plug & play conditional knockouts in Drosophila melanogaster. PMID:34095868
Chromatin accessibility changes at intergenic regions are associated with ovarian cancer drug resistance. PMID:34090482
SnoRNA copy regulation affects family size, genomic location and family abundance levels. PMID:34090325
Annotation of snoRNA abundance across human tissues reveals complex snoRNA-host gene relationships. PMID:34088344
Extensive pleiotropism and allelic heterogeneity mediate metabolic effects of IRX3 and IRX5. PMID:34083488
noisyR: enhancing biological signal in sequencing datasets by characterizing random technical noise. PMID:34076236
The stabilization of yes-associated protein by TGFβ-activated kinase 1 regulates the self-renewal and oncogenesis of gastric cancer stem cells. PMID:34075691
Widespread Exaptation of L1 Transposons for Transcription Factor Binding in Breast Cancer. PMID:34070697
The Detection and Bioinformatic Analysis of Alternative 3' UTR Isoforms as Potential Cancer Biomarkers. PMID:34070203
Hypoxia-induced lncHILAR promotes renal cancer metastasis via ceRNA for the miR-613/206/ 1-1-3p/Jagged-1/Notch/CXCR4 signaling pathway. PMID:34058384
snpXplorer: a web application to explore human SNP-associations and annotate SNP-sets. PMID:34048563
Novel loci and Mapuche genetic ancestry are associated with pubertal growth traits in Chilean boys. PMID:34047840
A cross-cohort analysis of autosomal DNA methylation sex differences in the term placenta. PMID:34044884
A workflow to identify novel proteins based on the direct mapping of peptide-spectrum-matches to genomic locations. PMID:34039272
CRISPECTOR provides accurate estimation of genome editing translocation and off-target activity from comparative NGS data. PMID:34031394
Mapping the transcriptomics landscape of post-traumatic stress disorder symptom dimensions in World Trade Center responders. PMID:34031375
NFAT5 Amplifies Antipathogen Responses by Enhancing Chromatin Accessibility, H3K27 Demethylation, and Transcription Factor Recruitment. PMID:34031145
The nuclear periphery is a scaffold for tissue-specific enhancers. PMID:34023908
Inducible expression quantitative trait locus analysis of the MUC5AC gene in asthma in urban populations of children. PMID:34019912
Very long intergenic non-coding (vlinc) RNAs directly regulate multiple genes in cis and trans. PMID:34016118
Transcription start site-level expression of thyroid transcription factor 1 isoforms in lung adenocarcinoma and its clinicopathological significance. PMID:34014042
RAS mutations drive proliferative chronic myelomonocytic leukemia via a KMT2A-PLK1 axis. PMID:34006870
Molecular Evolution of DNA Topoisomerase III Beta (TOP3B) in Metazoa. PMID:33999213
OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions. PMID:33999180
Polycomb Factor PHF19 Controls Cell Growth and Differentiation Toward Erythroid Pathway in Chronic Myeloid Leukemia Cells. PMID:33996816
Genome-wide analysis of primary microRNA expression using H3K36me3 ChIP-seq data. PMID:33995896
LncRNA ZNF674-AS1 regulates granulosa cell glycolysis and proliferation by interacting with ALDOA. PMID:33993190
High-throughput full-length single-cell RNA-seq automation. PMID:33990801
Downregulation of both mismatch repair and non-homologous end-joining pathways in hypoxic brain tumour cell lines. PMID:33986995
PhyloPrimer: a taxon-specific oligonucleotide design platform. PMID:33986979
Tissue-specific activation of gene expression by the Synergistic Activation Mediator (SAM) CRISPRa system in mice. PMID:33986266
piRNA-mediated gene regulation and adaptation to sex-specific transposon expression in D. melanogaster male germline. PMID:33985970
CRISPRi-mediated functional analysis of NKX2-1-binding sites in the lung. PMID:33980985
Profiling of Primary and Mature miRNA Expression in Atherosclerosis-Associated Cell Types. PMID:33980036
Chromatin accessibility governs the differential response of cancer and T cells to arginine starvation. PMID:33979616
Comprehensive cell type decomposition of circulating cell-free DNA with CelFiE. PMID:33976150
SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. PMID:33976134
Identification of missense MAB21L1 variants in microphthalmia and aniridia. PMID:33973683
Knowledge bases and software support for variant interpretation in precision oncology. PMID:33971666
Genome-wide association study of cardiac troponin I in the general population. PMID:33961016
Screening and identification of LMNB1 and DLGAP5, two key biomarkers in gliomas. PMID:33956061
A highly multiplexed droplet digital PCR assay to measure the intact HIV-1 proviral reservoir. PMID:33948574
ZFP90 drives the initiation of colitis-associated colorectal cancer via a microbiota-dependent strategy. PMID:33947304
Elephant Genomes Reveal Accelerated Evolution in Mechanisms Underlying Disease Defenses. PMID:33944920
Deep sequencing of pre-translational mRNPs reveals hidden flux through evolutionarily conserved alternative splicing nonsense-mediated decay pathways. PMID:33941243
A maximum flow-based network approach for identification of stable noncoding biomarkers associated with the multigenic neurological condition, autism. PMID:33941233
SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses. PMID:33932985
IBDDB: a manually curated and text-mining-enhanced database of genes involved in inflammatory bowel disease. PMID:33929018
Identification and Characterization of Alternatively Spliced Transcript Isoforms of IRX4 in Prostate Cancer. PMID:33919200
Human Endogenous Retroviruses in Glioblastoma Multiforme. PMID:33917421
Integrative RNA-Seq and H3 Trimethylation ChIP-Seq Analysis of Human Lung Cancer Cells Isolated by Laser-Microdissection. PMID:33916417
Chromatin occupancy and target genes of the haematopoietic master transcription factor MYB. PMID:33903675
Transcriptional Silencing of ALDH2 Confers a Dependency on Fanconi Anemia Proteins in Acute Myeloid Leukemia. PMID:33893150
Estimating sequencing error rates using families. PMID:33892748
A unified atlas of CD8 T cell dysfunctional states in cancer and infection. PMID:33891860
An intron variant of the GLI family zinc finger 3 (GLI3) gene differentiates resistance training-induced muscle fiber hypertrophy in younger men. PMID:33891350
Co-regulation and function of FOXM1/RHNO1 bidirectional genes in cancer. PMID:33890574
BAP1 constrains pervasive H2AK119ub1 to control the transcriptional potential of the genome. PMID:33888563
Single nucleotide polymorphisms affect miRNA target prediction in bovine. PMID:33882076
Genome-wide strand asymmetry in massively parallel reporter activity favors genic strands. PMID:33879525
FOXP4-AS1 is a favorable prognostic-related enhancer RNA in ovarian cancer. PMID:33870423
Conserved long-range base pairings are associated with pre-mRNA processing of human genes. PMID:33863890
Deletion of CTCF sites in the SHH locus alters enhancer-promoter interactions and leads to acheiropodia. PMID:33863876
Chromatin accessibility landscapes of immune cells in rheumatoid arthritis nominate monocytes in disease pathogenesis. PMID:33863328
Single-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacy. PMID:33861994
Variable kinship patterns in Neolithic Anatolia revealed by ancient genomes. PMID:33857427
Panels and models for accurate prediction of tumor mutation burden in tumor samples. PMID:33850256
Integrated transcription factor profiling with transcriptome analysis identifies L1PA2 transposons as global regulatory modulators in a breast cancer model. PMID:33850167
Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney. PMID:33850129
Genome-wide characterization of human minisatellite VNTRs: population-specific alleles and gene expression differences. PMID:33849068
CNGB1-related rod-cone dystrophy: A mutation review and update. PMID:33847019
A novel KCNQ4 gene variant (c.857A>G; p.Tyr286Cys) in an extended family with non‑syndromic deafness 2A. PMID:33846771
Minor intron retention drives clonal hematopoietic disorders and diverse cancer predisposition. PMID:33846634
Go Get Data (GGD) is a framework that facilitates reproducible access to genomic data. PMID:33846313
Genetic alterations in Thai adult patients with acute myeloid leukemia and myelodysplastic syndrome-excess blasts detected by next-generation sequencing technique. PMID:33839881
A distal Foxp3 enhancer enables interleukin-2 dependent thymic Treg cell lineage commitment for robust immune tolerance. PMID:33838102
Whole-exome sequencing reveals the etiology of the rare primary hepatic mucoepidermoid carcinoma. PMID:33832503
Multi-Staged Data-Integrated Multi-Omics Analysis for Symptom Science Research. PMID:33827270
Distinct dynamics and functions of H2AK119ub1 and H3K27me3 in mouse preimplantation embryos. PMID:33821005
Enhort: a platform for deep analysis of genomic positions. PMID:33816851
Pan-Cancer Genome-Wide DNA Methylation Analyses Revealed That Hypermethylation Influences 3D Architecture and Gene Expression Dysregulation in HOXA Locus During Carcinogenesis of Cancers. PMID:33816499
Founder mutation in the PMM2 promotor causes hyperinsulinemic hypoglycaemia/polycystic kidney disease (HIPKD). PMID:33811480
Evaluation of a Custom Design Gene Panel as a Diagnostic Tool for Human Non-Syndromic Infertility. PMID:33809228
Selective Activation of CNS and Reference PPARGC1A Promoters Is Associated with Distinct Gene Programs Relevant for Neurodegenerative Diseases. PMID:33804860
Translational Research in the Era of Precision Medicine: Where We Are and Where We Will Go. PMID:33803592
Genetic Variation in the Vascular Endothelial Growth Factor (VEGFA) Gene at rs13207351 Is Associated with Overall Survival of Patients with Head and Neck Cancer. PMID:33800431
Integrative Analysis of the Expression of SIGLEC Family Members in Lung Adenocarcinoma via Data Mining. PMID:33796453
Presence of complete murine viral genome sequences in patient-derived xenografts. PMID:33795676
Human OMICs and Computational Biology Research in Africa: Current Challenges and Prospects. PMID:33794662
Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements. PMID:33793741
Associations between childhood family emotional health, fronto-limbic grey matter volume, and saliva 5mC in young adulthood. PMID:33789736
Epigenomic tensor predicts disease subtypes and reveals constrained tumor evolution. PMID:33789109
Asterix/Gtsf1 links tRNAs and piRNA silencing of retrotransposons. PMID:33789107
Single-cell chromatin accessibility landscape identifies tissue repair program in human regulatory T cells. PMID:33789089
Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies. PMID:33789087
Machine learning predicts nucleosome binding modes of transcription factors. PMID:33784978
Expanding the Phenotype of TUBB2A-Related Tubulinopathy: Three Cases of a Novel, Heterozygous TUBB2A Pathogenic Variant p.Gly98Arg. PMID:33776625
Early cis-regulatory events in the formation of retinal horizontal cells. PMID:33774011
A proof-of-concept study for the pathogenetic role of enhancer hypomethylation of MYBPHL in multiple myeloma. PMID:33772052
Primate innate immune responses to bacterial and viral pathogens reveals an evolutionary trade-off between strength and specificity. PMID:33771921
Neuronal enhancers are hotspots for DNA single-strand break repair. PMID:33767446
Temporal gene regulation by p53 is associated with the rotational setting of its binding sites in nucleosomes. PMID:33764853
Tunable, division-independent control of gene activation timing by a polycomb switch. PMID:33761349
A cohesin cancer mutation reveals a role for the hinge domain in genome organization and gene expression. PMID:33760811
Functional genomics study of protein inhibitor of activated STAT1 in mouse hippocampal neuronal cells revealed by RNA sequencing. PMID:33759814
Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research. PMID:33758196
Hovlinc is a recently evolved class of ribozyme found in human lncRNA. PMID:33753927
An exon-biased biophysical approach and NMR spectroscopy define the secondary structure of a conserved helical element within the HOTAIR long non-coding RNA. PMID:33753203
Field-deployable, rapid diagnostic testing of saliva for SARS-CoV-2. PMID:33750853
Implication of TIGIT+ human memory B cells in immune regulation. PMID:33750787
Identification of 11 candidate structured noncoding RNA motifs in humans by comparative genomics. PMID:33750298
Developmental Accumulation of Gene Body and Transposon Non-CpG Methylation in the Zebrafish Brain. PMID:33748137
Remus: A Web Application for Prioritization of Regulatory Regions and Variants in Monogenic Diseases. PMID:33747049
Statistical integration of two omics datasets using GO2PLS. PMID:33736604
POINT technology illuminates the processing of polymerase-associated intact nascent transcripts. PMID:33735606
Identification of Four Novel Variants and Determination of Genotype-Phenotype Correlations for ABCA4 Variants Associated With Inherited Retinal Degenerations. PMID:33732702
Use of Mathematical Methods for the Biosafety Assessment of Agricultural Crops. PMID:33727728
A unified framework for inferring the multi-scale organization of chromatin domains from Hi-C. PMID:33724986
The Long Non-Coding RNA HOTAIR Is a Critical Epigenetic Mediator of Angiogenesis in Diabetic Retinopathy. PMID:33724292
Experimental Resurrection of Ancestral Mammalian CPEB3 Ribozymes Reveals Deep Functional Conservation. PMID:33720319
Interpretable Machine Learning Reveals Dissimilarities Between Subtypes of Autism Spectrum Disorder. PMID:33719335
An optimized protocol for rapid, sensitive and robust on-bead ChIP-seq from primary cells. PMID:33718886
Aptardi predicts polyadenylation sites in sample-specific transcriptomes using high-throughput RNA sequencing and DNA sequence. PMID:33712618
aniFOUND: analysing the associated proteome and genomic landscape of the repaired nascent non-replicative chromatin. PMID:33693861
Aging and pathological aging signatures of the brain: through the focusing lens of SIRT6. PMID:33690173
Genetic variation and microRNA targeting of A-to-I RNA editing fine tune human tissue transcriptomes. PMID:33685485
S3V2-IDEAS: a package for normalizing, denoising and integrating epigenomic datasets across different cell types. PMID:33681991
MACMIC Reveals A Dual Role of CTCF in Epigenetic Regulation of Cell Identity Genes. PMID:33677108
Characterization of axolotl lampbrush chromosomes by fluorescence in situ hybridization and immunostaining. PMID:33675804
IRF8 Is an AML-Specific Susceptibility Factor That Regulates Signaling Pathways and Proliferation of AML Cells. PMID:33673123
Common Treatment, Common Variant: Evolutionary Prediction of Functional Pharmacogenomic Variants. PMID:33669176
Conversion of the death inhibitor ARC to a killer activates pancreatic β cell death in diabetes. PMID:33667344
Germline mutation in POLR2A: a heterogeneous, multi-systemic developmental disorder characterized by transcriptional dysregulation. PMID:33665635
IL10 hypomethylation is associated with the risk of gastric cancer. PMID:33664805
The evolution of hemocyanin genes in Tectipleura: a multitude of conserved introns in highly diverse gastropods. PMID:33663373
MMP7 as a potential biomarker of colon cancer and its prognostic value by bioinformatics analysis. PMID:33655961
The relationship between donor-recipient genetic distance and long-term kidney transplant outcome. PMID:33655195
Proximity-dependent Mapping of the Androgen Receptor Identifies Kruppel-like Factor 4 as a Functional Partner. PMID:33640491
rs1944919 on chromosome 11q23.1 and its effector genes COLCA1/COLCA2 confer susceptibility to primary biliary cholangitis. PMID:33633225
Integrated analysis of behavioral, epigenetic, and gut microbiome analyses in AppNL-G-F, AppNL-F, and wild type mice. PMID:33633159
Haplotype-resolved diverse human genomes and integrated analysis of structural variation. PMID:33632895
How to Use Online Tools to Generate New Hypotheses for Mammary Gland Biology Research: A Case Study for Wnt7b. PMID:33625717
Annotation of chromatin states in 66 complete mouse epigenomes during development. PMID:33619351
Mitochondria Autoimmunity and MNRR1 in Breast Carcinogenesis: A Review. PMID:33615312
Characterising open chromatin in chick embryos identifies cis-regulatory elements important for paraxial mesoderm formation and axis extension. PMID:33608545
GWAS of peptic ulcer disease implicates Helicobacter pylori infection, other gastrointestinal disorders and depression. PMID:33608531
Rare KMT2A-ELL and Novel ZNF56-KMT2A Fusion Genes in Pediatric T-cell Acute Lymphoblastic Leukemia. PMID:33608309
Ush regulates hemocyte-specific gene expression, fatty acid metabolism and cell cycle progression and cooperates with dNuRD to orchestrate hematopoiesis. PMID:33600407
Telomeres reforged with non-telomeric sequences in mouse embryonic stem cells. PMID:33597549
Cross-species examination of X-chromosome inactivation highlights domains of escape from silencing. PMID:33597016
Identification of a novel genetic locus associated with immune-mediated thrombotic thrombocytopenic purpura. PMID:33596643
Divergence in alternative polyadenylation contributes to gene regulatory differences between humans and chimpanzees. PMID:33595436
The Impact of Purifying and Background Selection on the Inference of Population History: Problems and Prospects. PMID:33591322
circTulp4 functions in Alzheimer's disease pathogenesis by regulating its parental gene, Tulp4. PMID:33578037
Screening and identification of hub genes in bladder cancer by bioinformatics analysis and KIF11 is a potential prognostic biomarker. PMID:33574944
Integrated bioinformatic analysis identifies COL4A3, COL4A4, and KCNJ1 as key biomarkers in Wilms tumor. PMID:33564352
Live-cell single particle tracking of PRC1 reveals a highly dynamic system with low target site occupancy. PMID:33563969
Aberrant gene expression induced by a high fat diet is linked to H3K9 acetylation in the promoter-proximal region. PMID:33556624
Pancreatic progenitor epigenome maps prioritize type 2 diabetes risk genes with roles in development. PMID:33544077
ESR1 ChIP-Seq Identifies Distinct Ligand-Free ESR1 Genomic Binding Sites in Human Hepatocytes and Liver Tissue. PMID:33540646
Enhancers predominantly regulate gene expression during differentiation via transcription initiation. PMID:33539786
A gene-environment-induced epigenetic program initiates tumorigenesis. PMID:33536616
Identification of SNPs Associated with Somatic Cell Score in Candidate Genes in Italian Holstein Friesian Bulls. PMID:33535694
Human MiniPromoters for ocular-rAAV expression in ON bipolar, cone, corneal, endothelial, Müller glial, and PAX6 cells. PMID:33531684
Epigenome-Wide Study of Posttraumatic Stress Disorder Symptom Severity in a Treatment-Seeking Adolescent Sample. PMID:33529416
Structural and Genetic Determinants of Convergence in the Drosophila tRNA Structure-Function Map. PMID:33528599
Insight into formation propensity of pseudocircular DNA G-hairpins. PMID:33524154
Direct diagnostic testing of SARS-CoV-2 without the need for prior RNA extraction. PMID:33510181
Sensitive and specific multi-cancer detection and localization using methylation signatures in cell-free DNA. PMID:33506766
Transcriptionally active enhancers in human cancer cells. PMID:33502116
The impact of purifying and background selection on the inference of population history: problems and prospects. PMID:33501439
Forkhead box F1 induces columnar phenotype and epithelial-to-mesenchymal transition in esophageal squamous cells to initiate Barrett's like metaplasia. PMID:33495575
Fetuin-A is a HIF target that safeguards tissue integrity during hypoxic stress. PMID:33483479
Polymorphism rs368234815 of interferon lambda 4 gene and spontaneous clearance of hepatitis C virus in haemodialysis patients: a case-control study. PMID:33482747
A comprehensive microsatellite landscape of human Y-DNA at kilobase resolution. PMID:33482734
Analysis of ovarian transcriptomes reveals thousands of novel genes in the insect vector Rhodnius prolixus. PMID:33479356
RAFFI: Accurate and fast familial relationship inference in large scale biobank studies using RaPID. PMID:33476339
Association analysis of repetitive elements and R-loop formation across species. PMID:33472695
Genome-wide prediction of topoisomerase IIβ binding by architectural factors and chromatin accessibility. PMID:33465072
Giant lungfish genome elucidates the conquest of land by vertebrates. PMID:33461212
Secondary Structural Model of MALAT1 Becomes Unstructured in Chronic Myeloid Leukemia and Undergoes Structural Rearrangement in Cervical Cancer. PMID:33450947
The pioneer and differentiation factor FOXA2 is a key driver of yolk-sac tumour formation and a new biomarker for paediatric and adult yolk-sac tumours. PMID:33448076
Patterns of de novo tandem repeat mutations and their role in autism. PMID:33442040
Heritability and family-based GWAS analyses of the N-acyl ethanolamine and ceramide plasma lipidome. PMID:33437986
Allele-specific expression of Parkinson's disease susceptibility genes in human brain. PMID:33436766
Childhood DNA methylation as a marker of early life rapid weight gain and subsequent overweight. PMID:33436068
Exploration of Coding and Non-coding Variants in Cancer Using GenomePaint. PMID:33434514
Strategies to Identify Genetic Variants Causing Infertility. PMID:33431240
Therapy-induced Deletion in 11q23 Leading to Fusion of KMT2A With ARHGEF12 and Development of B Lineage Acute Lymphoplastic Leukemia in a Child Treated for Acute Myeloid Leukemia Caused by t(9;11)(p21;q23)/KMT2A-MLLT3. PMID:33419897
Whole exome sequencing and establishment of an organoid culture of the carcinoma showing thymus-like differentiation (CASTLE) of the parotid gland. PMID:33415446
Dynamic regulation of CTCF stability and sub-nuclear localization in response to stress. PMID:33411704
Genome-wide association study of circulating levels of glucagon during an oral glucose tolerance test. PMID:33407418
Cell-specific characterization of the placental methylome. PMID:33407091
MEF2 (Myocyte Enhancer Factor 2) Is Essential for Endothelial Homeostasis and the Atheroprotective Gene Expression Program. PMID:33406884
A Poorly Differentiated Non-keratinizing Sinonasal Squamous Cell Carcinoma with a Novel ETV6-TNFRSF8 Fusion Gene. PMID:33394379
CRISPR-Cas9-Mediated Genomic Deletions Protocol in Zebrafish. PMID:33377102
Genome-wide Interrogation of Protein-DNA Interactions in Mammalian Cells Using ChIPmentation. PMID:33377081
Genome-wide detection of short tandem repeat expansions by long-read sequencing. PMID:33371889
Signatures of host-pathogen evolutionary conflict reveal MISTR-A conserved MItochondrial STress Response network. PMID:33370271
On the NF-Y regulome as in ENCODE (2019). PMID:33370256
Neuron type-specific increase in lamin B1 contributes to nuclear dysfunction in Huntington's disease. PMID:33369245
Usher syndrome and Nebulin-associated myopathy in a single patient due to variants in MYO7A and NEB. PMID:33363762
Novel CRISPR-based sequence specific enrichment methods for target loci and single base mutations. PMID:33362267
Biparental contributions of the H2A.B histone variant control embryonic development in mice. PMID:33362208
Dark Matter of Primate Genomes: Satellite DNA Repeats and Their Evolutionary Dynamics. PMID:33352976
Chemical carcinogen-induced rat mammary carcinogenesis is a potential model of p21-activated kinase positive female breast cancer. PMID:33346690
The lncRNA Toolkit: Databases and In Silico Tools for lncRNA Analysis. PMID:33339309
Confined placental mosaicism of Duchenne muscular dystrophy: a case report. PMID:33334361
Integrative characterization of the near-minimal bacterium Mesoplasma florum. PMID:33331123
Oncology and Pharmacogenomics Insights in Polycystic Ovary Syndrome: An Integrative Analysis. PMID:33329391
AnnoLnc: A One-Stop Portal to Systematically Annotate Novel Human Long Noncoding RNAs. PMID:33326073
Transcriptome Analysis Illuminates a Hub Role of SREBP2 in Cholesterol Metabolism by α-Mangostin. PMID:33324821
Hybrid sequencing resolves two germline ultra-complex chromosomal rearrangements consisting of 137 breakpoint junctions in a single carrier. PMID:33315133
Fc γ receptor IIIa/CD16a processing correlates with the expression of glycan-related genes in human natural killer cells. PMID:33310702
Is there any intron sliding in mammals? PMID:33308147
Efficient homing of antibody-secreting cells to the bone marrow requires RNA-binding protein ZFP36L1. PMID:33306108
Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework. PMID:33304457
In-Depth Analysis of Genetic Variation Associated with Severe West Nile Viral Disease. PMID:33302579
Genomic Analysis of Natural Rough Brucella melitensis Rev.1 Vaccine Strains: Identification and Characterization of Mutations in Key Genes Associated with Bacterial LPS Biosynthesis and Virulence. PMID:33302421
A reference catalog of DNA palindromes in the human genome and their variations in 1000 Genomes. PMID:33298903
Hepatic transcriptome and DNA methylation patterns following perinatal and chronic BPS exposure in male mice. PMID:33297965
Msuite: A High-Performance and Versatile DNA Methylation Data-Analysis Toolkit. PMID:33294868
Intronic tRNAs of mitochondrial origin regulate constitutive and alternative splicing. PMID:33292386
Urinary metabolite quantitative trait loci in children and their interaction with dietary factors. PMID:33283231
Informatics Inference of Exercise-Induced Modulation of Brain Pathways Based on Cerebrospinal Fluid Micro-RNAs in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome. PMID:33274349
Predicting sites of epitranscriptome modifications using unsupervised representation learning based on generative adversarial networks. PMID:33274189
Identification of novel alternative splicing biomarkers for breast cancer with LC/MS/MS and RNA-Seq. PMID:33272210
Developmental remodelling of non-CG methylation at satellite DNA repeats. PMID:33271598
GENCODE 2021. PMID:33270111
Transcriptome and regulatory maps of decidua-derived stromal cells inform gene discovery in preterm birth. PMID:33268355
Impact of AHR Ligand TCDD on Human Embryonic Stem Cells and Early Differentiation. PMID:33260776
ncVarDB: a manually curated database for pathogenic non-coding variants and benign controls. PMID:33258967
SNP-SNP Interaction in Genes Encoding PD-1/PD-L1 Axis as a Potential Risk Factor for Clear Cell Renal Cell Carcinoma. PMID:33255938
Whole-Transcriptome Analysis in Peripheral Blood Mononuclear Cells from Patients with Lipid-Specific Oligoclonal IgM Band Characterization Reveals Two Circular RNAs and Two Linear RNAs as Biomarkers of Highly Active Disease. PMID:33255923
Evaluating the Genomic Parameters Governing rAAV-Mediated Homologous Recombination. PMID:33248247
c-KIT-ERK1/2 signaling activated ELK1 and upregulated carcinoembryonic antigen expression to promote colorectal cancer progression. PMID:33247506
DIANA-miRGen v4: indexing promoters and regulators for more than 1500 microRNAs. PMID:33245765
ProTECT-Prediction of T-Cell Epitopes for Cancer Therapy. PMID:33244314
An Integrated Epigenomic and Transcriptomic Map of Mouse and Human αβ T Cell Development. PMID:33242395
Accessing NCBI data using the NCBI Sequence Viewer and Genome Data Viewer (GDV). PMID:33239395
Site-Specific Phosphorylation of Histone H1.4 Is Associated with Transcription Activation. PMID:33238524
DNMT3A Haploinsufficiency Results in Behavioral Deficits and Global Epigenomic Dysregulation Shared across Neurodevelopmental Disorders. PMID:33238114
Qtlizer: comprehensive QTL annotation of GWAS results. PMID:33235230
A developmental stage-specific network approach for studying dynamic co-regulation of transcription factors and microRNAs during craniofacial development. PMID:33234712
GTRD: an integrated view of transcription regulation. PMID:33231677
cGAS-mediated induction of type I interferon due to inborn errors of histone pre-mRNA processing. PMID:33230297
Multi-Omics Identifies Circulating miRNA and Protein Biomarkers for Facioscapulohumeral Dystrophy. PMID:33228131
The UCSC Genome Browser database: 2021 update. PMID:33221922
Optimized design of antisense oligomers for targeted rRNA depletion. PMID:33221877
Are spliced ncRNA host genes distinct classes of lncRNAs? PMID:33219910
Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1-positive pediatric leukemia identifies drug-targetable transcription factor activities. PMID:33218352
ANK2 Hypermethylation in Canine Mammary Tumors and Human Breast Cancer. PMID:33218035
Polymorphic variants of drug-metabolizing enzymes alter the risk and survival of oral cancer patients. PMID:33214976
Altered immune phenotype and DNA methylation in panic disorder. PMID:33208194
XPC deficiency increases risk of hematologic malignancies through mutator phenotype and characteristic mutational signature. PMID:33203900
Genetic Predictors of Severe Skin Toxicity in Patients with Stage III Colon Cancer Treated with Cetuximab: NCCTG N0147 (Alliance). PMID:33203692
YY1 interacts with guanine quadruplexes to regulate DNA looping and gene expression. PMID:33199912
Control of adipogenic commitment by a STAT3-VSTM2A axis. PMID:33196296
Varying Expression of Mu and Kappa Opioid Receptors in Cockatiels (Nymphicus hollandicus) and Domestic Pigeons (Columba livia domestica). PMID:33193624
Brd/BET Proteins Influence the Genome-Wide Localization of the Kaposi's Sarcoma-Associated Herpesvirus and Murine Gammaherpesvirus Major Latency Proteins. PMID:33193257
Neurexins in autism and schizophrenia-a review of patient mutations, mouse models and potential future directions. PMID:33191396
High levels of LINE-1 transposable elements expressed in Kaposi's sarcoma-associated herpesvirus-related primary effusion lymphoma. PMID:33188297
A human cell atlas of fetal chromatin accessibility. PMID:33184180
Upregulated lnc‑HRK‑2:1 prompts nucleus pulposus cell senescence in intervertebral disc degeneration. PMID:33174041
A functional variant on 20q13.33 related to glioma risk alters enhancer activity and modulates expression of multiple genes. PMID:33169458
LSH mediates gene repression through macroH2A deposition. PMID:33159050
Argonaut: A Web Platform for Collaborative Multi-omic Data Visualization and Exploration. PMID:33154995
A zebrafish functional genomics model to investigate the role of human A20 variants in vivo. PMID:33154446
Towards a better understanding of the low recall of insertion variants with short-read based variant callers. PMID:33148192
The transition from primary colorectal cancer to isolated peritoneal malignancy is associated with an increased tumour mutational burden. PMID:33144643
Broad genic repression domains signify enhanced silencing of oncogenes. PMID:33144558
H4K20me3 methyltransferase SUV420H2 shapes the chromatin landscape of pluripotent embryonic stem cells. PMID:33144397
NRF2-Dependent Bioactivation of Mitomycin C as a Novel Strategy To Target KEAP1-NRF2 Pathway Activation in Human Cancer. PMID:33139492
Transfer learning enables prediction of CYP2D6 haplotype function. PMID:33137098
Characterization of Organoid Cultures to Study the Effects of Pregnancy Hormones on the Epigenome and Transcriptional Output of Mammary Epithelial Cells. PMID:33131024
Effects of NT5C2 Germline Variants on 6-Mecaptopurine Metabolism in Children With Acute Lymphoblastic Leukemia. PMID:33124053
Involvement of Essential Signaling Cascades and Analysis of Gene Networks in Diabesity. PMID:33113859
Voltage-Gated Calcium Channels in Nonexcitable Tissues. PMID:33106102
Alternative isoforms of KDM2A and KDM2B lysine demethylases negatively regulate canonical Wnt signaling. PMID:33104714
Identification of Specific Circular RNA Expression Patterns and MicroRNA Interaction Networks in Mesial Temporal Lobe Epilepsy. PMID:33101384
Selective DNA Demethylation Accompanies T Cell Homeostatic Proliferation and Gene Regulation in Lupus-Prone lpr Mice. PMID:33097564
RING1B recruits EWSR1-FLI1 and cooperates in the remodeling of chromatin necessary for Ewing sarcoma tumorigenesis. PMID:33097530
Genetically predicted telomere length is associated with clonal somatic copy number alterations in peripheral leukocytes. PMID:33090998
Downregulation of PUMA underlies resistance to FGFR1 inhibitors in the stem cell leukemia/lymphoma syndrome. PMID:33082322
Identification of a competing endogenous RNA axis related to gastric cancer. PMID:33080572
Cruciform DNA in mouse growing oocytes: Its dynamics and its relationship with DNA transcription. PMID:33079963
Evolutionary History of Alpha Satellite DNA Repeats Dispersed within Human Genome Euchromatin. PMID:33078196
HIF1α is not a target of 14q deletion in clear cell renal cancer. PMID:33077781
Detecting Selection from Linked Sites Using an F-Model. PMID:33067324
CHD7 promotes neural progenitor differentiation in embryonic stem cells via altered chromatin accessibility and nascent gene expression. PMID:33060836
Ultrafast and scalable variant annotation and prioritization with big functional genomics data. PMID:33060171
Emergent Coordination of the CHKB and CPT1B Genes in Eutherian Mammals: Implications for the Origin of Brown Adipose Tissue. PMID:33058877
dbGuide: a database of functionally validated guide RNAs for genome editing in human and mouse cells. PMID:33051688
Aberrantly Expressed RECQL4 Helicase Supports Proliferation and Drug Resistance of Human Glioma Cells and Glioma Stem Cells. PMID:33050631
Environmental Epigenetics of Diesel Particulate Matter Toxicogenomics. PMID:33050454
Exploring chromosomal structural heterogeneity across multiple cell lines. PMID:33047670
LncExpDB: an expression database of human long non-coding RNAs. PMID:33045751
Association of Common Variants of TNFSF13 and TNFRSF13B Genes with CLL Risk and Clinical Picture, as Well as Expression of Their Products-APRIL and TACI Molecules. PMID:33036273
Bioinformatic Identification of Potential Hub Genes in Muscle-Invasive Bladder Urothelial Carcinoma. PMID:33035117
Prostate cancer evolution from multilineage primary to single lineage metastases with implications for liquid biopsy. PMID:33033260
The mole genome reveals regulatory rearrangements associated with adaptive intersexuality. PMID:33033216
inCNV: An Integrated Analysis Tool for Copy Number Variation on Whole Exome Sequencing. PMID:33029071
Rescuing Over-activated Microglia Restores Cognitive Performance in Juvenile Animals of the Dp(16) Mouse Model of Down Syndrome. PMID:33027640
SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. PMID:33024961
Transcript Isoforms of SLC7A11-AS1 Are Associated With Varicocele-Related Male Infertility. PMID:33024440
HIV-1 infection activates endogenous retroviral promoters regulating antiviral gene expression. PMID:33021676
Modulating gene regulation to treat genetic disorders. PMID:33020616
Novel 199 base pair NEFH promoter drives expression in retinal ganglion cells. PMID:33020509
HIV-1 viremia not suppressible by antiretroviral therapy can originate from large T cell clones producing infectious virus. PMID:33016926
A Novel Microduplication Spanning Exons 8-16 of ATP2C1 That Was Undetectable by Standard Sanger Sequencing in a Japanese Patient With Hailey-Hailey Disease. PMID:33015087
Screening and Identification of Key Biomarkers in Acquired Lapatinib-Resistant Breast Cancer. PMID:33013420
Combined proteomic and transcriptomic approaches reveal externalized keratin 8 as a potential therapeutic target involved in invasiveness of head and neck cancers. PMID:33010552
Large-scale variation in single nucleotide polymorphism density within the laboratory axolotl (Ambystoma mexicanum). PMID:33001517
Repeat expansions confer WRN dependence in microsatellite-unstable cancers. PMID:32999459
Causal Associations Between Modifiable Risk Factors and the Alzheimer's Phenome. PMID:32996171
Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder. PMID:32991838
An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer's disease. PMID:32989324
A Model-Driven Quantitative Analysis of Retrotransposon Distributions in the Human Genome. PMID:32986810
Genetic background dependent modifiers of craniosynostosis severity. PMID:32976998
Detection of a somatic GREB1-NCOA1 gene fusion in a uterine tumor resembling ovarian sex cord tumor (UTROSCT). PMID:32964092
Theoretical characterisation of strand cross-correlation in ChIP-seq. PMID:32962634
Clearing of Foreign Episomal DNA from Human Cells by CRISPRa-Mediated Activation of Cytidine Deaminases. PMID:32962129
Targeting the histone demethylase PHF8-mediated PKCα-Src-PTEN axis in HER2-negative gastric cancer. PMID:32958674
A novel low-grade nasopharyngeal adenocarcinoma characterized by a GOLGB1-BRAF fusion gene. PMID:32951290
Ovarian Cancer Risk Variants Are Enriched in Histotype-Specific Enhancers and Disrupt Transcription Factor Binding Sites. PMID:32946763
The qBED track: a novel genome browser visualization for point processes. PMID:32941613
Scanning window analysis of non-coding regions within normal-tumor whole-genome sequence samples. PMID:32940334
Phenotypic expansion in KIF1A-related dominant disorders: A description of novel variants and review of published cases. PMID:32935419
Characterization of rare ABCC8 variants identified in Spanish pulmonary arterial hypertension patients. PMID:32934261
Molecular basis of a new ovine model for human 3M syndrome-2. PMID:32933480
The Role of Chromosome X in Intraocular Pressure Variation and Sex-Specific Effects. PMID:32926103
Adiponectin GWAS loci harboring extensive allelic heterogeneity exhibit distinct molecular consequences. PMID:32915782
sn-spMF: matrix factorization informs tissue-specific genetic regulation of gene expression. PMID:32912314
Using genomic resources for linkage analysis in Peromyscus with an application for characterizing Dominant Spot. PMID:32912160
The UCSC SARS-CoV-2 Genome Browser. PMID:32908258
Identification of Immune-Related Prognostic Biomarkers Based on the Tumor Microenvironment in 20 Malignant Tumor Types With Poor Prognosis. PMID:32903590
A novel identified circular RNA, circ_0000491, aggravates the extracellular matrix of diabetic nephropathy glomerular mesangial cells through suppressing miR‑101b by targeting TGFβRI. PMID:32901868
Role of the Transcription Factor Yin Yang 1 and Its Selectively Identified Target Survivin in High-Grade B-Cells Non-Hodgkin Lymphomas: Potential Diagnostic and Therapeutic Targets. PMID:32899428
Histone chaperone FACT represses retrotransposon MERVL and MERVL-derived cryptic promoters. PMID:32894293
A LINE-1 insertion situated in the promoter of IMPG2 is associated with autosomal recessive progressive retinal atrophy in Lhasa Apso dogs. PMID:32894063
A long non-coding RNA (Lrap) modulates brain gene expression and levels of alcohol consumption in rats. PMID:32893479
Repurposing of KLF5 activates a cell cycle signature during the progression from a precursor state to oesophageal adenocarcinoma. PMID:32880368
Cancer SLC43A2 alters T cell methionine metabolism and histone methylation. PMID:32879489
Pooled analysis of radiation hybrids identifies loci for growth and drug action in mammalian cells. PMID:32878976
The Evolution of the Mammalian ABCA6-like Genes: Analysis of Phylogenetic, Expression, and Population Genetic Data Reveals Complex Evolutionary Histories. PMID:32877505
β-actin contributes to open chromatin for activation of the adipogenic pioneer factor CEBPA during transcriptional reprograming. PMID:32877276
Evolutionary and Functional Analysis of Korean Native Pig Using Single Nucleotide Polymorphisms. PMID:32868490
Oncogenic Orphan Nuclear Receptor NR4A3 Interacts and Cooperates with MYB in Acinic Cell Carcinoma. PMID:32867110
In silico identification of pseudo-exon activation events in personal genome and transcriptome data. PMID:32865117
Bioinformatics Analysis Revealed Novel 3'UTR Variants Associated with Intellectual Disability. PMID:32858868
Microarray analysis of long non-coding RNA expression profiles in Marfan syndrome. PMID:32855713
Bidirectional Wnt signaling between endoderm and mesoderm confers tracheal identity in mouse and human cells. PMID:32855415
PreLnc: An Accurate Tool for Predicting lncRNAs Based on Multiple Features. PMID:32842486
Emerging Insights into the Distinctive Neuronal Methylome. PMID:32839016
Abundance and localization of human UBE3A protein isoforms. PMID:32833011
The Polycomb-associated factor PHF19 controls hematopoietic stem cell state and differentiation. PMID:32821835
H. pylori infection confers resistance to apoptosis via Brd4-dependent BIRC3 eRNA synthesis. PMID:32820150
Novel, abundant Drosha isoforms are deficient in miRNA processing in cancer cells. PMID:32819190
Motto: Representing Motifs in Consensus Sequences with Minimum Information Loss. PMID:32816922
SUMOylation of E2F1 Regulates Expression of EZH2. PMID:32816857
Prevention of dsRNA-induced interferon signaling by AGO1x is linked to breast cancer cell proliferation. PMID:32812257
Deficiency of pseudogene UPAT leads to hepatocellular carcinoma progression and forms a positive feedback loop with ZEB1. PMID:32808348
The Long Noncoding RNA CCAT2 Induces Chromosomal Instability Through BOP1-AURKB Signaling. PMID:32805281
Genetic analyses identify GSDMB associated with asthma severity, exacerbations, and antiviral pathways. PMID:32795586
Sequence-based prediction of SARS-CoV-2 vaccine targets using a mass spectrometry-based bioinformatics predictor identifies immunogenic T cell epitopes. PMID:32791978
Mutations in m6A consensus motifs are suppressed in the m6A modified genes in human cancer cells. PMID:32790688
Genetic variants modulate gene expression statin response in human lymphoblastoid cell lines. PMID:32787775
Predictive and prognostic value of EPIC1 in patients with breast cancer receiving neoadjuvant chemotherapy. PMID:32782487
An Unbiased Molecular Approach Using 3'-UTRs Resolves the Avian Family-Level Tree of Life. PMID:32781465
SOX10-regulated promoter use defines isoform-specific gene expression in Schwann cells. PMID:32770939
Predictive features of gene expression variation reveal mechanistic link with differential expression. PMID:32767663
Ribbon: intuitive visualization for complex genomic variation. PMID:32766814
Korean Genome Project: 1094 Korean personal genomes with clinical information. PMID:32766443
Systematic Analysis of Differential H3K27me3 and H3K4me3 Deposition in Callus and Seedling Reveals the Epigenetic Regulatory Mechanisms Involved in Callus Formation in Rice. PMID:32765593
Analysis of a Chinese Pedigree With Familial Chylomicronemia Syndrome Reveals Two Novel LPL Mutations by Whole-Exome Sequencing. PMID:32765589
Disease-modifying effects of an SCAF4 structural variant in a predominantly SOD1 ALS cohort. PMID:32754644
MYBPC3 Haplotype Linked to Hypertrophic Cardiomyopathy in Rhesus Macaques (Macaca mulatta). PMID:32753092
Analysis of Ugandan cervical carcinomas identifies human papillomavirus clade-specific epigenome and transcriptome landscapes. PMID:32747824
Mapping and Quantification of Non-Coding RNA Originating from the rDNA in Human Glioma Cells. PMID:32731436
Spatiotemporal DNA methylome dynamics of the developing mouse fetus. PMID:32728242
The multicomparative 2-n-way genome suite. PMID:32727870
Contributions of de novo variants to systemic lupus erythematosus. PMID:32724065
Human L1 Transposition Dynamics Unraveled with Functional Data Analysis. PMID:32722770
Multiple FGF4 Retrocopies Recently Derived within Canids. PMID:32717834
SNPs in lncRNA Regions and Breast Cancer Risk. PMID:32714364
The RNA exosome shapes the expression of key protein-coding genes. PMID:32710631
Accounting for diverse evolutionary forces reveals mosaic patterns of selection on human preterm birth loci. PMID:32709900
Emergence of a High-Plasticity Cell State during Lung Cancer Evolution. PMID:32707077
Genome‑wide analysis of DNA methylation and gene expression changes in an ovalbumin‑induced asthma mouse model. PMID:32705270
Genome‑wide copy number analysis of circulating tumor cells in breast cancer patients with liver metastasis. PMID:32705227
Epigenetic alterations in cytochrome P450 oxidoreductase (Por) in sperm of rats exposed to tetrahydrocannabinol (THC). PMID:32704063
Optical mapping of the 22q11.2DS region reveals complex repeat structures and preferred locations for non-allelic homologous recombination (NAHR). PMID:32699385
Epigenome-wide cross-tissue correlation of human bone and blood DNA methylation - can blood be used as a surrogate for bone? PMID:32692944
A novel CACNA1A variant in a child with early stroke and intractable epilepsy. PMID:32692472
Enhancer prediction in the human genome by probabilistic modelling of the chromatin feature patterns. PMID:32689977
NRF2 is a key regulator of endothelial microRNA expression under proatherogenic stimuli. PMID:32683448
Tumors induce de novo steroid biosynthesis in T cells to evade immunity. PMID:32680985
IL6/STAT3 Signaling Hijacks Estrogen Receptor α Enhancers to Drive Breast Cancer Metastasis. PMID:32679107
Nuclear role for human Argonaute-1 as an estrogen-dependent transcription coactivator. PMID:32673398
Trait-associated noncoding variant regions affect TBX3 regulation and cardiac conduction. PMID:32672536
Human bone marrow stem/stromal cell osteogenesis is regulated via mechanically activated osteocyte-derived extracellular vesicles. PMID:32672416
NCOA4 is regulated by HIF and mediates mobilization of murine hepatic iron stores after blood loss. PMID:32659785
The chromatin remodeling enzyme Chd4 regulates genome architecture in the mouse brain. PMID:32647123
A single-nucleotide polymorphism (rs8176070) of lncRNA PART1 may reflect the risk for knee osteoarthritis. PMID:32644930
Population bias in somatic measurement of microsatellite instability status. PMID:32644297
A Conserved Notochord Enhancer Controls Pancreas Development in Vertebrates. PMID:32640228
Single-cell ATAC sequencing analysis: From data preprocessing to hypothesis generation. PMID:32637041
A user guide for the online exploration and visualization of PCAWG data. PMID:32636365
Targeted sequencing of genes associated with the mismatch repair pathway in patients with endometrial cancer. PMID:32634176
SOAT1 promotes mevalonate pathway dependency in pancreatic cancer. PMID:32633781
Sequence Compression Benchmark (SCB) database-A comprehensive evaluation of reference-free compressors for FASTA-formatted sequences. PMID:32627830
Epiviz File Server: Query, transform and interactively explore data from indexed genomic files. PMID:32618995
The -514C>T polymorphism in the LIPC gene modifies type 2 diabetes risk through modulation of HDL-cholesterol levels in Mexicans. PMID:32617858
URMAP, an ultra-fast read mapper. PMID:32612885
Replicative aging is associated with loss of genetic heterogeneity from extrachromosomal circular DNA in Saccharomyces cerevisiae. PMID:32609810
Nonsense-mediated decay factor SMG7 sensitizes cells to TNFα-induced apoptosis via CYLD tumor suppressor and the noncoding oncogene Pvt1. PMID:32602581
Genomic analyses implicate noncoding de novo variants in congenital heart disease. PMID:32601476
Structural variation of the malaria-associated human glycophorin A-B-E region. PMID:32600246
A unified view of the sequence and functional organization of the human RNA polymerase II promoter. PMID:32597978
A CLN6-CLN8 complex recruits lysosomal enzymes at the ER for Golgi transfer. PMID:32597833
Trans-generational epigenetic regulation associated with the amelioration of Duchenne Muscular Dystrophy. PMID:32596946
Allele-specific DNA methylation is increased in cancers and its dense mapping in normal plus neoplastic cells increases the yield of disease-associated regulatory SNPs. PMID:32594908
An Insulin-Sensitive Circular RNA that Regulates Lifespan in Drosophila. PMID:32592682
Intrinsic and Extrinsic Factors Governing the Transcriptional Regulation of ESR1. PMID:32592004
Detection of copy-number variations from NGS data using read depth information: a diagnostic performance evaluation. PMID:32591635
Shared genetic etiology underlying late-onset Alzheimer's disease and posttraumatic stress syndrome. PMID:32588970
Alternative polyadenylation mediates genetic regulation of gene expression. PMID:32584258
HMTase Inhibitors as a Potential Epigenetic-Based Therapeutic Approach for Friedreich's Ataxia. PMID:32582297
SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. PMID:32577641
Conserved Small Nucleotidic Elements at the Origin of Concerted piRNA Biogenesis from Genes and lncRNAs. PMID:32570966
Molecular Pathogenesis and Interventional Strategies for Alzheimer's Disease: Promises and Pitfalls. PMID:32566913
Clinical Characteristics and Mutation Analyses of Ovarian Sertoli-Leydig Cell Tumors. PMID:32557933
miR-410-3p is induced by vemurafenib via ER stress and contributes to resistance to BRAF inhibitor in melanoma. PMID:32555626
Nibbling 405 kb off the X: Viable deletion alleles eliminating 50 protein coding genes, including a chromatin factor involved in neuronal development. PMID:32550431
Recurrent inversion toggling and great ape genome evolution. PMID:32541924
Resource: A multi-species multi-timepoint transcriptome database and webpage for the pineal gland and retina. PMID:32533862
Proteogenomic analysis of Inhibitor of Differentiation 4 (ID4) in basal-like breast cancer. PMID:32527287
Highly expressed STAT1 contributes to the suppression of stemness properties in human paclitaxel-resistant ovarian cancer cells. PMID:32516753
Folding Keratin Gene Clusters during Skin Regional Specification. PMID:32516596
IRESbase: A Comprehensive Database of Experimentally Validated Internal Ribosome Entry Sites. PMID:32512182
Shear stimulation of FOXC1 and FOXC2 differentially regulates cytoskeletal activity during lymphatic valve maturation. PMID:32510325
CRISPRi-mediated functional analysis of lung disease-associated loci at non-coding regions. PMID:32500120
GC-AG Introns Features in Long Non-coding and Protein-Coding Genes Suggest Their Role in Gene Expression Regulation. PMID:32499820
Complement genes contribute sex-biased vulnerability in diverse disorders. PMID:32499649
A low-bias and sensitive small RNA library preparation method using randomized splint ligation. PMID:32496547
G-quadruplexes offer a conserved structural motif for NONO recruitment to NEAT1 architectural lncRNA. PMID:32496517
Insights into variation in meiosis from 31,228 human sperm genomes. PMID:32494014
An Independent Locus Upstream of ASIP Controls Variation in the Shade of the Bay Coat Colour in Horses. PMID:32486210
Machine learning uncovers cell identity regulator by histone code. PMID:32483223
Diacylglycerol Kinase Alpha in Radiation-Induced Fibrosis: Potential as a Predictive Marker or Therapeutic Target. PMID:32477950
Pervasive promoter hypermethylation of silenced TERT alleles in human cancers. PMID:32468444
halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments. PMID:32463100
Flexible Mixture Model Approaches That Accommodate Footprint Size Variability for Robust Detection of Balancing Selection. PMID:32462188
Transcript expression-aware annotation improves rare variant interpretation. PMID:32461655
Landscape of multi-nucleotide variants in 125,748 human exomes and 15,708 genomes. PMID:32461613
Synergistic CRISPRa-Regulated Chondrogenic Extracellular Matrix Deposition Without Exogenous Growth Factors. PMID:32460686
EpiRegio: analysis and retrieval of regulatory elements linked to genes. PMID:32459338
Clinical Genetics of Prolidase Deficiency: An Updated Review. PMID:32455636
Opposing Functions of BRD4 Isoforms in Breast Cancer. PMID:32446320
SNHG7 is a lncRNA oncogene controlled by Insulin-like Growth Factor signaling through a negative feedback loop to tightly regulate proliferation. PMID:32444795
PTSD and the klotho longevity gene: Evaluation of longitudinal effects on inflammation via DNA methylation. PMID:32438247
Differential Regulation of Wnt Signaling Components During Hippocampal Reorganization After Entorhinal Cortex Lesion. PMID:32435957
Genetic Determinants of Reduced Arsenic Metabolism Efficiency in the 10q24.32 Region Are Associated With Reduced AS3MT Expression in Multiple Human Tissue Types. PMID:32433756
Multi-omic signatures identify pan-cancer classes of tumors beyond tissue of origin. PMID:32433524
Differential Glucocorticoid-Dependent Regulation and Function of the ERRFI1 Gene in Triple-Negative Breast Cancer. PMID:32432675
Protection from DNA re-methylation by transcription factors in primordial germ cells and pre-implantation embryos can explain trans-generational epigenetic inheritance. PMID:32423419
The Evolution of Human Cancer Gene Duplications across Mammals. PMID:32421773
Quantitative phenotype scan statistic (QPSS) reveals rare variant associations with Alzheimer's disease endophenotypes. PMID:32414344
Tropomyosin 1 genetically constrains in vitro hematopoiesis. PMID:32408895
Application of Multiplex Bisulfite PCR-Ligase Detection Reaction-Real-Time Quantitative PCR Assay in Interrogating Bioinformatically Identified, Blood-Based Methylation Markers for Colorectal Cancer. PMID:32407802
AnnoLnc2: the one-stop portal to systematically annotate novel lncRNAs for human and mouse. PMID:32406920
CNN-Peaks: ChIP-Seq peak detection pipeline using convolutional neural networks that imitate human visual inspection. PMID:32404971
Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats. PMID:32398234
Oviz-Bio: a web-based platform for interactive cancer genomics data visualization. PMID:32392343
Clinical and prognostic association of oncogene cadherin 11 in gastric cancer. PMID:32391104
Differentiation of Hispanic biogeographic ancestry with 80 ancestry informative markers. PMID:32385290
Tet2-mediated epigenetic drive for astrocyte differentiation from embryonic neural stem cells. PMID:32377393
Ampliconic Genes on the Great Ape Y Chromosomes: Rapid Evolution of Copy Number but Conservation of Expression Levels. PMID:32374870
Desmoplakin Cardiomyopathy, a Fibrotic and Inflammatory Form of Cardiomyopathy Distinct From Typical Dilated or Arrhythmogenic Right Ventricular Cardiomyopathy. PMID:32372669
The Role of lncRNAs TAPIR-1 and -2 as Diagnostic Markers and Potential Therapeutic Targets in Prostate Cancer. PMID:32365858
Novel Compound Heterozygous Variants of ETHE1 Causing Ethylmalonic Encephalopathy in a Chinese Patient: A Case Report. PMID:32362910
Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis. PMID:32362324
DNA Barcoding in Nonhuman Primates Reveals Important Limitations in Retrovirus Integration Site Analysis. PMID:32355868
Analysis of computational codon usage models and their association with translationally slow codons. PMID:32352987
LSD1-mediated enhancer silencing attenuates retinoic acid signalling during pancreatic endocrine cell development. PMID:32350257
Combined neurodevelopmental exposure to deltamethrin and corticosterone is associated with Nr3c1 hypermethylation in the midbrain of male mice. PMID:32348866
ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data. PMID:32345345
VarFish: comprehensive DNA variant analysis for diagnostics and research. PMID:32338743
HSF1: Primary Factor in Molecular Chaperone Expression and a Major Contributor to Cancer Morbidity. PMID:32331382
O-GlcNAc regulates gene expression by controlling detained intron splicing. PMID:32329777
TFmotifView: a webserver for the visualization of transcription factor motifs in genomic regions. PMID:32324215
STAT3-dependent analysis reveals PDK4 as independent predictor of recurrence in prostate cancer. PMID:32323921
ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation. PMID:32321567
Retinoic acid receptor-related orphan receptor α reduces lipid droplets by upregulating neutral cholesterol ester hydrolase 1 in macrophages. PMID:32321446
The Set7 Lysine Methyltransferase Regulates Plasticity in Oxidative Phosphorylation Necessary for Trained Immunity Induced by β-Glucan. PMID:32320649
Partial loss of CFIm25 causes learning deficits and aberrant neuronal alternative polyadenylation. PMID:32319885
Multi-level evidence of an allelic hierarchy of USH2A variants in hearing, auditory processing and speech/language outcomes. PMID:32313182
Molecular networks in Network Medicine: Development and applications. PMID:32307915
DolphinNext: a distributed data processing platform for high throughput genomics. PMID:32306927
Sex-Specific Role for the Long Non-coding RNA LINC00473 in Depression. PMID:32304628
Estrogen regulation of germline stem cell differentiation as a mechanism contributing to female reproductive aging. PMID:32302290
Whole-genome genotyping and resequencing reveal the association of a deletion in the complex interferon alpha gene cluster with hypothyroidism in dogs. PMID:32299354
Automated 3D light-sheet screening with high spatiotemporal resolution reveals mitotic phenotypes. PMID:32295847
A WIZ/Cohesin/CTCF Complex Anchors DNA Loops to Define Gene Expression and Cell Identity. PMID:32294452
A negative storage model for precise but compact storage of genetic variation data. PMID:32293013
Simultaneous measurement of biochemical phenotypes and gene expression in single cells. PMID:32286626
Transposable elements contribute to cell and species-specific chromatin looping and gene regulation in mammalian genomes. PMID:32286261
LARP1 isoform expression in human cancer cell lines. PMID:32286153
Integrating structural and evolutionary data to interpret variation and pathogenicity in adapter protein complex 4. PMID:32285480
Merkel cell polyomavirus activates LSD1-mediated blockade of non-canonical BAF to regulate transformation and tumorigenesis. PMID:32284543
Copy number variation in human genomes from three major ethno-linguistic groups in Africa. PMID:32272904
HIPPIE2: a method for fine-scale identification of physically interacting chromatin regions. PMID:32270138
Genome-Wide Association of Genetic Variants With Refraction, Axial Length, and Corneal Curvature: A Longitudinal Study of Chinese Schoolchildren. PMID:32269590
Whole-Genome and RNA Sequencing Reveal Variation and Transcriptomic Coordination in the Developing Human Prefrontal Cortex. PMID:32268104
A genome-wide association study implicates the BMP7 locus as a risk factor for nonsyndromic metopic craniosynostosis. PMID:32266521
The UCSC repeat browser allows discovery and visualization of evolutionary conflict across repeat families. PMID:32266012
A Shared Regulatory Element Controls the Initiation of Tcf7 Expression During Early T Cell and Innate Lymphoid Cell Developments. PMID:32265924
Empowering Retinal Gene Therapy with a Specific Promoter for Human Rod and Cone ON-Bipolar Cells. PMID:32258214
Rapid Identification of Biallelic SPTB Mutation in a Neonate with Severe Congenital Hemolytic Anemia and Liver Failure. PMID:32256302
TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription. PMID:32241291
DNA methylation profiling identifies a high effect genetic variant for lipoprotein(a) levels. PMID:32237968
Proteomics-Based Characterization of miR-574-5p Decoy to CUGBP1 Suggests Specificity for mPGES-1 Regulation in Human Lung Cancer Cells. PMID:32231562
RNA-seq data of soleus muscle tissue after spinal cord injury under conditions of inactivity and applied exercise. PMID:32226812
A Functional Synonymous Variant in PDGFRA Is Associated with Better Survival in Acral Melanoma. PMID:32226509
DNA methylation and histone acetylation changes to cytochrome P450 2E1 regulation in normal aging and impact on rates of drug metabolism in the liver. PMID:32221779
Evolutionary Selection and Constraint on Human Knee Chondrocyte Regulation Impacts Osteoarthritis Risk. PMID:32220312
Genetic Architecture of Gene Expression in European and African Americans: An eQTL Mapping Study in GENOA. PMID:32220292
Accessing a New Dimension in TP53 Biology: Multiplex Long Amplicon Digital PCR to Specifically Detect and Quantitate Individual TP53 Transcripts. PMID:32213968
Quantification, Dynamic Visualization, and Validation of Bias in ATAC-Seq Data with ataqv. PMID:32213349
Expression Changes Confirm Genomic Variants Predicted to Result in Allele-Specific, Alternative mRNA Splicing. PMID:32211018
Janus effect of glucocorticoids on differentiation of muscle fibro/adipogenic progenitors. PMID:32210313
Inflammatory and mitogenic signals drive interleukin 23 subunit alpha (IL23A) secretion independent of IL12B in intestinal epithelial cells. PMID:32209656
Conditional Single Vector CRISPR/SaCas9 Viruses for Efficient Mutagenesis in the Adult Mouse Nervous System. PMID:32209486
RNAseq expression patterns of canine invasive urothelial carcinoma reveal two distinct tumor clusters and shared regions of dysregulation with human bladder tumors. PMID:32209086
Long non-coding RNA GRASLND enhances chondrogenesis via suppression of the interferon type II signaling pathway. PMID:32202492
Reply to: MIDN locus structural variants and Parkinson's disease risk. PMID:32200577
Metastasis-initiating cells induce and exploit a fibroblast niche to fuel malignant colonization of the lungs. PMID:32198421
Genome-wide association meta-analysis of corneal curvature identifies novel loci and shared genetic influences across axial length and refractive error. PMID:32193507
Cis-regulatory analysis of Onecut1 expression in fate-restricted retinal progenitor cells. PMID:32192535
Modeling methylation dynamics with simultaneous changes in CpG islands. PMID:32183713
Identification and Characterization of a Non-muscular Myostatin in the Nile Tilapia. PMID:32180761
Somatic selection distinguishes oncogenes and tumor suppressor genes. PMID:32176769
Circular RNA expression profile in blood according to ischemic stroke etiology. PMID:32175077
Gene Polymorphisms in Boar Spermatozoa and Their Associations with Post-Thaw Semen Quality. PMID:32164368
Epigenetic Regulation of WNT3A Enhancer during Regeneration of Injured Cortical Neurons. PMID:32164275
Mapping of the chicken cleft primary palate mutation on chromosome 11 and sequencing of the 4.9 Mb linked region. PMID:32162363
Genomic loci susceptible to systematic sequencing bias in clinical whole genomes. PMID:32156711
Estrogen Receptor, Inflammatory, and FOXO Transcription Factors Regulate Expression of Myasthenia Gravis-Associated Circulating microRNAs. PMID:32153563
Shared genetic etiology underlying Alzheimer's disease and major depressive disorder. PMID:32152295
Deficiency in the endocytic adaptor proteins PHETA1/2 impairs renal and craniofacial development. PMID:32152089
Complete Genome Sequence of Streptococcus ratti JH145. PMID:32139573
KRGDB: the large-scale variant database of 1722 Koreans based on whole genome sequencing. PMID:32133509
Locally acting transcription factors regulate p53-dependent cis-regulatory element activity. PMID:32133495
BACH family members regulate angiogenesis and lymphangiogenesis by modulating VEGFC expression. PMID:32132179
Single-Cell Analysis of Foxp1-Driven Mechanisms Essential for Striatal Development. PMID:32130906
Dnmt3a and Dnmt3b-Decommissioned Fetal Enhancers are Linked to Kidney Disease. PMID:32127410
Evolutionary Analysis of the Zinc Finger and Homeoboxes Family of Proteins Identifies Multiple Conserved Domains and a Common Early Chordate Ancestor. PMID:32125369
BedSect: An Integrated Web Server Application to Perform Intersection, Visualization, and Functional Annotation of Genomic Regions From Multiple Datasets. PMID:32117432
A novel NGS library preparation method to characterize native termini of fragmented DNA. PMID:32112100
Genome-wide association and multi-omic analyses reveal ACTN2 as a gene linked to heart failure. PMID:32111823
Amhr2-Cre-Mediated Global Tspo Knockout. PMID:32099945
GenEpi: gene-based epistasis discovery using machine learning. PMID:32093643
The Length and Distribution of Plasma Cell-Free DNA Fragments in Stroke Patients. PMID:32090114
Dynamic Evolution of De Novo DNA Methyltransferases in Rodent and Primate Genomes. PMID:32077945
Mobile genomics: tools and techniques for tackling transposons. PMID:32075565
Widespread correlation of KRAB zinc finger protein binding with brain-developmental gene expression patterns. PMID:32075554
Identification of universal and cell-type specific p53 DNA binding. PMID:32070277
From astrocytoma to glioblastoma: a clonal evolution study. PMID:32069381
Large epigenome-wide association study of childhood ADHD identifies peripheral DNA methylation associated with disease and polygenic risk burden. PMID:32066674
Suppressing proteasome mediated processing of topoisomerase II DNA-protein complexes preserves genome integrity. PMID:32057297
Exploration of databases and methods supporting drug repurposing: a comprehensive survey. PMID:32055842
Field cricket genome reveals the footprint of recent, abrupt adaptation in the wild. PMID:32055408
Deletion of a conserved Gata2 enhancer impairs haemogenic endothelium programming and adult Zebrafish haematopoiesis. PMID:32054973
Effect of Grilled Nux Vomica on Differential RNA Expression Profile of Gastrocnemius Muscle and Toll‑Like Receptor 4 (TLR-4)/Nuclear Factor kappa B (NF-κB) Signaling in Experimental Autoimmune Myasthenia Gravis Rats. PMID:32052794
ATM and PRDM9 regulate SPO11-bound recombination intermediates during meiosis. PMID:32051414
GsmPlot: a web server to visualize epigenome data in NCBI. PMID:32050905
ETV4 Is Necessary for Estrogen Signaling and Growth in Endometrial Cancer Cells. PMID:32046982
Pan-mammalian analysis of molecular constraints underlying extended lifespan. PMID:32043462
4See: A Flexible Browser to Explore 4C Data. PMID:32038719
pCADD: SNV prioritisation in Sus scrofa. PMID:32033531
Skin Irritation Testing beyond Tissue Viability: Fucoxanthin Effects on Inflammation, Homeostasis, and Metabolism. PMID:32033492
Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. PMID:32024996
Interstitial 4q Deletion Syndrome Including NR3C2 Causing Pseudohypoaldosteronism. PMID:32021607
A CRISPR/Cas13-based approach demonstrates biological relevance of vlinc class of long non-coding RNAs in anticancer drug response. PMID:32020014
REXTAL: Regional Extension of Assemblies Using Linked-Reads. PMID:32016171
An optimized chemical-genetic method for cell-specific metabolic labeling of RNA. PMID:32015544
Concentration-Dependent Recruitment of Mammalian Odorant Receptors. PMID:32015097
Evolutionary dynamics of microRNA target sites across vertebrate evolution. PMID:32012152
Promoter methylation status of ASC/TMS1/PYCARD is associated with decreased overall survival and TNM status in patients with early stage non-small cell lung cancer (NSCLC). PMID:32010578
Identification of Novel Genes and Biological Pathways That Overlap in Infectious and Nonallergic Diseases of the Upper and Lower Airways Using Network Analyses. PMID:32010199
HLA-H: Transcriptional Activity and HLA-E Mobilization. PMID:32010122
Prediction of blood-based biomarkers and subsequent design of bisulfite PCR-LDR-qPCR assay for breast cancer detection. PMID:32005108
MakeHub: Fully Automated Generation of UCSC Genome Browser Assembly Hubs. PMID:32001327
Epistatic interaction between PKD2 and ABCG2 influences the pathogenesis of hyperuricemia and gout. PMID:32000861
Triangular correlation (TrC) between cancer aggressiveness, cell uptake capability, and cell deformability. PMID:31998832
Transcriptome Analysis of Pineal Glands in the Mouse Model of Alzheimer's Disease. PMID:31998073
Case report: recurrent pituitary adenoma has increased load of somatic variants. PMID:31996211
Developing a virus-microRNA interactome using cytoscape. PMID:31993337
Assessment of branch point prediction tools to predict physiological branch points and their alteration by variants. PMID:31992191
ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets. PMID:31978042
Osteoporosis- and obesity-risk interrelationships: an epigenetic analysis of GWAS-derived SNPs at the developmental gene TBX15. PMID:31975641
Quantification of aminobutyric acids and their clinical applications as biomarkers for osteoporosis. PMID:31969651
Cohesin Disrupts Polycomb-Dependent Chromosome Interactions in Embryonic Stem Cells. PMID:31968256
The stress-responsive gene GDPGP1/mcp-1 regulates neuronal glycogen metabolism and survival. PMID:31968056
Galaxy External Display Applications: closing a dataflow interoperability loop. PMID:31959996
Genome organization in proximity to the BAP1 locus appears to play a pivotal role in a variety of cancers. PMID:31957195
CHROMATIX: computing the functional landscape of many-body chromatin interactions in transcriptionally active loci from deconvolved single cells. PMID:31948478
Enhancer-gene maps in the human and zebrafish genomes using evolutionary linkage conservation. PMID:31943068
Transgenic Testing Does Not Support a Role for Additional Candidate Genes in Wolbachia Male Killing or Cytoplasmic Incompatibility. PMID:31937677
Pigment Intensity in Dogs is Associated with a Copy Number Variant Upstream of KITLG. PMID:31936656
IGF-1 Signalling Regulates Mitochondria Dynamics and Turnover through a Conserved GSK-3β-Nrf2-BNIP3 Pathway. PMID:31936236
A meta-analysis of genome-wide association studies of multiple myeloma among men and women of African ancestry. PMID:31935283
Construction of the gene regulatory network identifies MYC as a transcriptional regulator of SWI/SNF complex. PMID:31932624
shinyChromosome: An R/Shiny Application for Interactive Creation of Non-circular Plots of Whole Genomes. PMID:31931182
FilTar: using RNA-Seq data to improve microRNA target prediction accuracy in animals. PMID:31930382
Negligible senescence in naked mole rats may be a consequence of well-maintained splicing regulation. PMID:31927681
Clonal kinetics and single-cell transcriptional profiling of CAR-T cells in patients undergoing CD19 CAR-T immunotherapy. PMID:31924795
Precursors for Nonlymphoid-Tissue Treg Cells Reside in Secondary Lymphoid Organs and Are Programmed by the Transcription Factor BATF. PMID:31924477
Head and neck squamous cancer progression is marked by CLIC4 attenuation in tumor epithelium and reciprocal stromal upregulation of miR-142-3p, a novel post-transcriptional regulator of CLIC4. PMID:31921386
Comparative analysis on the expression of L1 loci using various RNA-Seq preparations. PMID:31921361
Exonic Variants in Aging-Related Genes Are Predictive of Phenotypic Aging Status. PMID:31921313
Analysis of retrotransposon subfamily DNA methylation reveals novel early epigenetic changes in chronic lymphocytic leukemia. PMID:31919093
DNA methylation changes in Down syndrome derived neural iPSCs uncover co-dysregulation of ZNF and HOX3 families of transcription factors. PMID:31915063
DNA hypermethylation associated with upregulated gene expression in prostate cancer demonstrates the diversity of epigenetic regulation. PMID:31914996
Constitutively bound CTCF sites maintain 3D chromatin architecture and long-range epigenetically regulated domains. PMID:31911579
Ezh2-dependent H3K27me3 modification dynamically regulates vitamin D3-dependent epigenetic control of CYP24A1 gene expression in osteoblastic cells. PMID:31907922
DDX3X Multifunctionally Modulates Tumor Progression and Serves as a Prognostic Indicator to Predict Cancer Outcomes. PMID:31906196
THAP11F80L cobalamin disorder-associated mutation reveals normal and pathogenic THAP11 functions in gene expression and cell proliferation. PMID:31905202
Differential Expression Gene Explorer (DrEdGE): a tool for generating interactive online visualizations of gene expression datasets. PMID:31899488
Elucidation of de novo small insertion/deletion biology with parent-of-origin phasing. PMID:31898844
Recapitulation of previously reported associations for type 2 diabetes and metabolic traits in the 126K East Asians. PMID:31896248
Targeted viral vector transduction of relaxin-3 neurons in the rat nucleus incertus using a novel cell-type specific promoter. PMID:31890981
Long walk to genomics: History and current approaches to genome sequencing and assembly. PMID:31890139
MECoRank: cancer driver genes discovery simultaneously evaluating the impact of SNVs and differential expression on transcriptional networks. PMID:31888623
Human protein-RNA interaction network is highly stable across mammals. PMID:31888461
Next Generation Sequencing Identifies Five Novel Mutations in Lebanese Patients with Bardet-Biedl and Usher Syndromes. PMID:31888296
Enhancer jungles establish robust tissue-specific regulatory control in the human genome. PMID:31887344
PRC1 Catalytic Activity Is Central to Polycomb System Function. PMID:31883950
Chromosome Translocation t(14;21)(q11;q22) Activates Both OLIG1 and OLIG2 in Pediatric T-cell Lymphoblastic Malignancies and May Signify Adverse Prognosis. PMID:31882550
Venn-diaNet : venn diagram based network propagation analysis framework for comparing multiple biological experiments. PMID:31881980
A ligation-based single-stranded library preparation method to analyze cell-free DNA and synthetic oligos. PMID:31881841
Intra-Vκ Cluster Recombination Shapes the Ig Kappa Locus Repertoire. PMID:31875554
Reduced TRPM8 expression underpins reduced migraine risk and attenuated cold pain sensation in humans. PMID:31873179
Yield of comparative genomic hybridization microarray in pediatric neurology practice. PMID:31872051
SYCP2 Translocation-Mediated Dysregulation and Frameshift Variants Cause Human Male Infertility. PMID:31866047
Deletion of the serine protease CAP2/Tmprss4 leads to dysregulated renal water handling upon dietary potassium depletion. PMID:31863073
Novel approach reveals genomic landscapes of single-strand DNA breaks with nucleotide resolution in human cells. PMID:31862872
MethylToSNP: identifying SNPs in Illumina DNA methylation array data. PMID:31861999
Targeted sequencing of the LRRTM gene family in suicide attempters with bipolar disorder. PMID:31854516
Identification and characterization of occult human-specific LINE-1 insertions using long-read sequencing technology. PMID:31853540
Activity of the poly(A) binding protein MSUT2 determines susceptibility to pathological tau in the mammalian brain. PMID:31852801
Integrated Epigenome, Exome, and Transcriptome Analyses Reveal Molecular Subtypes and Homeotic Transformation in Uterine Fibroids. PMID:31851934
Topologically Associated Domains Delineate Susceptibility to Somatic Hypermutation. PMID:31851922
Enhancers Facilitate the Birth of De Novo Genes and Gene Integration into Regulatory Networks. PMID:31845961
Epigenomic analysis of gastrulation identifies a unique chromatin state for primed pluripotency. PMID:31844322
An Online Database for Exploring Over 2,000 Arabidopsis Small RNA Libraries. PMID:31843802
Systematic Analysis of Transcriptomic Profile of the Effects of Low Dose Atropine Treatment on Scleral Fibroblasts using Next-Generation Sequencing and Bioinformatics. PMID:31839753
TMRS: an algorithm for computing the time to the most recent substitution event from a multiple alignment column. PMID:31832082
Maintenance of active chromatin states by HMGN2 is required for stem cell identity in a pluripotent stem cell model. PMID:31831052
Sensitive detection of circular DNAs at single-nucleotide resolution using guided realignment of partially aligned reads. PMID:31830908
Molecular signature of different lesion types in the brain white matter of patients with progressive multiple sclerosis. PMID:31829262
Diversification of the Caenorhabditis heat shock response by Helitron transposable elements. PMID:31825311
Targeted deep-intronic sequencing in a cohort of unexplained cases of suspected Lynch syndrome. PMID:31822864
Association Between Side Effects and Blood microRNA Expression Levels and Their Targeted Pathways in Patients With Major Depressive Disorder Treated by a Selective Serotonin Reuptake Inhibitor, Escitalopram: A CAN-BIND-1 Report. PMID:31819986
Epigenetic therapy of novel tumour suppressor ZAR1 and its cancer biomarker function. PMID:31801617
The m6A Dynamics of Profilin in Neurogenesis. PMID:31798620
Cisplatin treatment of testicular cancer patients introduces long-term changes in the epigenome. PMID:31796056
Transcriptional Regulation of INSR, the Insulin Receptor Gene. PMID:31795422
Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle. PMID:31794382
Multiple selective sweeps of ancient polymorphisms in and around LTα located in the MHC class III region on chromosome 6. PMID:31791241
Alu insertion polymorphisms shared by Papio baboons and Theropithecus gelada reveal an intertwined common ancestry. PMID:31788036
Identification and Characterization of Cis-Regulatory Elements for Photoreceptor-Type-Specific Transcription in ZebraFish. PMID:31786786
Developmental Pathways from Genetic, Prenatal, Parenting and Emotional/Behavioral Risk to Cortisol Reactivity and Adolescent Substance Use: A TRAILS Study. PMID:31786769
Integrating the Ribonucleic Acid Sequencing Data From Various Studies for Exploring the Multiple Sclerosis-Related Long Noncoding Ribonucleic Acids and Their Functions. PMID:31781177
MySeq: privacy-protecting browser-based personal Genome analysis for genomics education and exploration. PMID:31775760
Bioinformatics analysis reveals 6 key biomarkers associated with non-small-cell lung cancer. PMID:31775549
A Comprehensive Analysis of Runs of Homozygosity of Eleven Cattle Breeds Representing Different Production Types. PMID:31775271
Unusual interplay of contrasting selective pressures on β-defensin genes implicated in male fertility of the Buffalo (Bubalus bubalis). PMID:31771505
Tasks, Techniques, and Tools for Genomic Data Visualization. PMID:31768085
Genome-wide histone modification profiling of inner cell mass and trophectoderm of bovine blastocysts by RAT-ChIP. PMID:31765427
Neutralization of Oxidized Phospholipids Ameliorates Non-alcoholic Steatohepatitis. PMID:31761566
FGF Signalling in the Self-Renewal of Colon Cancer Organoids. PMID:31758153
A guide to computational methods for G-quadruplex prediction. PMID:31754698
Genetic variants in humanin nuclear isoform gene regions show no association with coronary artery disease. PMID:31753007
The ENCODE Portal as an Epigenomics Resource. PMID:31751002
Alzheimer Disease Pathology-Associated Polymorphism in a Complex Variable Number of Tandem Repeat Region Within the MUC6 Gene, Near the AP2A2 Gene. PMID:31748784
Identification of novel common variants associated with chronic pain using conditional false discovery rate analysis with major depressive disorder and assessment of pleiotropic effects of LRFN5. PMID:31748543
CREB5 Promotes Resistance to Androgen-Receptor Antagonists and Androgen Deprivation in Prostate Cancer. PMID:31747605
ChiTaRS 5.0: the comprehensive database of chimeric transcripts matched with druggable fusions and 3D chromatin maps. PMID:31747015
Screening and identification of key biomarkers in prostate cancer using bioinformatics. PMID:31746380
Defining Signatures of Arm-Wise Copy Number Change and Their Associated Drivers in Kidney Cancers. PMID:31744086
The mutational footprints of cancer therapies. PMID:31740835
Expression of A New Endogenous Retrovirus-Associated Transcript in Hodgkin Lymphoma Cells. PMID:31731509
Overexpression of Na+/H+ exchanger 1 specifically induces cell death in human iPS cells via sustained activation of the Rho kinase ROCK. PMID:31723030
Hsa-miR-587 Regulates TGFβ/SMAD Signaling and Promotes Cell Cycle Progression. PMID:31721529
Characterization and Potential Applications of Dog Natural Killer Cells in Cancer Immunotherapy. PMID:31717876
Secondary Structural Model of Human MALAT1 Reveals Multiple Structure-Function Relationships. PMID:31717552
The Rich World of p53 DNA Binding Targets: The Role of DNA Structure. PMID:31717504
New developments on the Encyclopedia of DNA Elements (ENCODE) data portal. PMID:31713622
Low mutation rate in the TTN gene in paediatric patients with dilated cardiomyopathy - a pilot study. PMID:31712709
Cortical Foxp2 Supports Behavioral Flexibility and Developmental Dopamine D1 Receptor Expression. PMID:31711176
COPD-dependent effects of genetic variation in key inflammation pathway genes on lung cancer risk. PMID:31709530
Upregulation of Yy1 Suppresses Dilated Cardiomyopathy caused by Ttn insufficiency. PMID:31705051
Salt-inducible kinase inhibition suppresses acute myeloid leukemia progression in vivo. PMID:31697837
Free circular introns with an unusual branchpoint in neuronal projections. PMID:31697236
Yin Yang 1 facilitates hepatocellular carcinoma cell lipid metabolism and tumor progression by inhibiting PGC-1β-induced fatty acid oxidation. PMID:31695789
Lactate Efflux From Intervertebral Disc Cells Is Required for Maintenance of Spine Health. PMID:31692093
UCSC Genome Browser enters 20th year. PMID:31691824
A non-coding genetic variant associated with abdominal aortic aneurysm alters ERG gene regulation. PMID:31691800
SHH signaling mediated by a prechordal and brain enhancer controls forebrain organization. PMID:31685615
A genome-wide DNA methylation signature for SETD1B-related syndrome. PMID:31685013
Electrical Stimulation of C6 Glia-Precursor Cells In Vitro Differentially Modulates Gene Expression Related to Chronic Pain Pathways. PMID:31683631
Inference and analysis of population-specific fine-scale recombination maps across 26 diverse human populations. PMID:31681842
Condemned or Not to Die? Gene Polymorphisms Associated With Cell Death in Pemphigus Foliaceus. PMID:31681304
R-Loops Promote Antisense Transcription across the Mammalian Genome. PMID:31679819
The impact of short tandem repeat variation on gene expression. PMID:31676866
LSD1-mediated repression of GFI1 super-enhancer plays an essential role in erythroleukemia. PMID:31676828
Making multi-omics data accessible to researchers. PMID:31672978
Genomic architecture and introgression shape a butterfly radiation. PMID:31672890
Visualization tools for human structural variations identified by whole-genome sequencing. PMID:31666648
An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo. PMID:31666509
Synchronized replication of genes encoding the same protein complex in fast-proliferating cells. PMID:31662304
The transcription factor ETS1 promotes apoptosis resistance of senescent cholangiocytes by epigenetically up-regulating the apoptosis suppressor BCL2L1. PMID:31659122
Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits. PMID:31653862
53BP1 Enforces Distinct Pre- and Post-resection Blocks on Homologous Recombination. PMID:31653568
Deleterious Variants in WNT10A, EDAR, and EDA Causing Isolated and Syndromic Tooth Agenesis: A Structural Perspective from Molecular Dynamics Simulations. PMID:31652981
Association of the Rheumatoid Arthritis Severity Variant rs26232 with the Invasive Activity of Synovial Fibroblasts. PMID:31652652
FFPEcap-seq: a method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples. PMID:31649055
The Tudor SND1 protein is an m6A RNA reader essential for replication of Kaposi's sarcoma-associated herpesvirus. PMID:31647415
MTHFR and F5 genetic variations have association with preeclampsia in Pakistani patients: a case control study. PMID:31646966
Breakpoint junction features of seven DMD deletion mutations. PMID:31645977
ExonSkipDB: functional annotation of exon skipping event in human. PMID:31642488
Epigenome-Wide Association Study for All-Cause Mortality in a Cardiovascular Cohort Identifies Differential Methylation in Castor Zinc Finger 1 (CASZ1). PMID:31642367
Repression of eEF2K transcription by NF-κB tunes translation elongation to inflammation and dsDNA-sensing. PMID:31636182
Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction. PMID:31631012
TRIM39-RPP21 Variants (∆19InsCCC) Are Not Associated with Juvenile Idiopathic Epilepsy in Egyptian Arabian Horses. PMID:31623255
A pharmacogenetic risk score for the evaluation of major depression severity under treatment with antidepressants. PMID:31617956
DNA methylation modules associate with incident cardiovascular disease and cumulative risk factor exposure. PMID:31615550
A Highly Contiguous Reference Genome for Northern Bobwhite (Colinus virginianus). PMID:31611345
TNPO2 operates downstream of DYNC1I1 and promotes gastric cancer cell proliferation and inhibits apoptosis. PMID:31605449
The glucocorticoid receptor interferes with progesterone receptor-dependent genomic regulation in breast cancer cells. PMID:31598691
Building a Science Gateway For Processing and Modeling Sequencing Data Via Apache Airavata. PMID:31598610
Spliceosomal disruption of the non-canonical BAF complex in cancer. PMID:31597964
Single-Cell Chromatin Analysis of Mammary Gland Development Reveals Cell-State Transcriptional Regulators and Lineage Relationships. PMID:31597106
Immunochip meta-analysis in European and Argentinian populations identifies two novel genetic loci associated with celiac disease. PMID:31591516
Cronos Titin Is Expressed in Human Cardiomyocytes and Necessary for Normal Sarcomere Function. PMID:31587567
Characterization of GJB2 cis-regulatory elements in the DFNB1 locus. PMID:31586237
Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases. PMID:31584084
Unraveling the Heterogeneous Mutational Signature of Spontaneously Developing Tumors in MLH1-/- Mice. PMID:31581674
HTLV-1 viral oncogene HBZ drives bone destruction in adult T cell leukemia. PMID:31578308
Pedigree-based estimation of human mobile element retrotransposition rates. PMID:31575651
The CLN3 gene and protein: What we know. PMID:31568712
Mediator Condensates Localize Signaling Factors to Key Cell Identity Genes. PMID:31563432
Identifying Structural Domains and Conserved Regions in the Long Non-Coding RNA lncTCF7. PMID:31561429
T-cell receptor signal strength and epigenetic control of Bim predict memory CD8+ T-cell fate. PMID:31558776
Drosophila Heterochromatin Stabilization Requires the Zinc-Finger Protein Small Ovary. PMID:31558581
Endogenous fluctuations of OCT4 and SOX2 bias pluripotent cell fate decisions. PMID:31556488
Genome Improvement and Genetic Map Construction for Aethionema arabicum, the First Divergent Branch in the Brassicaceae Family. PMID:31554715
Driver gene alterations and activated signaling pathways toward malignant progression of gastrointestinal stromal tumors. PMID:31553483
Genetic associations of perinatal pain and depression. PMID:31552780
The Challenges of Chromosome Y Analysis and the Implications for Chronic Kidney Disease. PMID:31552093
Hypermethylation-associated downregulation of microRNA-4456 in hypersexual disorder with putative influence on oxytocin signalling: A DNA methylation analysis of miRNA genes. PMID:31542994
The inference of sex-biased human demography from whole-genome data. PMID:31539367
Comparative evaluation of RNA-Seq library preparation methods for strand-specificity and low input. PMID:31530843
NRXN1 is associated with enlargement of the temporal horns of the lateral ventricles in psychosis. PMID:31530798
A regression framework to uncover pleiotropy in large-scale electronic health record data. PMID:31529123
Bioinformatics Discovery of Putative Enhancers within Mouse Odorant Receptor Gene Clusters. PMID:31529021
Dosage regulation, and variation in gene expression and copy number of human Y chromosome ampliconic genes. PMID:31525193
SUMO-Chain-Regulated Proteasomal Degradation Timing Exemplified in DNA Replication Initiation. PMID:31519521
The first enhancer in an enhancer chain safeguards subsequent enhancer-promoter contacts from a distance. PMID:31514731
Targeted genotyping by sequencing: a new way to genome profile the cat. PMID:31512748
Socioeconomic status and DNA methylation from birth through mid-childhood: a prospective study in Project Viva. PMID:31509016
Possible Molecular Mechanisms for the Roles of MicroRNA-21 Played in Lung Cancer. PMID:31506038
Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning. PMID:31504766
The Impact of Natural Selection on the Evolution and Function of Placentally Expressed Galectins. PMID:31504490
MicroRNA 7 Impairs Insulin Signaling and Regulates Aβ Levels through Posttranscriptional Regulation of the Insulin Receptor Substrate 2, Insulin Receptor, Insulin-Degrading Enzyme, and Liver X Receptor Pathway. PMID:31501273
Retrotransposon insertions can initiate colorectal cancer and are associated with poor survival. PMID:31492840
H3K4me3, H3K9ac, H3K27ac, H3K27me3 and H3K9me3 Histone Tags Suggest Distinct Regulatory Evolution of Open and Condensed Chromatin Landmarks. PMID:31491936
Pituitary cell translation and secretory capacities are enhanced cell autonomously by the transcription factor Creb3l2. PMID:31481663
The 22q11 low copy repeats are characterized by unprecedented size and structural variability. PMID:31481461
Reactivation of super-enhancers by KLF4 in human Head and Neck Squamous Cell Carcinoma. PMID:31477832
Variants in the fetal genome near pro-inflammatory cytokine genes on 2q13 associate with gestational duration. PMID:31477735
A circRNA signature predicts postoperative recurrence in stage II/III colon cancer. PMID:31475771
Germline 16p11.2 Microdeletion Predisposes to Neuroblastoma. PMID:31474320
Landscape of Enhancer-Enhancer Cooperative Regulation during Human Cardiac Commitment. PMID:31465963
Duration of breastfeeding is associated with leptin (LEP) DNA methylation profiles and BMI in 10-year-old children. PMID:31464656
BMI1 is directly regulated by androgen receptor to promote castration-resistance in prostate cancer. PMID:31462713
Regulation of Cyclin E by transcription factors of the naïve pluripotency network in mouse embryonic stem cells. PMID:31462142
The role of Xist-mediated Polycomb recruitment in the initiation of X-chromosome inactivation. PMID:31456285
A germline alteration of ERBB2 increases the risk of breast cancer in Chinese Han women with a familial history of malignant tumors. PMID:31452768
Microsyntenic Clusters Reveal Conservation of lncRNAs in Chordates Despite Absence of Sequence Conservation. PMID:31450588
CNEr: A toolkit for exploring extreme noncoding conservation. PMID:31449516
Neoantigen vaccine: an emerging tumor immunotherapy. PMID:31443694
A de novo evolved gene in the house mouse regulates female pregnancy cycles. PMID:31436535
LSD1 Inhibition Promotes Epithelial Differentiation through Derepression of Fate-Determining Transcription Factors. PMID:31433976
Genome-wide association study of cerebral small vessel disease reveals established and novel loci. PMID:31430377
Genome-Wide Transcription Factor Binding in Leaves from C3 and C4 Grasses. PMID:31427470
PRAS: Predicting functional targets of RNA binding proteins based on CLIP-seq peaks. PMID:31425505
Separate Polycomb Response Elements control chromatin state and activation of the vestigial gene. PMID:31425502
Blood Leukocyte DNA Methylation Predicts Risk of Future Myocardial Infarction and Coronary Heart Disease. PMID:31424985
Diversification of Retinoblastoma Protein Function Associated with Cis and Trans Adaptations. PMID:31418797
Epigenetic silencing of a multifunctional plant stress regulator. PMID:31418686
A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing. PMID:31413257
Targeted sequencing reveals expanded genetic diversity of human transfer RNAs. PMID:31407949
ShapeShifter: a novel approach for identifying and quantifying stable lariat intronic species in RNAseq data. PMID:31404415
CAPN5 genetic inactivation phenotype supports therapeutic inhibition trials. PMID:31403230
Evolutionary history of disease-susceptibility loci identified in longitudinal exome-wide association studies. PMID:31402603
Profiling DNA methylation patterns of zebrafish liver associated with parental high dietary arachidonic acid. PMID:31398226
Simultaneous precise editing of multiple genes in human cells. PMID:31392986
Genome-wide mapping of DNA-binding sites identifies stemness-related genes as directly repressed targets of SNAIL1 in colorectal cancer cells. PMID:31391555
The small GTPase RAB1B promotes antiviral innate immunity by interacting with TNF receptor-associated factor 3 (TRAF3). PMID:31375559
DNA Rchitect: an R based visualizer for network analysis of chromatin interaction data. PMID:31373608
Dissection of acute stimulus-inducible nucleosome remodeling in mammalian cells. PMID:31371436
An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi). PMID:31367745
KDM2 proteins constrain transcription from CpG island gene promoters independently of their histone demethylase activity. PMID:31363749
Loss of the PTCH1 tumor suppressor defines a new subset of plexiform fibromyxoma. PMID:31362756
Mechanistic interpretation of non-coding variants for discovering transcriptional regulators of drug response. PMID:31362726
Genome-wide scan identifies opioid overdose risk locus close to MCOLN1. PMID:31362332
Challenges in funding and developing genomic software: roots and remedies. PMID:31358028
The IDO Metabolic Trap Hypothesis for the Etiology of ME/CFS. PMID:31357483
MicroRNA-193a-3p suppresses the colorectal cancer cell proliferation and progression through downregulating the PLAU expression. PMID:31354344
Human chromatin remodeler cofactor, RNA interactor, eraser and writer sperm RNAs responding to obesity. PMID:31354029
Cortical Neurogenesis Requires Bcl6-Mediated Transcriptional Repression of Multiple Self-Renewal-Promoting Extrinsic Pathways. PMID:31353074
An expanded landscape of human long noncoding RNA. PMID:31350901
Ribosome profiling of selenoproteins in vivo reveals consequences of pathogenic Secisbp2 missense mutations. PMID:31350336
Inherited genetic susceptibility to acute lymphoblastic leukemia in Down syndrome. PMID:31350265
Coordinated transcriptional regulation by thyroid hormone and glucocorticoid interaction in adult mouse hippocampus-derived neuronal cells. PMID:31348800
Integrated identification of key genes and pathways in Alzheimer's disease via comprehensive bioinformatical analyses. PMID:31346329
Non-coding variability at the APOE locus contributes to the Alzheimer's risk. PMID:31346172
Glucocorticoid-induced leucine zipper "quantifies" stressors and increases male susceptibility to PTSD. PMID:31346158
SLAMF9 regulates pDC homeostasis and function in health and disease. PMID:31346085
E2F1 Drives Breast Cancer Metastasis by Regulating the Target Gene FGF13 and Altering Cell Migration. PMID:31341204
Genetic analyses supporting colorectal, gastric, and prostate cancer syndromes. PMID:31334572
The Polycomb Repressor Complex 1 Drives Double-Negative Prostate Cancer Metastasis by Coordinating Stemness and Immune Suppression. PMID:31327655
Expanded potential stem cell media as a tool to study human developmental hematopoiesis in vitro. PMID:31326613
RepViz: a replicate-driven R tool for visualizing genomic regions. PMID:31324268
Reorganization of 3D genome structure may contribute to gene regulatory evolution in primates. PMID:31323043
Better prognostic determination and feature characterization of cutaneous melanoma through integrative genomic analysis. PMID:31322504
VariED: the first integrated database of gene annotation and expression profiles for variants related to human diseases. PMID:31317185
Analysis of the 4q35 chromatin organization reveals distinct long-range interactions in patients affected with Facio-Scapulo-Humeral Dystrophy. PMID:31316120
Stable enhancers are active in development, and fragile enhancers are associated with evolutionary adaptation. PMID:31307522
The Role of Zinc in Antiviral Immunity. PMID:31305906
MC4R and HNF4α promoter methylation at birth contribute to triglyceride levels in childhood: A prospective cohort study. PMID:31305461
CDKN2B upregulation prevents teratoma formation in multipotent fibromodulin-reprogrammed cells. PMID:31305260
NFAT5/TonEBP controls early acquisition of notochord phenotypic markers, collagen composition, and sonic hedgehog signaling during mouse intervertebral disc embryogenesis. PMID:31301300
Tumor mutation burden and circulating tumor DNA in combined CTLA-4 and PD-1 antibody therapy in metastatic melanoma - results of a prospective biomarker study. PMID:31300034
Cell type-specific epigenetic links to schizophrenia risk in the brain. PMID:31288836
Cas9-based enrichment and single-molecule sequencing for precise characterization of genomic duplications. PMID:31273287
Detecting the long non‑coding RNA signature related to spinal cord ependymal tumor subtype using a genome‑wide methylome analysis approach. PMID:31257484
Interleukin-18 as a drug repositioning opportunity for inflammatory bowel disease: A Mendelian randomization study. PMID:31253830
HTLV-1 basic leucine zipper factor protects cells from oxidative stress by upregulating expression of Heme Oxygenase I. PMID:31251786
De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication. PMID:31249862
Defining Genetic Variation in Widely Used Congenic and Backcrossed Mouse Models Reveals Varied Regulation of Genes Important for Immune Responses. PMID:31248780
Identification of Abundant and Evolutionarily Conserved Opioid Receptor Circular RNAs in the Nervous System Modulated by Morphine. PMID:31243060
On estimating evolutionary probabilities of population variants. PMID:31238981
Functionally Significant Features in the 5' Untranslated Region of the ABCA1 Gene and Their Comparison in Vertebrates. PMID:31234415
Comparative Analyses of Chromatin Landscape in White Adipose Tissue Suggest Humans May Have Less Beigeing Potential than Other Primates. PMID:31233101
Glycosylphosphatidylinositol biosynthesis and remodeling are required for neural tube closure, heart development, and cranial neural crest cell survival. PMID:31232685
Functional characterization of CNOT3 variants identified in familial adenomatous polyposis adenomas. PMID:31231471
Mass Spectrometry-Based Proteomics Approach Characterizes the Dual Functionality of miR-328 in Monocytes. PMID:31231226
The R941L mutation in MYH14 disrupts mitochondrial fission and associates with peripheral neuropathy. PMID:31231018
Atlas of Subcellular RNA Localization Revealed by APEX-Seq. PMID:31230715
RNA sequencing dataset characterizing transcriptomic responses to dietary changes in Caenorhabditis elegans. PMID:31223636
Navigating the Depths and Avoiding the Shallows of Pancreatic Islet Cell Transcriptomes. PMID:31221802
iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures. PMID:31218344
Deep sequencing of a recurrent oligodendroglioma and the derived xenografts reveals new insights into the evolution of human oligodendroglioma and candidate driver genes. PMID:31217899
Long-term, genome-wide kinetic analysis of the effect of the circadian clock and transcription on the repair of cisplatin-DNA adducts in the mouse liver. PMID:31217280
DNA methylation signature of human hippocampus in Alzheimer's disease is linked to neurogenesis. PMID:31217032
Somatic mutation that affects transcription factor binding upstream of CD55 in the temporal cortex of a late-onset Alzheimer disease patient. PMID:31216356
Comprehensive mapping of the methylation landscape of 16 CpG-dense regions in oral and pharyngeal squamous cell carcinoma. PMID:31215230
Signatures of Recent Positive Selection in Enhancers Across 41 Human Tissues. PMID:31213516
Simultaneous quantification of protein-DNA contacts and transcriptomes in single cells. PMID:31209373
Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. PMID:31209238
Topoisomerase II-Induced Chromosome Breakage and Translocation Is Determined by Chromosome Architecture and Transcriptional Activity. PMID:31202577
Analysis of pleiotropic genetic effects on cognitive impairment, systemic inflammation, and plasma lipids in the Health and Retirement Study. PMID:31201950
Two contrasting classes of nucleolus-associated domains in mouse fibroblast heterochromatin. PMID:31201210
Protein quality control in the nucleolus safeguards recovery of epigenetic regulators after heat shock. PMID:31199242
Activity/exercise-induced changes in the liver transcriptome after chronic spinal cord injury. PMID:31197156
Profiling the genome-wide landscape of tandem repeat expansions. PMID:31194863
BarkBase: Epigenomic Annotation of Canine Genomes. PMID:31181663
Transcriptome of dorsal root ganglia caudal to a spinal cord injury with modulated behavioral activity. PMID:31175296
An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. PMID:31169497
Adventitious Virus Detection in Cells by High-Throughput Sequencing of Newly Synthesized RNAs: Unambiguous Differentiation of Cell Infection from Carryover of Viral Nucleic Acids. PMID:31167947
WashU Epigenome Browser update 2019. PMID:31165883
Kidney cytosine methylation changes improve renal function decline estimation in patients with diabetic kidney disease. PMID:31165727
The HRP3 PWWP domain recognizes the minor groove of double-stranded DNA and recruits HRP3 to chromatin. PMID:31162607
RNA editing alterations in a multi-ethnic Alzheimer disease cohort converge on immune and endocytic molecular pathways. PMID:31162550
Comprehensive functional profiling of long non-coding RNAs through a novel pan-cancer integration approach and modular analysis of their protein-coding gene association networks. PMID:31159744
Modeling Steatohepatitis in Humans with Pluripotent Stem Cell-Derived Organoids. PMID:31155493
The perils of intralocus recombination for inferences of molecular convergence. PMID:31154973
Interpreting the MicroRNA-15/107 family: interaction identification by combining network based and experiment supported approach. PMID:31151434
Augmented Interval List: a novel data structure for efficient genomic interval search. PMID:31150060
Early divergence of mutational processes in human fetal tissues. PMID:31149636
Lentiviral CRISPR Epigenome Editing of Inflammatory Receptors as a Gene Therapy Strategy for Disc Degeneration. PMID:31140325
CORR® ORS Richard A. Brand Award: Disruption in Peroxisome Proliferator-Activated Receptor-γ (PPARG) Increases Osteonecrosis Risk Through Genetic Variance and Pharmacologic Modulation. PMID:31135556
The bipartite TAD organization of the X-inactivation center ensures opposing developmental regulation of Tsix and Xist. PMID:31133748
A Comprehensive Analysis of Ontogeny of Renal Drug Transporters: mRNA Analyses, Quantitative Proteomics, and Localization. PMID:31127606
Microhomologies are prevalent at Cas9-induced larger deletions. PMID:31127293
Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity. PMID:31124784
Genetic variant in SLC1A2 is associated with elevated anterior cingulate cortex glutamate and lifetime history of rapid cycling. PMID:31123248
Loss of TLE3 promotes the mitochondrial program in beige adipocytes and improves glucose metabolism. PMID:31123067
EpiAlignment: alignment with both DNA sequence and epigenomic data. PMID:31114924
Thermodynamically stable and genetically unstable G-quadruplexes are depleted in genomes across species. PMID:31114920
MEXPRESS update 2019. PMID:31114869
SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues. PMID:31110282
MethylSeqDesign: a framework for Methyl-Seq genome-wide power calculation and study design issues. PMID:31107532
Pergola-web: a web server for the visualization and analysis of longitudinal behavioral data using repurposed genomics tools and standards. PMID:31106365
CiliaCarta: An integrated and validated compendium of ciliary genes. PMID:31095607
Expression Analysis of Fibronectin Type III Domain-Containing (FNDC) Genes in Inflammatory Bowel Disease and Colorectal Cancer. PMID:31093274
The Paf1 Complex Broadly Impacts the Transcriptome of Saccharomyces cerevisiae. PMID:31092540
A novel FGF8 mutation in a female patient with isolated congenital anosmia. PMID:31087283
Targeting HIF-1α in combination with PPARα activation and postnatal factors promotes the metabolic maturation of human induced pluripotent stem cell-derived cardiomyocytes. PMID:31082397
INKA2, a novel p53 target that interacts with the serine/threonine kinase PAK4. PMID:31081062
Splice-Aware Multiple Sequence Alignment of Protein Isoforms. PMID:31080963
Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity. PMID:31080084
Heterozygous Variants in KMT2E Cause a Spectrum of Neurodevelopmental Disorders and Epilepsy. PMID:31079897
A Premature Stop Codon in RAF1 Is the Priority Candidate Causative Mutation of the Inherited Chicken Wingless-2 Developmental Syndrome. PMID:31075853
Generation, transcriptome profiling, and functional validation of cone-rich human retinal organoids. PMID:31072937
G-OnRamp: a Galaxy-based platform for collaborative annotation of eukaryotic genomes. PMID:31070714
Humans and Chimpanzees Display Opposite Patterns of Diversity in Arylamine N-Acetyltransferase Genes. PMID:31068377
Cardiac Toxicity From Ethanol Exposure in Human-Induced Pluripotent Stem Cell-Derived Cardiomyocytes. PMID:31059573
Germline Predisposition and Copy Number Alteration in Pre-stage Lung Adenocarcinomas Presenting as Ground-Glass Nodules. PMID:31058088
Determining the Cause of Recurrent Miscarriages in a Couple: Importance of NOR in the Era of NGS. PMID:31058056
Analysis of Subtelomeric REXTAL Assemblies Using QUAST. PMID:31056507
Modulation of Monoaminergic Systems by Antidepressants in the Frontal Cortex of Rats After Chronic Mild Stress Exposure. PMID:31054078
Profiling of chromatin accessibility and identification of general cis-regulatory mechanisms that control two ocular lens differentiation pathways. PMID:31053165
EpiAlign: an alignment-based bioinformatic tool for comparing chromatin state sequences. PMID:31045217
TAGOOS: genome-wide supervised learning of non-coding loci associated to complex phenotypes. PMID:31045203
Differential expression and bioinformatics analysis of circRNA in osteosarcoma. PMID:31036604
Synergy between Variant PRC1 Complexes Defines Polycomb-Mediated Gene Repression. PMID:31029541
Referee: Reference Assembly Quality Scores. PMID:31028392
High-Quality Library Preparation for NGS-Based Immunoglobulin Germline Gene Inference and Repertoire Expression Analysis. PMID:31024532
Unique RNA signature of different lesion types in the brain white matter in progressive multiple sclerosis. PMID:31023379
Human skin long noncoding RNA WAKMAR1 regulates wound healing by enhancing keratinocyte migration. PMID:31019085
An Intramolecular Salt Bridge Linking TDP43 RNA Binding, Protein Stability, and TDP43-Dependent Neurodegeneration. PMID:31018129
LightCpG: a multi-view CpG sites detection on single-cell whole genome sequence data. PMID:31014252
ChimeraMiner: An Improved Chimeric Read Detection Pipeline and Its Application in Single Cell Sequencing. PMID:31010074
Placental DNA methylation levels at CYP2E1 and IRS2 are associated with child outcome in a prospective autism study. PMID:31009952
Chromatin State-Based Analysis of Epigenetic H3K4me3 Marks of Arabidopsis in Response to Dark Stress. PMID:31001332
A novel CRISPR/Cas9 associated technology for sequence-specific nucleic acid enrichment. PMID:30998719
Methylation analysis of Gasdermin E shows great promise as a biomarker for colorectal cancer. PMID:30993897
Classification and monomer-by-monomer annotation dataset of suprachromosomal family 1 alpha satellite higher-order repeats in hg38 human genome assembly. PMID:30989093
The spatial correspondence and genetic influence of interhemispheric connectivity with white matter microstructure. PMID:30988526
Detection of NRG1 Gene Fusions in Solid Tumors. PMID:30988082
Rare variants in MYH15 modify amyotrophic lateral sclerosis risk. PMID:30985904
Dynamic repression by BCL6 controls the genome-wide liver response to fasting and steatosis. PMID:30983568
Use of FFPE-derived DNA in next generation sequencing: DNA extraction methods. PMID:30973937
A QTL for Number of Teats Shows Breed Specific Effects on Number of Vertebrae in Pigs: Bridging the Gap Between Molecular and Quantitative Genetics. PMID:30972109
Long noncoding RNAs in vascular smooth muscle cells regulate vascular calcification. PMID:30971745
Complex Formation between VEGFR2 and the β2-Adrenoceptor. PMID:30956148
The dyslexia susceptibility KIAA0319 gene shows a specific expression pattern during zebrafish development supporting a role beyond neuronal migration. PMID:30950042
A Pipeline for Faecal Host DNA Analysis by Absolute Quantification of LINE-1 and Mitochondrial Genomic Elements Using ddPCR. PMID:30944341
Mendelian Inconsistent Signatures from 1314 Ancestrally Diverse Family Trios Distinguish Biological Variation from Sequencing Error. PMID:30942611
The survey and reference assisted assembly of the Octopus vulgaris genome. PMID:30931949
Sequence and expression levels of circular RNAs in progenitor cell types during mouse corticogenesis. PMID:30926618
FactorNet: A deep learning framework for predicting cell type specific transcription factor binding from nucleotide-resolution sequential data. PMID:30922998
Diagnosis of fusion genes using targeted RNA sequencing. PMID:30918253
Integrative transcriptomic analysis suggests new autoregulatory splicing events coupled with nonsense-mediated mRNA decay. PMID:30916337
Evolution of replication origins in vertebrate genomes: rapid turnover despite selective constraints. PMID:30916335
Detection of Differentially Expressed Cleavage Site Intervals Within 3' Untranslated Regions Using CSI-UTR Reveals Regulated Interaction Motifs. PMID:30915105
Genomic Variants Among Threatened Acropora Corals. PMID:30914426
Phenotype and response to growth hormone therapy in siblings with B4GALT7 deficiency. PMID:30914273
Efficient Genomic Interval Queries Using Augmented Range Trees. PMID:30911095
A Genome-Wide Analysis of the Penumbral Volume in Inbred Mice following Middle Cerebral Artery Occlusion. PMID:30911049
Global DNA methylation of peripheral blood leukocytes from dogs bearing multicentric non-Hodgkin lymphomas and healthy dogs: A comparative study. PMID:30908498
Haploinsufficiency of ARHGAP42 is associated with hypertension. PMID:30903111
Tks5 and Dynamin-2 enhance actin bundle rigidity in invadosomes to promote myoblast fusion. PMID:30894403
Coalitional Game Theory Facilitates Identification of Non-Coding Variants Associated With Autism. PMID:30886520
Genome-wide association study and scan for signatures of selection point to candidate genes for body temperature maintenance under the cold stress in Siberian cattle populations. PMID:30885142
GMASS: a novel measure for genome assembly structural similarity. PMID:30885117
EZH2 Inhibition in Ewing Sarcoma Upregulates GD2 Expression for Targeting with Gene-Modified T Cells. PMID:30879952
Functional genomics analysis of Phelan-McDermid syndrome 22q13 region during human neurodevelopment. PMID:30875393
Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2. PMID:30864654
Outgroup Machine Learning Approach Identifies Single Nucleotide Variants in Noncoding DNA Associated with Autism Spectrum Disorder. PMID:30864328
Live imaging of marked chromosome regions reveals their dynamic resolution and compaction in mitosis. PMID:30858191
Long-read single-molecule maps of the functional methylome. PMID:30846530
Genome-wide data from the Bubi of Bioko Island clarifies the Atlantic fringe of the Bantu dispersal. PMID:30841922
UniProt genomic mapping for deciphering functional effects of missense variants. PMID:30840782
Impact of acceptor splice site NAGTAG motif on exon recognition. PMID:30840204
Making Sense of the Epigenome Using Data Integration Approaches. PMID:30837884
Cohesin-Mediated Genome Architecture Does Not Define DNA Replication Timing Domains. PMID:30836708
Selecting variants of unknown significance through network-based gene-association significantly improves risk prediction for disease-control cohorts. PMID:30824863
Comparative analysis of whole-genome sequencing pipelines to minimize false negative findings. PMID:30824715
PITX3 mutations associated with autosomal dominant congenital cataract in the Chinese population. PMID:30816539
Epigenome-Wide Association Study (EWAS) of Blood Lipids in Healthy Population from STANISLAS Family Study (SFS). PMID:30813608
Advancing Personalized Medicine Through the Application of Whole Exome Sequencing and Big Data Analytics. PMID:30809243
BCL-3 promotes a cancer stem cell phenotype by enhancing β-catenin signalling in colorectal tumour cells. PMID:30792270
Mitochondrial hypoxic stress induces widespread RNA editing by APOBEC3G in natural killer cells. PMID:30791937
Systematical Identification of Breast Cancer-Related Circular RNA Modules for Deciphering circRNA Functions Based on the Non-Negative Matrix Factorization Algorithm. PMID:30791568
Novel Missense Mutations in BEST1 Are Associated with Bestrophinopathies in Lebanese Patients. PMID:30781664
Attenuated chromatin compartmentalization in meiosis and its maturation in sperm development. PMID:30778237
Mycobacterium avium subsp. paratuberculosis induces differential cytosine methylation at miR-21 transcription start site region. PMID:30774666
Evolution of Immune Systems From Viruses and Transposable Elements. PMID:30761103
Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks. PMID:30760546
Nucleotide Resolution Comparison of Transcription of Human Cytomegalovirus and Host Genomes Reveals Universal Use of RNA Polymerase II Elongation Control Driven by Dissimilar Core Promoter Elements. PMID:30755505
Integrated epigenomic analysis stratifies chromatin remodellers into distinct functional groups. PMID:30755246
C/EBPβ Is a Transcriptional Regulator of Wee1 at the G₂/M Phase of the Cell Cycle. PMID:30754676
Significant Strain Variation in the Mutation Spectra of Inbred Laboratory Mice. PMID:30753674
Tourette-Like Syndrome in a Patient with RBFOX1 Deletion. PMID:30746397
Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity. PMID:30744673
Nkx2-5 Second Heart Field Target Gene Ccdc117 Regulates DNA Metabolism and Proliferation. PMID:30742009
A genome-wide association study identifies single nucleotide polymorphisms associated with time-to-metastasis in colorectal cancer. PMID:30738427
Mitochondrial acetyl-CoA reversibly regulates locus-specific histone acetylation and gene expression. PMID:30737248
Modeling double strand break susceptibility to interrogate structural variation in cancer. PMID:30736820
Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation. PMID:30735170
The interplay of renal potassium and sodium handling in blood pressure regulation: critical role of the WNK-SPAK-NCC pathway. PMID:30723251
Comprehensive bioinformatics analysis of critical lncRNAs, mRNAs and miRNAs in non‑alcoholic fatty liver disease. PMID:30720100
Bioinformatic analysis of next‑generation sequencing data to identify dysregulated genes in fibroblasts of idiopathic pulmonary fibrosis. PMID:30720061
Mesoscale modeling reveals formation of an epigenetically driven HOXC gene hub. PMID:30718394
GenESysV: a fast, intuitive and scalable genome exploration open source tool for variants generated from high-throughput sequencing projects. PMID:30704396
An integrated transcriptional analysis of the developing human retina. PMID:30696714
Venous identity requires BMP signalling through ALK3. PMID:30692543
Data Lakes, Clouds, and Commons: A Review of Platforms for Analyzing and Sharing Genomic Data. PMID:30691868
HIV-1 infection increases microRNAs that inhibit Dicer1, HRB and HIV-EP2, thereby reducing viral replication. PMID:30682089
Functional SNPs in the Human Autoimmunity-Associated Locus 17q12-21. PMID:30678091
Systems biology reveals how altered TGFβ signalling with age reduces protection against pro-inflammatory stimuli. PMID:30677026
Exploring the landscape of focal amplifications in cancer using AmpliconArchitect. PMID:30674876
Genome-wide association study and a post replication analysis revealed a promising genomic region and candidate genes for chicken eggshell blueness. PMID:30673708
PLZF targets developmental enhancers for activation during osteogenic differentiation of human mesenchymal stem cells. PMID:30672466
Inflammation in Traumatic Brain Injury: Roles for Toxic A1 Astrocytes and Microglial-Astrocytic Crosstalk. PMID:30661228
High-throughput ChIPmentation: freely scalable, single day ChIPseq data generation from very low cell-numbers. PMID:30658577
Expression Changes of Structural Protein Genes May Be Related to Adaptive Skin Characteristics Specific to Humans. PMID:30657921
The complex architecture and epigenomic impact of plant T-DNA insertions. PMID:30657772
Integrative genomic analysis predicts novel functional enhancer-SNPs for bone mineral density. PMID:30656451
SP1 and STAT3 Functionally Synergize to Induce the RhoU Small GTPase and a Subclass of Non-canonical WNT Responsive Genes Correlating with Poor Prognosis in Breast Cancer. PMID:30654518
A near-chromosome-scale genome assembly of the gemsbok (Oryx gazella): an iconic antelope of the Kalahari desert. PMID:30649288
Improved indel detection in DNA and RNA via realignment with ABRA2. PMID:30649250
Expression of long non-coding RNA ENSG00000226738 (LncKLHDC7B) is enriched in the immunomodulatory triple-negative breast cancer subtype and its alteration promotes cell migration, invasion, and resistance to cell death. PMID:30648789
POGLUT1, the putative effector gene driven by rs2293370 in primary biliary cholangitis susceptibility locus chromosome 3q13.33. PMID:30643196
ATDC mediates a TP63-regulated basal cancer invasive program. PMID:30643195
The mir-465 family is upregulated with age and attenuates growth hormone signaling in mouse liver. PMID:30637918
SQuIRE reveals locus-specific regulation of interspersed repeat expression. PMID:30624635
The long non-coding RNA LINC00941 and SPRR5 are novel regulators of human epidermal homeostasis. PMID:30622217
microRNA-22 promotes megakaryocyte differentiation through repression of its target, GFI1. PMID:30617215
Single-Cell Applications of Next-Generation Sequencing. PMID:30617056
An upstream enhancer regulates Gpihbp1 expression in a tissue-specific manner. PMID:30598475
Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy. PMID:30598455
Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication. PMID:30595451
An extended regulatory landscape drives Tbx18 activity in a variety of prostate-associated cell lineages. PMID:30594504
High-Throughput Sequencing in Respiratory, Critical Care, and Sleep Medicine Research. An Official American Thoracic Society Workshop Report. PMID:30592451
Inherited selective cobalamin malabsorption in Komondor dogs associated with a CUBN splice site variant. PMID:30591068
Genome-wide maps of distal gene regulatory enhancers active in the human placenta. PMID:30589856
Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling. PMID:30586358
Low STYK1 expression indicates poor prognosis in gastric cancer. PMID:30584361
RGAAT: A Reference-based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes. PMID:30583062
MicroRNA-31 Reduces the Motility of Proinflammatory T Helper 1 Lymphocytes. PMID:30574141
HLA-DO Modulates the Diversity of the MHC-II Self-peptidome. PMID:30573663
Chorioamnionitis exposure remodels the unique histone modification landscape of neonatal monocytes and alters the expression of immune pathway genes. PMID:30565411
Bracketing phenogenotypic limits of mammalian hybridization. PMID:30564397
Identification of novel pathogenic ABCA4 variants in a Han Chinese family with Stargardt disease. PMID:30563929
Dichotomy in redundant enhancers points to presence of initiators of gene regulation. PMID:30563465
DAWN: a resource for yielding insights into the diversity among wheat genomes. PMID:30558550
Human sex reversal is caused by duplication or deletion of core enhancers upstream of SOX9. PMID:30552336
Spatiotemporal transcriptomic divergence across human and macaque brain development. PMID:30545855
HDAC is indispensable for IFN-γ-induced B7-H1 expression in gastric cancer. PMID:30537988
PopViz: a webserver for visualizing minor allele frequencies and damage prediction scores of human genetic variations. PMID:30535305
NFKB1 and MANBA Confer Disease Susceptibility to Primary Biliary Cholangitis via Independent Putative Primary Functional Variants. PMID:30528300
UM-HACC-2A: MYB-NFIB fusion-positive human adenoid cystic carcinoma cell line. PMID:30527239
Cannabinoid exposure and altered DNA methylation in rat and human sperm. PMID:30521419
ShapeGTB: the role of local DNA shape in prioritization of functional variants in human promoters with machine learning. PMID:30519505
Multiple Sequence Alignments Enhance Boundary Definition of RNA Structures. PMID:30518121
A map of direct TF-DNA interactions in the human genome. PMID:30517703
Genetic Characterization of Indubrasil Cattle Breed Population. PMID:30513897
Childhood adversity and DNA methylation in two population-based cohorts. PMID:30510187
Molecular analysis of NPAS3 functional domains and variants. PMID:30509165
Biosynthesis of histone messenger RNA employs a specific 3' end endonuclease. PMID:30507380
A Transcription Factor Addiction in Leukemia Imposed by the MLL Promoter Sequence. PMID:30503706
Genome-wide search of nucleosome patterns using visual analytics. PMID:30496344
Integrated Genomic and Proteomic Analyses Reveal Novel Mechanisms of the Methyltransferase SETD2 in Renal Cell Carcinoma Development. PMID:30487242
Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus. PMID:30487138
Topoisomerase 3β interacts with RNAi machinery to promote heterochromatin formation and transcriptional silencing in Drosophila. PMID:30470739
Targets and genomic constraints of ectopic Dnmt3b expression. PMID:30468428
Genetic variation is associated with PTSD risk and aversive memory: Evidence from two trauma-Exposed African samples and one healthy European sample. PMID:30467376
HDAC stimulates gene expression through BRD4 availability in response to IFN and in interferonopathies. PMID:30463877
Hepatic gene body hypermethylation is a shared epigenetic signature of murine longevity. PMID:30462643
Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis. PMID:30462313
The Phosphorylated Estrogen Receptor α (ER) Cistrome Identifies a Subset of Active Enhancers Enriched for Direct ER-DNA Binding and the Transcription Factor GRHL2. PMID:30455249
DMD Open-access Variant Explorer (DOVE): A scalable, open-access, web-based tool to aid in clinical interpretation of genetic variants in the DMD gene. PMID:30450799
Translating Alzheimer's disease-associated polymorphisms into functional candidates: a survey of IGAP genes and SNPs. PMID:30448613
Methylation-Based Classification of Cervical Squamous Cell Carcinoma into Two New Subclasses Differing in Immune-Related Gene Expression. PMID:30445744
Two Pif1 Family DNA Helicases Cooperate in Centromere Replication and Segregation in Saccharomyces cerevisiae. PMID:30442759
Mapping the Pax6 3' untranslated region microRNA regulatory landscape. PMID:30442116
Mutation of the gene encoding the circadian clock component PERIOD2 in oncogenic cells confers chemoresistance by up-regulating the Aldh3a1 gene. PMID:30429219
Genomes reveal marked differences in the adaptive evolution between orangutan species. PMID:30428903
A fast adaptive algorithm for computing whole-genome homology maps. PMID:30423094
Prolonged central apnoea after intravenous morphine administration in a 12-year-old male with a UGT1A1 loss-of-function polymorphism. PMID:30421550
Pergola: Boosting Visualization and Analysis of Longitudinal Data by Unlocking Genomic Analysis Tools. PMID:30419504
TFmapper: A Tool for Searching Putative Factors Regulating Gene Expression Using ChIP-seq Data. PMID:30416387
CRM Discovery Beyond Model Insects. PMID:30414115
ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data. PMID:30413482
DNA methylation in blood as a mediator of the association of mid-childhood body mass index with cardio-metabolic risk score in early adolescence. PMID:30412002
AFLP-AFLP in silico-NGS approach reveals polymorphisms in repetitive elements in the malignant genome. PMID:30408048
FusionGDB: fusion gene annotation DataBase. PMID:30407583
The UCSC Genome Browser database: 2019 update. PMID:30407534
The Drosophila Dot Chromosome: Where Genes Flourish Amidst Repeats. PMID:30401762
Detection of copy number variations in brown and white layers based on genotyping panels with different densities. PMID:30400769
Metastasis Suppressor NME1 Directly Activates Transcription of the ALDOC Gene in Melanoma Cells. PMID:30396920
Wingless promotes EGFR signaling in follicle stem cells to maintain self-renewal. PMID:30389852
Loss-of-function mutations in KIF14 cause severe microcephaly and kidney development defects in humans and zebrafish. PMID:30388224
Detection of Shared Balancing Selection in the Absence of Trans-Species Polymorphism. PMID:30380122
Non-invasive genotyping with a massively parallel sequencing panel for the detection of SNPs in HPA-axis genes. PMID:30374157
piRBase: a comprehensive database of piRNA sequences. PMID:30371818
HJURP antagonizes CENP-A mislocalization driven by the H3.3 chaperones HIRA and DAXX. PMID:30365520
BitterDB: taste ligands and receptors database in 2019. PMID:30357384
Gene expression variability across cells and species shapes innate immunity. PMID:30356220
Argonaute2 attenuates active transcription by limiting RNA Polymerase II elongation in Drosophila melanogaster. PMID:30356106
Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes. PMID:30355328
Defective transcription elongation in a subset of cancers confers immunotherapy resistance. PMID:30353012
Prolonged Idasanutlin (RG7388) Treatment Leads to the Generation of p53-Mutated Cells. PMID:30352966
Expression of calcium pumps is differentially regulated by histone deacetylase inhibitors and estrogen receptor alpha in breast cancer cells. PMID:30352569
Impact of PYROXD1 deficiency on cellular respiration and correlations with genetic analyses of limb-girdle muscular dystrophy in Saudi Arabia and Sudan. PMID:30345904
FANCA D1359Y mutation in a patient with gastric polyposis and cancer susceptibility: A case report and review of literature. PMID:30344425
Chromatin accessibility landscape of articular knee cartilage reveals aberrant enhancer regulation in osteoarthritis. PMID:30341348
Expression of renal cell markers and detection of 3p loss links endolymphatic sac tumor to renal cell carcinoma and warrants careful evaluation to avoid diagnostic pitfalls. PMID:30340515
ComPaSS-GWAS: A method to reduce type I error in genome-wide association studies when replication data are not available. PMID:30334581
A parallel algorithm for N-way interval set intersection. PMID:30333632
Integrated genetic, epigenetic, and gene set enrichment analyses identify NOTCH as a potential mediator for PTSD risk after trauma: Results from two independent African cohorts. PMID:30328613
Genome-Wide Association and Mechanistic Studies Indicate That Immune Response Contributes to Alzheimer's Disease Development. PMID:30319691
Identification of the Transcription Factor Relationships Associated with Androgen Deprivation Therapy Response and Metastatic Progression in Prostate Cancer. PMID:30314329
Genomic coordinates and continental distribution of 120 blood group variants reported by the 1000 Genomes Project. PMID:30312480
IRE1α-XBP1 controls T cell function in ovarian cancer by regulating mitochondrial activity. PMID:30305738
Going the Distance: Optimizing RNA-Seq Strategies for Transcriptomic Analysis of Complex Viral Genomes. PMID:30305358
Ceramide Synthase 6: Comparative Analysis, Phylogeny and Evolution. PMID:30297675
Lead Modulates trans- and cis-Expression Quantitative Trait Loci (eQTLs) in Drosophila melanogaster Heads. PMID:30294342
Long non-coding RNA LINC-01572:28 inhibits granulosa cell growth via a decrease in p27 (Kip1) degradation in patients with polycystic ovary syndrome. PMID:30293818
Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes. PMID:30290830
Hand Factors in Cardiac Development. PMID:30288953
Direct-to-consumer DNA testing of 6,000 dogs reveals 98.6-kb duplication associated with blue eyes and heterochromia in Siberian Huskies. PMID:30286082
Impact of ZBTB7A hypomethylation and expression patterns on treatment response to hydroxyurea. PMID:30285874
Colon-specific eQTL analysis to inform on functional SNPs. PMID:30283144
Replication of a rare risk haplotype on 1p36.33 for autism spectrum disorder. PMID:30276537
Analysis of the association of EPHB6, EFNB1 and EFNB3 variants with hypertension risks in males with hypogonadism. PMID:30262919
Epigenetic Study in Parkinson's Disease: A Pilot Analysis of DNA Methylation in Candidate Genes in Brain. PMID:30261625
Role of post-translational modification of the Y box binding protein 1 in human cancers. PMID:30258867
Coordinate systems for supergenomes. PMID:30258487
Co-dependent Assembly of Drosophila piRNA Precursor Complexes and piRNA Cluster Heterochromatin. PMID:30257203
De novo pattern discovery enables robust assessment of functional consequences of non-coding variants. PMID:30256891
The gene repressor complex NuRD interacts with the histone variant H3.3 at promoters of active genes. PMID:30254051
Risk Locus Identification Ties Alcohol Withdrawal Symptoms to SORCS2. PMID:30252935
Mutations of genes including DNMT3A detected by next-generation sequencing in thyroid cancer. PMID:30252567
Pseudogenes Provide Evolutionary Evidence for the Competitive Endogenous RNA Hypothesis. PMID:30252115
A moderate form of osteogenesis imperfecta caused by compound heterozygous LEPRE1 mutations. PMID:30246063
Functional Genetic Variants Revealed by Massively Parallel Precise Genome Editing. PMID:30245013
Epigenome-Wide Analyses Identify Two Novel Associations With Recurrent Stroke in the Vitamin Intervention for Stroke Prevention Clinical Trial. PMID:30237808
Transcription Promotes the Interaction of the FAcilitates Chromatin Transactions (FACT) Complex with Nucleosomes in Saccharomyces cerevisiae. PMID:30237209
Functional and phylogenetic characterization of noncanonical vitamin B12-binding proteins in zebrafish suggests involvement in cobalamin transport. PMID:30237171
Transcriptome profiling of the cardiac neural crest reveals a critical role for MafB. PMID:30236445
GC4S: A bioinformatics-oriented Java software library of reusable graphical user interface components. PMID:30235322
Early nurture epigenetically tunes the oxytocin receptor. PMID:30227351
X-Chromosome Inactivation and Escape from X Inactivation in Mouse. PMID:30218369
Autosomal genetic variation is associated with DNA methylation in regions variably escaping X-chromosome inactivation. PMID:30218040
GePMI: A statistical model for personal intestinal microbiome identification. PMID:30210803
PLD3 epigenetic changes in the hippocampus of Alzheimer's disease. PMID:30208929
An admixture mapping meta-analysis implicates genetic variation at 18q21 with asthma susceptibility in Latinos. PMID:30201514
Enhancer reprogramming in mammalian genomes. PMID:30200877
HeteroMeth: A Database of Cell-to-cell Heterogeneity in DNA Methylation. PMID:30196115
Extensive sex differences at the initiation of genetic recombination. PMID:30185906
Pairs of Adjacent Conserved Noncoding Elements Separated by Conserved Genomic Distances Act as Cis-Regulatory Units. PMID:30184074
Genotype-dependent associations between serotonin transporter gene (SLC6A4) DNA methylation and late-life depression. PMID:30180828
Ap4 is rate limiting for intestinal tumor formation by controlling the homeostasis of intestinal stem cells. PMID:30177706
Umap and Bismap: quantifying genome and methylome mappability. PMID:30169659
Targeted sequencing to identify novel genetic risk factors for deep vein thrombosis: a study of 734 genes. PMID:30168256
RNA Sequencing (RNA-Seq) Reveals Extremely Low Levels of Reticulocyte-Derived Globin Gene Transcripts in Peripheral Blood From Horses (Equus caballus) and Cattle (Bos taurus). PMID:30154823
Polycomb repressive complex 1 shapes the nucleosome landscape but not accessibility at target genes. PMID:30154222
The Evf2 Ultraconserved Enhancer lncRNA Functionally and Spatially Organizes Megabase Distant Genes in the Developing Forebrain. PMID:30146317
HiGlass: web-based visual exploration and analysis of genome interaction maps. PMID:30143029
Biotinylated amplicon sequencing: A method for preserving DNA samples of limited quantity. PMID:30140723
Genetic associations of hemoglobin in children with chronic kidney disease in the PediGFR Consortium. PMID:30140068
Predictability and persistence of prebiotic dietary supplementation in a healthy human cohort. PMID:30139999
Pathobiological Pseudohypoxia as a Putative Mechanism Underlying Myelodysplastic Syndromes. PMID:30139811
Independent erosion of conserved transcription factor binding sites points to shared hindlimb, vision and external testes loss in different mammals. PMID:30137416
Epiviz Web Components: reusable and extensible component library to visualize functional genomic datasets. PMID:30135734
bioSyntax: syntax highlighting for computational biology. PMID:30134911
Nuclear Receptor Nur77 Limits the Macrophage Inflammatory Response through Transcriptional Reprogramming of Mitochondrial Metabolism. PMID:30134173
Transfer RNA genes experience exceptionally elevated mutation rates. PMID:30127029
Promoter expression of HERV-K (HML-2) provirus-derived sequences is related to LTR sequence variation and polymorphic transcription factor binding sites. PMID:30126415
Functional characterization of alternatively spliced GSN in head and neck squamous cell carcinoma. PMID:30118659
The Role of Phylogenetically Conserved Elements in Shaping Patterns of Human Genomic Diversity. PMID:30113695
Methylomic Analysis of Ovarian Cancers Identifies Tumor-Specific Alterations Readily Detectable in Early Precursor Lesions. PMID:30108103
Revealing a human p53 universe. PMID:30107566
Epigenome-wide association study in whole blood on type 2 diabetes among sub-Saharan African individuals: findings from the RODAM study. PMID:30107520
Characterization of the ICCE Repeat in Mammals Reveals an Evolutionary Relationship with the DXZ4 Macrosatellite through Conserved CTCF Binding Motifs. PMID:30102341
Non-coding genetic variation shaping mental health. PMID:30099302
Identification of novel GLI1 target genes and regulatory circuits in human cancer cells. PMID:30098229
Whole Genome Sequencing, de Novo Assembly and Phenotypic Profiling for the New Budding Yeast Species Saccharomyces jurei. PMID:30097472
A clinical-pathogenetic approach on associated anomalies and chromosomal defects supports novel candidate critical regions and genes for gastroschisis. PMID:30094464
Ancient convergent losses of Paraoxonase 1 yield potential risks for modern marine mammals. PMID:30093596
Sequence diversity of the Rh blood group system in Basques. PMID:30089826
DoGFinder: a software for the discovery and quantification of readthrough transcripts from RNA-seq. PMID:30089468
LncFinder: an integrated platform for long non-coding RNA identification utilizing sequence intrinsic composition, structural information and physicochemical property. PMID:30084867
The SUMO protease SENP1 and the chromatin remodeler CHD3 interact and jointly affect chromatin accessibility and gene expression. PMID:30082317
Pan-Cancer Analysis Reveals Differential Susceptibility of Bidirectional Gene Promoters to DNA Methylation, Somatic Mutations, and Copy Number Alterations. PMID:30081598
No Evidence for Recent Selection at FOXP2 among Diverse Human Populations. PMID:30078708
Dual Roles of Poly(dA:dT) Tracts in Replication Initiation and Fork Collapse. PMID:30078706
Genetic and genomic stability across lymphoblastoid cell line expansions. PMID:30075799
Selection Has Countered High Mutability to Preserve the Ancestral Copy Number of Y Chromosome Amplicons in Diverse Human Lineages. PMID:30075113
RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates. PMID:30071678
Transcriptional profiling of HERV-K(HML-2) in amyotrophic lateral sclerosis and potential implications for expression of HML-2 proteins. PMID:30068350
New MiniPromoter Ple345 (NEFL) Drives Strong and Specific Expression in Retinal Ganglion Cells of Mouse and Primate Retina. PMID:30062914
Whole-genome sequencing analysis of CNV using low-coverage and paired-end strategies is efficient and outperforms array-based CNV analysis. PMID:30061371
High resolution annotation of zebrafish transcriptome using long-read sequencing. PMID:30061115
KDM2A/B lysine demethylases and their alternative isoforms in development and disease. PMID:30059280
The RNA binding protein EWS is broadly involved in the regulation of pri-miRNA processing in mammalian cells. PMID:30053258
Mitochondrial double-stranded RNA triggers antiviral signalling in humans. PMID:30046113
Functional characterization of enhancer evolution in the primate lineage. PMID:30045748
Computational Prediction of Position Effects of Human Chromosome Rearrangements. PMID:30038699
Epigenetic and transcriptional dysregulation of VWA2 associated with a MYC-driven oncogenic program in colorectal cancer. PMID:30038405
Predicting the clinical impact of human mutation with deep neural networks. PMID:30038395
Identification of additional regulatory RNPs that impact rRNA and U6 snRNA methylation. PMID:30037971
Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. PMID:30033119
Parvovirus minute virus of mice interacts with sites of cellular DNA damage to establish and amplify its lytic infection. PMID:30028293
Ascorbate Suppresses VEGF Expression in Retinal Pigment Epithelial Cells. PMID:30025088
Amino acid deprivation triggers a novel GCN2-independent response leading to the transcriptional reactivation of non-native DNA sequences. PMID:30020994
Characteristic of HPV Integration in the Genome and Transcriptome of Cervical Cancer Tissues. PMID:30018982
Heterogeneity and interplay of the extracellular vesicle small RNA transcriptome and proteome. PMID:30018314
An Evolutionary Mechanism for the Generation of Competing RNA Structures Associated with Mutually Exclusive Exons. PMID:30018239
Making genome browsers portable and personal. PMID:30016986
HRPDviewer: human ribosome profiling data viewer. PMID:30010738
Conflicts of CpG density and DNA methylation are proximally and distally involved in gene regulation in human and mouse tissues. PMID:30009687
miR-196b target screen reveals mechanisms maintaining leukemia stemness with therapeutic potential. PMID:29997117
A fast exact functional test for directional association and cancer biology applications. PMID:29993984
PTBP1-Mediated Alternative Splicing Regulates the Inflammatory Secretome and the Pro-tumorigenic Effects of Senescent Cells. PMID:29990503
Novel long-range regulatory mechanisms controlling PKD2 gene expression. PMID:29986647
Subclonal mutation selection in mouse lymphomagenesis identifies known cancer loci and suggests novel candidates. PMID:29985390
Horizontal transfer of BovB and L1 retrotransposons in eukaryotes. PMID:29983116
IL-6 Mediates Cross-Talk between Tumor Cells and Activated Fibroblasts in the Tumor Microenvironment. PMID:29976575
An antisense RNA capable of modulating the expression of the tumor suppressor microRNA-34a. PMID:29970884
Identification of an enhancer region within the TP63/LEPREL1 locus containing genetic variants associated with bladder cancer risk. PMID:29956121
Correlated Selection on Amino Acid Deletion and Replacement in Mammalian Protein Sequences. PMID:29955898
CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness. PMID:29945659
Associations of single nucleotide polymorphisms with mucinous colorectal cancer: genome-wide common variant and gene-based rare variant analyses. PMID:29942513
JDP2: An oncogenic bZIP transcription factor in T cell acute lymphoblastic leukemia. PMID:29941549
Post-transcriptional regulation of Pabpn1 by the RNA binding protein HuR. PMID:29939290
Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data. PMID:29936186
Identification and characterization of two novel alternatively spliced E2F1 transcripts in the rat CNS. PMID:29936143
Weak effects of common genetic variation in oxytocin and vasopressin receptor genes on rhesus macaque social behavior. PMID:29931777
Coactivator condensation at super-enhancers links phase separation and gene control. PMID:29930091
Single-cell whole-genome sequencing identifies human papillomavirus integration in cervical tumour cells prior to and following radiotherapy. PMID:29928338
Epigenetic maintenance of topological domains in the highly rearranged gibbon genome. PMID:29914971
CRISPR/Cas9-mediated knock-in of an optimized TetO repeat for live cell imaging of endogenous loci. PMID:29912475
Predicting human genes susceptible to genomic instability associated with Alu/Alu-mediated rearrangements. PMID:29907612
Development and application of an integrated allele-specific pipeline for methylomic and epigenomic analysis (MEA). PMID:29907088
Mammalian Glutamyl Aminopeptidase Genes (ENPEP) and Proteins: Comparative Studies of a Major Contributor to Arterial Hypertension. PMID:29900035
MicroRNA-30 modulates metabolic inflammation by regulating Notch signaling in adipose tissue macrophages. PMID:29899524
Modulation of Cellular CpG DNA Methylation by Kaposi's Sarcoma-Associated Herpesvirus. PMID:29899086
Association mapping from sequencing reads using k-mers. PMID:29897334
MMARGE: Motif Mutation Analysis for Regulatory Genomic Elements. PMID:29893919
A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes. PMID:29889196
Global miRNA expression profile reveals novel molecular players in aneurysmal subarachnoid haemorrhage. PMID:29884860
CREBBP/EP300 bromodomains are critical to sustain the GATA1/MYC regulatory axis in proliferation. PMID:29884215
Muscle miRNAome shows suppression of chronic inflammatory miRNAs with both prednisone and vamorolone. PMID:29883261
Discovery, fine-mapping, and conditional analyses of genetic variants associated with C-reactive protein in multiethnic populations using the Metabochip in the Population Architecture using Genomics and Epidemiology (PAGE) study. PMID:29878111
A survey of microRNA single nucleotide polymorphisms identifies novel breast cancer susceptibility loci in a case-control, population-based study of African-American women. PMID:29871690
mySyntenyPortal: an application package to construct websites for synteny block analysis. PMID:29871588
Yin Yang 1 promotes the Warburg effect and tumorigenesis via glucose transporter GLUT3. PMID:29869834
Choice of binding sites for CTCFL compared to CTCF is driven by chromatin and by sequence preference. PMID:29860503
Activity of Genes with Functions in Human Williams-Beuren Syndrome Is Impacted by Mobile Element Insertions in the Gray Wolf Genome. PMID:29860323
17p13.3 quadruplication: a prenatal and postpartum clinical characterization of a copy number variant. PMID:29858378
T Cell-Dependent Affinity Maturation and Innate Immune Pathways Differentially Drive Autoreactive B Cell Responses in Rheumatoid Arthritis. PMID:29855173
The rs13388259 Intergenic Polymorphism in the Genomic Context of the BCYRN1 Gene Is Associated with Parkinson's Disease in the Hungarian Population. PMID:29850016
Common genetic variation in the autoimmune regulator (AIRE) locus is associated with autoimmune Addison's disease in Sweden. PMID:29849176
Adaptive Landscape of Protein Variation in Human Exomes. PMID:29846678
Genome-wide microRNA screening in Nile tilapia reveals pervasive isomiRs' transcription, sex-biased arm switching and increasing complexity of expression throughout development. PMID:29844338
Sex-Specific Transcriptome Differences in Substantia Nigra Tissue: A Meta-Analysis of Parkinson's Disease Data. PMID:29799491
Mutalisk: a web-based somatic MUTation AnaLyIS toolKit for genomic, transcriptional and epigenomic signatures. PMID:29790943
Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function. PMID:29779944
Assessment of rosacea symptom severity by genome-wide association study and expression analysis highlights immuno-inflammatory and skin pigmentation genes. PMID:29771307
Adeno-associated Virus Genome Population Sequencing Achieves Full Vector Genome Resolution and Reveals Human-Vector Chimeras. PMID:29766023
Sequencing of exons 4, 5, 12 of COCH gene in patients with postlingual sensorineural hearing loss accompanied by vestibular lesion. PMID:29765451
PCGF5 is required for neural differentiation of embryonic stem cells. PMID:29765032
Preconception Carrier Screening by Genome Sequencing: Results from the Clinical Laboratory. PMID:29754767
Genome-wide binding of transcription factor ZEB1 in triple-negative breast cancer cells. PMID:29744893
Inherited Deletion of 1q, Hyperparathyroidism and Signs of Y-chromosomal Influence in a Patient with Turner Syndrome. PMID:29739732
Circular RNA expression and regulatory network prediction in posterior cingulate astrocytes in elderly subjects. PMID:29739336
Nuclear pore complex-mediated modulation of TCR signaling is required for naïve CD4+ T cell homeostasis. PMID:29736031
UTX-mediated enhancer and chromatin remodeling suppresses myeloid leukemogenesis through noncatalytic inverse regulation of ETS and GATA programs. PMID:29736013
MSIQ: JOINT MODELING OF MULTIPLE RNA-SEQ SAMPLES FOR ACCURATE ISOFORM QUANTIFICATION. PMID:29731954
RNA Helicase DDX1 Converts RNA G-Quadruplex Structures into R-Loops to Promote IgH Class Switch Recombination. PMID:29731414
Genomewide binding of transcription factor Snail1 in triple-negative breast cancer cells. PMID:29729076
Chronic Mild Stress Alters Kynurenine Pathways Changing the Glutamate Neurotransmission in Frontal Cortex of Rats. PMID:29725904
RNA editing in nascent RNA affects pre-mRNA splicing. PMID:29724793
Interferon regulatory factor 1 and a variant of heterogeneous nuclear ribonucleoprotein L coordinately silence the gene for adhesion protein CEACAM1. PMID:29720400
High-Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development. PMID:29719267
Reconstruction of a replication-competent ancestral murine endogenous retrovirus-L. PMID:29716624
A genome-wide assessment of conserved SNP alleles reveals a panel of regulatory SNPs relevant to the peripheral nerve. PMID:29716548
Insulin promoter in human pancreatic β cells contacts diabetes susceptibility loci and regulates genes affecting insulin metabolism. PMID:29712868
miRNA-based signatures in cerebrospinal fluid as potential diagnostic tools for early stage Parkinson's disease. PMID:29707120
Transcriptional Modulation of Human Endogenous Retroviruses in Primary CD4+ T Cells Following Vorinostat Treatment. PMID:29706951
Identification of substrates of the small RNA methyltransferase Hen1 in mouse spermatogonial stem cells and analysis of its methyl-transfer domain. PMID:29703750
An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder. PMID:29700473
DNA methylation, through DNMT1, has an essential role in the development of gastrointestinal smooth muscle cells and disease. PMID:29700293
Enhanced JBrowse plugins for epigenomics data visualization. PMID:29699480
MALAT1: An Epigenetic Regulator of Inflammation in Diabetic Retinopathy. PMID:29695738
Global profiling of protein-DNA and protein-nucleosome binding affinities using quantitative mass spectrometry. PMID:29695722
VariFunNet, an integrated multiscale modeling framework to study the effects of rare non-coding variants in Genome-Wide Association Studies: applied to Alzheimer's Disease. PMID:29692948
Unsupervised, Statistically Based Systems Biology Approach for Unraveling the Genetics of Complex Traits: A Demonstration with Ethanol Metabolism. PMID:29689131
Maser: one-stop platform for NGS big data from analysis to visualization. PMID:29688385
Association of copy number variation across the genome with neuropsychiatric traits in the general population. PMID:29687944
Sparking Fire Under the Skin? Answers From the Association of Complement Genes With Pemphigus Foliaceus. PMID:29686679
Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular. PMID:29678151
Divergent genome evolution caused by regional variation in DNA gain and loss between human and mouse. PMID:29677183
Cstf2t Regulates expression of histones and histone-like proteins in male germ cells. PMID:29673127
Dissecting the sources of gene expression variation in a pan-cancer analysis identifies novel regulatory mutations. PMID:29672706
Mitochondrial nicotinamide adenine dinucleotide reduced (NADH) oxidation links the tricarboxylic acid (TCA) cycle with methionine metabolism and nuclear DNA methylation. PMID:29668680
Distinct chromatin structures at the monoamine oxidase-A promoter correlate with allele-specific expression in SH-SY5Y cells. PMID:29667298
Worldwide distribution of the DCDC2 READ1 regulatory element and its relationship with phoneme variation across languages. PMID:29666269
The Genetic Polymorphism UGT1A4*3 Is Associated with Low Posaconazole Plasma Concentrations in Hematological Malignancy Patients Receiving the Oral Suspension. PMID:29661871
Synergistic co-regulation and competition by a SOX9-GLI-FOXA phasic transcriptional network coordinate chondrocyte differentiation transitions. PMID:29659575
Rare Splice Variants in Long Non-Coding RNAs. PMID:29657294
Micro-RNA Feedback Loops Modulating the Calcineurin/NFAT Signaling Pathway. PMID:29657261
Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome. PMID:29654302
Identification of somatic mutations in monozygotic twins discordant for psychiatric disorders. PMID:29654278
HIF1 mediates a switch in pyruvate kinase isoforms after myocardial infarction. PMID:29652636
Chromatin Accessibility-Based Characterization of the Gene Regulatory Network Underlying Plasmodium falciparum Blood-Stage Development. PMID:29649445
Inference of the human polyadenylation code. PMID:29648582
Smooth muscle cells differentiated from mesenchymal stem cells are regulated by microRNAs and suitable for vascular tissue grafts. PMID:29643181
Tracing the evolution of the heterotrimeric G protein α subunit in Metazoa. PMID:29642851
Type I Interferon Receptor Variants in Gene Regulatory Regions are Associated with Susceptibility to Cerebral Malaria in Malawi. PMID:29637882
Genotype imputation performance of three reference panels using African ancestry individuals. PMID:29637265
Orphan receptor GPR37L1 contributes to the sexual dimorphism of central cardiovascular control. PMID:29625592
TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets. PMID:29621972
iCopyDAV: Integrated platform for copy number variations-Detection, annotation and visualization. PMID:29621297
Mammalian genomic regulatory regions predicted by utilizing human genomics, transcriptomics, and epigenetics data. PMID:29618048
Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq. PMID:29599440
QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data. PMID:29592814
A comprehensive map coupling histone modifications with gene regulation in adult dopaminergic and serotonergic neurons. PMID:29581424
Improved methods of DNA extraction from human spermatozoa that mitigate experimentally-induced oxidative DNA damage. PMID:29579126
Common PIEZO1 Allele in African Populations Causes RBC Dehydration and Attenuates Plasmodium Infection. PMID:29576450
Systematic characterization of pan-cancer mutation clusters. PMID:29572294
A Role for Retrotransposons in Chromothripsis. PMID:29564824
In silico modeling of epigenetic-induced changes in photoreceptor cis-regulatory elements. PMID:29563767
Identification of potential regulatory mutations using multi-omics analysis and haplotyping of lung adenocarcinoma cell lines. PMID:29563587
Interleukin-1β Signaling in Dendritic Cells Induces Antiviral Interferon Responses. PMID:29559569
Statistical methods to detect novel genetic variants using publicly available GWAS summary data. PMID:29558699
Adult height is associated with increased risk of ovarian cancer: a Mendelian randomisation study. PMID:29555990
Peripubertal serum dioxin concentrations and subsequent sperm methylome profiles of young Russian adults. PMID:29550351
Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals. PMID:29549088
Maternal 5mCpG Imprints at the PARD6G-AS1 and GCSAML Differentially Methylated Regions Are Decoupled From Parent-of-Origin Expression Effects in Multiple Human Tissues. PMID:29545821
Allopregnanolone Alters the Gene Expression Profile of Human Glioblastoma Cells. PMID:29543748
Genome-Wide Association Study on Immunoglobulin G Glycosylation Patterns. PMID:29535710
Effects of Cadmium Exposure on DNA Methylation at Imprinting Control Regions and Genome-Wide in Mothers and Newborn Children. PMID:29529597
Metaviz: interactive statistical and visual analysis of metagenomic data. PMID:29529268
GAA•TTC repeat expansion in human cells is mediated by mismatch repair complex MutLγ and depends upon the endonuclease domain in MLH3 isoform one. PMID:29529236
Argonaute2 and LaminB modulate gene expression by controlling chromatin topology. PMID:29529026
LKB1, Salt-Inducible Kinases, and MEF2C Are Linked Dependencies in Acute Myeloid Leukemia. PMID:29526696
Prematurity, ventricular septal defect and dysmorphisms are independent predictors of pathogenic copy number variants: a retrospective study on array-CGH results and phenotypical features of 293 children with neurodevelopmental disorders and/or multiple congenital anomalies. PMID:29523172
A proteomic landscape of diffuse-type gastric cancer. PMID:29520031
Genome-wide transcriptome analysis identifies alternative splicing regulatory network and key splicing factors in mouse and human psoriasis. PMID:29515135
Identification of genes and pathways associated with MDR in MCF-7/MDR breast cancer cells by RNA-seq analysis. PMID:29512753
Comparison of discriminative motif optimization using matrix and DNA shape-based models. PMID:29510689
Dysregulation of the epigenetic landscape of normal aging in Alzheimer's disease. PMID:29507413
Intrinsic DNA binding properties demonstrated for lineage-specifying basic helix-loop-helix transcription factors. PMID:29500235
Developmentally linked human DNA hypermethylation is associated with down-modulation, repression, and upregulation of transcription. PMID:29498561
It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data. PMID:29490019
Mutations in DNA repair genes are associated with increased neo-antigen load and activated T cell infiltration in lung adenocarcinoma. PMID:29487705
Transcriptomes define distinct subgroups of salivary gland adenoid cystic carcinoma with different driver mutations and outcomes. PMID:29484115
A comparative bioinformatic analysis of C9orf72. PMID:29479499
Soluble syntaxin 3 functions as a transcriptional regulator. PMID:29475951
Genome-wide mapping of endogenous G-quadruplex DNA structures by chromatin immunoprecipitation and high-throughput sequencing. PMID:29470465
Drosophila Larval Brain Neoplasms Present Tumour-Type Dependent Genome Instability. PMID:29467187
Transcription start site profiling uncovers divergent transcription and enhancer-associated RNAs in Drosophila melanogaster. PMID:29466941
OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes. PMID:29463736
Identification of piRNA Binding Sites Reveals the Argonaute Regulatory Landscape of the C. elegans Germline. PMID:29456082
Identification of G-quadruplex clusters by high-throughput sequencing of whole-genome amplified products with a G-quadruplex ligand. PMID:29449667
Structure/Function Studies of the α4 Subunit Reveal Evolutionary Loss of a GlyR Subtype Involved in Startle and Escape Responses. PMID:29445326
Colorectal Cancer-Associated Genes Are Associated with Tooth Agenesis and May Have a Role in Tooth Development. PMID:29445242
Rett syndrome: a neurological disorder with metabolic components. PMID:29445033
Mutation in an alternative transcript of CDKL5 in a boy with early-onset seizures. PMID:29444904
Transcriptome analysis reveals TMPRSS6 isoforms with distinct functionalities. PMID:29441715
Chromosomal microarray analysis in the genetic evaluation of 279 patients with syndromic obesity. PMID:29441128
Characterization of TTN Novex Splicing Variants across Species and the Role of RBM20 in Novex-Specific Exon Splicing. PMID:29438341
Identification of genetic risk factors in the Chinese population implicates a role of immune system in Alzheimer's disease pathogenesis. PMID:29432188
Molecular Correlates of In Vitro Responses to Dacomitinib and Afatinib in Bladder Cancer. PMID:29430509
The curious case of peroxiredoxin-5: what its absence in aves can tell us and how it can be used. PMID:29422028
Stratification of TAD boundaries reveals preferential insulation of super-enhancers by strong boundaries. PMID:29416042
The complex genetics of human insulin-like growth factor 2 are not reflected in public databases. PMID:29414792
Integration of human pancreatic islet genomic data refines regulatory mechanisms at Type 2 Diabetes susceptibility loci. PMID:29412141
Mirna biogenesis pathway is differentially regulated during adipose derived stromal/stem cell differentiation. PMID:29411671
Skeletal cell YAP and TAZ combinatorially promote bone development. PMID:29401582
Structural analyses of NEAT1 lncRNAs suggest long-range RNA interactions that may contribute to paraspeckle architecture. PMID:29394378
Stop codon readthrough generates a C-terminally extended variant of the human vitamin D receptor with reduced calcitriol response. PMID:29386352
Whole Genome Methylation Analysis of Nondysplastic Barrett Esophagus that Progresses to Invasive Cancer. PMID:29384778
Polycomb group protein Suz12 is regulated by a novel miRNA-like small RNA. PMID:29379063
An integrative functional genomics framework for effective identification of novel regulatory variants in genome-phenome studies. PMID:29378629
Defining the earliest step of cardiovascular lineage segregation by single-cell RNA-seq. PMID:29371425
A system view and analysis of essential hypertension. PMID:29369145
Experience with genomic sequencing in pediatric patients with congenital cardiac defects in a large community hospital. PMID:29368431
Targeted deletion of a 170-kb cluster of LINE-1 repeats and implications for regional control. PMID:29367313
Expression profiling of snoRNAs in normal hematopoiesis and AML. PMID:29365324
Conserved and species-specific transcription factor co-binding patterns drive divergent gene regulation in human and mouse. PMID:29361190
Dynamic genome wide expression profiling of Drosophila head development reveals a novel role of Hunchback in retinal glia cell development and blood-brain barrier integrity. PMID:29360820
Homeostatic Response of Mouse renin Gene Transcription in a Hypertensive Environment Is Mediated by a Novel 5' Enhancer. PMID:29358217
HERV-W group evolutionary history in non-human primates: characterization of ERV-W orthologs in Catarrhini and related ERV groups in Platyrrhini. PMID:29351742
Dysregulation of miR-155-5p and miR-200-3p and the Anti-Non-Bilayer Phospholipid Arrangement Antibodies Favor the Development of Lupus in Three Novel Murine Lupus Models. PMID:29349090
Genome-wide association study of self-reported food reactions in Japanese identifies shrimp and peach specific loci in the HLA-DR/DQ gene region. PMID:29348432
MSH6 and PMS2 germ-line pathogenic variants implicated in Lynch syndrome are associated with breast cancer. PMID:29345684
Bone marrow failure may be caused by chromosome anomalies exerting effects on RUNX1T1 gene. PMID:29344089
Genome-wide association study in 79,366 European-ancestry individuals informs the genetic architecture of 25-hydroxyvitamin D levels. PMID:29343764
Intellectual disability and epilepsy due to the K/L-mediated Xq28 duplication: Further evidence of a distinct, dosage-dependent phenotype. PMID:29341460
Positive selection on human gamete-recognition genes. PMID:29340252
Evaluating the bias of circRNA predictions from total RNA-Seq data. PMID:29340026
Genome-Wide circRNA Profiling from RNA-seq Data. PMID:29322438
Phenotypic interpretation of complex chromosomal rearrangements informed by nucleotide-level resolution and structural organization of chromatin. PMID:29321672
Polymorphism in Tmem132d regulates expression and anxiety-related behavior through binding of RNA polymerase II complex. PMID:29317594
Coordinated expression and genetic polymorphisms in Grainyhead-like genes in human non-melanoma skin cancers. PMID:29301499
Lymphocytes eject interferogenic mitochondrial DNA webs in response to CpG and non-CpG oligodeoxynucleotides of class C. PMID:29295921
Detection of de novo single nucleotide variants in offspring of atomic-bomb survivors close to the hypocenter by whole-genome sequencing. PMID:29279608
Cancer transcriptome profiling at the juncture of clinical translation. PMID:29279605
Binding of high mobility group A proteins to the mammalian genome occurs as a function of AT-content. PMID:29267285
Circular RNA expression is abundant and correlated to aggressiveness in early-stage bladder cancer. PMID:29263845
Evolutionary expansion of DNA hypomethylation in the mammalian germline genome. PMID:29259021
Investigation of differential HDAC4 methylation patterns in eating disorders. PMID:29256967
Multiple enhancer regions govern the transcription of CCN2 during embryonic development. PMID:29256171
Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type I interferon responses. PMID:29253856
The interaction of lncRNA EZR-AS1 with SMYD3 maintains overexpression of EZR in ESCC cells. PMID:29253179
"DNA Methylation signatures in panic disorder". PMID:29249830
Effects of maternal obesity on Wharton's Jelly mesenchymal stromal cells. PMID:29242640
Efficient transgenesis and annotated genome sequence of the regenerative flatworm model Macrostomum lignano. PMID:29242515
Genome-wide dose-dependent inhibition of histone deacetylases studies reveal their roles in enhancer remodeling and suppression of oncogenic super-enhancers. PMID:29240919
Structural basis for genome wide recognition of 5-bp GC motifs by SMAD transcription factors. PMID:29234012
Integrated analysis of motif activity and gene expression changes of transcription factors. PMID:29233921
Oestrogen Receptor-α binds the FOXP3 promoter and modulates regulatory T-cell function in human cervical cancer. PMID:29229929
Timing of transcription during the cell cycle: Protein complexes binding to E2F, E2F/CLE, CDE/CHR, or CHR promoter elements define early and late cell cycle gene expression. PMID:29228647
YY1 Is a Structural Regulator of Enhancer-Promoter Loops. PMID:29224777
Conserved Gene Microsynteny Unveils Functional Interaction Between Protein Disulfide Isomerase and Rho Guanine-Dissociation Inhibitor Families. PMID:29222525
MiRIAD update: using alternative polyadenylation, protein interaction network analysis and additional species to enhance exploration of the role of intragenic miRNAs and their host genes. PMID:29220447
Leveraging putative enhancer-promoter interactions to investigate two-way epistasis in Type 2 Diabetes GWAS. PMID:29218913
The Anaerobically Induced sRNA PaiI Affects Denitrification in Pseudomonas aeruginosa PA14. PMID:29218039
DNA methylation levels in candidate genes associated with chronological age in mammals are not conserved in a long-lived seabird. PMID:29216256
Two large deletions extending beyond either end of the RHD gene and their red cell phenotypes. PMID:29215093
Transcriptional Profiling of Saccharomyces cerevisiae Reveals the Impact of Variation of a Single Transcription Factor on Differential Gene Expression in 4NQO, Fermentable, and Nonfermentable Carbon Sources. PMID:29208650
A population of innate myelolymphoblastoid effector cell expanded by inactivation of mTOR complex 1 in mice. PMID:29206103
Explorative visual analytics on interval-based genomic data and their metadata. PMID:29202689
The zebrafish as a model system for analyzing mammalian and native α-crystallin promoter function. PMID:29201567
Powerful Inference with the D-Statistic on Low-Coverage Whole-Genome Data. PMID:29196497
OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps. PMID:29195502
Adiposity QTL Adip20 decomposes into at least four loci when dissected using congenic strains. PMID:29194435
DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data. PMID:29187143
19p13 microduplications encompassing NFIX are responsible for intellectual disability, short stature and small head circumference. PMID:29184170
Software for rapid time dependent ChIP-sequencing analysis (TDCA). PMID:29178831
Exome Sequencing of Extended Families with Alzheimer's Disease Identifies Novel Genes Implicated in Cell Immunity and Neuronal Function. PMID:29177109
Epigenetic regulation of AXL and risk of childhood asthma symptoms. PMID:29177020
Genome-wide DNase hypersensitivity, and occupancy of RUNX2 and CTCF reveal a highly dynamic gene regulome during MC3T3 pre-osteoblast differentiation. PMID:29176792
Single suture craniosynostosis: Identification of rare variants in genes associated with syndromic forms. PMID:29168297
Rapid Gene Family Evolution of a Nematode Sperm Protein Despite Sequence Hyper-conservation. PMID:29162683
Compound Heterozygous Inheritance of Mutations in Coenzyme Q8A Results in Autosomal Recessive Cerebellar Ataxia and Coenzyme Q10 Deficiency in a Female Sib-Pair. PMID:29159460
GFZF, a Glutathione S-Transferase Protein Implicated in Cell Cycle Regulation and Hybrid Inviability, Is a Transcriptional Coactivator. PMID:29158293
Asymmetry between Activation and Deactivation during a Transcriptional Pulse. PMID:29153839
Identification of Pleiotropic Cancer Susceptibility Variants from Genome-Wide Association Studies Reveals Functional Characteristics. PMID:29150481
Comparative transcriptomics of 5 high-altitude vertebrates and their low-altitude relatives. PMID:29149296
Whole-genome re-sequencing of two Italian tomato landraces reveals sequence variations in genes associated with stress tolerance, fruit quality and long shelf-life traits. PMID:29149280
Convergence of topological domain boundaries, insulators, and polytene interbands revealed by high-resolution mapping of chromatin contacts in the early Drosophila melanogaster embryo. PMID:29148971
The Epstein-Barr Virus Episome Maneuvers between Nuclear Chromatin Compartments during Reactivation. PMID:29142137
LRH-1 expression patterns in breast cancer tissues are associated with tumour aggressiveness. PMID:29137369
Network inference from glycoproteomics data reveals new reactions in the IgG glycosylation pathway. PMID:29133956
Hit-and-run epigenetic editing prevents senescence entry in primary breast cells from healthy donors. PMID:29133799
Significance of functional disease-causal/susceptible variants identified by whole-genome analyses for the understanding of human diseases. PMID:29129848
DNA methylation regulates TMEM16A/ANO1 expression through multiple CpG islands in head and neck squamous cell carcinoma. PMID:29123240
Beyond genome-wide scan: Association of a cis-regulatory NCR3 variant with mild malaria in a population living in the Republic of Congo. PMID:29121672
Chromatin-state discovery and genome annotation with ChromHMM. PMID:29120462
Dynamic Visualization and Comparative Analysis of Multiple Collinear Genomic Data. PMID:29119144
Identification of a novel HERV-K(HML10): comprehensive characterization and comparative analysis in non-human primates provide insights about HML10 proviruses structure and diffusion. PMID:29118853
Identification of Splicing Quantitative Trait Loci (sQTL) in Drosophila melanogaster with Developmental Lead (Pb2+) Exposure. PMID:29114259
Selection of reference genes for gene expression studies in human bladder cancer using SYBR-Green quantitative polymerase chain reaction. PMID:29113238
STK38L kinase ablation promotes loss of cell viability in a subset of KRAS-dependent pancreatic cancer cell lines. PMID:29108249
ASpedia: a comprehensive encyclopedia of human alternative splicing. PMID:29106599
The UCSC Genome Browser database: 2018 update. PMID:29106570
Stability of Wake-Sleep Cycles Requires Robust Degradation of the PERIOD Protein. PMID:29103939
Polygenic risk score in postmortem diagnosed sporadic early-onset Alzheimer's disease. PMID:29103623
A distinct hematopoietic stem cell population for rapid multilineage engraftment in nonhuman primates. PMID:29093179
Loss of the Caenorhabditis elegans pocket protein LIN-35 reveals MuvB's innate function as the repressor of DREAM target genes. PMID:29091720
Identification of a novel CACNA1A mutation in a Chinese family with autosomal recessive progressive myoclonic epilepsy. PMID:29089769
Common, germline genetic variations in the novel tumor suppressor BAP1 and risk of developing different types of cancer. PMID:29088836
Odd skipped-related 1 identifies a population of embryonic fibro-adipogenic progenitors regulating myogenesis during limb development. PMID:29084951
Measurement of fetal fraction in cell-free DNA from maternal plasma using a panel of insertion/deletion polymorphisms. PMID:29084245
GATA2/3-TFAP2A/C transcription factor network couples human pluripotent stem cell differentiation to trophectoderm with repression of pluripotency. PMID:29078328
Denaturing CLIP, dCLIP, Pipeline Identifies Discrete RNA Footprints on Chromatin-Associated Proteins and Reveals that CBX7 Targets 3' UTRs to Regulate mRNA Expression. PMID:29073373
UTX-guided neural crest function underlies craniofacial features of Kabuki syndrome. PMID:29073101
FlyAtlas 2: a new version of the Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data. PMID:29069479
OverGeneDB: a database of 5' end protein coding overlapping genes in human and mouse genomes. PMID:29069459
Investigating transcription factor synergism in humans. PMID:29069301
RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education. PMID:29067736
Cell-Specific RNA Binding Protein Rbfox2 Regulates CaV2.2 mRNA Exon Composition and CaV2.2 Current Size. PMID:29067356
Cardamonin inhibits colonic neoplasia through modulation of MicroRNA expression. PMID:29066742
A cautionary tale of sense-antisense gene pairs: independent regulation despite inverse correlation of expression. PMID:29059299
Estimating the causal tissues for complex traits and diseases. PMID:29058715
Further Insights into the Ciliary Gene and Protein KIZ and Its Murine Ortholog PLK1S1 Mutated in Rod-Cone Dystrophy. PMID:29057815
Identification of candidate genes related to pancreatic cancer based on analysis of gene co-expression and protein-protein interaction network. PMID:29050346
Mechanisms of HERV-K (HML-2) Transcription during Human Mammary Epithelial Cell Transformation. PMID:29046454
The human PKP2/plakophilin-2 gene is induced by Wnt/β-catenin in normal and colon cancer-associated fibroblasts. PMID:29044515
A DNA Contact Map for the Mouse Runx1 Gene Identifies Novel Haematopoietic Enhancers. PMID:29042628
PCSD: a plant chromatin state database. PMID:29040761
Partial monosomy 8p and trisomy 16q in two children with developmental delay detected by array comparative genomic hybridization. PMID:29039589
Identification of genome variations in patients with lung adenocarcinoma using whole genome re‑sequencing. PMID:29039585
Biological Function of MicroRNA193a-3p in Health and Disease. PMID:29038785
Irys Extract. PMID:29036307
Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling. PMID:29035697
Clinical phenotype of ASD-associated DYRK1A haploinsufficiency. PMID:29034068
DNA methylation and transcriptional trajectories during human development and reprogramming of isogenic pluripotent stem cells. PMID:29030611
Early-life environmental exposures interact with genetic susceptibility variants in pediatric patients with eosinophilic esophagitis. PMID:29029802
The common oncogenomic program of NOTCH1 and NOTCH3 signaling in T-cell acute lymphoblastic leukemia. PMID:29023469
Genome-wide mapping of DNase I hypersensitive sites in rare cell populations using single-cell DNase sequencing. PMID:29022941
SHH signaling directed by two oral epithelium-specific enhancers controls tooth and oral development. PMID:29021530
DNA sequencing at 40: past, present and future. PMID:29019985
Applications of sequence coevolution in membrane protein biochemistry. PMID:28993150
Clinical utility of the low-density Infinium QC genotyping Array in a genomics-based diagnostics laboratory. PMID:28985730
An RNA editing/dsRNA binding-independent gene regulatory mechanism of ADARs and its clinical implication in cancer. PMID:28985428
Circular RNA expression profiles and features in human tissues: a study using RNA-seq data. PMID:28984197
Identification of genome-wide non-canonical spliced regions and analysis of biological functions for spliced sequences using Read-Split-Fly. PMID:28984182
A Novel Retinal Ganglion Cell Promoter for Utility in AAV Vectors. PMID:28983234
Viewing RNA-seq data on the entire human genome. PMID:28979763
CRISPR-mediated isolation of specific megabase segments of genomic DNA. PMID:28977642
Oxidative stress rapidly stabilizes promoter-proximal paused Pol II across the human genome. PMID:28977633
Fractionation iCLIP detects persistent SR protein binding to conserved, retained introns in chromatin, nucleoplasm and cytoplasm. PMID:28977534
Epigenetic regulation of gene expression in cancer: techniques, resources and analysis. PMID:28968850
MAJIQ-SPEL: web-tool to interrogate classical and complex splicing variations from RNA-Seq data. PMID:28968636
U1 snRNP telescripting regulates a size-function-stratified human genome. PMID:28967884
Nested Inversion Polymorphisms Predispose Chromosome 22q11.2 to Meiotic Rearrangements. PMID:28965848
An improved compound Poisson model for the number of motif hits in DNA sequences. PMID:28961747
Dysregulation of Alternative Poly-adenylation as a Potential Player in Autism Spectrum Disorder. PMID:28955198
VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences. PMID:28950836
Application of dual reading domains as novel reagents in chromatin biology reveals a new H3K9me3 and H3K36me2/3 bivalent chromatin state. PMID:28946896
Targeting H19, an Imprinted Long Non-Coding RNA, in Hepatic Functions and Liver Diseases. PMID:28933364
Detection of clinically relevant copy number alterations in oral cancer progression using multiplexed droplet digital PCR. PMID:28928368
C1orf64 is a novel androgen receptor target gene and coregulator that interacts with 14-3-3 protein in breast cancer. PMID:28915724
Alternative Polyadenylation of PRELID1 Regulates Mitochondrial ROS Signaling and Cancer Outcomes. PMID:28912168
Integration of Kinase and Calcium Signaling at the Level of Chromatin Underlies Inducible Gene Activation in T Cells. PMID:28904128
RNA-Seq of Human Neural Progenitor Cells Exposed to Lead (Pb) Reveals Transcriptome Dynamics, Splicing Alterations and Disease Risk Associations. PMID:28903495
Neanderthal and Denisova tooth protein variants in present-day humans. PMID:28902892
Screening and identification of key biomarkers in hepatocellular carcinoma: Evidence from bioinformatic analysis. PMID:28901457
Catalog of Differentially Expressed Long Non-Coding RNA following Activation of Human and Mouse Innate Immune Response. PMID:28900427
Associations of two-pore domain potassium channels and triple negative breast cancer subtype in The Cancer Genome Atlas: systematic evaluation of gene expression and methylation. PMID:28899398
Tissue-specific DNA methylation is conserved across human, mouse, and rat, and driven by primary sequence conservation. PMID:28899353
CDK10 Mutations in Humans and Mice Cause Severe Growth Retardation, Spine Malformations, and Developmental Delays. PMID:28886341
Incidence of pancreatic cancer is dramatically increased by a high fat, high calorie diet in KrasG12D mice. PMID:28886117
LncRNA ZNF503-AS1 promotes RPE differentiation by downregulating ZNF503 expression. PMID:28880276
Deep Sequencing Transcriptome Analysis of Murine Wound Healing: Effects of a Multicomponent, Multitarget Natural Product Therapy-Tr14. PMID:28879183
Overdominant Effect of a CHRNA4 Polymorphism on Cingulo-Opercular Network Activity and Cognitive Control. PMID:28877969
Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines. PMID:28869592
Stability of gene expression in human T cells in different gravity environments is clustered in chromosomal region 11p15.4. PMID:28868355
Evolution of Vertebrate Solute Carrier Family 9B Genes and Proteins (SLC9B): Evidence for a Marsupial Origin for Testis Specific SLC9B1 from an Ancestral Vertebrate SLC9B2 Gene. PMID:28868326
5C analysis of the Epidermal Differentiation Complex locus reveals distinct chromatin interaction networks between gene-rich and gene-poor TADs in skin epithelial cells. PMID:28863138
X Chromosome Evolution in Cetartiodactyla. PMID:28858207
A Rare Syndrome of GRID2 Deletion in 2 Siblings. PMID:28856174
The effect of Nipped-B-like (Nipbl) haploinsufficiency on genome-wide cohesin binding and target gene expression: modeling Cornelia de Lange syndrome. PMID:28855971
Genome-wide association and functional studies identify a role for matrix Gla protein in osteoarthritis of the hand. PMID:28855172
Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells. PMID:28854368
A heterochromatin-dependent transcription machinery drives piRNA expression. PMID:28847004
Induction of a novel isoform of the lncRNA HOTAIR in Claudin-low breast cancer cells attached to extracellular matrix. PMID:28846832
Fast, Quantitative and Variant Enabled Mapping of Peptides to Genomes. PMID:28837811
Population genetic structure of Guiana dolphin (Sotalia guianensis) from the southwestern Atlantic coast of Brazil. PMID:28837691
Differential alternative splicing coupled to nonsense-mediated decay of mRNA ensures dietary restriction-induced longevity. PMID:28824175
Sex chromosomes drive gene expression and regulatory dimorphisms in mouse embryonic stem cells. PMID:28818098
A demethylation deficient isoform of the lysine demethylase KDM2A interacts with pericentromeric heterochromatin in an HP1a-dependent manner. PMID:28816576
CCCTC-Binding Factor Translates Interleukin 2- and α-Ketoglutarate-Sensitive Metabolic Changes in T Cells into Context-Dependent Gene Programs. PMID:28813658
Joint Analysis of Nuclear and Mitochondrial Variants in Age-Related Macular Degeneration Identifies Novel Loci TRPM1 and ABHD2/RLBP1. PMID:28813576
Modeling of TREX1-Dependent Autoimmune Disease using Human Stem Cells Highlights L1 Accumulation as a Source of Neuroinflammation. PMID:28803918
Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation. PMID:28803781
Identification and characterization of a long non-coding RNA up-regulated during HIV-1 infection. PMID:28803142
STAT3-induced long noncoding RNAs in multiple myeloma cells display different properties in cancer. PMID:28801664
Whole gene sequencing identifies deep-intronic variants with potential functional impact in patients with hypertrophic cardiomyopathy. PMID:28797094
Smoking is associated with hypermethylation of the APC 1A promoter in colorectal cancer: the ColoCare Study. PMID:28791728
Tet-Mediated DNA Demethylation Is Required for SWI/SNF-Dependent Chromatin Remodeling and Histone-Modifying Activities That Trigger Expression of the Sp7 Osteoblast Master Gene during Mesenchymal Lineage Commitment. PMID:28784721
Characterization of the piRNA pathway during development of the sea anemone Nematostella vectensis. PMID:28783426
Structural variants in genes associated with human Williams-Beuren syndrome underlie stereotypical hypersociability in domestic dogs. PMID:28776031
Uracil Accumulation and Mutagenesis Dominated by Cytosine Deamination in CpG Dinucleotides in Mice Lacking UNG and SMUG1. PMID:28775312
Identification of candidate protective variants for common diseases and evaluation of their protective potential. PMID:28774272
Challenges for visualizing three-dimensional data in genomic browsers. PMID:28771695
T-Cell Lymphopenia Detected by Newborn Screening in Two Siblings with an Xq13.1 Duplication. PMID:28770187
Discovery of rare, diagnostic AluYb8/9 elements in diverse human populations. PMID:28770012
Comprehensive discovery of noncoding RNAs in acute myeloid leukemia cell transcriptomes. PMID:28760689
Genome-wide screen for differentially methylated long noncoding RNAs identifies Esrp2 and lncRNA Esrp2-as regulated by enhancer DNA methylation with prognostic relevance for human breast cancer. PMID:28759043
Population and allelic variation of A-to-I RNA editing in human transcriptomes. PMID:28754146
Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility. PMID:28750606
miR-130b directly targets ARHGAP1 to drive activation of a metastatic CDC42-PAK1-AP1 positive feedback loop in Ewing sarcoma. PMID:28748534
MED resulting from recessively inherited mutations in the gene encoding calcium-activated nucleotidase CANT1. PMID:28742282
Short (16-mer) locked nucleic acid splice-switching oligonucleotides restore dystrophin production in Duchenne Muscular Dystrophy myotubes. PMID:28742140
Germline EMSY sequence alterations in hereditary breast cancer and ovarian cancer families. PMID:28738860
Argonaute CLIP Defines a Deregulated miR-122-Bound Transcriptome that Correlates with Patient Survival in Human Liver Cancer. PMID:28735896
Computational Prediction of Position Effects of Apparently Balanced Human Chromosomal Rearrangements. PMID:28735859
Genome Organization Drives Chromosome Fragility. PMID:28735753
Genome-wide signals of positive selection in strongylocentrotid sea urchins. PMID:28732465
m6aViewer: software for the detection, analysis, and visualization of N6-methyladenosine peaks from m6A-seq/ME-RIP sequencing data. PMID:28724534
Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells. PMID:28722025
Pharmacogenomics study of thiazide diuretics and QT interval in multi-ethnic populations: the cohorts for heart and aging research in genomic epidemiology. PMID:28719597
Genetic determinants of susceptibility to silver nanoparticle-induced acute lung inflammation in mice. PMID:28716969
Selectivity and Kinetic Requirements of HDAC Inhibitors as Progranulin Enhancers for Treating Frontotemporal Dementia. PMID:28712747
Vertical sleeve gastrectomy reverses diet-induced gene-regulatory changes impacting lipid metabolism. PMID:28706189
A fourth Denisovan individual. PMID:28695206
Connected Gene Communities Underlie Transcriptional Changes in Cornelia de Lange Syndrome. PMID:28679547
CRISPR Epigenome Editing of AKAP150 in DRG Neurons Abolishes Degenerative IVD-Induced Neuronal Activation. PMID:28676344
Expression of a SOX1 overlapping transcript in neural differentiation and cancer models. PMID:28674729
The Stress-Responding miR-132-3p Shows Evolutionarily Conserved Pathway Interactions. PMID:28667373
Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells. PMID:28653622
An ancestral haplotype of the human PERIOD2 gene associates with reduced sensitivity to light-induced melatonin suppression. PMID:28650999
In Vivo Murine-Matured Human CD3+ Cells as a Preclinical Model for T Cell-Based Immunotherapies. PMID:28649577
Maternal serum PFOA concentration and DNA methylation in cord blood: A pilot study. PMID:28645023
Genome-wide mapping of DNase I hypersensitive sites reveals chromatin accessibility changes in Arabidopsis euchromatin and heterochromatin regions under extended darkness. PMID:28642500
Identification of a Sjögren's syndrome susceptibility locus at OAS1 that influences isoform switching, protein expression, and responsiveness to type I interferons. PMID:28640813
Ptbp2 Controls an Alternative Splicing Network Required for Cell Communication during Spermatogenesis. PMID:28636946
Reconstruction and evolutionary history of eutherian chromosomes. PMID:28630326
Genetic-epigenetic interactions in cis: a major focus in the post-GWAS era. PMID:28629478
Epigenome-wide association study of chronic obstructive pulmonary disease and lung function in Koreans. PMID:28621160
SoxF factors induce Notch1 expression via direct transcriptional regulation during early arterial development. PMID:28619820
Regulatory landscape fusion in rhabdomyosarcoma through interactions between the PAX3 promoter and FOXO1 regulatory elements. PMID:28615069
Hypoplastic Left Heart Syndrome Sequencing Reveals a Novel NOTCH1 Mutation in a Family with Single Ventricle Defects. PMID:28608148
GeneHancer: genome-wide integration of enhancers and target genes in GeneCards. PMID:28605766
Using nanoBRET and CRISPR/Cas9 to monitor proximity to a genome-edited protein in real-time. PMID:28600500
The regulatory role of miRNAs on VDR in breast cancer. PMID:28598255
Androgen receptor and miR-206 regulation in prostate cancer. PMID:28598253
Identification of the functional variant driving ORMDL3 and GSDMB expression in human chromosome 17q12-21 in primary biliary cholangitis. PMID:28588209
Genome-wide profiling and differential expression of microRNA in rat pluripotent stem cells. PMID:28584262
Repeated divergent selection on pigmentation genes in a rapid finch radiation. PMID:28560331
An environment-dependent transcriptional network specifies human microglia identity. PMID:28546318
The dynamic three-dimensional organization of the diploid yeast genome. PMID:28537556
The Damaging Effect of Passenger Mutations on Cancer Progression. PMID:28536279
Bioinformatic analysis of bacteria and host cell dual RNA-sequencing experiments. PMID:28535295
The microRNA miR-31 inhibits CD8+ T cell function in chronic viral infection. PMID:28530712
A genetic basis for molecular asymmetry at vertebrate electrical synapses. PMID:28530549
MicroRNAs 146a/b-5 and 425-3p and 24-3p are markers of antidepressant response and regulate MAPK/Wnt-system genes. PMID:28530238
Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes. PMID:28522611
Bioinformatic Analysis for Profiling Drug-induced Chromatin Modification Landscapes in Mouse Brain Using ChlP-seq Data. PMID:28516124
A computational approach for the functional classification of the epigenome. PMID:28515787
Comparative Analysis of Immune Checkpoint Molecules and Their Potential Role in the Transmissible Tasmanian Devil Facial Tumor Disease. PMID:28515726
Zinc is a potent and specific inhibitor of IFN-λ3 signalling. PMID:28513591
VEGFA links self-renewal and metastasis by inducing Sox2 to repress miR-452, driving Slug. PMID:28504716
Bioinformatic analysis of the effects and mechanisms of decitabine and cytarabine on acute myeloid leukemia. PMID:28498449
Epstein-Barr Virus Rta-Mediated Accumulation of DNA Methylation Interferes with CTCF Binding in both Host and Viral Genomes. PMID:28490592
Identification of a novel RASD1 somatic mutation in a USP8-mutated corticotroph adenoma. PMID:28487882
The More the Merrier-Complexity in Long Non-Coding RNA Loci. PMID:28487673
Functional Characterization of the GUCY1A3 Coronary Artery Disease Risk Locus. PMID:28487391
Firmiana: towards a one-stop proteomic cloud platform for data processing and analysis. PMID:28486446
Soft Sweeps Are the Dominant Mode of Adaptation in the Human Genome. PMID:28482049
An Integrating Approach for Genome-Wide Screening of MicroRNA Polymorphisms Mediated Drug Response Alterations. PMID:28480217
CHARGE and Kabuki Syndromes: Gene-Specific DNA Methylation Signatures Identify Epigenetic Mechanisms Linking These Clinically Overlapping Conditions. PMID:28475860
DNA methylation and Transcriptome Changes Associated with Cisplatin Resistance in Ovarian Cancer. PMID:28473707
IGF2 mRNA binding protein 3 (IMP3) promotes glioma cell migration by enhancing the translation of RELA/p65. PMID:28465487
Similarity in viral and host promoters couples viral reactivation with host cell migration. PMID:28462923
Small RNA sequencing reveals metastasis-related microRNAs in lung adenocarcinoma. PMID:28460486
Genome-wide association study of red blood cell traits in Hispanics/Latinos: The Hispanic Community Health Study/Study of Latinos. PMID:28453575
A Chromosome-Scale Assembly of the Bactrocera cucurbitae Genome Provides Insight to the Genetic Basis of white pupae. PMID:28450369
Evolutionary history of Tibetans inferred from whole-genome sequencing. PMID:28448578
Small copy-number variations involving genes of the FGF pathway in differences in sex development. PMID:28446957
A Novel Long Non-coding RNA, durga Modulates Dendrite Density and Expression of kalirin in Zebrafish. PMID:28442991
Dysregulation of Blimp1 transcriptional repressor unleashes p130Cas/ErbB2 breast cancer invasion. PMID:28442738
Mutational screening of SLC39A5, LEPREL1 and LRPAP1 in a cohort of 187 high myopia patients. PMID:28442722
The BAF (BRG1/BRM-Associated Factor) chromatin-remodeling complex exhibits ethanol sensitivity in fetal neural progenitor cells and regulates transcription at the miR-9-2 encoding gene locus. PMID:28438527
Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells. PMID:28436944
FLI1 level during megakaryopoiesis affects thrombopoiesis and platelet biology. PMID:28432223
Loss of Dnmt3a and Dnmt3b does not affect epidermal homeostasis but promotes squamous transformation through PPAR-γ. PMID:28425913
Vitamin C Prevents Offspring DNA Methylation Changes Associated with Maternal Smoking in Pregnancy. PMID:28422514
Integrative analysis unveils new functions for the Drosophila Cutoff protein in noncoding RNA biogenesis and gene regulation. PMID:28420675
Stratified polygenic risk prediction model with application to CAGI bipolar disorder sequencing data. PMID:28419606
The histone demethylase KDM3A regulates the transcriptional program of the androgen receptor in prostate cancer cells. PMID:28416760
Drosophila melanogaster retrotransposon and inverted repeat-derived endogenous siRNAs are differentially processed in distinct cellular locations. PMID:28415970
gb4gv: a genome browser for geminivirus. PMID:28413726
Search for rare protein altering variants influencing susceptibility to multiple myeloma. PMID:28404951
ORIO (Online Resource for Integrative Omics): a web-based platform for rapid integration of next generation sequencing data. PMID:28402545
Comparative studies of vertebrate iduronate 2-sulfatase (IDS) genes and proteins: evolution of A mammalian X-linked gene. PMID:28401457
LADD syndrome with glaucoma is caused by a novel gene. PMID:28400699
Rare copy number variants in patients with congenital conotruncal heart defects. PMID:28398664
Toil enables reproducible, open source, big biomedical data analyses. PMID:28398314
Co-option of an endogenous retrovirus envelope for host defense in hominid ancestors. PMID:28397686
Association between CACNA1C gene polymorphisms and ritodrine-induced adverse events in preterm labor patients. PMID:28391406
Physical Confirmation and Comparative Genomics of the Rat Mammary carcinoma susceptibility 3 Quantitative Trait Locus. PMID:28391240
Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data. PMID:28388874
Cancer-associated noncoding mutations affect RNA G-quadruplex-mediated regulation of gene expression. PMID:28386116
Genome-wide TOP2A DNA cleavage is biased toward translocated and highly transcribed loci. PMID:28385713
Short template switch events explain mutation clusters in the human genome. PMID:28385709
Genetic Predisposition of Polymorphisms in HMGB1-Related Genes to Breast Cancer Prognosis in Korean Women. PMID:28382092
Virgin Beta Cells Persist throughout Life at a Neogenic Niche within Pancreatic Islets. PMID:28380380
The crown-of-thorns starfish genome as a guide for biocontrol of this coral reef pest. PMID:28379940
DNA Methylation Divergence and Tissue Specialization in the Developing Mouse Placenta. PMID:28379409
A CD47-associated super-enhancer links pro-inflammatory signalling to CD47 upregulation in breast cancer. PMID:28378740
Integrated analysis of gene expression and copy number identified potential cancer driver genes with amplification-dependent overexpression in 1,454 solid tumors. PMID:28377632
Characterizing Genetic Susceptibility to Breast Cancer in Women of African Ancestry. PMID:28377418
AD-LIBS: inferring ancestry across hybrid genomes using low-coverage sequence data. PMID:28376731
An epigenetic aging clock for dogs and wolves. PMID:28373601
The haploinsufficient tumor suppressor, CUX1, acts as an analog transcriptional regulator that controls target genes through distal enhancers that loop to target promoters. PMID:28369554
The impact of structural variation on human gene expression. PMID:28369037
Non-coding cancer driver candidates identified with a sample- and position-specific model of the somatic mutation rate. PMID:28362259
A sequence-based method to predict the impact of regulatory variants using random forest. PMID:28361702
Genomic profiling reveals mutational landscape in parathyroid carcinomas. PMID:28352668
Dietary restriction protects from age-associated DNA methylation and induces epigenetic reprogramming of lipid metabolism. PMID:28351387
Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus. PMID:28348391
Weighted pseudolikelihood for SNP set analysis with multiple secondary outcomes in case-control genetic association studies. PMID:28346824
Hepatic cyclooxygenase-2 overexpression induced spontaneous hepatocellular carcinoma formation in mice. PMID:28346420
Suppression of indoleamine-2,3-dioxygenase 1 expression by promoter hypermethylation in ER-positive breast cancer. PMID:28344890
Translation of CircRNAs. PMID:28344080
Functional Architectures of Local and Distal Regulation of Gene Expression in Multiple Human Tissues. PMID:28343628
Variants in the host genome may inhibit tumour growth in devil facial tumours: evidence from genome-wide association. PMID:28341828
Small chromosomal regions position themselves autonomously according to their chromatin class. PMID:28341771
GWAS identifies population-specific new regulatory variants in FUT6 associated with plasma B12 concentrations in Indians. PMID:28334792
swga: a primer design toolkit for selective whole genome amplification. PMID:28334194
Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells. PMID:28332981
PML nuclear bodies contribute to the basal expression of the mTOR inhibitor DDIT4. PMID:28332630
Hypoxia-Inducible Lipid Droplet-Associated Is Not a Direct Physiological Regulator of Lipolysis in Adipose Tissue. PMID:28323980
NEUROD2 Regulates Stim1 Expression and Store-Operated Calcium Entry in Cortical Neurons. PMID:28303257
The RNA-binding protein Tristetraprolin (TTP) is a critical negative regulator of the NLRP3 inflammasome. PMID:28302726
Autism gene Ube3a and seizures impair sociability by repressing VTA Cbln1. PMID:28297715
Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data. PMID:28288115
Custom Array Comparative Genomic Hybridization: the Importance of DNA Quality, an Expert Eye, and Variant Validation. PMID:28287439
Adaptation of A-to-I RNA editing in Drosophila. PMID:28282384
The birth of a human-specific neural gene by incomplete duplication and gene fusion. PMID:28279197
Identifying Novel Transcriptional and Epigenetic Features of Nuclear Lamina-associated Genes. PMID:28273906
The Characterization of GSDMB Splicing and Backsplicing Profiles Identifies Novel Isoforms and a Circular RNA That Are Dysregulated in Multiple Sclerosis. PMID:28272342
A potent antimalarial benzoxaborole targets a Plasmodium falciparum cleavage and polyadenylation specificity factor homologue. PMID:28262680
Elevated Fibroblast growth factor 21 (FGF21) in obese, insulin resistant states is normalised by the synthetic retinoid Fenretinide in mice. PMID:28256636
Evolutionarily conserved serum microRNAs predict radiation-induced fatality in nonhuman primates. PMID:28251902
TOP2 synergizes with BAF chromatin remodeling for both resolution and formation of facultative heterochromatin. PMID:28250416
Conserved expression of transposon-derived non-coding transcripts in primate stem cells. PMID:28245871
An atlas of human long non-coding RNAs with accurate 5' ends. PMID:28241135
The single nucleotide variant rs12722489 determines differential estrogen receptor binding and enhancer properties of an IL2RA intronic region. PMID:28234966
Evolution of Brain Active Gene Promoters in Human Lineage Towards the Increased Plasticity of Gene Regulation. PMID:28233272
Exploratory bioinformatics investigation reveals importance of "junk" DNA in early embryo development. PMID:28231763
Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting. PMID:28202815
Genome-Wide Identification of Basic Helix-Loop-Helix and NF-1 Motifs Underlying GR Binding Sites in Male Rat Hippocampus. PMID:28200020
Enhancer of polycomb coordinates multiple signaling pathways to promote both cyst and germline stem cell differentiation in the Drosophila adult testis. PMID:28196077
Improved regulatory element prediction based on tissue-specific local epigenomic signatures. PMID:28193886
Computational identification of the selenocysteine tRNA (tRNASec) in genomes. PMID:28192430
ETS Proto-oncogene 1 Transcriptionally Up-regulates the Cholangiocyte Senescence-associated Protein Cyclin-dependent Kinase Inhibitor 2A. PMID:28184004
Small genomic insertions form enhancers that misregulate oncogenes. PMID:28181482
Challenges of CRISPR/Cas9 applications for long non-coding RNA genes. PMID:28180319
Selective RNA targeting and regulated signaling by RIG-I is controlled by coordination of RNA and ATP binding. PMID:28180316
Comparative genomics of canine hemoglobin genes reveals primacy of beta subunit delta in adult carnivores. PMID:28178945
Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity. PMID:28178237
Interstitial deletion of chromosome 1 (1p21.1p12) in an infant with congenital diaphragmatic hernia, hydrops fetalis, and interrupted aortic arch. PMID:28174644
Modeling complex patterns of differential DNA methylation that associate with gene expression changes. PMID:28168293
Genomic rearrangement screening of the BRCA1 from seventy Iranian high-risk breast cancer families. PMID:28163741
Software tools for visualizing Hi-C data. PMID:28159004
MetaPlotR: a Perl/R pipeline for plotting metagenes of nucleotide modifications and other transcriptomic sites. PMID:28158328
Aspirin-Induced Chemoprevention and Response Kinetics Are Enhanced by PIK3CA Mutations in Colorectal Cancer Cells. PMID:28154202
Tdp-43 cryptic exons are highly variable between cell types. PMID:28153034
Next-Generation Sequencing in Oncology: Genetic Diagnosis, Risk Prediction and Cancer Classification. PMID:28146134
Whole-genome view of the consequences of a population bottleneck using 2926 genome sequences from Finland and United Kingdom. PMID:28145424
Identification and evolutionary analysis of long non-coding RNAs in zebra finch. PMID:28143393
Systematic analysis of telomere length and somatic alterations in 31 cancer types. PMID:28135248
Gene-based association study of genes linked to hippocampal sclerosis of aging neuropathology: GRN, TMEM106B, ABCC9, and KCNMB2. PMID:28131462
Primary Human Placental Trophoblasts are Permissive for Zika Virus (ZIKV) Replication. PMID:28128342
HS3ST1 genotype regulates antithrombin's inflammomodulatory tone and associates with atherosclerosis. PMID:28126521
Comparative Analysis of Mitochondrial N-Termini from Mouse, Human, and Yeast. PMID:28122942
Roles of MIWI, MILI and PLD6 in small RNA regulation in mouse growing oocytes. PMID:28115634
Who Scared the Cat? A Molecular Crime Scene Investigation Laboratory Exercise. PMID:28101273
PBrowse: a web-based platform for real-time collaborative exploration of genomic data. PMID:28100700
Myofibril breakdown during atrophy is a delayed response requiring the transcription factor PAX4 and desmin depolymerization. PMID:28096335
pH, Lactate, and Hypoxia: Reciprocity in Regulating High-Affinity Monocarboxylate Transporter Expression in Glioblastoma. PMID:28092823
Whole-Genome DNA Methylation Profiling Identifies Epigenetic Signatures of Uterine Carcinosarcoma. PMID:28088687
Alternative intronic promoters in development and disease. PMID:28078440
KTCNlncDB-a first platform to investigate lncRNAs expressed in human keratoconus and non-keratoconus corneas. PMID:28077570
Comparative Analysis of Vertebrate Diurnal/Circadian Transcriptomes. PMID:28076377
Accurate Breakpoint Mapping in Apparently Balanced Translocation Families with Discordant Phenotypes Using Whole Genome Mate-Pair Sequencing. PMID:28072833
TRIM28 interacts with EZH2 and SWI/SNF to activate genes that promote mammosphere formation. PMID:28068325
Visualizing the secondary and tertiary architectural domains of lncRNA RepA. PMID:28068310
Maintenance of Genome Integrity: How Mammalian Cells Orchestrate Genome Duplication by Coordinating Replicative and Specialized DNA Polymerases. PMID:28067843
The Effects of Increasing the Number of Taxa on Inferences of Molecular Convergence. PMID:28057728
Identification of coding and non-coding mutational hotspots in cancer genomes. PMID:28056774
Temperature-dependent sRNA transcriptome of the Lyme disease spirochete. PMID:28056764
Long Noncoding RNA Identification: Comparing Machine Learning Based Tools for Long Noncoding Transcripts Discrimination. PMID:28042575
Combined alpha-delta platelet storage pool deficiency is associated with mutations in GFI1B. PMID:28041820
Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive. PMID:28038678
Androgen receptor transcriptionally regulates semaphorin 3C in a GATA2-dependent manner. PMID:28038451
Targeted Sequencing of FKBP5 in Suicide Attempters with Bipolar Disorder. PMID:28030643
Scalable Genomics with R and Bioconductor. PMID:28018047
A developmental transcriptomic analysis of Pax1 and Pax9 in embryonic intervertebral disc development. PMID:28011632
Proposed association between the hexanucleotide repeat of C9orf72 and opposability index of the thumb. PMID:28010125
Bioinformatic tools for analysis of CLIP ribonucleoprotein data. PMID:28008714
Primate-specific oestrogen-responsive long non-coding RNAs regulate proliferation and viability of human breast cancer cells. PMID:28003470
The small GTPase ARF6 regulates protein trafficking to control cellular function during development and in disease. PMID:28001501
Cross-regulation by CrcZ RNA controls anoxic biofilm formation in Pseudomonas aeruginosa. PMID:28000785
A pipeline for local assembly of minisatellite alleles from single-molecule sequencing data. PMID:27998939
RNA sequencing analysis of the developing chicken retina. PMID:27996968
Intragenic CFTR Duplication and 5T/12TG Variant in a Patient with Non-Classic Cystic Fibrosis. PMID:27996019
A common class of transcripts with 5'-intron depletion, distinct early coding sequence features, and N1-methyladenosine modification. PMID:27994090
Alternative splicing of the OCC-1 gene generates three splice variants and a novel exonic microRNA, which regulate the Wnt signaling pathway. PMID:27986894
Improved Prediction of Non-methylated Islands in Vertebrates Highlights Different Characteristic Sequence Patterns. PMID:27984582
The intron-enriched HERV-K(HML-10) family suppresses apoptosis, an indicator of malignant transformation. PMID:27980690
Mutation Rate Variation is a Primary Determinant of the Distribution of Allele Frequencies in Humans. PMID:27977673
Fatty acid amide hydrolase-morphine interaction influences ventilatory response to hypercapnia and postoperative opioid outcomes in children. PMID:27977335
The novel homozygous KCNJ10 c.986T>C (p.(Leu329Pro)) variant is pathogenic for the SeSAME/EAST homologue in Malinois dogs. PMID:27966545
Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes. PMID:27965291
Large-scale pharmacogenomic study of sulfonylureas and the QT, JT and QRS intervals: CHARGE Pharmacogenomics Working Group. PMID:27958378
Ankyrin-G isoform imbalance and interneuronopathy link epilepsy and bipolar disorder. PMID:27956739
MicroRNA-183 Family in Inner Ear: Hair Cell Development and Deafness. PMID:27942598
DNA methylation in lung cells is associated with asthma endotypes and genetic risk. PMID:27942592
CIB1 contributes to oncogenic signalling by Ras via modulating the subcellular localisation of sphingosine kinase 1. PMID:27941888
Transcriptional programs that control expression of the autoimmune regulator gene Aire. PMID:27941786
RPAN: rice pan-genome browser for ∼3000 rice genomes. PMID:27940610
Genome sequence, population history, and pelage genetics of the endangered African wild dog (Lycaon pictus). PMID:27938335
CASP9 germline mutation in a family with multiple brain tumors. PMID:27935156
A novel mutation in the fibrinogen Aα chain (Gly13Arg, fibrinogen Nanning) causes congenital dysfibrinogenemia associated with defective peptide A release. PMID:27933517
Host genome integration and giant virus-induced reactivation of the virophage mavirus. PMID:27929021
DNA methylation and substance-use risk: a prospective, genome-wide study spanning gestation to adolescence. PMID:27922636
TRPM2 SNP genotype previously associated with susceptibility to Rhodococcus equi pneumonia in Quarter Horse foals displays differential gene expression identified using RNA-Seq. PMID:27919223
A human microprotein that interacts with the mRNA decapping complex. PMID:27918561
Disease variants alter transcription factor levels and methylation of their binding sites. PMID:27918535
A Novel Mechanism for Human Cardiac Ankyrin-B Syndrome due to Reciprocal Chromosomal Translocation. PMID:27916589
Clonal conversion of B lymphoid leukemia reveals cross-lineage transfer of malignant states. PMID:27913602
Association of 5-hydroxymethylation and 5-methylation of DNA cytosine with tissue-specific gene expression. PMID:27911668
Integrative genomic analysis identifies ancestry-related expression quantitative trait loci on DNA polymerase β and supports the association of genetic ancestry with survival disparities in head and neck squamous cell carcinoma. PMID:27906459
Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set. PMID:27903645
Methylation of Breast Cancer Predisposition Genes in Early-Onset Breast Cancer: Australian Breast Cancer Family Registry. PMID:27902704
The UCSC Genome Browser database: 2017 update. PMID:27899642
The ExAC browser: displaying reference data information from over 60 000 exomes. PMID:27899611
Prediction of human miRNA target genes using computationally reconstructed ancestral mammalian sequences. PMID:27899600
The KDM5 family is required for activation of pro-proliferative cell cycle genes during adipocyte differentiation. PMID:27899593
Adaptively introgressed Neandertal haplotype at the OAS locus functionally impacts innate immune responses in humans. PMID:27899133
ADARB1 catalyzes circadian A-to-I editing and regulates RNA rhythm. PMID:27893733
Circular RNAs are down-regulated in KRAS mutant colon cancer cells and can be transferred to exosomes. PMID:27892494
Cancer somatic mutations cluster in a subset of regulatory sites predicted from the ENCODE data. PMID:27887606
IL1A rs1800587 associates with chronic noncrisis pain in sickle cell disease. PMID:27883292
An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes. PMID:27882922
Gene regulatory networks in neural cell fate acquisition from genome-wide chromatin association of Geminin and Zic1. PMID:27881878
Assessing characteristics of RNA amplification methods for single cell RNA sequencing. PMID:27881084
Gender-Specific Expression of Ubiquitin-Specific Peptidase 9 Modulates Tau Expression and Phosphorylation: Possible Implications for Tauopathies. PMID:27878758
Identification of urinary exosomal noncoding RNAs as novel biomarkers in chronic kidney disease. PMID:27872161
Reprogramming mouse fibroblasts into engraftable myeloerythroid and lymphoid progenitors. PMID:27869129
Molecular genetic contributions to self-rated health. PMID:27864402
The BLUEPRINT Data Analysis Portal. PMID:27863955
Successful transmission and transcriptional deployment of a human chromosome via mouse male meiosis. PMID:27855777
Whole genome sequencing of Guzerá cattle reveals genetic variants in candidate genes for production, disease resistance, and heat tolerance. PMID:27853861
SBE6: a novel long-range enhancer involved in driving sonic hedgehog expression in neural progenitor cells. PMID:27852806
EYS Is a Protein Associated with the Ciliary Axoneme in Rods and Cones. PMID:27846257
JUN is a key transcriptional regulator of the unfolded protein response in acute myeloid leukemia. PMID:27840425
Transcriptional Categorization of the Etiology of Pneumonia Syndrome in Pediatric Patients in Malaria-Endemic Areas. PMID:27837008
Precise mapping of the transcription start sites of human microRNAs using DROSHA knockout cells. PMID:27835943
Resolving Cypriniformes relationships using an anchored enrichment approach. PMID:27829363
SORL1 mutations in early- and late-onset Alzheimer disease. PMID:27822510
Stringent comparative sequence analysis reveals SOX10 as a putative inhibitor of glial cell differentiation. PMID:27821050
Copy number variation analysis reveals additional variants contributing to endometriosis development. PMID:27817035
Developmental mechanisms of stripe patterns in rodents. PMID:27806375
Genetic variant rs3750625 in the 3'UTR of ADRA2A affects stress-dependent acute pain severity after trauma and alters a microRNA-34a regulatory site. PMID:27805929
Transcriptional Dynamics During Human Adipogenesis and Its Link to Adipose Morphology and Distribution. PMID:27803022
Specification of osteoblast cell fate by canonical Wnt signaling requires Bmp2. PMID:27802170
Platform-Independent Genome-Wide Pattern of DNA Copy-Number Alterations Predicting Astrocytoma Survival and Response to Treatment Revealed by the GSVD Formulated as a Comparative Spectral Decomposition. PMID:27798635
Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning. PMID:27797775
NGSmethDB 2017: enhanced methylomes and differential methylation. PMID:27794041
Control of embryonic stem cell self-renewal and differentiation via coordinated alternative splicing and translation of YY2. PMID:27791185
Test for association of common variants in GRM7 with alcohol consumption. PMID:27788777
Local regulation of gene expression by lncRNA promoters, transcription and splicing. PMID:27783602
Computational pan-genomics: status, promises and challenges. PMID:27769991
e-GRASP: an integrated evolutionary and GRASP resource for exploring disease associations. PMID:27766955
The antihypertensive MTHFR gene polymorphism rs17367504-G is a possible novel protective locus for preeclampsia. PMID:27755385
Vitamin D in hematological disorders and malignancies. PMID:27743385
NDE1 and NDEL1 from genes to (mal)functions: parallel but distinct roles impacting on neurodevelopmental disorders and psychiatric illness. PMID:27742926
Visualizing the geography of genetic variants. PMID:27742697
Smad2 and Smad3 Regulate Chondrocyte Proliferation and Differentiation in the Growth Plate. PMID:27741240
DNApi: A De Novo Adapter Prediction Algorithm for Small RNA Sequencing Data. PMID:27736901
Selection-free genome editing of the sickle mutation in human adult hematopoietic stem/progenitor cells. PMID:27733558
Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells. PMID:27713552
MyoD Regulates Skeletal Muscle Oxidative Metabolism Cooperatively with Alternative NF-κB. PMID:27705798
LINEs between Species: Evolutionary Dynamics of LINE-1 Retrotransposons across the Eukaryotic Tree of Life. PMID:27702814
Novel Genetic Variants for Cartilage Thickness and Hip Osteoarthritis. PMID:27701424
Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. PMID:27701403
RNA-seq analysis identifies key long non-coding RNAs connected to the pathogenesis of alcohol-associated head and neck squamous cell carcinoma. PMID:27698869
Insertion of an Alu element in a lncRNA leads to primate-specific modulation of alternative splicing. PMID:27694840
MSP-HTPrimer: a high-throughput primer design tool to improve assay design for DNA methylation analysis in epigenetics. PMID:27688817
SMAR1 binds to T(C/G) repeat and inhibits tumor progression by regulating miR-371-373 cluster. PMID:27671416
MeCP2 and histone deacetylases 1 and 2 in dorsal striatum collectively suppress repetitive behaviors. PMID:27668390
Chocó, Colombia: a hotspot of human biodiversity. PMID:27668076
Mutations in Human Accelerated Regions Disrupt Cognition and Social Behavior. PMID:27667684
Genetic analysis of hyperemesis gravidarum reveals association with intracellular calcium release channel (RYR2). PMID:27663074
Neonatal monocytes exhibit a unique histone modification landscape. PMID:27660665
The Impact of Endurance Training on Human Skeletal Muscle Memory, Global Isoform Expression and Novel Transcripts. PMID:27657503
NDST1 Preferred Promoter Confirmation and Identification of Corresponding Transcriptional Inhibitors as Substrate Reduction Agents for Multiple Mucopolysaccharidosis Disorders. PMID:27657498
Founder mutation in KCNJ10 in Pakistani patients with EAST syndrome. PMID:27652280
Identification of a novel distal regulatory element of the human Neuroglobin gene by the chromosome conformation capture approach. PMID:27651453
MBD3 expression and DNA binding patterns are altered in a rat model of temporal lobe epilepsy. PMID:27650712
The Contribution of Mosaic Variants to Autism Spectrum Disorder. PMID:27632392
The power of fission: yeast as a tool for understanding complex splicing. PMID:27628706
Identification of Pathway-Specific Serum Biomarkers of Response to Glucocorticoid and Infliximab Treatment in Children with Inflammatory Bowel Disease. PMID:27628422
Transcriptional Timers Regulating Mitosis in Early Drosophila Embryos. PMID:27626650
Systems Medicine as an Emerging Tool for Cardiovascular Genetics. PMID:27626034
Identification of non-coding genetic variants in samples from hypoxemic respiratory disease patients that affect the transcriptional response to hypoxia. PMID:27625398
Refinement of the androgen response element based on ChIP-Seq in androgen-insensitive and androgen-responsive prostate cancer cell lines. PMID:27623747
Lower Placental Leptin Promoter Methylation in Association with Fine Particulate Matter Air Pollution during Pregnancy and Placental Nitrosative Stress at Birth in the ENVIRONAGE Cohort. PMID:27623604
Pathway Analysis Incorporating Protein-Protein Interaction Networks Identified Candidate Pathways for the Seven Common Diseases. PMID:27622767
Genomic resources for wild populations of the house mouse, Mus musculus and its close relative Mus spretus. PMID:27622383
L1-associated genomic regions are deleted in somatic cells of the healthy human brain. PMID:27618310
Pax6 associates with H3K4-specific histone methyltransferases Mll1, Mll2, and Set1a and regulates H3K4 methylation at promoters and enhancers. PMID:27617035
PGD: a pangolin genome hub for the research community. PMID:27616775
Positive Selection Linked with Generation of Novel Mammalian Dentition Patterns. PMID:27613398
Contribution of type W human endogenous retroviruses to the human genome: characterization of HERV-W proviral insertions and processed pseudogenes. PMID:27613107
GenToS: Use of Orthologous Gene Information to Prioritize Signals from Human GWAS. PMID:27612175
Evolutionary Dynamics of Abundant Stop Codon Readthrough. PMID:27604222
Fine scale mapping of the 17q22 breast cancer locus using dense SNPs, genotyped within the Collaborative Oncological Gene-Environment Study (COGs). PMID:27600471
The Drosophila melanogaster homolog of UBE3A is not imprinted in neurons. PMID:27599063
Rail-RNA: scalable analysis of RNA-seq splicing and coverage. PMID:27592709
Multi-focal control of mitochondrial gene expression by oncogenic MYC provides potential therapeutic targets in cancer. PMID:27590350
Global Mapping of Small RNA-Target Interactions in Bacteria. PMID:27588604
Alu-miRNA interactions modulate transcript isoform diversity in stress response and reveal signatures of positive selection. PMID:27586304
Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA). PMID:27585267
Genome-Wide Ultrabithorax Binding Analysis Reveals Highly Targeted Genomic Loci at Developmental Regulators and a Potential Connection to Polycomb-Mediated Regulation. PMID:27575958
Long noncoding RNA linc00598 regulates CCND2 transcription and modulates the G1 checkpoint. PMID:27572135
Within-pair differences of DNA methylation levels between monozygotic twins are different between male and female pairs. PMID:27561550
Fine-Mapping of the 1p11.2 Breast Cancer Susceptibility Locus. PMID:27556229
A Robust Protocol for Using Multiplexed Droplet Digital PCR to Quantify Somatic Copy Number Alterations in Clinical Tissue Specimens. PMID:27537682
The Brain-Enriched MicroRNA miR-9-3p Regulates Synaptic Plasticity and Memory. PMID:27535911
Cross-species Conservation of context-specific networks. PMID:27531214
Structure and regulation of human troponin genes. PMID:27520667
iTAR: a web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data. PMID:27519564
EnhancerAtlas: a resource for enhancer annotation and analysis in 105 human cell/tissue types. PMID:27515742
Specificity of Pitx3-Dependent Gene Regulatory Networks in Subsets of Midbrain Dopamine Neurons. PMID:27514757
Susceptibility to Childhood Pneumonia: A Genome-Wide Analysis. PMID:27508494
Determining the Effect of Natural Selection on Linked Neutral Divergence across Species. PMID:27508305
MEF2C protects bone marrow B-lymphoid progenitors during stress haematopoiesis. PMID:27507714
MiR-31 and miR-128 regulates poliovirus receptor-related 4 mediated measles virus infectivity in tumors. PMID:27507538
Genes Interacting with Occupational Exposures to Low Molecular Weight Agents and Irritants on Adult-Onset Asthma in Three European Studies. PMID:27504716
Genetic mapping of canine fear and aggression. PMID:27503363
Mechanistically Distinct Pathways of Divergent Regulatory DNA Creation Contribute to Evolution of Human-Specific Genomic Regulatory Networks Driving Phenotypic Divergence of Homo sapiens. PMID:27503290
Association of variations in HLA class II and other loci with susceptibility to EGFR-mutated lung adenocarcinoma. PMID:27501781
Transcription factors GAF and HSF act at distinct regulatory steps to modulate stress-induced gene activation. PMID:27492368
A 1.35 Mb DNA fragment is inserted into the DHMN1 locus on chromosome 7q34-q36.2. PMID:27487800
Specific detection of interferon regulatory factor 5 (IRF5): A case of antibody inequality. PMID:27481535
On the study of microbial transcriptomes using second- and third-generation sequencing technologies. PMID:27480632
A targeted sequencing study of glutamatergic candidate genes in suicide attempters with bipolar disorder. PMID:27480506
Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder. PMID:27479844
DNA Breaks and End Resection Measured Genome-wide by End Sequencing. PMID:27477910
Characterizing polymorphic inversions in human genomes by single-cell sequencing. PMID:27472961
Musashi1 Impacts Radio-Resistance in Glioblastoma by Controlling DNA-Protein Kinase Catalytic Subunit. PMID:27470713
Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers. PMID:27467908
Influence of Repressive Histone and DNA Methylation upon D4Z4 Transcription in Non-Myogenic Cells. PMID:27467759
SOX10 regulates an alternative promoter at the Charcot-Marie-Tooth disease locus MTMR2. PMID:27466180
Tissue damage drives co-localization of NF-κB, Smad3, and Nrf2 to direct Rev-erb sensitive wound repair in mouse macrophages. PMID:27462873
BATCH-GE: Batch analysis of Next-Generation Sequencing data for genome editing assessment. PMID:27461955
eIF2β is critical for eIF5-mediated GDP-dissociation inhibitor activity and translational control. PMID:27458202
ASPP2 deficiency causes features of 1q41q42 microdeletion syndrome. PMID:27447114
A scientist's guide for submitting data to ZFIN. PMID:27443940
Chromatin immunoprecipitation and an open chromatin assay in zebrafish erythrocytes. PMID:27443937
Epigenetic activation of MGAT3 and corresponding bisecting GlcNAc shortens the survival of cancer patients. PMID:27429195
Genomics era and complex disorders: Implications of GWAS with special reference to coronary artery disease, type 2 diabetes mellitus, and cancers. PMID:27424552
Genetic contribution to variation in DNA methylation at maternal smoking-sensitive loci in exposed neonates. PMID:27403598
An intergenic risk locus containing an enhancer deletion in 2q35 modulates breast cancer risk by deregulating IGFBP5 expression. PMID:27402876
FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki. PMID:27402679
Chromatin variation associated with liver metabolism is mediated by transposable elements. PMID:27398095
Leukaemia cell of origin identified by chromatin landscape of bulk tumour cells. PMID:27397025
Sip1 regulates the generation of the inner nuclear layer retinal cell lineages in mammals. PMID:27385012
Multiple mechanisms disrupt the let-7 microRNA family in neuroblastoma. PMID:27383785
Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. PMID:27380939
Fine-Mapping of Common Genetic Variants Associated with Colorectal Tumor Risk Identified Potential Functional Variants. PMID:27379672
Genetic dissection of the α-globin super-enhancer in vivo. PMID:27376235
Transcriptome Analysis on Monocytes from Patients with Neovascular Age-Related Macular Degeneration. PMID:27374485
MDM2 facilitates adipocyte differentiation through CRTC-mediated activation of STAT3. PMID:27362806
Optimizing sgRNA position markedly improves the efficiency of CRISPR/dCas9-mediated transcriptional repression. PMID:27353328
Genetic influences on nicotinic α5 receptor (CHRNA5) CpG methylation and mRNA expression in brain and adipose tissue. PMID:27350810
Computational Analysis of Single Nucleotide Polymorphisms Associated with Altered Drug Responsiveness in Type 2 Diabetes. PMID:27347941
MonoSeq Variant Caller Reveals Novel Mononucleotide Run Indel Mutations in Tumors with Defective DNA Mismatch Repair. PMID:27346418
TOX expression and role in CTCL. PMID:27345620
GORpipe: a query tool for working with sequence data based on a Genomic Ordered Relational (GOR) architecture. PMID:27339714
QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks. PMID:27336171
Overexpression of CHOP in Myelinating Cells Does Not Confer a Significant Phenotype under Normal or Metabolic Stress Conditions. PMID:27335410
Genomewide meta-analysis identifies loci associated with IGF-I and IGFBP-3 levels with impact on age-related traits. PMID:27329260
Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia. PMID:27322744
Trans-ethnic Meta-analysis and Functional Annotation Illuminates the Genetic Architecture of Fasting Glucose and Insulin. PMID:27321945
Somatically Acquired LINE-1 Insertions in Normal Esophagus Undergo Clonal Expansion in Esophageal Squamous Cell Carcinoma. PMID:27319353
phRAIDER: Pattern-Hunter based Rapid Ab Initio Detection of Elementary Repeats. PMID:27307619
A novel method for discovering local spatial clusters of genomic regions with functional relationships from DNA contact maps. PMID:27307607
Construction of an integrative regulatory element and variation map of the murine Tst locus. PMID:27287690
Explaining the disease phenotype of intergenic SNP through predicted long range regulation. PMID:27280978
A catalog of hemizygous variation in 127 22q11 deletion patients. PMID:27274857
Antimalarial Benzoxaboroles Target Plasmodium falciparum Leucyl-tRNA Synthetase. PMID:27270277
Clonal evolution of glioblastoma under therapy. PMID:27270107
Defining the identity of mouse embryonic dermal fibroblasts. PMID:27265328
Spatial distribution of predicted transcription factor binding sites in Drosophila ChIP peaks. PMID:27264535
A Primate lncRNA Mediates Notch Signaling during Neuronal Development by Sequestering miRNA. PMID:27263970
Identification of mutations in the MYO9A gene in patients with congenital myasthenic syndrome. PMID:27259756
The Third Intron of the Interferon Regulatory Factor-8 Is an Initiator of Repressed Chromatin Restricting Its Expression in Non-Immune Cells. PMID:27257682
Detection and visualization of differential splicing in RNA-Seq data with JunctionSeq. PMID:27257077
Goldmine integrates information placing genomic ranges into meaningful biological contexts. PMID:27257071
Experimental and Computational Considerations in the Study of RNA-Binding Protein-RNA Interactions. PMID:27256380
Vcfanno: fast, flexible annotation of genetic variants. PMID:27250555
Combinatorial Gene Regulatory Functions Underlie Ultraconserved Elements in Drosophila. PMID:27247329
Bioinformatic Studies to Predict MicroRNAs with the Potential of Uncoupling RECK Expression from Epithelial-Mesenchymal Transition in Cancer Cells. PMID:27226706
JUMPg: An Integrative Proteogenomics Pipeline Identifying Unannotated Proteins in Human Brain and Cancer Cells. PMID:27225868
PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions. PMID:27224906
Prediction and Quantification of Splice Events from RNA-Seq Data. PMID:27218464
Foxc1 and Foxc2 deletion causes abnormal lymphangiogenesis and correlates with ERK hyperactivation. PMID:27214551
Improved definition of the mouse transcriptome via targeted RNA sequencing. PMID:27197243
Variants within the SP110 nuclear body protein modify risk of canine degenerative myelopathy. PMID:27185954
CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering. PMID:27185894
Genetic and neuroendocrine regulation of the postpartum brain. PMID:27184829
Tristetraprolin binding site atlas in the macrophage transcriptome reveals a switch for inflammation resolution. PMID:27178967
Fine-Scale Crossover Rate Variation on the Caenorhabditis elegans X Chromosome. PMID:27172189
Maternal Smoking during Pregnancy and DNA-Methylation in Children at Age 5.5 Years: Epigenome-Wide-Analysis in the European Childhood Obesity Project (CHOP)-Study. PMID:27171005
Development of new PCR multiplex system by the simultaneous detection of 10 miniSTRs, SE33, Penta E, Penta D, and four Y-STRs. PMID:27166705
Integrated Genomics for Pinpointing Survival Loci within Arm-Level Somatic Copy Number Alterations. PMID:27165745
The potential for adaptive maintenance of diversity in insect antimicrobial peptides. PMID:27160594
Mapping the chemical chromatin reactivation landscape identifies BRD4-TAF1 cross-talk. PMID:27159579
A hybrid approach for de novo human genome sequence assembly and phasing. PMID:27159086
Genomic analysis of mouse VL30 retrotransposons. PMID:27158269
Multivariate eQTL mapping uncovers functional variation on the X-chromosome associated with complex disease traits. PMID:27155841
High-performance web services for querying gene and variant annotation. PMID:27154141
DensityMap: a genome viewer for illustrating the densities of features. PMID:27153821
Goldilocks: a tool for identifying genomic regions that are 'just right'. PMID:27153673
TnT: a set of libraries for visualizing trees and track-based annotations for the web. PMID:27153646
pileup.js: a JavaScript library for interactive and in-browser visualization of genomic data. PMID:27153605
Integrated genome browser: visual analytics platform for genomics. PMID:27153568
Genome Sequencing and Comparative Analysis of Saccharomyces cerevisiae Strains of the Peterhof Genetic Collection. PMID:27152522
Improvements to the HITS-CLIP protocol eliminate widespread mispriming artifacts. PMID:27150721
CADD score has limited clinical validity for the identification of pathogenic variants in noncoding regions in a hereditary cancer panel. PMID:27148939
Genome-wide variant analysis of simplex autism families with an integrative clinical-bioinformatics pipeline. PMID:27148569
Identifying Network Perturbation in Cancer. PMID:27145341
Enrichment of rare variants in population isolates: single AICDA mutation responsible for hyper-IgM syndrome type 2 in Finland. PMID:27142677
Setd1a and NURF mediate chromatin dynamics and gene regulation during erythroid lineage commitment and differentiation. PMID:27141965
Data in support of transcriptional regulation and function of Fas-antisense long noncoding RNA during human erythropoiesis. PMID:27141526
Dopamine pathway is highly diverged in primate species that differ markedly in social behavior. PMID:27140612
Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing. PMID:27135536
Profiling and Validation of the Circular RNA Repertoire in Adult Murine Hearts. PMID:27132142
Cofactors of LIM Domains Associate with Estrogen Receptor α to Regulate the Expression of Noncoding RNA H19 and Corneal Epithelial Progenitor Cell Function. PMID:27129775
Genotype imputation in the domestic dog. PMID:27129452
Enhanced snoMEN Vectors Facilitate Establishment of GFP-HIF-1α Protein Replacement Human Cell Lines. PMID:27128805
ImiRP: a computational approach to microRNA target site mutation. PMID:27122020
Analysis of SLC4A11, ZEB1, LOXHD1, COL8A2 and TCF4 gene sequences in a multi-generational family with late-onset Fuchs corneal dystrophy. PMID:27121161
Metabolic Characterization of a Rare Genetic Variation Within APOC3 and Its Lipoprotein Lipase-Independent Effects. PMID:27114411
Separating the wheat from the chaff: systematic identification of functionally relevant noncoding variants in ADHD. PMID:27113999
A CRISPR Path to Engineering New Genetic Mouse Models for Cardiovascular Research. PMID:27102963
Trisomy 21 Alters DNA Methylation in Parent-of-Origin-Dependent and -Independent Manners. PMID:27100087
GeNemo: a search engine for web-based functional genomic data. PMID:27098038
CRTC1 gene is differentially methylated in the human hippocampus in Alzheimer's disease. PMID:27094739
Ebola virus encodes a miR-155 analog to regulate importin-α5 expression. PMID:27094387
A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals. PMID:27089393
DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets. PMID:27084938
Effects of vitamin A deficiency in the postnatal mouse heart: role of hepatic retinoid stores. PMID:27084391
Identification of ITPA on chromosome 20 as a susceptibility gene for young-onset tuberculosis. PMID:27081565
An Intronic Flk1 Enhancer Directs Arterial-Specific Expression via RBPJ-Mediated Venous Repression. PMID:27079877
Functional Divergence of the Nuclear Receptor NR2C1 as a Modulator of Pluripotentiality During Hominid Evolution. PMID:27075724
JBrowse: a dynamic web platform for genome visualization and analysis. PMID:27072794
A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer. PMID:27067391
Common Genetic Variants in FOXP2 Are Not Associated with Individual Differences in Language Development. PMID:27064276
Genetic Dissection of Dual Roles for the Transcription Factor six7 in Photoreceptor Development and Patterning in Zebrafish. PMID:27058886
A Hox Transcription Factor Collective Binds a Highly Conserved Distal-less cis-Regulatory Module to Generate Robust Transcriptional Outcomes. PMID:27058369
Clustered mutations in hominid genome evolution are consistent with APOBEC3G enzymatic activity. PMID:27056836
De Novo Genes Arise at a Slow but Steady Rate along the Primate Lineage and Have Been Subject to Incomplete Lineage Sorting. PMID:27056411
82-kDa choline acetyltransferase and SATB1 localize to β-amyloid induced matrix attachment regions. PMID:27052102
TREM2 upregulation correlates with 5-hydroxymethycytosine enrichment in Alzheimer's disease hippocampus. PMID:27051467
The necrosome promotes pancreatic oncogenesis via CXCL1 and Mincle-induced immune suppression. PMID:27049944
Global Intersection of Long Non-Coding RNAs with Processed and Unprocessed Pseudogenes in the Human Genome. PMID:27047535
Ancient human sialic acid variant restricts an emerging zoonotic malaria parasite. PMID:27041489
Unlinking an lncRNA from Its Associated cis Element. PMID:27041223
System-Wide Associations between DNA-Methylation, Gene Expression, and Humoral Immune Response to Influenza Vaccination. PMID:27031986
Multivariate models from RNA-Seq SNVs yield candidate molecular targets for biomarker discovery: SNV-DA. PMID:27029813
Genetic diversity analysis of two commercial breeds of pigs using genomic and pedigree data. PMID:27029213
Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites. PMID:27023428
Meta-analysis of gene-environment-wide association scans accounting for education level identifies additional loci for refractive error. PMID:27020472
Nuc-ErbB3 regulates H3K27me3 levels and HMT activity to establish epigenetic repression during peripheral myelination. PMID:27017927
Deletions at 22q11.2 in idiopathic Parkinson's disease: a combined analysis of genome-wide association data. PMID:27017469
Mutation in IRF2BP2 is responsible for a familial form of common variable immunodeficiency disorder. PMID:27016798
Activation of individual L1 retrotransposon instances is restricted to cell-type dependent permissive loci. PMID:27016617
Epigenetic Regulatory Effect of Exercise on Glutathione Peroxidase 1 Expression in the Skeletal Muscle of Severely Dyslipidemic Mice. PMID:27010651
Long noncoding RNAs expressed in human hepatic stellate cells form networks with extracellular matrix proteins. PMID:27007663
Persistent Chromatin Modifications Induced by High Fat Diet. PMID:27006400
ROBO2 gene variants in children with primary nonsyndromic vesicoureteral reflux with or without renal hypoplasia/dysplasia. PMID:27002985
Functional annotation of the vlinc class of non-coding RNAs using systems biology approach. PMID:27001520
Genome-wide DNA methylation levels and altered cortisol stress reactivity following childhood trauma in humans. PMID:26997371
MiR144/451 Expression Is Repressed by RUNX1 During Megakaryopoiesis and Disturbed by RUNX1/ETO. PMID:26990877
Bioinformatic analyses of sense and antisense expression from terminal inverted repeat transposons in Drosophila somatic cells. PMID:26986720
Characterization of Disease-Associated Mutations in Human Transmembrane Proteins. PMID:26986070
Mechanosensory and ATP Release Deficits following Keratin14-Cre-Mediated TRPA1 Deletion Despite Absence of TRPA1 in Murine Keratinocytes. PMID:26978657
S/HIC: Robust Identification of Soft and Hard Sweeps Using Machine Learning. PMID:26977894
Supporting data for characterization of non-coding RNAs associated with the Neuronal growth regulator 1 (NEGR1) adhesion protein. PMID:26977442
Recurrent copy number variants associated with bronchopulmonary dysplasia. PMID:26974307
Testing candidate genes for attention-deficit/hyperactivity disorder in fruit flies using a high throughput assay for complex behavior. PMID:26954609
MSRE-HTPrimer: a high-throughput and genome-wide primer design pipeline optimized for epigenetic research. PMID:26949424
Sister chromatid telomere fusions, but not NHEJ-mediated inter-chromosomal telomere fusions, occur independently of DNA ligases 3 and 4. PMID:26941250
High-throughput discovery of post-transcriptional cis-regulatory elements. PMID:26941072
An interactive environment for agile analysis and visualization of ChIP-sequencing data. PMID:26926434
The Human Toxome Collaboratorium: A Shared Environment for Multi-Omic Computational Collaboration within a Consortium. PMID:26924983
Mutational Landscape of Aggressive Prostate Tumors in African American Men. PMID:26921337
Glutamate-system defects behind psychiatric manifestations in a familial hemiplegic migraine type 2 disease-mutation mouse model. PMID:26911348
The MazF-regulon: a toolbox for the post-transcriptional stress response in Escherichia coli. PMID:26908653
The handedness-associated PCSK6 locus spans an intronic promoter regulating novel transcripts. PMID:26908617
The effect of non-coding DNA variations on P53 and cMYC competitive inhibition at cis-overlapping motifs. PMID:26908612
Genotoxicity in Mice Following AAV Gene Delivery: A Safety Concern for Human Gene Therapy? PMID:26906613
Resolving rates of mutation in the brain using single-neuron genomics. PMID:26901440
Genome-Wide Chromatin Landscape Transitions Identify Novel Pathways in Early Commitment to Osteoblast Differentiation. PMID:26890492
Mapping of Variable DNA Methylation Across Multiple Cell Types Defines a Dynamic Regulatory Landscape of the Human Genome. PMID:26888867
Pitfalls of haplotype phasing from amplicon-based long-read sequencing. PMID:26883533
TOPORS, a Dual E3 Ubiquitin and Sumo1 Ligase, Interacts with 26 S Protease Regulatory Subunit 4, Encoded by the PSMC1 Gene. PMID:26872363
Mutations in the Mitochondrial Citrate Carrier SLC25A1 are Associated with Impaired Neuromuscular Transmission. PMID:26870663
GMOL: An Interactive Tool for 3D Genome Structure Visualization. PMID:26868282
Sequence Diversity, Intersubgroup Relationships, and Origins of the Mouse Leukemia Gammaretroviruses of Laboratory and Wild Mice. PMID:26865715
Enhancer RNA-driven looping enhances the transcription of the long noncoding RNA DHRS4-AS1, a controller of the DHRS4 gene cluster. PMID:26864944
Natural selection in a population of Drosophila melanogaster explained by changes in gene expression caused by sequence variation in core promoter regions. PMID:26860869
Detection bias in microarray and sequencing transcriptomic analysis identified by housekeeping genes. PMID:26858976
CressInt: a user-friendly web resource for genome-scale exploration of gene regulation in Arabidopsis thaliana. PMID:26855883
Systematic Evaluation of Sanger Validation of Next-Generation Sequencing Variants. PMID:26847218
Erosion of Conserved Binding Sites in Personal Genomes Points to Medical Histories. PMID:26845687
MutAid: Sanger and NGS Based Integrated Pipeline for Mutation Identification, Validation and Annotation in Human Molecular Genetics. PMID:26840129
Rapid detection of germline mutations for hereditary gastrointestinal polyposis/cancers using HaloPlex target enrichment and high-throughput sequencing technologies. PMID:26837502
Sequential activation and distinct functions for distal and proximal modules within the IgH 3' regulatory region. PMID:26831080
NEAT: a framework for building fully automated NGS pipelines and analyses. PMID:26830846
HLA class II sequence variants influence tuberculosis risk in populations of European ancestry. PMID:26829749
Insulin-like growth factor axis in pregnancies affected by fetal growth disorders. PMID:26823688
A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation. PMID:26823433
A survey of best practices for RNA-seq data analysis. PMID:26813401
Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCs. PMID:26812582
Epigenetic silencing of CREB3L1 by DNA methylation is associated with high-grade metastatic breast cancers with poor prognosis and is prevalent in triple negative breast cancers. PMID:26810754
Cascade: an RNA-seq visualization tool for cancer genomics. PMID:26810393
Quantification of read species behavior within whole genome sequencing of cancer genomes for the stratification and visualization of genomic variation. PMID:26809676
RUNX1B Expression Is Highly Heterogeneous and Distinguishes Megakaryocytic and Erythroid Lineage Fate in Adult Mouse Hematopoiesis. PMID:26808730
Purifying Selection on Exonic Splice Enhancers in Intronless Genes. PMID:26802218
Genome-wide methylation profiling identifies novel methylated genes in neuroblastoma tumors. PMID:26786290
Expression of a Novel D4 Dopamine Receptor in the Lamprey Brain. Evolutionary Considerations about Dopamine Receptors. PMID:26778974
KNOWLEDGE DRIVEN BINNING AND PHEWAS ANALYSIS IN MARSHFIELD PERSONALIZED MEDICINE RESEARCH PROJECT USING BIOBIN. PMID:26776191
B-cell survival and development controlled by the coordination of NF-κB family members RelB and cRel. PMID:26773039
De novo 9q gain in an infant with tetralogy of Fallot with absent pulmonary valve: Patient report and review of congenital heart disease in 9q duplication syndrome. PMID:26768185
PTESFinder: a computational method to identify post-transcriptional exon shuffling (PTES) events. PMID:26758031
Establishment of two quantitative nested qPCR assays targeting the human EPO transgene. PMID:26752352
Genome-wide association analysis identifies TXNRD2, ATXN2 and FOXC1 as susceptibility loci for primary open-angle glaucoma. PMID:26752265
ELF5 isoform expression is tissue-specific and significantly altered in cancer. PMID:26738740
Comprehensive nucleosome mapping of the human genome in cancer progression. PMID:26735342
DNA repair in species with extreme lifespan differences. PMID:26729707
ConBind: motif-aware cross-species alignment for the identification of functional transcription factor binding sites. PMID:26721389
The transcriptome of nitrofen-induced pulmonary hypoplasia in the rat model of congenital diaphragmatic hernia. PMID:26720608
Two patients with small chromosome 22q11.21 alterations and central nervous system abnormalities. PMID:26719767
Epigenomic Landscape of Human Fetal Brain, Heart, and Liver. PMID:26719341
The RNA-binding protein LARP1 is a post-transcriptional regulator of survival and tumorigenesis in ovarian cancer. PMID:26717985
Tissue Restricted Splice Junctions Originate Not Only from Tissue-Specific Gene Loci, but Gene Loci with a Broad Pattern of Expression. PMID:26713731
Transcription Factor Hepatocyte Nuclear Factor-1β Regulates Renal Cholesterol Metabolism. PMID:26712526
Identifying rhesus macaque gene orthologs using heterospecific human CNV probes. PMID:26697375
Genome-wide epigenetic cross-talk between DNA methylation and H3K27me3 in zebrafish embryos. PMID:26697317
Identification of methylated deoxyadenosines in vertebrates reveals diversity in DNA modifications. PMID:26689968
Transcriptome profiling of human FoxP3+ regulatory T cells. PMID:26686412
Pathogenic and likely pathogenic variant prevalence among the first 10,000 patients referred for next-generation cancer panel testing. PMID:26681312
Estradiol differentially induces progesterone receptor isoforms expression through alternative promoter regulation in a mouse embryonic hypothalamic cell line. PMID:26676302
Competition between DNA methylation and transcription factors determines binding of NRF1. PMID:26675734
RNA-Seq workflow: gene-level exploratory analysis and differential expression. PMID:26674615
MethylAction: detecting differentially methylated regions that distinguish biological subtypes. PMID:26673711
Genome-wide association study of dental caries in the Hispanic Communities Health Study/Study of Latinos (HCHS/SOL). PMID:26662797
Identifying transcription start sites and active enhancer elements using BruUV-seq. PMID:26656874
Genetic Determinants of RNA Editing Levels of ADAR Targets in Drosophila melanogaster. PMID:26656153
A human 3'UTR clone collection to study post-transcriptional gene regulation. PMID:26645212
Identifying Novel Transcriptional Regulators with Circadian Expression. PMID:26644408
Genome-Wide Studies Reveal that H3K4me3 Modification in Bivalent Genes Is Dynamically Regulated during the Pluripotent Cell Cycle and Stabilized upon Differentiation. PMID:26644406
ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly. PMID:26643039
Abundant contribution of short tandem repeats to gene expression variation in humans. PMID:26642241
Segmenting the Human Genome into Isochores. PMID:26640363
The Role of H3K4me3 in Transcriptional Regulation Is Altered in Huntington's Disease. PMID:26636336
SIFT missense predictions for genomes. PMID:26633127
ADMIRE: analysis and visualization of differential methylation in genomic regions using the Infinium HumanMethylation450 Assay. PMID:26628921
Evaluation of preprocessing, mapping and postprocessing algorithms for analyzing whole genome bisulfite sequencing data. PMID:26628557
Quantifying the heritability of glioma using genome-wide complex trait analysis. PMID:26625949
Analysis of long-range interactions in primary human cells identifies cooperative CFTR regulatory elements. PMID:26615198
PExFInS: An Integrative Post-GWAS Explorer for Functional Indels and SNPs. PMID:26612672
Genome-wide scan for selection signatures in six cattle breeds in South Africa. PMID:26612660
Identification of RNA Oligonucleotides Binding to Several Proteins from Potential G-Quadruplex Forming Regions in Transcribed Pre-mRNA. PMID:26610452
Functional analysis of the 11q23.3 glioma susceptibility locus implicates PHLDB1 and DDX6 in glioma susceptibility. PMID:26610392
Variants Near CCK Receptors are Associated With Electrophysiological Responses to Pre-pulse Startle Stimuli in a Mexican American Cohort. PMID:26608796
Δ9-Tetrahydrocannabinol (Δ9-THC) Promotes Neuroimmune-Modulatory MicroRNA Profile in Striatum of Simian Immunodeficiency Virus (SIV)-Infected Macaques. PMID:26607731
Trans effects of chromosome aneuploidies on DNA methylation patterns in human Down syndrome and mouse models. PMID:26607552
Hepatic Interferon-λ3 (IFNL3) Gene Expression Reveals Not to Be Attenuated in Non-Favorable IFNL3 rs4803217 or IFNL4 rs368234815 Minor Allele Carriers in Chronic Hepatitis C. PMID:26606750
Using Disease-Associated Coding Sequence Variation to Investigate Functional Compensation by Human Paralogous Proteins. PMID:26604664
Indirect p53-dependent transcriptional repression of Survivin, CDC25C, and PLK1 genes requires the cyclin-dependent kinase inhibitor p21/CDKN1A and CDE/CHR promoter sites binding the DREAM complex. PMID:26595675
A resource of ribosomal RNA-depleted RNA-Seq data from different normal adult and fetal human tissues. PMID:26594381
MicroRNA expression is altered in lateral septum across reproductive stages. PMID:26592715
SBR-Blood: systems biology repository for hematopoietic cells. PMID:26590403
The UCSC Genome Browser database: 2016 update. PMID:26590259
deepBase v2.0: identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data. PMID:26590255
Inferring Selective Constraint from Population Genomic Data Suggests Recent Regulatory Turnover in the Human Brain. PMID:26590212
Genome-Wide Association Study of Golden Retrievers Identifies Germ-Line Risk Factors Predisposing to Mast Cell Tumours. PMID:26588071
Pooled Sequencing of Candidate Genes Implicates Rare Variants in the Development of Asthma Following Severe RSV Bronchiolitis in Infancy. PMID:26587832
Assembly: a resource for assembled genomes at NCBI. PMID:26578580
Distinguishing the immunostimulatory properties of noncoding RNAs expressed in cancer cells. PMID:26575629
Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism. PMID:26560027
Automated amplicon design suitable for analysis of DNA variants by melting techniques. PMID:26559640
Mutation screening of SCN2A in schizophrenia and identification of a novel loss-of-function mutation. PMID:26555645
Selective sweeps versus introgression - population genetic dynamics of the murine leukemia virus receptor Xpr1 in wild populations of the house mouse (Mus musculus). PMID:26555287
Characterization of the biological processes shaping the genetic structure of the Italian population. PMID:26553317
Three Residues Make an Evolutionary Switch for Folding and RNA-Destabilizing Activity in the TTP Family of Proteins. PMID:26551835
High-density P300 enhancers control cell state transitions. PMID:26546038
A potential endophenotype for Alzheimer's disease: cerebrospinal fluid clusterin. PMID:26545630
Spatio-temporal regulation of circular RNA expression during porcine embryonic brain development. PMID:26541409
Comprehensive transcriptional landscape of aging mouse liver. PMID:26541291
Classification of Cancer Primary Sites Using Machine Learning and Somatic Mutations. PMID:26539502
Antisense Transcription of Retrotransposons in Drosophila: An Origin of Endogenous Small Interfering RNA Precursors. PMID:26534950
Differential expression analysis of human endogenous retroviruses based on ENCODE RNA-seq data. PMID:26530187
Identification and functional studies of regulatory variants responsible for the association of NRG3 with a delusion phenotype in schizophrenia. PMID:26528484
sORFs.org: a repository of small ORFs identified by ribosome profiling. PMID:26527729
Application of Functional Genomics for Bovine Respiratory Disease Diagnostics. PMID:26526746
Construction and analysis of dynamic transcription factor regulatory networks in the progression of glioma. PMID:26526635
Expression of young HERV-H loci in the course of colorectal carcinoma and correlation with molecular subtypes. PMID:26517682
Decline of FOXN1 gene expression in human thymus correlates with age: possible epigenetic regulation. PMID:26516334
Transcription factor trapping by RNA in gene regulatory elements. PMID:26516199
Exploring DNA methylation changes in promoter, intragenic, and intergenic regions as early and late events in breast cancer formation. PMID:26510686
Genetics of RA susceptibility, what comes next? PMID:26509058
Gene copy number variation analysis reveals dosage-insensitive expression of CYP2E1. PMID:26503817
Discovery and characterization of Alu repeat sequences via precise local read assembly. PMID:26503250
Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud. PMID:26501966
Deciphering the Developmental Dynamics of the Mouse Liver Transcriptome. PMID:26496202
Strong Constraint on Human Genes Escaping X-Inactivation Is Modulated by their Expression Level and Breadth in Both Sexes. PMID:26494842
Identification and Characterization of Circular RNAs As a New Class of Putative Biomarkers in Human Blood. PMID:26485708
A ChIP-on-chip tiling array approach detects functional histone-free regions associated with boundaries at vertebrate HOX genes. PMID:26484075
A conformational RNA zipper promotes intron ejection during non-conventional XBP1 mRNA splicing. PMID:26483401
Genome-Wide Chromatin Immunoprecipitation in Candida albicans and Other Yeasts. PMID:26483022
Constitutional de novo deletion of the FBXW7 gene in a patient with focal segmental glomerulosclerosis and multiple primitive tumors. PMID:26482194
Structure and Sequence Analyses of Clustered Protocadherins Reveal Antiparallel Interactions that Mediate Homophilic Specificity. PMID:26481813
Identification of linc-NeD125, a novel long non coding RNA that hosts miR-125b-1 and negatively controls proliferation of human neuroblastoma cells. PMID:26480000
Genome and transcriptome delineation of two major oncogenic pathways governing invasive ductal breast cancer development. PMID:26474389
Next-Generation Sequencing in Clinical Molecular Diagnostics of Cancer: Advantages and Challenges. PMID:26473927
Multiple breast cancer risk variants are associated with differential transcript isoform expression in tumors. PMID:26472073
Nanopublications for exposing experimental data in the life-sciences: a Huntington's Disease case study. PMID:26464783
Genome-wide association study of body mass index in subjects with alcohol dependence. PMID:26458734
Tumour-suppression function of KLF12 through regulation of anoikis. PMID:26455320
The Hox cluster microRNA miR-615: a case study of intronic microRNA evolution. PMID:26451238
Design, measurement and processing of region-specific DNA methylation assays: the mass spectrometry-based method EpiTYPER. PMID:26442105
Ethnicity and Smoking-Associated DNA Methylation Changes at HIV Co-Receptor GPR15. PMID:26441693
Shared Enhancer Activity in the Limbs and Phallus and Functional Divergence of a Limb-Genital cis-Regulatory Element in Snakes. PMID:26439399
Prioritizing Clinically Relevant Copy Number Variation from Genetic Interactions and Gene Function Data. PMID:26437450
MicroRNA-148a regulates LDL receptor and ABCA1 expression to control circulating lipoprotein levels. PMID:26437365
Re-Annotator: Annotation Pipeline for Microarray Probe Sequences. PMID:26426330
Frequent DPH3 promoter mutations in skin cancers. PMID:26416425
Partitioning heritability by functional annotation using genome-wide association summary statistics. PMID:26414678
Long Noncoding RNA Expression during Human B-Cell Development. PMID:26394393
Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments. PMID:26392541
Identification of novel small ncRNAs in pollen of tomato. PMID:26385469
Next-generation sequencing of 100 candidate genes in young victims of suspected sudden cardiac death with structural abnormalities of the heart. PMID:26383259
Aberrant Retinoblastoma (RB)-E2F Transcriptional Regulation Defines Molecular Phenotypes of Osteosarcoma. PMID:26378234
Gene activity in primary T cells infected with HIV89.6: intron retention and induction of genomic repeats. PMID:26377088
Genome-wide linkage analyses of non-Hispanic white families identify novel loci for familial late-onset Alzheimer's disease. PMID:26365416
Molecular Characterization of the NLRC4 Expression in Relation to Interleukin-18 Levels. PMID:26362438
High-efficiency reprogramming of fibroblasts into cardiomyocytes requires suppression of pro-fibrotic signalling. PMID:26354680
Genetic investigations of sudden unexpected deaths in infancy using next-generation sequencing of 100 genes associated with cardiac diseases. PMID:26350513
Comparative Analyses of QTLs Influencing Obesity and Metabolic Phenotypes in Pigs and Humans. PMID:26348622
IRF6 mutation screening in non-syndromic orofacial clefting: analysis of 1521 families. PMID:26346622
Endotoxemia Induces IκBβ/NF-κB-Dependent Endothelin-1 Expression in Hepatic Macrophages. PMID:26342031
Tiling Assembly: a new tool for reference annotation-independent transcript assembly and novel gene identification by RNA-sequencing. PMID:26341416
Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data. PMID:26338770
Data integration in biological research: an overview. PMID:26336651
Epiviz: a view inside the design of an integrated visual analysis software for genomics. PMID:26328750
VisRseq: R-based visual framework for analysis of sequencing data. PMID:26328469
Network analysis reveals stage-specific changes in zebrafish embryo development using time course whole transcriptome profiling and prior biological knowledge. PMID:26322129
Histoimmunogenetics Markup Language 1.0: Reporting next generation sequencing-based HLA and KIR genotyping. PMID:26319908
Sequence Analysis and Characterization of Active Human Alu Subfamilies Based on the 1000 Genomes Pilot Project. PMID:26319576
Fast and accurate approximate inference of transcript expression from RNA-seq data. PMID:26315907
Hepatitis C Virus Driven AXL Expression Suppresses the Hepatic Type I Interferon Response. PMID:26313459
Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future. PMID:26309733
Identification of a Novel MYO15A Mutation in a Chinese Family with Autosomal Recessive Nonsyndromic Hearing Loss. PMID:26308726
MEXPRESS: visualizing expression, DNA methylation and clinical TCGA data. PMID:26306699
Generation of a synthetic GlcNAcylated nucleosome reveals regulation of stability by H2A-Thr101 GlcNAcylation. PMID:26305776
A mitochondria-anchored isoform of the actin-nucleating spire protein regulates mitochondrial division. PMID:26305500
Specificity and sensitivity of glucocorticoid signaling in health and disease. PMID:26303082
Meta-analysis of shared genetic architecture across ten pediatric autoimmune diseases. PMID:26301688
Repression of CD24 surface protein expression by oncogenic Ras is relieved by inhibition of Raf but not MEK or PI3K. PMID:26301220
A chromosomal rearrangement in a child with severe speech and language disorder separates FOXP2 from a functional enhancer. PMID:26300977
YAP1 Exerts Its Transcriptional Control via TEAD-Mediated Activation of Enhancers. PMID:26295846
DIS3 shapes the RNA polymerase II transcriptome in humans by degrading a variety of unwanted transcripts. PMID:26294688
Androgen-Regulated SPARCL1 in the Tumor Microenvironment Inhibits Metastatic Progression. PMID:26294211
Transcription Factor Hepatocyte Nuclear Factor-1β (HNF-1β) Regulates MicroRNA-200 Expression through a Long Noncoding RNA. PMID:26292219
Targeted DNA Methylation Screen in the Mouse Mammary Genome Reveals a Parity-Induced Hypermethylation of Igf1r That Persists Long after Parturition. PMID:26290394
Evolution of the unspliced transcriptome. PMID:26289325
Read clouds uncover variation in complex regions of the human genome. PMID:26286554
Assessing Recent Selection and Functionality at Long Noncoding RNA Loci in the Mouse Genome. PMID:26272717
Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions. PMID:26268681
Molecular and phenotypic distinction of the very recently evolved insular subspecies Mus musculus helgolandicus ZIMMERMANN, 1953. PMID:26268354
Social exclusion changes histone modifications H3K4me3 and H3K27ac in liver tissue of wild house mice. PMID:26267652
Predicting effective microRNA target sites in mammalian mRNAs. PMID:26267216
Applying Novel Methods for Assessing Individual- and Neighborhood-Level Social and Psychosocial Environment Interactions with Genetic Factors in the Prediction of Depressive Symptoms in the Multi-Ethnic Study of Atherosclerosis. PMID:26254610
Bipartite structure of the inactive mouse X chromosome. PMID:26248554
BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data. PMID:26248465
A call for benchmarking transposable element annotation methods. PMID:26244060
Whole-genome sequencing identifies a novel ABCB7 gene mutation for X-linked congenital cerebellar ataxia in a large family of Mongolian ancestry. PMID:26242992
Differential Effects of Hepatocyte Nuclear Factor 4α Isoforms on Tumor Growth and T-Cell Factor 4/AP-1 Interactions in Human Colorectal Cancer Cells. PMID:26240283
Genome-wide meta-analysis identifies five new susceptibility loci for cutaneous malignant melanoma. PMID:26237428
Can Characteristics of Reciprocal Translocations Predict the Chance of Transferable Embryos in PGD Cycles? PMID:26237378
The frequent evolutionary birth and death of functional promoters in mouse and human. PMID:26228054
Population-specific genotype imputations using minimac or IMPUTE2. PMID:26226460
Evolutionary History of Cathepsin L (L-like) Family Genes in Vertebrates. PMID:26221069
Inferring 3D chromatin structure using a multiscale approach based on quaternions. PMID:26220581
Transcriptional profiling of predator-induced phenotypic plasticity in Daphnia pulex. PMID:26213557
GESPA: classifying nsSNPs to predict disease association. PMID:26206375
Whole exome sequencing in extended families with autism spectrum disorder implicates four candidate genes. PMID:26204995
Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. PMID:26202974
Novel mutations of NFIX gene causing Marshall-Smith syndrome or Sotos-like syndrome: one gene, two phenotypes. PMID:26200704
Genome-wide Gene-Asbestos Exposure Interaction Association Study Identifies a Common Susceptibility Variant on 22q13.31 Associated with Lung Cancer Risk. PMID:26199339
POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans. PMID:26198033
QoRTs: a comprehensive toolset for quality control and data processing of RNA-Seq experiments. PMID:26187896
Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates. PMID:26184873
p53-Regulated Networks of Protein, mRNA, miRNA, and lncRNA Expression Revealed by Integrated Pulsed Stable Isotope Labeling With Amino Acids in Cell Culture (pSILAC) and Next Generation Sequencing (NGS) Analyses. PMID:26183718
The microRNA-183 cluster: the family that plays together stays together. PMID:26170234
Regulation of human MAPT gene expression. PMID:26170022
DNA methylation of oestrogen-regulated enhancers defines endocrine sensitivity in breast cancer. PMID:26169690
Epigenetic Regulation of Cytosolic Phospholipase A2 in SH-SY5Y Human Neuroblastoma Cells. PMID:26162318
Novel scripts for improved annotation and selection of variants from whole exome sequencing in cancer research. PMID:26150983
NKX2-5 mutations causative for congenital heart disease retain functionality and are directed to hundreds of targets. PMID:26146939
Venus trap in the mouse embryo reveals distinct molecular dynamics underlying specification of first embryonic lineages. PMID:26142281
The Convergence of Systems and Reductionist Approaches in Complex Trait Analysis. PMID:26140590
Cancer, Warts, or Asymptomatic Infections: Clinical Presentation Matches Codon Usage Preferences in Human Papillomaviruses. PMID:26139833
DNAseq Workflow in a Diagnostic Context and an Example of a User Friendly Implementation. PMID:26137478
High-throughput RNA sequencing reveals structural differences of orthologous brain-expressed genes between western lowland gorillas and humans. PMID:26132897
Biomarker discovery: quantification of microRNAs and other small non-coding RNAs using next generation sequencing. PMID:26130076
QuickNGS elevates Next-Generation Sequencing data analysis to a new level of automation. PMID:26126663
Use of RNA sequencing to evaluate rheumatic disease patients. PMID:26126608
CTCF-dependent co-localization of canonical Smad signaling factors at architectural protein binding sites in D. melanogaster. PMID:26125535
Sequencing of the TBX6 Gene in Families with Familial Idiopathic Scoliosis. PMID:26120555
Wanderer, an interactive viewer to explore DNA methylation and gene expression data in human cancer. PMID:26113876
Acute TNF-induced repression of cell identity genes is mediated by NFκB-directed redistribution of cofactors from super-enhancers. PMID:26113076
Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction. PMID:26110515
Comparison of the Equine Reference Sequence with Its Sanger Source Data and New Illumina Reads. PMID:26107638
Annotation of the Protein Coding Regions of the Equine Genome. PMID:26107351
PHF6 Degrees of Separation: The Multifaceted Roles of a Chromatin Adaptor Protein. PMID:26103525
Np9, a cellular protein of retroviral ancestry restricted to human, chimpanzee and gorilla, binds and regulates ubiquitin ligase MDM2. PMID:26103464
RNA-Binding Protein Musashi1 Is a Central Regulator of Adhesion Pathways in Glioblastoma. PMID:26100017
DELTA: A Distal Enhancer Locating Tool Based on AdaBoost Algorithm and Shape Features of Chromatin Modifications. PMID:26091399
Exonic Re-Sequencing of the Chromosome 2q24.3 Parkinson's Disease Locus. PMID:26090850
Associations of Haplotypes Upstream of IRS1 with Insulin Resistance, Type 2 Diabetes, Dyslipidemia, Preclinical Atherosclerosis, and Skeletal Muscle LOC646736 mRNA Levels. PMID:26090471
Efficient conditional knockout targeting vector construction using co-selection BAC recombineering (CoSBR). PMID:26089387
Structural variation on the human Y chromosome from population-scale resequencing. PMID:26088844
Analysis of Low Frequency Protein Truncating Stop-Codon Variants and Fasting Concentration of Growth Hormone. PMID:26086970
Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort. PMID:26084464
Epigenetic modifications of the glucocorticoid receptor gene are associated with the vulnerability to psychopathology in childhood maltreatment. PMID:26080088
Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes. PMID:26079130
Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures. PMID:26075601
Global Survey of Variation in a Human Olfactory Receptor Gene Reveals Signatures of Non-Neutral Evolution. PMID:26072518
Regulation of cholesteryl ester transfer protein expression by upstream polymorphisms: reduced expression associated with rs247616. PMID:26061659
Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation. PMID:26056000
Tracks through the genome to physiological events. PMID:26053180
GeIST: a pipeline for mapping integrated DNA elements. PMID:26049161
The sea lamprey meiotic map improves resolution of ancient vertebrate genome duplications. PMID:26048246
High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9. PMID:26048245
Polymorphism Analysis Reveals Reduced Negative Selection and Elevated Rate of Insertions and Deletions in Intrinsically Disordered Protein Regions. PMID:26047845
Genome-Wide DNA Methylation Profiling Reveals Epigenetic Changes in the Rat Nucleus Accumbens Associated With Cross-Generational Effects of Adolescent THC Exposure. PMID:26044905
Molecular Mechanisms and Evolutionary Processes Contributing to Accelerated Divergence of Gene Expression on the Drosophila X Chromosome. PMID:26041937
C/D-box snoRNA-derived RNA production is associated with malignant transformation and metastatic progression in prostate cancer. PMID:26041889
Defining bacterial regulons using ChIP-seq. PMID:26032817
Novel and rare functional genomic variants in multiple autoimmune syndrome and Sjögren's syndrome. PMID:26031516
Coherence analysis discriminates between retroviral integration patterns in CD34(+) cells transduced under differing clinical trial conditions. PMID:26029726
Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cells. PMID:26025802
Brachyury and SMAD signalling collaboratively orchestrate distinct mesoderm and endoderm gene regulatory networks in differentiating human embryonic stem cells. PMID:26015544
Transcriptional upregulation of microtubule-associated protein 2 is involved in the protein kinase A-induced decrease in the invasiveness of glioma cells. PMID:26014048
Connecting Anxiety and Genomic Copy Number Variation: A Genome-Wide Analysis in CD-1 Mice. PMID:26011321
Proteogenomic Analysis Identifies a Novel Human SHANK3 Isoform. PMID:25997006
Association between Stress Response Genes and Features of Diurnal Cortisol Curves in the Multi-Ethnic Study of Atherosclerosis: A New Multi-Phenotype Approach for Gene-Based Association Tests. PMID:25993632
A low-latency, big database system and browser for storage, querying and visualization of 3D genomic data. PMID:25990738
A novel DNA sequence motif in human and mouse genomes. PMID:25990515
Genome-wide patterns and properties of de novo mutations in humans. PMID:25985141
Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility. PMID:25984238
Sequence variants from whole genome sequencing a large group of Icelanders. PMID:25977816
Human Enhancers Are Fragile and Prone to Deactivating Mutations. PMID:25976354
A multi-SNP association test for complex diseases incorporating an optimal P-value threshold algorithm in nuclear families. PMID:25975968
Common Variants at Putative Regulatory Sites of the Tissue Nonspecific Alkaline Phosphatase Gene Influence Circulating Pyridoxal 5'-Phosphate Concentration in Healthy Adults. PMID:25972531
CSR-1 and P granules suppress sperm-specific transcription in the C. elegans germline. PMID:25968310
Mutant U2AF1 Expression Alters Hematopoiesis and Pre-mRNA Splicing In Vivo. PMID:25965570
Compound hierarchical correlated beta mixture with an application to cluster mouse transcription factor DNA binding data. PMID:25964663
Coordinated epigenetic remodelling of transcriptional networks occurs during early breast carcinogenesis. PMID:25960784
Disruption of BRD4 at H3K27Ac-enriched enhancer region correlates with decreased c-Myc expression in Merkel cell carcinoma. PMID:25941994
HDAC inhibition attenuates cardiac hypertrophy by acetylation and deacetylation of target genes. PMID:25941940
CONSERTING: integrating copy-number analysis with structural-variation detection. PMID:25938371
Relaxing the Molecular Clock to Different Degrees for Different Substitution Types. PMID:25931515
Genome-wide co-occupancy of AML1-ETO and N-CoR defines the t(8;21) AML signature in leukemic cells. PMID:25928846
Destabilization of pluripotency in the absence of Mad2l2. PMID:25928475
Dual 3'Seq using deepSuperSAGE uncovers transcriptomes of interacting Salmonella enterica Typhimurium and human host cells. PMID:25927313
A cluster of noncoding RNAs activates the ESR1 locus during breast cancer adaptation. PMID:25923108
Ten new cases further delineate the syndromic intellectual disability phenotype caused by mutations in DYRK1A. PMID:25920557
CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool. PMID:25909470
Alu-mediated diverse and complex pathogenic copy-number variants within human chromosome 17 at p13.3. PMID:25908615
XomAnnotate: Analysis of Heterogeneous and Complex Exome- A Step towards Translational Medicine. PMID:25905921
RAR/RXR binding dynamics distinguish pluripotency from differentiation associated cis-regulatory elements. PMID:25897113
Association analyses confirm five susceptibility loci for systemic lupus erythematosus in the Han Chinese population. PMID:25890262
Natural variation of gene models in Drosophila melanogaster. PMID:25888292
EVI1 promotes tumor growth via transcriptional repression of MS4A3. PMID:25886616
Modulation of human endogenous retrovirus (HERV) transcription during persistent and de novo HIV-1 infection. PMID:25886562
Mason: a JavaScript web site widget for visualizing and comparing annotated features in nucleotide or protein sequences. PMID:25884379
Polycomb repressive complex 2 epigenomic signature defines age-associated hypermethylation and gene expression changes. PMID:25880792
ClusTrack: feature extraction and similarity measures for clustering of genome-wide data sets. PMID:25879845
Retinoic acid promotes myogenesis in myoblasts by antagonizing transforming growth factor-beta signaling via C/EBPβ. PMID:25878769
Tensor GSVD of patient- and platform-matched tumor and normal DNA copy-number profiles uncovers chromosome arm-wide patterns of tumor-exclusive platform-consistent alterations encoding for cell transformation and predicting ovarian cancer survival. PMID:25875127
An Ontology-Based GIS for Genomic Data Management of Rumen Microbes. PMID:25873847
Constraint and divergence of global gene expression in the mammalian embryo. PMID:25871848
TALE-mediated epigenetic suppression of CDKN2A increases replication in human fibroblasts. PMID:25866970
The methylcytosine dioxygenase Tet2 promotes DNA demethylation and activation of cytokine gene expression in T cells. PMID:25862091
The recently identified modifier of murine metastable epialleles, Rearranged L-Myc Fusion, is involved in maintaining epigenetic marks at CpG island shores and enhancers. PMID:25857663
NexGenEx-Tom: a gene expression platform to investigate the functionalities of the tomato genome. PMID:25849067
Genomic heterogeneity of osteosarcoma - shift from single candidates to functional modules. PMID:25848766
Mapping regulatory factors by immunoprecipitation from native chromatin. PMID:25827087
RNA polymerase II pausing can be retained or acquired during activation of genes involved in the epithelial to mesenchymal transition. PMID:25820424
Genetics of cardiovascular disease: Importance of sex and ethnicity. PMID:25817330
SNPfisher: tools for probing genetic variation in laboratory-reared zebrafish. PMID:25813542
Demonstration of the presence of the "deleted" MIR122 gene in HepG2 cells. PMID:25811611
Improved inherited peripheral neuropathy genetic diagnosis by whole-exome sequencing. PMID:25802885
Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT): A Hybridization Capture-Based Next-Generation Sequencing Clinical Assay for Solid Tumor Molecular Oncology. PMID:25801821
Sensitive detection of chromatin-altering polymorphisms reveals autoimmune disease mechanisms. PMID:25799442
De novo origin of VCY2 from autosome to Y-transposed amplicon. PMID:25799347
A statistical approach for rare-variant association testing in affected sibships. PMID:25799106
Evidence for widespread subfunctionalization of splice forms in vertebrate genomes. PMID:25792610
iTagPlot: an accurate computation and interactive drawing tool for tag density plot. PMID:25792550
Foamy viral vector integration sites in SCID-repopulating cells after MGMTP140K-mediated in vivo selection. PMID:25786870
Involvement of RNA Polymerase III in Immune Responses. PMID:25776554
Effect of minichromosome maintenance protein 2 deficiency on the locations of DNA replication origins. PMID:25762552
Transcriptional regulation of microRNA-100, -146a, and -150 genes by p53 and NFκB p65/RelA in mouse striatal STHdh(Q7)/ Hdh(Q7) cells and human cervical carcinoma HeLa cells. PMID:25757558
Genome-wide CIITA-binding profile identifies sequence preferences that dictate function versus recruitment. PMID:25753668
The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment. PMID:25752243
Genome-Wide Analysis of ChREBP Binding Sites on Male Mouse Liver and White Adipose Chromatin. PMID:25751637
Complex genomic rearrangements at the PLP1 locus include triplication and quadruplication. PMID:25749076
Differential expression of HERV-K (HML-2) proviruses in cells and virions of the teratocarcinoma cell line Tera-1. PMID:25746218
Genetic variant rs17225178 in the ARNT2 gene is associated with Asperger Syndrome. PMID:25745553
Landscape of insertion polymorphisms in the human genome. PMID:25745018
Enhanced reduced representation bisulfite sequencing for assessment of DNA methylation at base pair resolution. PMID:25742437
Computational methodology for ChIP-seq analysis. PMID:25741452
Drosophila muller f elements maintain a distinct set of genomic properties over 40 million years of evolution. PMID:25740935
Control of a neuronal morphology program by an RNA-binding zinc finger protein, Unkempt. PMID:25737280
The Mechanism of Interferon Refractoriness During Hepatitis C Virus Infection and Its Reversal with a Peroxisome Proliferator-Activated Receptor α Agonist. PMID:25734487
Microprocessor mediates transcriptional termination of long noncoding RNA transcripts hosting microRNAs. PMID:25730776
Defining the gene repertoire and spatiotemporal expression profiles of adhesion G protein-coupled receptors in zebrafish. PMID:25715737
Rock, paper, scissors: harnessing complementarity in ortholog detection methods improves comparative genomic inference. PMID:25711833
A survey of imprinted gene expression in mouse trophoblast stem cells. PMID:25711832
Species differential regulation of COX2 can be described by an NFκB-dependent logic AND gate. PMID:25697863
Gene expression analysis of human induced pluripotent stem cell-derived neurons carrying copy number variants of chromosome 15q11-q13.1. PMID:25694803
Targeted next generation sequencing identifies novel mutations in RP1 as a relatively common cause of autosomal recessive rod-cone dystrophy. PMID:25692139
Identification of mammalian proteins that collaborate with type III secretion system function: involvement of a chemokine receptor in supporting translocon activity. PMID:25691588
The Genome 10K Project: a way forward. PMID:25689317
The UCSC Ebola Genome Portal. PMID:25685613
Non-coding genomic regions possessing enhancer and silencer potential are associated with healthy aging and exceptional survival. PMID:25682868
Genomic and network patterns of schizophrenia genetic variation in human evolutionary accelerated regions. PMID:25681384
Active secretion of CXCL10 and CCL5 from colorectal cancer microenvironments associates with GranzymeB+ CD8+ T-cell infiltration. PMID:25671296
Exon-intron circular RNAs regulate transcription in the nucleus. PMID:25664725
Global O-GlcNAc Levels Modulate Transcription of the Adipocyte Secretome during Chronic Insulin Resistance. PMID:25657638
Amplification of pico-scale DNA mediated by bacterial carrier DNA for small-cell-number transcription factor ChIP-seq. PMID:25652644
Coordinated regulatory variation associated with gestational hyperglycaemia regulates expression of the novel hexokinase HKDC1. PMID:25648650
Addressing population-specific multiple testing burdens in genetic association studies. PMID:25644736
Zeb1 affects epithelial cell adhesion by diverting glycosphingolipid metabolism. PMID:25643708
Identification of a recently active mammalian SINE derived from ribosomal RNA. PMID:25637222
The role of DNA insertions in phenotypic differentiation between humans and other primates. PMID:25635043
Prioritizing causal disease genes using unbiased genomic features. PMID:25633252
Using the canary genome to decipher the evolution of hormone-sensitive gene regulation in seasonal singing birds. PMID:25631560
1. Alternative splicing of viral receptors: A review of the diverse morphologies and physiologies of adenoviral receptors. PMID:25621323
Quantitative visualization of alternative exon expression from RNA-seq data. PMID:25617416
3USS: a web server for detecting alternative 3'UTRs from RNA-seq experiments. PMID:25617413
Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements. PMID:25616342
Genome-wide analyses of LINE-LINE-mediated nonallelic homologous recombination. PMID:25613453
TNFα signalling primes chromatin for NF-κB binding and induces rapid and widespread nucleosome repositioning. PMID:25608606
Vector design influences hepatic genotoxicity after adeno-associated virus gene therapy. PMID:25607839
BTB-ZF transcriptional regulator PLZF modifies chromatin to restrain inflammatory signaling programs. PMID:25605927
Associations between DNA methylation and schizophrenia-related intermediate phenotypes - a gene set enrichment analysis. PMID:25598502
Interleukin polymorphisms associated with overall survival, disease-free survival, and recurrence in non-small cell lung cancer patients. PMID:25597281
Recurrent ZFX mutations in human sporadic parathyroid adenomas. PMID:25594030
Novel transcription factor variants through RNA-sequencing: the importance of being "alternative". PMID:25590302
Effects of copy number variable regions on local gene expression in white blood cells of Mexican Americans. PMID:25585699
Concerted copy number variation balances ribosomal DNA dosage in human and mouse genomes. PMID:25583482
Genetic mapping of MAPK-mediated complex traits Across S. cerevisiae. PMID:25569670
iRNA-seq: computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data. PMID:25564527
Identification and computational analysis of gene regulatory elements. PMID:25561628
The evolution and functional impact of human deletion variants shared with archaic hominin genomes. PMID:25556237
Conformational dynamics of nonsynonymous variants at protein interfaces reveals disease association. PMID:25546381
SIRT6 minor allele genotype is associated with >5-year decrease in lifespan in an aged cohort. PMID:25541994
Are special read alignment strategies necessary and cost-effective when handling sequencing reads from patient-derived tumor xenografts? PMID:25539684
Empowering biologists with multi-omics data: colorectal cancer as a paradigm. PMID:25527095
Genetic association between germline JAK2 polymorphisms and myeloproliferative neoplasms in Hong Kong Chinese population: a case-control study. PMID:25526816
TXNDC5, a newly discovered disulfide isomerase with a key role in cell physiology and pathology. PMID:25526565
Genetic contributions to urgency urinary incontinence in women. PMID:25524241
Using Mendelian inheritance errors as quality control criteria in whole genome sequencing data set. PMID:25519373
Pathway analysis for genetic association studies: to do, or not to do? That is the question. PMID:25519357
SNPAAMapperT2K: A genome-wide SNP downstream analysis and annotation pipeline for species annotated with NCBI.tbl data files. PMID:25512690
An integrative computational approach for prioritization of genomic variants. PMID:25506935
Browning of human adipocytes requires KLF11 and reprogramming of PPARγ superenhancers. PMID:25504365
RNA-Seq and ChIP-Seq reveal SQSTM1/p62 as a key mediator of JunB suppression of NF-κB-dependent inflammation. PMID:25501661
A pathway switch directs BAFF signaling to distinct NFκB transcription factors in maturing and proliferating B cells. PMID:25497099
Comparative genomics reveals molecular features unique to the songbird lineage. PMID:25494627
Functional redundancy in the nuclear compartmentalization of the late-replicating genome. PMID:25493640
Functions of lncRNA HOTAIR in lung cancer. PMID:25491133
Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond. PMID:25486472
What do drug transporters really do? PMID:25475361
Open source libraries and frameworks for biological data visualisation: a guide for developers. PMID:25475079
Next-generation sequencing of 34 genes in sudden unexplained death victims in forensics and in patients with channelopathic cardiac diseases. PMID:25467552
Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes. PMID:25437436
Mosquito genomics. Extensive introgression in a malaria vector species complex revealed by phylogenomics. PMID:25431491
The UCSC Genome Browser database: 2015 update. PMID:25428374
piRBase: a web resource assisting piRNA functional study. PMID:25425034
Type I Interferon Regulates the Expression of Long Non-Coding RNAs. PMID:25414701
Identification of highly conserved putative developmental enhancers bound by SOX3 in neural progenitors using ChIP-Seq. PMID:25409526
Massively parallel sequencing of forensically relevant single nucleotide polymorphisms using TruSeq™ forensic amplicon. PMID:25408291
Maintenance of nucleosomal balance in cis by conserved AAA-ATPase Yta7. PMID:25406467
RADIA: RNA and DNA integrated analysis for somatic mutation detection. PMID:25405470
Biological knowledge-driven analysis of epistasis in human GWAS with application to lipid traits. PMID:25403526
A recurrent de novo mutation in KCNC1 causes progressive myoclonus epilepsy. PMID:25401298
SuRFing the genomics wave: an R package for prioritising SNPs by functionality. PMID:25400697
Detection theory in identification of RNA-DNA sequence differences using RNA-sequencing. PMID:25396741
Genomic landscape of metastatic colorectal cancer. PMID:25394515
Role of recurrent hypoxia-ischemia in preterm white matter injury severity. PMID:25390897
Evolution of an expanded mannose receptor gene family. PMID:25390371
Expression analysis in intestinal mucosa reveals complex relations among genes under the association peaks in celiac disease. PMID:25388004
Expression profiles of PIWIL2 short isoforms differ in testicular germ cell tumors of various differentiation subtypes. PMID:25384072
Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. PMID:25383968
Nutrient-sensing nuclear receptors coordinate autophagy. PMID:25383539
Amplicon rearrangements during the extrachromosomal and intrachromosomal amplification process in a glioma. PMID:25378339
Genomic evidence of rapid and stable adaptive oscillations over seasonal time scales in Drosophila. PMID:25375361
Pseudoautosomal region 1 length polymorphism in the human population. PMID:25375121
Pigment cell interactions and differential xanthophore recruitment underlying zebrafish stripe reiteration and Danio pattern evolution. PMID:25374113
Differential nuclease sensitivity profiling of chromatin reveals biochemical footprints coupled to gene expression and functional DNA elements in maize. PMID:25361955
Assessing copy number from exome sequencing and exome array CGH based on CNV spectrum in a large clinical cohort. PMID:25356966
Evidence of convergent evolution in humans and macaques supports an adaptive role for copy number variation of the β-defensin-2 gene. PMID:25349268
The genomic landscape of polymorphic human nuclear mitochondrial insertions. PMID:25348406
A novel virus-inducible enhancer of the interferon-β gene with tightly linked promoter and enhancer activities. PMID:25348400
Navigating protected genomics data with UCSC Genome Browser in a Box. PMID:25348212
Host and viral determinants for MxB restriction of HIV-1 infection. PMID:25348155
Generation of a neuro-specific microarray reveals novel differentially expressed noncoding RNAs in mouse models for neurodegenerative diseases. PMID:25344396
Zinc finger protein Zfp335 is required for the formation of the naïve T cell compartment. PMID:25343476
Hybrid mice reveal parent-of-origin and Cis- and trans-regulatory effects in the retina. PMID:25340786
Fra-1 regulation of Matrix Metallopeptidase-1 (MMP-1) in metastatic variants of MDA-MB-231 breast cancer cells. PMID:25339983
Aggregation of the protein TRIOBP-1 and its potential relevance to schizophrenia. PMID:25333879
SummonChimera infers integrated viral genomes with nucleotide precision from NGS data. PMID:25331652
Transcriptomic portrait of human Mesenchymal Stromal/Stem Cells isolated from bone marrow and placenta. PMID:25326687
Incorporating computational resources in a cancer research program. PMID:25324189
Databases for lncRNAs: a comparative evaluation of emerging tools. PMID:25323317
Widespread contribution of transposable elements to the innovation of gene regulatory networks. PMID:25319995
Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis. PMID:25319994
A comparison of control samples for ChIP-seq of histone modifications. PMID:25309581
A novel single base pair duplication in WDR62 causes primary microcephaly. PMID:25303973
Transcriptome analysis elucidates key developmental components of bryozoan lophophore development. PMID:25300304
Association of common variants in TCF4 and PTPRG with Fuchs' corneal dystrophy: a systematic review and meta-analysis. PMID:25299301
Epigenetic signatures of alcohol abuse and hepatitis infection during human hepatocarcinogenesis. PMID:25294808
Sequence specificity incompletely defines the genome-wide occupancy of Myc. PMID:25287278
Comparative DNA methylome analysis of endometrial carcinoma reveals complex and distinct deregulation of cancer promoters and enhancers. PMID:25286960
Combined analysis of copy number alterations by single-nucleotide polymorphism array and MYC status in non-metastatic breast cancer patients: comparison according to the circulating tumor cell status. PMID:25286758
DaVIE: Database for the Visualization and Integration of Epigenetic data. PMID:25278960
An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons. PMID:25274305
Genetic variation in the oxytocin receptor (OXTR) gene is associated with Asperger Syndrome. PMID:25264479
TMPRSS2:ERG blocks neuroendocrine and luminal cell differentiation to maintain prostate cancer proliferation. PMID:25263440
Dopamine signaling leads to loss of Polycomb repression and aberrant gene activation in experimental parkinsonism. PMID:25254549
Systematic assessment of imputation performance using the 1000 Genomes reference panels. PMID:25246238
Meta-analysis of genome-wide association studies identifies novel loci that influence cupping and the glaucomatous process. PMID:25241763
G9a/GLP-dependent H3K9me2 patterning alters chromatin structure at CpG islands in hematopoietic progenitors. PMID:25237399
Mu-8: visualizing differences between proteins and their families. PMID:25237392
FixingTIM: interactive exploration of sequence and structural data to identify functional mutations in protein families. PMID:25237390
DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. PMID:25236618
circBase: a database for circular RNAs. PMID:25234927
Molecular characterization of common fragile sites as a strategy to discover cancer susceptibility genes. PMID:25231336
A systems biology approach reveals a link between systemic cytokines and skeletal muscle energy metabolism in a rodent smoking model and human COPD. PMID:25228925
Tangram: a comprehensive toolbox for mobile element insertion detection. PMID:25228379
PDYN, a gene implicated in brain/mental disorders, is targeted by REST in the adult human brain. PMID:25220237
Global MEF2 target gene analysis in cardiac and skeletal muscle reveals novel regulation of DUSP6 by p38MAPK-MEF2 signaling. PMID:25217591
visPIG--a web tool for producing multi-region, multi-track, multi-scale plots of genetic data. PMID:25208325
We are all individuals... bioinformatics in the personalized medicine era. PMID:25204962
Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins. PMID:25203624
BEDTools: The Swiss-Army Tool for Genome Feature Analysis. PMID:25199790
Identification of species-specific nuclear insertions of mitochondrial DNA (numts) in gorillas and their potential as population genetic markers. PMID:25194325
A dominant mutation in hexokinase 1 (HK1) causes retinitis pigmentosa. PMID:25190649
CITED2-mediated human hematopoietic stem cell maintenance is critical for acute myeloid leukemia. PMID:25184385
Identification of TERRA locus unveils a telomere protection role through association to nearly all chromosomes. PMID:25182072
Common variants near ABCA1, AFAP1 and GMDS confer risk of primary open-angle glaucoma. PMID:25173105
Birth weight, working memory and epigenetic signatures in IGF2 and related genes: a MZ twin study. PMID:25171170
Ankylosing spondylitis is associated with the anthrax toxin receptor 2 gene (ANTXR2). PMID:25169729
Modeling DNA methylation dynamics with approaches from phylogenetics. PMID:25161227
MendeLIMS: a web-based laboratory information management system for clinical genome sequencing. PMID:25159034
Purifying selection on splice-related motifs, not expression level nor RNA folding, explains nearly all constraint on human lincRNAs. PMID:25158797
A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites. PMID:25156699
Condensins are Required for Maintenance of Nuclear Architecture. PMID:25153163
Next-generation sequencing technologies: breaking the sound barrier of human genetics. PMID:25150023
Systematic identification of 3'-UTR regulatory elements in activity-dependent mRNA stability in hippocampal neurons. PMID:25135970
Alternative polyadenylation regulates CELF1/CUGBP1 target transcripts following T cell activation. PMID:25123787
The bone-specific Runx2-P1 promoter displays conserved three-dimensional chromatin structure with the syntenic Supt3h promoter. PMID:25120271
ARID3B expression in primary breast cancers and breast cancer-derived cell lines. PMID:25120063
The miR-124-prolyl hydroxylase P4HA1-MMP1 axis plays a critical role in prostate cancer progression. PMID:25115393
BRG1/SMARCA4 inactivation promotes non-small cell lung cancer aggressiveness by altering chromatin organization. PMID:25115300
The CHR site: definition and genome-wide identification of a cell cycle transcriptional element. PMID:25106871
De novo missense mutations in the NAA10 gene cause severe non-syndromic developmental delay in males and females. PMID:25099252
Cell fate inclination within 2-cell and 4-cell mouse embryos revealed by single-cell RNA sequencing. PMID:25096407
Preserving sequence annotations across reference sequences. PMID:25093075
Glucocorticoid receptor binds half sites as a monomer and regulates specific target genes. PMID:25085117
MixMir: microRNA motif discovery from gene expression data using mixed linear models. PMID:25081207
5meCpG epigenetic marks neighboring a primate-conserved core promoter short tandem repeat indicate X-chromosome inactivation. PMID:25078280
SOX2 is a cancer-specific regulator of tumour initiating potential in cutaneous squamous cell carcinoma. PMID:25077433
The associations between immunity-related genes and breast cancer prognosis in Korean women. PMID:25075970
Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation. PMID:25074712
CRTC1/MAML2 gain-of-function interactions with MYC create a gene signature predictive of cancers with CREB-MYC involvement. PMID:25071166
The genome and linkage map of the northern pike (Esox lucius): conserved synteny revealed between the salmonid sister group and the Neoteleostei. PMID:25069045
APADB: a database for alternative polyadenylation and microRNA regulation events. PMID:25052703
Functional repeat-derived RNAs often originate from retrotransposon-propagated ncRNAs. PMID:25045147
Characterization of rat serum amyloid A4 (SAA4): a novel member of the SAA superfamily. PMID:25044109
Noncoding origins of anthropoid traits and a new null model of transposon functionalization. PMID:25043600
Variant detection sensitivity and biases in whole genome and exome sequencing. PMID:25038816
SpliceNet: recovering splicing isoform-specific differential gene networks from RNA-Seq data of normal and diseased samples. PMID:25034693
Microsatellite interruptions stabilize primate genomes and exist as population-specific single nucleotide polymorphisms within individual human genomes. PMID:25033203
Annotation of functional variation within non-MHC MS susceptibility loci through bioinformatics analysis. PMID:25030428
KIFCI, a novel putative prognostic biomarker for ovarian adenocarcinomas: delineating protein interaction networks and signaling circuitries. PMID:25028599
Whole-exome imputation of sequence variants identified two novel alleles associated with adult body height in African Americans. PMID:25027330
Reproducible combinatorial regulatory networks elucidate novel oncogenic microRNAs in non-small cell lung cancer. PMID:25024357
Fine mapping and functional studies of risk variants for type 1 diabetes at chromosome 16p13.13. PMID:25008175
MicroRNA profiling of novel African American and Caucasian Prostate Cancer cell lines reveals a reciprocal regulatory relationship of miR-152 and DNA methyltranferase 1. PMID:25004396
Placental Nkx2-5 and target gene expression in early-onset and severe preeclampsia. PMID:24987805
Epigenetic remodelling and dysregulation of DLGAP4 is linked with early-onset cerebellar ataxia. PMID:24986922
Comparative validation of the D. melanogaster modENCODE transcriptome annotation. PMID:24985915
Insulator function and topological domain border strength scale with architectural protein occupancy. PMID:24981874
Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7. PMID:24973960
CD1d-mediated presentation of endogenous lipid antigens by adipocytes requires microsomal triglyceride transfer protein. PMID:24966328
Sequence-level mechanisms of human epigenome evolution. PMID:24966180
Using beta-binomial regression for high-precision differential methylation analysis in multifactor whole-genome bisulfite sequencing experiments. PMID:24962134
BLAT-based comparative analysis for transposable elements: BLATCAT. PMID:24959585
Did Neanderthals and Denisovans have our de novo genes? PMID:24952670
Engineered TAL Effector modulators for the large-scale gain-of-function screening. PMID:24939900
Investigation of the involvement of MIR185 and its target genes in the development of schizophrenia. PMID:24936775
The Cavβ1a subunit regulates gene expression and suppresses myogenin in muscle progenitor cells. PMID:24934157
Sorting signal targeting mRNA into hepatic extracellular vesicles. PMID:24921245
A meta-analysis of Hodgkin lymphoma reveals 19p13.3 TCF3 as a novel susceptibility locus. PMID:24920014
Novel H3K4me3 marks are enriched at human- and chimpanzee-specific cytogenetic structures. PMID:24916972
Discovering functional DNA elements using population genomic information: a proof of concept using human mtDNA. PMID:24916662
miR-1202 is a primate-specific and brain-enriched microRNA involved in major depression and antidepressant treatment. PMID:24908571
Population-specific common SNPs reflect demographic histories and highlight regions of genomic plasticity with functional relevance. PMID:24906912
Testicular differentiation factor SF-1 is required for human spleen development. PMID:24905461
Using semantic web technologies to annotate and align microarray designs. PMID:24904201
A bioinformatic and computational study of myosin phosphatase subunit diversity. PMID:24898838
Intergenerational genomic DNA methylation patterns in mouse hybrid strains. PMID:24887417
Functional annotation signatures of disease susceptibility loci improve SNP association analysis. PMID:24886216
Regression hidden Markov modeling reveals heterogeneous gene expression regulation: a case study in mouse embryonic stem cells. PMID:24884369
Epigenetic landscape during osteoblastogenesis defines a differentiation-dependent Runx2 promoter region. PMID:24881813
BiQ Analyzer HiMod: an interactive software tool for high-throughput locus-specific analysis of 5-methylcytosine and its oxidized derivatives. PMID:24875479
SPIB and BATF provide alternate determinants of IRF4 occupancy in diffuse large B-cell lymphoma linked to disease heterogeneity. PMID:24875472
Distinct and separable roles for EZH2 in neurogenic astroglia. PMID:24867641
HeatMapViewer: interactive display of 2D data in biology. PMID:24860644
An enhancer polymorphism at the cardiomyocyte intercalated disc protein NOS1AP locus is a major regulator of the QT interval. PMID:24857694
Specific glycosylation of membrane proteins in epithelial ovarian cancer cell lines: glycan structures reflect gene expression and DNA methylation status. PMID:24855066
Motif-based analysis of large nucleotide data sets using MEME-ChIP. PMID:24853928
Genome-wide quantitative analysis of histone H3 lysine 4 trimethylation in wild house mouse liver: environmental change causes epigenetic plasticity. PMID:24849289
Contrasting X-linked and autosomal diversity across 14 human populations. PMID:24836452
Understanding the Dynamics of Gene Regulatory Systems; Characterisation and Clinical Relevance of cis-Regulatory Polymorphisms. PMID:24832652
Convergent and divergent cellular responses by ErbB4 isoforms in mammary epithelial cells. PMID:24829397
Wnt signaling directs a metabolic program of glycolysis and angiogenesis in colon cancer. PMID:24825347
A naturally occurring, noncanonical GTP aptamer made of simple tandem repeats. PMID:24824832
The RNA-binding protein hnRNPA2 regulates β-catenin protein expression and is overexpressed in prostate cancer. PMID:24823909
Abundant local interactions in the 4p16.1 region suggest functional mechanisms underlying SLC2A9 associations with human serum uric acid. PMID:24821702
Genetic association study of adiposity and melanocortin-4 receptor (MC4R) common variants: replication and functional characterization of non-coding regions. PMID:24820477
Non-inhibited miRNAs shape the cellular response to anti-miR. PMID:24810853
Genomic landscape of human, bat, and ex vivo DNA transposon integrations. PMID:24809961
Genome-wide association study and ancestral origins of the slick-hair coat in tropically adapted cattle. PMID:24808908
Epigenetic variation in monozygotic twins: a genome-wide analysis of DNA methylation in buccal cells. PMID:24802513
The personal genome browser: visualizing functions of genetic variants. PMID:24799434
Engineered zinc-finger transcription factors activate OCT4 (POU5F1), SOX2, KLF4, c-MYC (MYC) and miR302/367. PMID:24792165
Reducing pervasive false-positive identical-by-descent segments detected by large-scale pedigree analysis. PMID:24784137
RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE). PMID:24779366
Rare and low-frequency coding variants in CXCR2 and other genes are associated with hematological traits. PMID:24777453
Characterization of genomic vitamin D receptor binding sites through chromatin looping and opening. PMID:24763502
Fos-dependent induction of Chk1 protects osteoblasts from replication stress. PMID:24762558
Retrotransposon hypomethylation in melanoma and expression of a placenta-specific gene. PMID:24759919
A novel tRNA variable number tandem repeat at human chromosome 1q23.3 is implicated as a boundary element based on conservation of a CTCF motif in mouse. PMID:24753417
VAP: a versatile aggregate profiler for efficient genome-wide data representation and discovery. PMID:24753414
Describing sequencing results of structural chromosome rearrangements with a suggested next-generation cytogenetic nomenclature. PMID:24746958
Long-read sequencing of chicken transcripts and identification of new transcript isoforms. PMID:24736250
ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases. PMID:24735413
Vascular histone deacetylation by pharmacological HDAC inhibition. PMID:24732587
TGFBI (βIG-H3) is a diabetes-risk gene based on mouse and human genetic studies. PMID:24728038
Multiscale representation of genomic signals. PMID:24727652
Inferring the evolutionary history of primate microRNA binding sites: overcoming motif counting biases. PMID:24723422
Recurrent duplications of the annexin A1 gene (ANXA1) in autism spectrum disorders. PMID:24720851
Cross-tissue comparisons of leptin and adiponectin: DNA methylation profiles. PMID:24719787
Recurrent epimutations activate gene body promoters in primary glioblastoma. PMID:24709822
VCGDB: a dynamic genome database of the Chinese population. PMID:24708222
ELFN1-AS1: a novel primate gene with possible microRNA function expressed predominantly in human tumors. PMID:24707484
ATR checkpoint kinase and CRL1βTRCP collaborate to degrade ASF1a and thus repress genes overlapping with clusters of stalled replication forks. PMID:24700029
Deep sequencing to identify the causes of viral encephalitis. PMID:24699691
Site-specific association with host and viral chromatin by Kaposi's sarcoma-associated herpesvirus LANA and its reversal during lytic reactivation. PMID:24696474
Studying the system-level involvement of microRNAs in Parkinson's disease. PMID:24690883
Transcriptional regulation of YWHAZ, the gene encoding 14-3-3ζ. PMID:24690670
CEH-28 activates dbl-1 expression and TGF-β signaling in the C. elegans M4 neuron. PMID:24690231
Hypoxic stress facilitates acute activation and chronic downregulation of fanconi anemia proteins. PMID:24688021
Subtelomeric CTCF and cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline. PMID:24676094
Identification of new genetic polymorphisms that alter the dietary requirement for choline and vary in their distribution across ethnic and racial groups. PMID:24671709
Assessing the impact of copy number variants on miRNA genes in autism by Monte Carlo simulation. PMID:24667286
Genomic occupancy of Runx2 with global expression profiling identifies a novel dimension to control of osteoblastogenesis. PMID:24655370
Microsatellite stable colorectal cancers stratified by the BRAF V600E mutation show distinct patterns of chromosomal instability. PMID:24651849
Long non-coding RNA and alternative splicing modulations in Parkinson's leukocytes identified by RNA sequencing. PMID:24651478
Obesity-associated variants within FTO form long-range functional connections with IRX3. PMID:24646999
Quantitative theory of entropic forces acting on constrained nucleotide sequences applied to viruses. PMID:24639520
DNA methylation biomarkers predict progression-free and overall survival of metastatic renal cell cancer (mRCC) treated with antiangiogenic therapies. PMID:24633192
mrSNP: software to detect SNP effects on microRNA binding. PMID:24629096
Genomic convergence and network analysis approach to identify candidate genes in Alzheimer's disease. PMID:24628925
Novel transcripts from a distinct promoter that encode the full-length AKT1 in human breast cancer cells. PMID:24628780
The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation. PMID:24618464
A course-based research experience: how benefits change with increased investment in instructional time. PMID:24591510
Systems genetics of liver fibrosis: identification of fibrogenic and expression quantitative trait loci in the BXD murine reference population. PMID:24586654
Identification and initial functional characterization of a human vascular cell-enriched long noncoding RNA. PMID:24578380
Regulation of human telomerase splicing by RNA:RNA pairing. PMID:24577044
Tempo and mode of regulatory evolution in Drosophila. PMID:24567308
Novel alternative splicing isoform biomarkers identification from high-throughput plasma proteomics profiling of breast cancer. PMID:24565027
AnnotateGenomicRegions: a web application. PMID:24564446
The chromatin regulator Brg1 suppresses formation of intraductal papillary mucinous neoplasm and pancreatic ductal adenocarcinoma. PMID:24561622
pY RNA1-s2: a highly retina-enriched small RNA that selectively binds to Matrin 3 (Matr3). PMID:24558381
GATA5 CpG island hypermethylation is an independent predictor for poor clinical outcome in renal cell carcinoma. PMID:24549248
Inherited variation in the PARP1 gene and survival from melanoma. PMID:24535833
Gene Expression and Gene Ontology Enrichment Analysis for H3K4me3 and H3K4me1 in Mouse Liver and Mouse Embryonic Stem Cell Using ChIP-Seq and RNA-Seq. PMID:24526835
Distinguishing hypertrophic cardiomyopathy-associated mutations from background genetic noise. PMID:24510615
Whole genome analyses of a well-differentiated liposarcoma reveals novel SYT1 and DDR2 rearrangements. PMID:24505276
Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development. PMID:24497530
SegAnnDB: interactive Web-based genomic segmentation. PMID:24493034
Targeted methylation of the epithelial cell adhesion molecule (EpCAM) promoter to silence its expression in ovarian cancer cells. PMID:24489952
Molecular evolution of multiple-level control of heme biosynthesis pathway in animal kingdom. PMID:24489775
bwtool: a tool for bigWig files. PMID:24489365
Genome-wide histone state profiling of fibroblasts from the opossum, Monodelphis domestica, identifies the first marsupial-specific imprinted gene. PMID:24484454
Searching for Alternatively Spliced Variants of Phospholipase Domain-Containing 2 (Pnpla2), a Novel Gene in the Retina. PMID:24482734
The imprinted NPAP1 gene in the Prader-Willi syndrome region belongs to a POM121-related family of retrogenes. PMID:24482533
Clinical and genomic evaluation of 201 patients with Phelan-McDermid syndrome. PMID:24481935
The receptor for advanced glycation end-products (RAGE) is only present in mammals, and belongs to a family of cell adhesion molecules (CAMs). PMID:24475194
Significant overlap between human genome-wide association-study nominated breast cancer risk alleles and rat mammary cancer susceptibility loci. PMID:24467842
Identification of rare DNA sequence variants in high-risk autism families and their prevalence in a large case/control population. PMID:24467814
ArchiLD: hierarchical visualization of linkage disequilibrium in human populations. PMID:24466224
MLV integration site selection is driven by strong enhancers and active promoters. PMID:24464997
Neurofilament Heavy polypeptide CpG island methylation associates with prognosis of renal cell carcinoma and prediction of antivascular endothelial growth factor therapy response. PMID:24464810
Identification of low-frequency and rare sequence variants associated with elevated or reduced risk of type 2 diabetes. PMID:24464100
Tau promotes neurodegeneration through global chromatin relaxation. PMID:24464041
The degree of segmental aneuploidy measured by total copy number abnormalities predicts survival and recurrence in superficial gastroesophageal adenocarcinoma. PMID:24454681
MafFilter: a highly flexible and extensible multiple genome alignment files processor. PMID:24447531
Evidence for a crucial role of a host non-coding RNA in influenza A virus replication. PMID:24440876
T-KDE: a method for genome-wide identification of constitutive protein binding sites from multiple ChIP-seq data sets. PMID:24428924
ISAAC - InterSpecies Analysing Application using Containers. PMID:24428905
Efficient haplotype block recognition of very long and dense genetic sequences. PMID:24423111
Differential protein occupancy profiling of the mRNA transcriptome. PMID:24417896
Genomic analysis of primordial dwarfism reveals novel disease genes. PMID:24389050
MBD3 localizes at promoters, gene bodies and enhancers of active genes. PMID:24385926
An online bioinformatics tool predicts zinc finger and TALE nuclease off-target cleavage. PMID:24381193
Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes. PMID:24380390
Peroxisome proliferator-activated receptor γ and C/EBPα synergistically activate key metabolic adipocyte genes by assisted loading. PMID:24379442
Galaxy tools to study genome diversity. PMID:24377391
Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties. PMID:24373287
Prolyl-4-hydroxylase 3 (PHD3) expression is downregulated during epithelial-to-mesenchymal transition. PMID:24367580
POMO--Plotting Omics analysis results for Multiple Organisms. PMID:24365393
A guide to bioinformatics for immunologists. PMID:24363654
Widespread misinterpretable ChIP-seq bias in yeast. PMID:24349523
A coregulatory network of NR2F1 and microRNA-140. PMID:24349493
KIAA1462, a coronary artery disease associated gene, is a candidate gene for late onset Alzheimer disease in APOE carriers. PMID:24349219
Large-scale quality analysis of published ChIP-seq data. PMID:24347632
Deep sequencing and high-resolution imaging reveal compartment-specific localization of Bdnf mRNA in hippocampal neurons. PMID:24345682
Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments. PMID:24335146
Copy number variants are produced in response to low-dose ionizing radiation in cultured cells. PMID:24327335
A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics. PMID:24324667
SIOMICS: a novel approach for systematic identification of motifs in ChIP-seq data. PMID:24322294
Genetic variation in GABRB3 is associated with Asperger syndrome and multiple endophenotypes relevant to autism. PMID:24321478
Status quo of annotation of human disease variants. PMID:24305467
Detection limit of intragenic deletions with targeted array comparative genomic hybridization. PMID:24304607
Genome-wide DNA methylation changes with age in disease-free human skeletal muscle. PMID:24304487
A point mutation in the gene for asparagine-linked glycosylation 10B (Alg10b) causes nonsyndromic hearing impairment in mice (Mus musculus). PMID:24303013
Alternative polyadenylation and differential expression of Shank mRNAs in the synaptic neuropil. PMID:24298140
BCL-XL mediates the strong selective advantage of a 20q11.21 amplification commonly found in human embryonic stem cell cultures. PMID:24286026
Lysine and arginine content of proteins: computational analysis suggests a new tool for solubility design. PMID:24283752
SVD identifies transcript length distribution functions from DNA microarray data and reveals evolutionary forces globally affecting GBM metabolism. PMID:24282503
Rates of evolution of hominoid seminal proteins are correlated with function and expression, rather than mating system. PMID:24281413
Compartmental genomics in living cells revealed by single-cell nanobiopsy. PMID:24279711
DUX4 binding to retroelements creates promoters that are active in FSHD muscle and testis. PMID:24278031
1000 Genomes Selection Browser 1.0: a genome browser dedicated to signatures of natural selection in modern humans. PMID:24275494
The UCSC Genome Browser database: 2014 update. PMID:24270787
Joint linkage and association analysis with exome sequence data implicates SLC25A40 in hypertriglyceridemia. PMID:24268658
Target analysis by integration of transcriptome and ChIP-seq data with BETA. PMID:24263090
Analysis of western lowland gorilla (Gorilla gorilla gorilla) specific Alu repeats. PMID:24262036
Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors. PMID:24257477
Neuropathology of brain and spinal malformations in a case of monosomy 1p36. PMID:24252393
Deep sequencing identification of novel glucocorticoid-responsive miRNAs in apoptotic primary lymphocytes. PMID:24250753
Primary 1,25-dihydroxyvitamin D3 response of the interleukin 8 gene cluster in human monocyte- and macrophage-like cells. PMID:24250750
SNPAAMapper: An efficient genome-wide SNP variant analysis pipeline for next-generation sequencing data. PMID:24250114
Practical guidelines for the comprehensive analysis of ChIP-seq data. PMID:24244136
The dynamic architectural and epigenetic nuclear landscape: developing the genomic almanac of biology and disease. PMID:24242872
HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics. PMID:24240322
Epigenetic regulation and functional characterization of microRNA-142 in mesenchymal cells. PMID:24236112
Transcription factor abundance controlled by an auto-regulatory mechanism involving a transcription start site switch. PMID:24234445
A common set of DNA regulatory elements shapes Drosophila appendages. PMID:24229644
STaRRRT: a table of short tandem repeats in regulatory regions of the human genome. PMID:24228761
Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. PMID:24227676
Efficient cellular fractionation improves RNA sequencing analysis of mature and nascent transcripts from human tissues. PMID:24225116
Polymorphisms of the homologous recombination gene RAD51 in keratoconus and Fuchs endothelial corneal dystrophy. PMID:24223453
General triallelic frequency spectrum under demographic models with variable population size. PMID:24214345
Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki). PMID:24209455
Acetylation of RNA polymerase II regulates growth-factor-induced gene transcription in mammalian cells. PMID:24207025
CanDrA: cancer-specific driver missense mutation annotation with optimized features. PMID:24205039
Transcriptional reprogramming of CD11b+Esam(hi) dendritic cell identity and function by loss of Runx3. PMID:24204843
Coordination of cell proliferation and cell fate determination by CES-1 snail. PMID:24204299
Functional characterization of SIM1-associated enhancers. PMID:24203700
Vitamin D receptor-mediated control of Soggy, Wise, and Hairless gene expression in keratinocytes. PMID:24190897
Using Google blogs and discussions to recommend biomedical resources: a case study. PMID:24180648
Hox in motion: tracking HoxA cluster conformation during differentiation. PMID:24174538
Transcriptome interrogation of human myometrium identifies differentially expressed sense-antisense pairs of protein-coding and long non-coding RNA genes in spontaneous labor at term. PMID:24168098
An evolutionary screen highlights canonical and noncanonical candidate antiviral genes within the primate TRIM gene family. PMID:24158625
Sequence signatures extracted from proximal promoters can be used to predict distal enhancers. PMID:24156763
Mitochondrial sequence variation in African-American primary open-angle glaucoma patients. PMID:24146900
The human constitutive androstane receptor promotes the differentiation and maturation of hepatic-like cells. PMID:24144921
CRISPR interference (CRISPRi) for sequence-specific control of gene expression. PMID:24136345
Sense-antisense gene pairs: sequence, transcription, and structure are not conserved between human and mouse. PMID:24133500
A novel large in-frame deletion within the CACNA1F gene associates with a cone-rod dystrophy 3-like phenotype. PMID:24124559
HTS-DB: an online resource to publish and query data from functional genomics high-throughput siRNA screening projects. PMID:24122843
Dynamic analysis of gene expression and genome-wide transcription factor binding during lineage specification of multipotent progenitors. PMID:24120743
Comprehensive analysis of human endogenous retrovirus group HERV-W locus transcription in multiple sclerosis brain lesions by high-throughput amplicon sequencing. PMID:24109235
Functions and regulation of MUC13 mucin in colon cancer cells. PMID:24097071
afterParty: turning raw transcriptomes into permanent resources. PMID:24093729
Bench-to-bedside review: future novel diagnostics for sepsis - a systems biology approach. PMID:24093155
Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data. PMID:24088262
Eeyore: a novel mouse model of hereditary deafness. PMID:24086324
Female-specific induction of rat pituitary dentin matrix protein-1 by GnRH. PMID:24085820
STAR: an integrated solution to management and visualization of sequencing data. PMID:24078702
BBGRE: brain and body genetic resource exchange. PMID:24077841
Hominoid fission of chromosome 14/15 and the role of segmental duplications. PMID:24077392
The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex. PMID:24076601
A computational model for histone mark propagation reproduces the distribution of heterochromatin in different human cell types. PMID:24069233
Functional analysis of limb enhancers in the developing fin. PMID:24068387
Comparative analysis of context-dependent mutagenesis using human and mouse models. PMID:24058920
46,XY disorder of sex development and developmental delay associated with a novel 9q33.3 microdeletion encompassing NR5A1. PMID:24056159
The Human Genome Project: big science transforms biology and medicine. PMID:24040834
Network-based stratification of tumor mutations. PMID:24037242
CruzDB: software for annotation of genomic intervals with UCSC genome-browser database. PMID:24037212
HINCUTs in cancer: hypoxia-induced noncoding ultraconserved transcripts. PMID:24037088
BAIT: Organizing genomes and mapping rearrangements in single cells. PMID:24028793
An epidemiological investigation of a Forkhead box protein E3 founder mutation underlying the high frequency of sclerocornea, aphakia, and microphthalmia in a Mexican village. PMID:24019743
Selective regulation of lymphopoiesis and leukemogenesis by individual zinc fingers of Ikaros. PMID:24013668
Lizards and LINEs: selection and demography affect the fate of L1 retrotransposons in the genome of the green anole (Anolis carolinensis). PMID:24013105
An X-linked cobalamin disorder caused by mutations in transcriptional coregulator HCFC1. PMID:24011988
Divergent evolutionary and expression patterns between lineage specific new duplicate genes and their parental paralogs in Arabidopsis thaliana. PMID:24009676
Cauli: a mouse strain with an Ift140 mutation that results in a skeletal ciliopathy modelling Jeune syndrome. PMID:24009529
How microRNA and transcription factor co-regulatory networks affect osteosarcoma cell proliferation. PMID:24009496
PAVIS: a tool for Peak Annotation and Visualization. PMID:24008416
Pathway-PDT: a flexible pathway analysis tool for nuclear families. PMID:24006871
Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome. PMID:24003029
Haplotype structure and positive selection at TLR1. PMID:24002163
Consed: a graphical editor for next-generation sequencing. PMID:23995391
Genome-wide copy number variation in sporadic amyotrophic lateral sclerosis in the Turkish population: deletion of EPHA3 is a possible protective factor. PMID:23991104
Spatial compartmentalization at the nuclear periphery characterized by genome-wide mapping. PMID:23987233
A large animal model for CNGB1 autosomal recessive retinitis pigmentosa. PMID:23977260
Identification and dissection of a key enhancer mediating cranial neural crest specific expression of transcription factor, Ets-1. PMID:23969311
Gentrepid V2.0: a web server for candidate disease gene prediction. PMID:23947436
Discovery of cell-type specific regulatory elements in the human genome using differential chromatin modification analysis. PMID:23945931
Accurate molecular diagnosis of phenylketonuria and tetrahydrobiopterin-deficient hyperphenylalaninemias using high-throughput targeted sequencing. PMID:23942198
Bilateral radial ulnar synostosis and vertebral anomalies in a child with a de novo 16p13.3 interstitial deletion. PMID:23936691
A mutation in mouse Pak1ip1 causes orofacial clefting while human PAK1IP1 maps to 6p24 translocation breaking points associated with orofacial clefting. PMID:23935987
Type I IFNs downregulate myeloid cell IFN-γ receptor by inducing recruitment of an early growth response 3/NGFI-A binding protein 1 complex that silences ifngr1 transcription. PMID:23935197
Mapping the human reference genome's missing sequence by three-way admixture in Latino genomes. PMID:23932108
Identification and systematic annotation of tissue-specific differentially methylated regions using the Illumina 450k array. PMID:23919675
HTR4 gene structure and altered expression in the developing lung. PMID:23890215
Detecting and comparing non-coding RNAs in the high-throughput era. PMID:23887659
Computational detection of abundant long-range nucleotide covariation in Drosophila genomes. PMID:23887147
Unraveling genomic variation from next generation sequencing data. PMID:23885890
Discovery of structural alterations in solid tumor oligodendroglioma by single molecule analysis. PMID:23885787
VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer. PMID:23876380
Plot protein: visualization of mutations. PMID:23876180
Major histocompatibility complex genomics and human disease. PMID:23875801
Inhibition of inducible heat shock protein-70 (hsp72) enhances bortezomib-induced cell death in human bladder cancer cells. PMID:23874968
GEMINI: integrative exploration of genetic variation and genome annotations. PMID:23874191
The strength of combined cytogenetic and mate-pair sequencing techniques illustrated by a germline chromothripsis rearrangement involving FOXP2. PMID:23860044
ATP5H/KCTD2 locus is associated with Alzheimer's disease risk. PMID:23857120
Positive effects of methylphenidate on hyperactivity are moderated by monoaminergic gene variants in children with autism spectrum disorders. PMID:23856854
Detection of Human Endogenous Retrovirus K (HERV-K) Transcripts in Human Prostate Cancer Cell Lines. PMID:23847768
lncRNome: a comprehensive knowledgebase of human long noncoding RNAs. PMID:23846593
Genome-wide identification of chromatin transitional regions reveals diverse mechanisms defining the boundary of facultative heterochromatin. PMID:23840609
Connectivity Mapping for Candidate Therapeutics Identification Using Next Generation Sequencing RNA-Seq Data. PMID:23840550
TNFRSF10B polymorphisms and haplotypes associated with increased risk of death in non-small cell lung cancer. PMID:23839018
Combinatorial effects of transposable elements on gene expression and phenotypic robustness in Drosophila melanogaster development. PMID:23833214
The developmental transcriptome of the mosquito Aedes aegypti, an invasive species and major arbovirus vector. PMID:23833213
Germline missense variants in the BTNL2 gene are associated with prostate cancer susceptibility. PMID:23833122
Genomics of sablefish (Anoplopoma fimbria): expressed genes, mitochondrial phylogeny, linkage map and identification of a putative sex gene. PMID:23829495
Browsing (Epi)genomes: a guide to data resources and epigenome browsers for stem cell researchers. PMID:23827707
Ribosomal protein S27-like in colorectal cancer: a candidate for predicting prognoses. PMID:23826192
Modeling exon expression using histone modifications. PMID:23825663
Characterization at nucleotide resolution of the homogeneously staining region sites of insertion in two cancer cell lines. PMID:23821669
Identifying Mendelian disease genes with the variant effect scoring tool. PMID:23819870
Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks. PMID:23818646
IB4-binding sensory neurons in the adult rat express a novel 3' UTR-extended isoform of CaMK4 that is associated with its localization to axons. PMID:23817991
Coordinate expression of transcripts and proteins in platelets. PMID:23813941
NetGestalt: integrating multidimensional omics data over biological networks. PMID:23807191
Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods. PMID:23804401
Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm. PMID:23804400
Reprogramming the chromatin landscape: interplay of the estrogen and glucocorticoid receptors at the genomic level. PMID:23803465
Proteogenomic database construction driven from large scale RNA-seq data. PMID:23802565
Moderation of antipsychotic-induced weight gain by energy balance gene variants in the RUPP autism network risperidone studies. PMID:23799528
Cellular re- and de-programming by microenvironmental memory: why short TGF-β1 pulses can have long effects. PMID:23782569
Distribution of recombination hotspots in the human genome--a comparison of computer simulations with real data. PMID:23776462
Molecular determinants of nucleosome retention at CpG-rich sequences in mouse spermatozoa. PMID:23770822
Viral categorization and discovery in human circulation by transcriptome sequencing. PMID:23764402
Vitamin D induces interleukin-1β expression: paracrine macrophage epithelial signaling controls M. tuberculosis infection. PMID:23762029
Detection of selective sweeps in cattle using genome-wide SNP data. PMID:23758707
Web-based visual analysis for high-throughput genomics. PMID:23758618
Characterization of the DNA methylome and its interindividual variation in human peripheral blood monocytes. PMID:23750642
Characterization of a large human transgene following invasin-mediated delivery in a bacterial artificial chromosome. PMID:23749207
Genome Maps, a new generation genome browser. PMID:23748955
Increased Intragenic IGF2 Methylation is Associated with Repression of Insulator Activity and Elevated Expression in Serous Ovarian Carcinoma. PMID:23745176
Structural dynamics flexibility informs function and evolution at a proteome scale. PMID:23745135
Latent transforming growth factor β-binding protein 4 is downregulated in esophageal cancer via promoter methylation. PMID:23741501
Paleoproteomic study of the Iceman's brain tissue. PMID:23739949
Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast. PMID:23720455
hnRNP A1 and secondary structure coordinate alternative splicing of Mag. PMID:23704325
ELK1 transcription factor linked to dysregulated striatal mu opioid receptor signaling network and OPRM1 polymorphism in human heroin abusers. PMID:23702428
Extensive polymerase pausing during Drosophila axis patterning enables high-level and pliable transcription. PMID:23699410
BAF complexes facilitate decatenation of DNA by topoisomerase IIα. PMID:23698369
The majority of primate-specific regulatory sequences are derived from transposable elements. PMID:23675311
MicroRNA-22 and promoter motif polymorphisms at the Chga locus in genetic hypertension: functional and therapeutic implications for gene expression and the pathogenesis of hypertension. PMID:23674521
High mobility group protein N5 (HMGN5) and lamina-associated polypeptide 2α (LAP2α) interact and reciprocally affect their genome-wide chromatin organization. PMID:23673662
Draft genome sequence of the Tibetan antelope. PMID:23673643
Differences in gastric carcinoma microenvironment stratify according to EBV infection intensity: implications for possible immune adjuvant therapy. PMID:23671415
r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data. PMID:23671339
LMNA-associated cardiocutaneous progeria: an inherited autosomal dominant premature aging syndrome with late onset. PMID:23666920
Twine: display and analysis of cis-regulatory modules. PMID:23658420
DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types. PMID:23657885
DDBJ read annotation pipeline: a cloud computing-based pipeline for high-throughput analysis of next-generation sequencing data. PMID:23657089
Discovering chromatin motifs using FAIRE sequencing and the human diploid genome. PMID:23656909
eXclusion: toward integrating the X chromosome in genome-wide association analyses. PMID:23643377
Hypertension and genetic variation in endothelial-specific genes. PMID:23637959
Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PMID:23637635
C. elegans GATA factors EGL-18 and ELT-6 function downstream of Wnt signaling to maintain the progenitor fate during larval asymmetric divisions of the seam cells. PMID:23633508
The Genomic HyperBrowser: an analysis web server for genome-scale data. PMID:23632163
Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq. PMID:23629695
A comprehensive analysis of adiponectin QTLs using SNP association, SNP cis-effects on peripheral blood gene expression and gene expression correlation identified novel metabolic syndrome (MetS) genes with potential role in carcinogenesis and systemic inflammation. PMID:23628382
ContigScape: a Cytoscape plugin facilitating microbial genome gap closing. PMID:23627759
AnsNGS: An Annotation System to Sequence Variations of Next Generation Sequencing Data for Disease-Related Phenotypes. PMID:23626918
Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. PMID:23622248
Phylogenomics of strongylocentrotid sea urchins. PMID:23617542
Reduced mRNA expression level of corticotropin-releasing hormone-binding protein is associated with aggressive human kidney cancer. PMID:23607589
A powerful and efficient set test for genetic markers that handles confounders. PMID:23599503
Models incorporating chromatin modification data identify functionally important p53 binding sites. PMID:23599002
COHCAP: an integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis. PMID:23598999
Regional modulation of a stochastically expressed factor determines photoreceptor subtypes in the Drosophila retina. PMID:23597484
Characteristics of cross-hybridization and cross-alignment of expression in pseudo-xenograft samples by RNA-Seq and microarrays. PMID:23594746
Divergence of mammalian higher order chromatin structure is associated with developmental loci. PMID:23592965
Alternative promoters regulate cold inducible RNA-binding (CIRP) gene expression and enhance transgene expression in mammalian cells. PMID:23589278
Resources for methylome analysis suitable for gene knockout studies of potential epigenome modifiers. PMID:23587164
Monocular inhibition reveals temporal and spatial changes in gene expression in the primary visual cortex of marmoset. PMID:23576954
Genome-wide prediction of nucleosome occupancy in maize reveals plant chromatin structural features at genes and other elements at multiple scales. PMID:23572549
Rapid and widespread suppression of self-renewal by microRNA-203 during epidermal differentiation. PMID:23571213
Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing. PMID:23562324
Careful selection of reference genes is required for reliable performance of RT-qPCR in human normal and cancer cell lines. PMID:23554992
Biological database of images and genomes: tools for community annotations linking image and genomic information. PMID:23550062
Enabling interspecies epigenomic comparison with CEpBrowser. PMID:23543396
The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. PMID:23537068
Fine-mapping identifies multiple prostate cancer risk loci at 5p15, one of which associates with TERT expression. PMID:23535824
Epigenetic regulation of CD34 and HIF1A expression during the differentiation of human mast cells. PMID:23529663
Soluble guanylate cyclase α1-deficient mice: a novel murine model for primary open angle glaucoma. PMID:23527308
RFECS: a random-forest based algorithm for enhancer identification from chromatin state. PMID:23526891
Elevated rate of fixation of endogenous retroviral elements in Haplorhini TRIM5 and TRIM22 genomic sequences: impact on transcriptional regulation. PMID:23516500
Multiple transcription factor binding sites predict AID targeting in non-Ig genes. PMID:23514741
Dynamic regulation of epigenomic landscapes during hematopoiesis. PMID:23510235
Fatty acid binding protein 3 (fabp3) is associated with insulin, lipids and cardiovascular phenotypes of the metabolic syndrome through epigenetic modifications in a Northern European family population. PMID:23510163
CistromeFinder for ChIP-seq and DNase-seq data reuse. PMID:23508969
Kdm2b maintains murine embryonic stem cell status by recruiting PRC1 complex to CpG islands of developmental genes. PMID:23502314
Modular Digital Course in Undergraduate Neuroscience Education (MDCUNE): A Website Offering Free Digital Tools for Neuroscience Educators. PMID:23494065
An engineering view on megatrends in radiology: digitization to quantitative tools of medicine. PMID:23482650
Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions. PMID:23482648
Meta-analysis of genome-wide association studies in five cohorts reveals common variants in RBFOX1, a regulator of tissue-specific splicing, associated with refractive error. PMID:23474815
Identity-by-descent mapping to detect rare variants conferring susceptibility to multiple sclerosis. PMID:23472070
Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates. PMID:23467541
Increased copy-number and not DNA hypomethylation causes overexpression of the candidate proto-oncogene CYP24A1 in colorectal cancer. PMID:23463632
Hepatocyte nuclear factor 4 alpha and farnesoid X receptor co-regulates gene transcription in mouse livers on a genome-wide scale. PMID:23462932
Self-catalytic DNA depurination underlies human β-globin gene mutations at codon 6 that cause anemias and thalassemias. PMID:23457306
Accurate identification and analysis of human mRNA isoforms using deep long read sequencing. PMID:23450794
Mature microsatellites: mechanisms underlying dinucleotide microsatellite mutational biases in human cells. PMID:23450065
Circular RNAs are a large class of animal RNAs with regulatory potency. PMID:23446348
New insights from existing sequence data: generating breakthroughs without a pipette. PMID:23438857
Identification of candidate transcription factor binding sites in the cattle genome. PMID:23433959
Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution. PMID:23433480
Phospholipase A2 receptor (PLA2R1) sequence variants in idiopathic membranous nephropathy. PMID:23431073
DNA replication timing and higher-order nuclear organization determine single-nucleotide substitution patterns in cancer genomes. PMID:23422670
The genomic signature of trait-associated variants. PMID:23418889
Mutations in SETD2 and genes affecting histone H3K36 methylation target hemispheric high-grade gliomas. PMID:23417712
Identifying recent adaptations in large-scale genomic data. PMID:23415221
Massive-scale gene co-expression network construction and robustness testing using random matrix theory. PMID:23409071
Congenital myasthenic syndromes due to mutations in ALG2 and ALG14. PMID:23404334
pseudoMap: an innovative and comprehensive resource for identification of siRNA-mediated mechanisms in human transcribed pseudogenes. PMID:23396300
TGF-β/Smad2/3 signaling directly regulates several miRNAs in mouse ES cells and early embryos. PMID:23390484
Next-generation sequencing of small RNAs from HIV-infected cells identifies phased microrna expression patterns and candidate novel microRNAs differentially expressed upon infection. PMID:23386435
PRISM offers a comprehensive genomic approach to transcription factor function prediction. PMID:23382538
Application of Top-Down and Bottom-up Systems Approaches in Ruminant Physiology and Metabolism. PMID:23372424
Potential roles of microRNAs in regulating long intergenic noncoding RNAs. PMID:23369519
Atypical rearrangement involving 3'-IGH@ and a breakpoint at least 400 Kb upstream of an intact MYC in a CLL patient with an apparently balanced t(8;14)(q24.1;q32) and negative MYC expression. PMID:23369149
A multispecies polyadenylation site model. PMID:23368518
Visualizing multidimensional cancer genomics data. PMID:23363777
Comparative SRY incorporation on the regulatory regions of pluripotency/differentiation genes in human embryonic carcinoma cells after retinoic acid induction. PMID:23361361
Effects of DNA methylation on nucleosome stability. PMID:23355616
Genome-wide analysis of histone modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica. PMID:23355544
DIP-STR: highly sensitive markers for the analysis of unbalanced genomic mixtures. PMID:23355272
Using whole-exome sequencing to identify inherited causes of autism. PMID:23352163
Identification of rare recurrent copy number variants in high-risk autism families and their prevalence in a large ASD population. PMID:23341896
Human disease-associated genetic variation impacts large intergenic non-coding RNA expression. PMID:23341781
A systematic mapping approach of 16q12.2/FTO and BMI in more than 20,000 African Americans narrows in on the underlying functional variation: results from the Population Architecture using Genomics and Epidemiology (PAGE) study. PMID:23341774
Transcriptional profiling of human endogenous retrovirus group HERV-K(HML-2) loci in melanoma. PMID:23338945
Brk regulates wing disc growth in part via repression of Myc expression. PMID:23337628
Genetic and pathologic evolution of early secondary gliosarcoma. PMID:23324827
Hsa-mir-124-3 CpG island methylation is associated with advanced tumours and disease recurrence of patients with clear cell renal cell carcinoma. PMID:23321515
Birth, decay, and reconstruction of an ancient TRIMCyp gene fusion in primate genomes. PMID:23319649
NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets. PMID:23314324
Genetic variation associated with circulating monocyte count in the eMERGE Network. PMID:23314186
Reference-assisted chromosome assembly. PMID:23307812
Discovery, validation and characterization of Erbb4 and Nrg1 haplotypes using data from three genome-wide association studies of schizophrenia. PMID:23301017
The cytochrome P450 genesis locus: the origin and evolution of animal cytochrome P450s. PMID:23297357
Genetic signatures in choline and 1-carbon metabolism are associated with the severity of hepatic steatosis. PMID:23292069
RNA-guided human genome engineering via Cas9. PMID:23287722
Micro-scale genomic DNA copy number aberrations as another means of mutagenesis in breast cancer. PMID:23284754
StRAP: an integrated resource for profiling high-throughput cancer genomic data from stress response studies. PMID:23284744
CTF: a CRF-based transcription factor binding sites finding system. PMID:23282203
Alt Event Finder: a tool for extracting alternative splicing events from RNA-seq data. PMID:23281921
Genetic studies of complex human diseases: characterizing SNP-disease associations using Bayesian networks. PMID:23281790
Genetic markers of comorbid depression and alcoholism in women. PMID:23278386
First evidence for functional vomeronasal 2 receptor genes in primates. PMID:23269843
CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize. PMID:23269663
GBSA: a comprehensive software for analysing whole genome bisulfite sequencing data. PMID:23268441
1,25-dihydroxyvitamin D(3) regulation of fibroblast growth factor-23 expression in bone cells: evidence for primary and secondary mechanisms modulated by leptin and interleukin-6. PMID:23263654
AT-rich sequence elements promote nascent transcript cleavage leading to RNA polymerase II termination. PMID:23258704
Genome-wide sequencing for the identification of rearrangements associated with Tourette syndrome and obsessive-compulsive disorder. PMID:23253088
Inner ear morphology is perturbed in two novel mouse models of recessive deafness. PMID:23251483
Detecting rare variants for psychiatric disorders using next generation sequencing: a methods primer. PMID:23250814
Respiratory syncytial virus regulates human microRNAs by using mechanisms involving beta interferon and NF-κB. PMID:23249809
miRNA-mediated risk for schizophrenia in 22q11.2 deletion syndrome. PMID:23248646
Evolutionarily conserved histone methylation dynamics during seed life-cycle transitions. PMID:23240039
Histone demethylase Jumonji D3 (JMJD3) as a tumor suppressor by regulating p53 protein nuclear stabilization. PMID:23236496
Analyzing illumina gene expression microarray data from different tissues: methodological aspects of data analysis in the metaxpress consortium. PMID:23236413
TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells. PMID:23233547
Determination of haplotypes at structurally complex regions using emulsion haplotype fusion PCR. PMID:23231411
Sequences associated with centromere competency in the human genome. PMID:23230266
Analysis of copy number variation in Alzheimer's disease in a cohort of clinically characterized and neuropathologically verified individuals. PMID:23227193
iPiG: integrating peptide spectrum matches into genome browser visualizations. PMID:23226516
Somatic neurofibromatosis type 1 (NF1) inactivation characterizes NF1-associated pilocytic astrocytoma. PMID:23222849
Evolution of hemoglobin and its genes. PMID:23209182
A genome-wide association study implicates the APOE locus in nonpathological cognitive ageing. PMID:23207651
Next generation sequencing of CLU, PICALM and CR1: pitfalls and potential solutions. PMID:23205178
Bioinformatics tools allow targeted selection of chromosome enumeration probes and aneuploidy detection. PMID:23204113
Multiple cis-elements and trans-acting factors regulate dynamic spatio-temporal transcription of let-7 in Caenorhabditis elegans. PMID:23201578
Molecular cytogenetic characterization of a non-robertsonian dicentric chromosome 14;19 identified in a girl with short stature and amenorrhea. PMID:23198188
CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization. PMID:23193294
ENCODE data in the UCSC Genome Browser: year 5 update. PMID:23193274
The evolution of the class A scavenger receptors. PMID:23181696
Position-dependent splicing activation and repression by SR and hnRNP proteins rely on common mechanisms. PMID:23175589
Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web. PMID:23172864
The rs1024611 regulatory region polymorphism is associated with CCL2 allelic expression imbalance. PMID:23166687
Polyadenylation-dependent control of long noncoding RNA expression by the poly(A)-binding protein nuclear 1. PMID:23166521
Congenital diaphragmatic hernia interval on chromosome 8p23.1 characterized by genetics and protein interaction networks. PMID:23165946
Telomerase directly regulates NF-κB-dependent transcription. PMID:23159929
Transcriptional silencing of transposons by Piwi and maelstrom and its impact on chromatin state and gene expression. PMID:23159368
Multiple regulatory variants modulate expression of 5-hydroxytryptamine 2A receptors in human cortex. PMID:23158458
The UCSC Genome Browser database: extensions and updates 2013. PMID:23155063
NRE: a tool for exploring neutral loci in the human genome. PMID:23151206
Adaptive efficient compression of genomes. PMID:23146997
HERV-E-mediated modulation of PLA2G4A transcription in urothelial carcinoma. PMID:23145155
Elongation factor 1 alpha1 and genes associated with Usher syndromes are downstream targets of GBX2. PMID:23144817
Expression and promoter analysis of a highly restricted integrin alpha gene in vascular smooth muscle. PMID:23142384
NGS analyses by visualization with Trackster. PMID:23138293
Binary Interval Search: a scalable algorithm for counting interval intersections. PMID:23129298
Cell cycle-related genes as modifiers of age of onset of colorectal cancer in Lynch syndrome: a large-scale study in non-Hispanic white patients. PMID:23125224
Cancer cells preferentially lose small chromosomes. PMID:23124507
Genome-wide association study reveals novel genetic determinants of DNA repair capacity in lung cancer. PMID:23108145
A hybrid distance measure for clustering expressed sequence tags originating from the same gene family. PMID:23071763
Heterogeneity in white blood cells has potential to confound DNA methylation measurements. PMID:23071618
The selector gene Pax7 dictates alternate pituitary cell fates through its pioneer action on chromatin remodeling. PMID:23070814
Demethylation of the aryl hydrocarbon receptor repressor as a biomarker for nascent smokers. PMID:23070629
PDGFR blockade is a rational and effective therapy for NPM-ALK-driven lymphomas. PMID:23064464
Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. PMID:23064229
Defining the status of RNA polymerase at promoters. PMID:23062713
Factors affecting the relative abundance of nuclear copies of mitochondrial DNA (numts) in hominoids. PMID:23053193
CloudMap: a cloud-based pipeline for analysis of mutant genome sequences. PMID:23051646
miR-BAG: bagging based identification of microRNA precursors. PMID:23049860
Extensive evolutionary and functional diversity among mammalian AIM2-like receptors. PMID:23045604
Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity. PMID:23034120
A genome-wide signature of glucocorticoid receptor binding in neuronal PC12 cells. PMID:23031785
Intrafamilial variability for novel TAZ gene mutation: Barth syndrome with dilated cardiomyopathy and heart failure in an infant and left ventricular noncompaction in his great-uncle. PMID:23031367
Stem cell selection in vivo using foamy vectors cures canine pyruvate kinase deficiency. PMID:23028826
Variation in genes related to cochlear biology is strongly associated with adult-onset deafness in border collies. PMID:23028339
CHMP1A encodes an essential regulator of BMI1-INK4A in cerebellar development. PMID:23023333
G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes. PMID:23020263
A model of spatially restricted transcription in opposing gradients of activators and repressors. PMID:23010997
Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells. PMID:23006825
IκBKβ and NFκB1, NSAID use and risk of colorectal cancer in the Colon Cancer Family Registry. PMID:23002237
The Ruby UCSC API: accessing the UCSC genome database using Ruby. PMID:22994508
Transcriptional expression patterns triggered by chemically distinct neuroprotective molecules. PMID:22986168
Evolutionary history and genome organization of DUF1220 protein domains. PMID:22973535
Hypoxic induction of the regulator of G-protein signalling 4 gene is mediated by the hypoxia-inducible factor pathway. PMID:22970249
A complex immunodeficiency is based on U1 snRNP-mediated poly(A) site suppression. PMID:22968171
Expanding the MTM1 mutational spectrum: novel variants including the first multi-exonic duplication and development of a locus-specific database. PMID:22968136
From next-generation sequencing alignments to accurate comparison and validation of single-nucleotide variants: the pibase software. PMID:22965131
Alkbh1 and Tzfp repress a non-repeat piRNA cluster in pachytene spermatocytes. PMID:22965116
Sex-biased genetic effects on gene regulation in humans. PMID:22960374
Spark: a navigational paradigm for genomic data exploration. PMID:22960372
Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse (Mus musculus). PMID:22956910
Teasing apart translational and transcriptional components of stochastic variations in eukaryotic gene expression. PMID:22956896
Linking disease associations with regulatory information in the human genome. PMID:22955986
A highly integrated and complex PPARGC1A transcription factor binding network in HepG2 cells. PMID:22955979
Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values. PMID:22954632
HighSSR: high-throughput SSR characterization and locus development from next-gen sequencing data. PMID:22954626
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. PMID:22950945
Phylogenetic and physicochemical analyses enhance the classification of rare nonsynonymous single nucleotide variants in type 1 and 2 long-QT syndrome. PMID:22949429
Deciphering the transcriptional regulation of microRNA genes in humans with ACTLocater. PMID:22941648
siSPOTR: a tool for designing highly specific and potent siRNAs for human and mouse. PMID:22941647
Contribution of global rare copy-number variants to the risk of sporadic congenital heart disease. PMID:22939634
Gene isoform specificity through enhancer-associated antisense transcription. PMID:22937057
Transcriptome sequencing in Sezary syndrome identifies Sezary cell and mycosis fungoides-associated lncRNAs and novel transcripts. PMID:22936659
Transcriptional architecture and chromatin landscape of the core circadian clock in mammals. PMID:22936566
Identifying ChIP-seq enrichment using MACS. PMID:22936215
Tissue-restricted transcription from a conserved intragenic CpG island in the Klf1 gene in mice. PMID:22933519
Identification and analysis of pig chimeric mRNAs using RNA sequencing data. PMID:22925561
H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells. PMID:22920947
Prediction of gene network models in limb muscle precursors. PMID:22917675
Genetics and regulatory impact of alternative polyadenylation in human B-lymphoblastoid cells. PMID:22916029
Functional characterization of tissue-specific enhancers in the DLX5/6 locus. PMID:22914741
Hydrogen peroxide alters splicing of soluble guanylyl cyclase and selectively modulates expression of splicing regulators in human cancer cells. PMID:22911749
Detecting transcription of ribosomal protein pseudogenes in diverse human tissues from RNA-seq data. PMID:22908858
The UCSC genome browser and associated tools. PMID:22908213
Mating of the stichotrichous ciliate Oxytricha trifallax induces production of a class of 27 nt small RNAs derived from the parental macronucleus. PMID:22900016
Next-generation sequencing data interpretation: enhancing reproducibility and accessibility. PMID:22898652
Mild paroxysmal kinesigenic dyskinesia caused by PRRT2 missense mutation with reduced penetrance. PMID:22895590
Genome-wide association study of obsessive-compulsive disorder. PMID:22889921
A beginners guide to SNP calling from high-throughput DNA-sequencing data. PMID:22886560
Copy number variation of the APC gene is associated with regulation of bone mineral density. PMID:22884971
Points of view: Managing deep data in genome browsers. PMID:22874978
ChIPnorm: a statistical method for normalizing and identifying differential regions in histone modification ChIP-seq libraries. PMID:22870189
X chromosome gene methylation in peripheral lymphocytes from monozygotic twins discordant for scleroderma. PMID:22861365
EnigmaVis: online interactive visualization of genome-wide association studies of the Enhancing NeuroImaging Genetics through Meta-Analysis (ENIGMA) consortium. PMID:22856375
PACSIN2 polymorphism influences TPMT activity and mercaptopurine-related gastrointestinal toxicity. PMID:22846425
Genomic imprinting absent in Drosophila melanogaster adult females. PMID:22840398
Uncovering MicroRNA and Transcription Factor Mediated Regulatory Networks in Glioblastoma. PMID:22829753
Seqcrawler: biological data indexing and browsing platform. PMID:22827839
The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding. PMID:22827163
Composition and organization of active centromere sequences in complex genomes. PMID:22817545
Human centromere genomics: now it's personal. PMID:22801774
Regulatory element copy number differences shape primate expression profiles. PMID:22797897
REST regulates the pool size of the different neural lineages by restricting the generation of neurons and oligodendrocytes from neural stem/progenitor cells. PMID:22791895
CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis. PMID:22789590
The cis-regulatory code of Hox function in Drosophila. PMID:22781127
Chemical and biochemical approaches in the study of histone methylation and demethylation. PMID:22777714
Use of mutagenesis, genetic mapping and next generation transcriptomics to investigate insecticide resistance mechanisms. PMID:22768270
ABCC6 expression is regulated by CCAAT/enhancer-binding protein activating a primate-specific sequence located in the first intron of the gene. PMID:22763786
Do human transposable element small RNAs serve primarily as genome defenders or genome regulators? PMID:22754749
Mutations in DPAGT1 cause a limb-girdle congenital myasthenic syndrome with tubular aggregates. PMID:22742743
piRNAs can trigger a multigenerational epigenetic memory in the germline of C. elegans. PMID:22738725
Bovine polledness--an autosomal dominant trait with allelic heterogeneity. PMID:22737241
SplicerEX: a tool for the automated detection and classification of mRNA changes from conventional and splice-sensitive microarray expression data. PMID:22736799
Deletion of a conserved regulatory element required for Hmx1 expression in craniofacial mesenchyme in the dumbo rat: a newly identified cause of congenital ear malformation. PMID:22736458
Research resource: whole transcriptome RNA sequencing detects multiple 1α,25-dihydroxyvitamin D(3)-sensitive metabolic pathways in developing zebrafish. PMID:22734042
Molecular evaluation of human ubiquilin 2 gene PXX domain in familial frontotemporal dementia patients. PMID:22729385
Genome-wide DNA methylation profiling of non-small cell lung carcinomas. PMID:22726460
Regulation of alternative splicing by the circadian clock and food related cues. PMID:22721557
Leukocyte function-associated antigen-1/intercellular adhesion molecule-1 interaction induces a novel genetic signature resulting in T-cells refractory to transforming growth factor-β signaling. PMID:22707713
Prioritizing cancer-related key miRNA-target interactions by integrative genomics. PMID:22705797
Developing and applying heterogeneous phylogenetic models with XRate. PMID:22693624
The NIH Roadmap Epigenomics Program data resource. PMID:22690667
Evidence for additional FREM1 heterogeneity in Manitoba oculotrichoanal syndrome. PMID:22690109
Multi-locus phylogeographic and population genetic analysis of Anolis carolinensis: historical demography of a genomic model species. PMID:22685573
Probing the Xenopus laevis inner ear transcriptome for biological function. PMID:22676585
Transcriptional networks driving enhancer function in the CFTR gene. PMID:22671145
Regulated Expression of Chromobox Homolog 5 Revealed in Tumors of Apc(Min) (/+) ROSA11 Gene Trap Mice. PMID:22670227
Prenatal famine and genetic variation are independently and additively associated with DNA methylation at regulatory loci within IGF2/H19. PMID:22666415
Inference of tumor phylogenies from genomic assays on heterogeneous samples. PMID:22654484
Transcripts with in silico predicted RNA structure are enriched everywhere in the mouse brain. PMID:22651826
Transcriptome of the adult female malaria mosquito vector Anopheles albimanus. PMID:22646700
Mutation at the human D1S80 minisatellite locus. PMID:22645469
Genetics of IL28B and HCV--response to infection and treatment. PMID:22641049
ILF-3 is a regulator of the neural plate border marker Zic1 in chick embryos. PMID:22639388
Savant Genome Browser 2: visualization and analysis for population-scale genomics. PMID:22638571
Frequent gain and loss of intronic splicing regulatory elements during the evolution of vertebrates. PMID:22619362
CpG island hypermethylation-associated silencing of small nucleolar RNAs in human cancer. PMID:22617881
iHAT: interactive hierarchical aggregation table for genetic association data. PMID:22607364
Rapid transcriptional pulsing dynamics of high expressing retroviral transgenes in embryonic stem cells. PMID:22606340
Comparative Genomics Reveals Key Gain-of-Function Events in Foxp3 during Regulatory T Cell Evolution. PMID:22590469
Tyrosine hydroxylase gene: another piece of the genetic puzzle of Parkinson's disease. PMID:22583432
Genomics and proteomics of vertebrate cholesterol ester lipase (LIPA) and cholesterol 25-hydroxylase (CH25H). PMID:22582164
Comparative studies of glycosylphosphatidylinositol-anchored high-density lipoprotein-binding protein 1: evidence for a eutherian mammalian origin for the GPIHBP1 gene from an LY6-like gene. PMID:22582156
A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance. PMID:22581228
BEDOPS: high-performance genomic feature operations. PMID:22576172
Genome-wide association study of multiple sclerosis confirms a novel locus at 5p13.1. PMID:22570697
Shape-based alignment of genomic landscapes in multi-scale resolution. PMID:22561376
Linking the epigenome to the genome: correlation of different features to DNA methylation of CpG islands. PMID:22558141
A high-throughput resequencing microarray for autosomal dominant spastic paraplegia genes. PMID:22552817
Gene regulation is governed by a core network in hepatocellular carcinoma. PMID:22548756
The super elongation complex family of RNA polymerase II elongation factors: gene target specificity and transcriptional output. PMID:22547686
Orangutan Alu quiescence reveals possible source element: support for ancient backseat drivers. PMID:22541534
Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution. PMID:22539649
Pathway analyses identify TGFBR2 as potential breast cancer susceptibility gene: results from a consortium study among Asians. PMID:22539603
Meiosis-induced alterations in transcript architecture and noncoding RNA expression in S. cerevisiae. PMID:22539527
Primates and mouse NumtS in the UCSC Genome Browser. PMID:22536961
Comparative analysis and visualization of multiple collinear genomes. PMID:22536897
Dark Matter RNA: Existence, Function, and Controversy. PMID:22536205
The distribution of a germline methylation marker suggests a regional mechanism of LINE-1 silencing by the piRNA-PIWI system. PMID:22530917
PSORS2 is due to mutations in CARD14. PMID:22521418
Sequence and expression analysis of gaps in human chromosome 20. PMID:22510267
Global methylation patterns in idiopathic pulmonary fibrosis. PMID:22506007
Case-control admixture mapping in Latino populations enriches for known asthma-associated genes. PMID:22502797
Normalization, bias correction, and peak calling for ChIP-seq. PMID:22499706
Adaptor protein LNK is a negative regulator of brain neural stem cell proliferation after stroke. PMID:22496561
Search for an aetiological virus candidate in chronic lymphocytic leukaemia by extensive transcriptome analysis. PMID:22489537
Analysis of copy number variation in Alzheimer's disease: the NIALOAD/ NCRAD Family Study. PMID:22486522
Diverse forms of RPS9 splicing are part of an evolving autoregulatory circuit. PMID:22479208
"Guilt by association" is the exception rather than the rule in gene networks. PMID:22479173
Meta-analyses of genome-wide linkage scans of anxiety-related phenotypes. PMID:22473089
Integration of microarray technology into prenatal diagnosis: counselling issues generated during the NICHD clinical trial. PMID:22467170
A novel ChREBP isoform in adipose tissue regulates systemic glucose metabolism. PMID:22466288
TACC2 is an androgen-responsive cell cycle regulator promoting androgen-mediated and castration-resistant growth of prostate cancer. PMID:22456197
Distinct contributions of replication and transcription to mutation rate variation of human genomes. PMID:22449396
An integrative genomic analysis of the superior fecundity phenotype in QSi5 mice. PMID:22447533
The SLC4A1 gene is under differential selective pressure in primates infected by Plasmodium falciparum and related parasites. PMID:22426110
Proteome-wide discovery of evolutionary conserved sequences in disordered regions. PMID:22416277
Visualizing next-generation sequencing data with JBrowse. PMID:22411711
Vertebrate hepatic lipase genes and proteins: a review supported by bioinformatic studies. PMID:22408368
Functional and genetic analysis of haplotypic sequence variation at the nicastrin genomic locus. PMID:22405046
Bioinformatic Resources of microRNA Sequences, Gene Targets, and Genetic Variation. PMID:22403585
Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas. PMID:22403401
Identification and properties of 1,119 candidate lincRNA loci in the Drosophila melanogaster genome. PMID:22403033
Reactive oxygen species suppress cardiac NaV1.5 expression through Foxo1. PMID:22400069
Mapping and functional characterisation of a CTCF-dependent insulator element at the 3' border of the murine Scl transcriptional domain. PMID:22396734
REST-mediated recruitment of polycomb repressor complexes in mammalian cells. PMID:22396653
The MuvB complex sequentially recruits B-Myb and FoxM1 to promote mitotic gene expression. PMID:22391450
Evolutionary meta-analysis of association studies reveals ancient constraints affecting disease marker discovery. PMID:22389448
Transcription factor binding site redundancy in embryonic enhancers of the Drosophila bithorax complex. PMID:22384371
Genome-wide analysis of Epstein-Barr virus Rta DNA binding. PMID:22379087
Dynamic microRNA gene transcription and processing during T cell development. PMID:22379031
ChromHMM: automating chromatin-state discovery and characterization. PMID:22373907
Prioritizing single-nucleotide variations that potentially regulate alternative splicing. PMID:22373210
A transcriptional regulatory role of the THAP11-HCF-1 complex in colon cancer cell function. PMID:22371484
Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics. PMID:22369646
Polycomb repressive complex 2-dependent and -independent functions of Jarid2 in transcriptional regulation in Drosophila. PMID:22354997
Modeling RNA degradation for RNA-Seq with applications. PMID:22353193
Depletion of RUNX1/ETO in t(8;21) AML cells leads to genome-wide changes in chromatin structure and transcription factor binding. PMID:22343733
Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function. PMID:22328084
Target gene expression levels and competition between transfected and endogenous microRNAs are strong confounding factors in microRNA high-throughput experiments. PMID:22325809
Resequencing candidate genes implicates rare variants in asthma susceptibility. PMID:22325360
RYBP-PRC1 complexes mediate H2A ubiquitylation at polycomb target sites independently of PRC2 and H3K27me3. PMID:22325148
Allelic imbalance in Drosophila hybrid heads: exons, isoforms, and evolution. PMID:22319150
Elevated and sustained expression of the transcription factors Egr1 and Egr2 controls NKT lineage differentiation in response to TCR signaling. PMID:22306690
Small-molecule-induced DNA damage identifies alternative DNA structures in human genes. PMID:22306580
Improved measurements of RNA structure conservation with generalized centroid estimators. PMID:22303350
Genome-wide landscape of liver X receptor chromatin binding and gene regulation in human macrophages. PMID:22292898
GSVD comparison of patient-matched normal and tumor aCGH profiles reveals global copy-number alterations predicting glioblastoma multiforme survival. PMID:22291905
Global analysis of DNA methylation in early-stage liver fibrosis. PMID:22281153
Molecular diagnosis of infantile mitochondrial disease with targeted next-generation sequencing. PMID:22277967
miRdSNP: a database of disease-associated SNPs and microRNA target sites on 3'UTRs of human genes. PMID:22276777
ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites. PMID:22253291
RNA deep sequencing reveals differential microRNA expression during development of sea urchin and sea star. PMID:22216218
"Calling cards" for DNA-binding proteins in mammalian cells. PMID:22214611
Acute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity. PMID:22210859
Identifying elemental genomic track types and representing them uniformly. PMID:22208806
Human box C/D snoRNA processing conservation across multiple cell types. PMID:22199253
Phenotype-specific effect of chromosome 1q21.1 rearrangements and GJA5 duplications in 2436 congenital heart disease patients and 6760 controls. PMID:22199024
OPRM1 and EGFR contribute to skin pigmentation differences between Indigenous Americans and Europeans. PMID:22198722
Molecular mechanisms of EGF signaling-dependent regulation of pipe, a gene crucial for dorsoventral axis formation in Drosophila. PMID:22198544
The little elongation complex regulates small nuclear RNA transcription. PMID:22195968
Identification of novel androgen-regulated pathways and mRNA isoforms through genome-wide exon-specific profiling of the LNCaP transcriptome. PMID:22194994
A distal modular enhancer complex acts to control pituitary- and nervous system-specific expression of the LHX3 regulatory gene. PMID:22194342
A computational pipeline for comparative ChIP-seq analyses. PMID:22179591
Parent-of-origin effects in SOX2 anophthalmia syndrome. PMID:22171155
Analysis of cancer metabolism with high-throughput technologies. PMID:22166000
Comparative Structures and Evolution of Vertebrate Carboxyl Ester Lipase (CEL) Genes and Proteins with a Major Role in Reverse Cholesterol Transport. PMID:22162806
Polymorphic NumtS trace human population relationships. PMID:22160368
Integration of Elf-4 into stem/progenitor and erythroid regulatory networks through locus-wide chromatin studies coupled with in vivo functional validation. PMID:22158964
Leiomodin 1, a new serum response factor-dependent target gene expressed preferentially in differentiated smooth muscle cells. PMID:22157009
Overview of biological database mapping services for interoperation between different 'omics' datasets. PMID:22155608
Increased copy number for methylated maternal 15q duplications leads to changes in gene and protein expression in human cortical samples. PMID:22152151
The chromatin-binding protein HMGN3 stimulates histone acetylation and transcription across the Glyt1 gene. PMID:22150271
Identification of a genomic reservoir for new TRIM genes in primate genomes. PMID:22144910
RecountDB: a database of mapped and count corrected transcribed sequences. PMID:22139942
Genome-wide copy number variation study associates metabotropic glutamate receptor gene networks with attention deficit hyperactivity disorder. PMID:22138692
Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster. PMID:22135405
Global mapping of H3K4me1 and H3K4me3 reveals the chromatin state-based cell type-specific gene regulation in human Treg cells. PMID:22132139
Gene Array Analyzer: alternative usage of gene arrays to study alternative splicing events. PMID:22123740
Using Sybil for interactive comparative genomics of microbes on the web. PMID:22121156
Erroneous attribution of relevant transcription factor binding sites despite successful prediction of cis-regulatory modules. PMID:22115527
The chromosome 2p21 region harbors a complex genetic architecture for association with risk for renal cell carcinoma. PMID:22113997
Heat shock factor binding in Alu repeats expands its involvement in stress through an antisense mechanism. PMID:22112862
The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome. PMID:22102592
GenomeView: a next-generation genome browser. PMID:22102585
Distinct association between aberrant methylation of Wnt inhibitors and genetic alterations in acute myeloid leukaemia. PMID:22095226
Characterizing complex structural variation in germline and somatic genomes. PMID:22094265
Functional analysis of APOE locus genetic variation implicates regional enhancers in the regulation of both TOMM40 and APOE. PMID:22089642
DBTSS: DataBase of Transcriptional Start Sites progress report in 2012. PMID:22086958
The UCSC Genome Browser database: extensions and updates 2011. PMID:22086951
DARC alleles and Duffy phenotypes in African Americans. PMID:22082243
RNA targets of wild-type and mutant FET family proteins. PMID:22081015
Tbx20 regulates a genetic program essential to adult mouse cardiomyocyte function. PMID:22080862
The UCSC Archaeal Genome Browser: 2012 update. PMID:22080555
ENCODE whole-genome data in the UCSC Genome Browser: update 2012. PMID:22075998
Genome-wide binding map of the HIV-1 Tat protein to the human genome. PMID:22073215
A role for insulator elements in the regulation of gene expression response to hypoxia. PMID:22067454
The CHR promoter element controls cell cycle-dependent gene transcription and binds the DREAM and MMB complexes. PMID:22064854
HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. PMID:22064851
Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain. PMID:22056773
Cluster K mycobacteriophages: insights into the evolutionary origins of mycobacteriophage TM4. PMID:22053209
SNOntology: Myriads of novel snoRNAs or just a mirage? PMID:22047601
C21orf91 genotypes correlate with herpes simplex labialis (cold sore) frequency: description of a cold sore susceptibility gene. PMID:22039568
TIP: a probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles. PMID:22039215
Genetic variants associated with the white blood cell count in 13,923 subjects in the eMERGE Network. PMID:22037903
SOX10 regulates expression of the SH3-domain kinase binding protein 1 (Sh3kbp1) locus in Schwann cells via an alternative promoter. PMID:22037207
Exploratory analysis of genomic segmentations with Segtools. PMID:22029426
Characterization and potential functional significance of human-chimpanzee large INDEL variation. PMID:22024410
Intronic L1 retrotransposons and nested genes cause transcriptional interference by inducing intron retention, exonization and cryptic polyadenylation. PMID:22022525
Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping. PMID:22022279
The reference human nuclear mitochondrial sequences compilation validated and implemented on the UCSC genome browser. PMID:22013967
In utero exposures, infant growth, and DNA methylation of repetitive elements and developmentally related genes in human placenta. PMID:22005006
Tumor-specific usage of alternative transcription start sites in colorectal cancer identified by genome-wide exon array analysis. PMID:21999571
Proceedings of the Tenth Annual UT-ORNL-KBRIN Bioinformatics Summit 2011. PMID:21999392
S-MART, a software toolbox to aid RNA-Seq data analysis. PMID:21998740
Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes. PMID:21994248
Evidence of abundant stop codon readthrough in Drosophila and other metazoa. PMID:21994247
Pico-inplace-inversions between human and chimpanzee. PMID:21994225
Hydroxyurea induces de novo copy number variants in human cells. PMID:21987784
Genome-wide mapping of Sox6 binding sites in skeletal muscle reveals both direct and indirect regulation of muscle terminal differentiation by Sox6. PMID:21985497
The UCSC Genome Browser. PMID:21975940
A method for inferring the rate of occurrence and fitness effects of advantageous mutations. PMID:21954160
Beyond genome-wide association studies: new strategies for identifying genetic determinants of hypertension. PMID:21953487
Pybedtools: a flexible Python library for manipulating genomic datasets and annotations. PMID:21949271
iCTNet: a Cytoscape plugin to produce and analyze integrative complex traits networks. PMID:21943367
BitterDB: a database of bitter compounds. PMID:21940398
Dissecting the transcriptional regulatory properties of human chromosome 16 highly conserved non-coding regions. PMID:21935474
Neisseria Base: a comparative genomics database for Neisseria meningitidis. PMID:21930505
An integrative genomic approach identifies p73 and p63 as activators of miR-200 microRNA family transcription. PMID:21917857
A novel application of pattern recognition for accurate SNP and indel discovery from high-throughput data: targeted resequencing of the glucocorticoid receptor co-chaperone FKBP5 in a Caucasian population. PMID:21917492
4040 SNPs for genomic analysis in the rhesus macaque (Macaca mulatta). PMID:21907785
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. PMID:21890647
FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context. PMID:21884636
Protein-binding microarray analysis of tumor suppressor AP2α target gene specificity. PMID:21876733
Hypomethylation of functional retrotransposon-derived genes in the human placenta. PMID:21874386
Evaluation of candidate genes from orphan FEB and GEFS+ loci by analysis of human brain gene expression atlases. PMID:21858011
PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data. PMID:21851591
Variants on chromosome 6p22.3 associated with blood pressure in the HyperGEN study: follow-up of FBPP quantitative trait loci. PMID:21850057
Molecular characterization of Tob1 in muscle development in pigs. PMID:21845080
Hormone-dependent expression of a steroidogenic acute regulatory protein natural antisense transcript in MA-10 mouse tumor Leydig cells. PMID:21829656
Molecular dissection of cis-regulatory modules at the Drosophila bithorax complex reveals critical transcription factor signature motifs. PMID:21821017
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. PMID:21816040
Sequencing of high-complexity DNA pools for identification of nucleotide and structural variants in regions associated with complex traits. PMID:21811304
Clinical validation of a genetic model to estimate the risk of developing choroidal neovascular age-related macular degeneration. PMID:21807600
A whole-genome analysis of premature termination codons. PMID:21803148
ChIP-seq defined genome-wide map of TGFβ/SMAD4 targets: implications with clinical outcome of ovarian cancer. PMID:21799915
In vivo neuronal subtype-specific targets of Atoh1 (Math1) in dorsal spinal cord. PMID:21795538
Efficient internal exon recognition depends on near equal contributions from the 3' and 5' splice sites. PMID:21795381
High resolution detection and analysis of CpG dinucleotides methylation using MBD-Seq technology. PMID:21779396
Identification of an epigenetic biomarker panel with high sensitivity and specificity for colorectal cancer and adenomas. PMID:21777459
Making whole genome multiple alignments usable for biologists. PMID:21775304
Identifying functional single nucleotide polymorphisms in the human CArGome. PMID:21771879
Evidence for post-transcriptional regulation of clustered microRNAs in Drosophila. PMID:21771325
Alzheimer's disease genes are associated with measures of cognitive ageing in the lothian birth cohorts of 1921 and 1936. PMID:21766012
Deletions of 11q22.3-q25 are associated with atypical lung carcinoids and poor clinical outcome. PMID:21763262
Long range regulation of human FXN gene expression. PMID:21760943
Reactome pathway analysis to enrich biological discovery in proteomics data sets. PMID:21751369
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. PMID:21750106
Evolution of the Alx homeobox gene family: parallel retention and independent loss of the vertebrate Alx3 gene. PMID:21740507
Mutational analysis of 12 patients with the phenotype of Ehlers-Danlos syndrome type VIB shows no linkage to the zinc transporter gene SLC39A13. PMID:21739577
Sch9 regulates ribosome biogenesis via Stb3, Dot6 and Tod6 and the histone deacetylase complex RPD3L. PMID:21730963
Transcription factor AP1 potentiates chromatin accessibility and glucocorticoid receptor binding. PMID:21726817
Exploring the selective constraint on the sizes of insertions and deletions in 5' untranslated regions in mammals. PMID:21726469
Activation of Src and transformation by an RPTPα splice mutant found in human tumours. PMID:21725282
Tissue-specific prediction of directly regulated genes. PMID:21724591
A peroxisome proliferator-activated receptor gamma (PPARgamma)/PPARgamma coactivator 1beta autoregulatory loop in adipocyte mitochondrial function. PMID:21719705
Differential activity by polymorphic variants of a remote enhancer that supports galanin expression in the hypothalamus and amygdala: implications for obesity, depression and alcoholism. PMID:21716262
Association of Rad51 polymorphism with DNA repair in BRCA1 mutation carriers and sporadic breast cancer risk. PMID:21708019
High-throughput mapping of the promoters of the mouse olfactory receptor genes reveals a new type of mammalian promoter and provides insight into olfactory receptor gene regulation. PMID:21705439
The Strategies WDK: a graphical search interface and web development kit for functional genomics databases. PMID:21705364
Chromatin structure characteristics of pre-miRNA genomic sequences. PMID:21702984
Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spots. PMID:21697099
Identification of ATPAF1 as a novel candidate gene for asthma in children. PMID:21696813
Proteomic patterns of cervical cancer cell lines, a network perspective. PMID:21696634
Comprehensive field synopsis and systematic meta-analyses of genetic association studies in cutaneous melanoma. PMID:21693730
MicroRNA regulation of expression of the cystic fibrosis transmembrane conductance regulator gene. PMID:21689072
Neurexin-1 and frontal lobe white matter: an overlapping intermediate phenotype for schizophrenia and autism spectrum disorders. PMID:21687627
The role of the effective population size in compensatory evolution. PMID:21680889
Characterization of autosomal copy-number variation in African Americans: the HyperGEN Study. PMID:21673747
Substitution patterns are GC-biased in divergent sequences across the metazoans. PMID:21670083
Three tiers of genome evolution in reptiles. PMID:21669810
Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences. PMID:21669002
Genomic Copy Number Analysis in Alzheimer's Disease and Mild Cognitive Impairment: An ADNI Study. PMID:21660214
Discrete regulatory regions control early and late expression of D-Pax2 during external sensory organ development. PMID:21644243
Analysis of DNA repair gene polymorphisms and survival in low-grade and anaplastic gliomas. PMID:21643987
Identification of novel targets of CSL-dependent Notch signaling in hematopoiesis. PMID:21637838
Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis. PMID:21636662
Retrotransposition of marked SVA elements by human L1s in cultured cells. PMID:21636526
Distinguishing arrhythmogenic right ventricular cardiomyopathy/dysplasia-associated mutations from background genetic noise. PMID:21636032
Cyclic regulation of apoptotic gene expression in the mouse oviduct. PMID:21635812
Using MACS to identify peaks from ChIP-Seq data. PMID:21633945
17p13.3 microduplications are associated with split-hand/foot malformation and long-bone deficiency (SHFLD). PMID:21629300
The membrane-spanning 4-domains, subfamily A (MS4A) gene cluster contains a common variant associated with Alzheimer's disease. PMID:21627779
Physical confirmation and mapping of overlapping rat mammary carcinoma susceptibility QTLs, Mcs2 and Mcs6. PMID:21625632
Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project. PMID:21596777
RAD21 cooperates with pluripotency transcription factors in the maintenance of embryonic stem cell identity. PMID:21589869
PSAR: measuring multiple sequence alignment reliability by probabilistic sampling. PMID:21576232
Complete exon sequencing of all known Usher syndrome genes greatly improves molecular diagnosis. PMID:21569298
Comparative studies of vertebrate lipoprotein lipase: a key enzyme of very low density lipoprotein metabolism. PMID:21561822
mirConnX: condition-specific mRNA-microRNA network integrator. PMID:21558324
An evolutionarily conserved three-dimensional structure in the vertebrate Irx clusters facilitates enhancer sharing and coregulation. PMID:21556064
The role of indirect connections in gene networks in predicting function. PMID:21551147
Genome-wide copy-number variation analysis identifies common genetic variants at 20p13 associated with aggressiveness of prostate cancer. PMID:21551127
Genomic and biochemical insights into the specificity of ETS transcription factors. PMID:21548782
Polymorphisms in WNT6 and WNT10A and colorectal adenoma risk. PMID:21547848
Novel copy number variants in children with autism and additional developmental anomalies. PMID:21547721
Neuroimaging measures as endophenotypes in Alzheimer's disease. PMID:21547229
CompaGB: An open framework for genome browsers comparison. PMID:21542900
Brief communication: DNA from early Holocene American dog. PMID:21541929
A sustained dietary change increases epigenetic variation in isogenic mice. PMID:21541011
Replication of TCF4 through association and linkage studies in late-onset Fuchs endothelial corneal dystrophy. PMID:21533127
Targeting of the SUN protein Mps3 to the inner nuclear membrane by the histone variant H2A.Z. PMID:21518795
Comparative analysis of the primate X-inactivation center region and reconstruction of the ancestral primate XIST locus. PMID:21518738
Adaptive informatics for multifactorial and high-content biological data. PMID:21516115
A multiplex RNA-seq strategy to profile poly(A+) RNA: application to analysis of transcription response and 3' end formation. PMID:21515359
cis-regulatory mutations are a genetic cause of human limb malformations. PMID:21509892
Methylation and loss of Secreted Frizzled-Related Protein 3 enhances melanoma cell migration and invasion. PMID:21494614
BamTools: a C++ API and toolkit for analyzing and managing BAM files. PMID:21493652
High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species. PMID:21478888
Serum response factor-dependent MicroRNAs regulate gastrointestinal smooth muscle cell phenotypes. PMID:21473868
The FaceBase Consortium: a comprehensive program to facilitate craniofacial research. PMID:21458441
A genome-wide comparison of the functional properties of rare and common genetic variants in humans. PMID:21457907
Control of pelvic girdle development by genes of the Pbx family and Emx2. PMID:21455939
hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data. PMID:21450710
Rice-Map: a new-generation rice genome browser. PMID:21450055
MISC-1/OGC links mitochondrial metabolism, apoptosis and insulin secretion. PMID:21448454
Genome-wide target profiling of piggyBac and Tol2 in HEK 293: pros and cons for gene discovery and gene therapy. PMID:21447194
Replication stress induces 53BP1-containing OPT domains in G1 cells. PMID:21444690
Mapping and analysis of chromatin state dynamics in nine human cell types. PMID:21441907
MicroRNA genes derived from repetitive elements and expanded by segmental duplication events in mammalian genomes. PMID:21436881
HOCTAR database: a unique resource for microRNA target prediction. PMID:21435384
Systematic polymorphism discovery after genome-wide identification of potential susceptibility loci in a hereditary rodent model of human hypertension. PMID:21428728
A genome-wide view of mutation rate co-variation using multivariate analyses. PMID:21426544
A method for visualization of "omic" datasets for sphingolipid metabolism to predict potentially interesting differences. PMID:21415121
Cross species comparison of C/EBPα and PPARγ profiles in mouse and human adipocytes reveals interdependent retention of binding sites. PMID:21410980
Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PMID:21408061
Ordered progression of stage-specific miRNA profiles in the mouse B2 B-cell lineage. PMID:21403133
The accumulation of gene regulation through time. PMID:21398425
hzAnalyzer: detection, quantification, and visualization of contiguous homozygosity in high-density genotyping datasets. PMID:21396103
David Haussler. PMID:21390032
A Slit/miR-218/Robo regulatory loop is required during heart tube formation in zebrafish. PMID:21385766
Genome-wide association study of personality traits in bipolar patients. PMID:21368711
NAViGaTing the micronome--using multiple microRNA prediction databases to identify signalling pathway-associated microRNAs. PMID:21364759
Genome studies at the PAG 2011 conference. PMID:21360134
Meet me halfway: when genomics meets structural bioinformatics. PMID:21350909
Differential expression of non-coding RNAs and continuous evolution of the X chromosome in testicular transcriptome of two mouse species. PMID:21347268
Toward the commoditization of translational genomic research: Design and implementation features of the Galaxy genomic workbench. PMID:21347127
Global analysis of disease-related DNA sequence variation in 10 healthy individuals: implications for whole genome-based clinical diagnostics. PMID:21325948
Perturbation with intrabodies reveals that calpain cleavage is required for degradation of huntingtin exon 1. PMID:21304966
Cocaine dynamically regulates heterochromatin and repetitive element unsilencing in nucleus accumbens. PMID:21300862
Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution. PMID:21298013
Functional relevance of CpG island length for regulation of gene expression. PMID:21288871
Natural and experimental infection of Caenorhabditis nematodes by novel viruses related to nodaviruses. PMID:21283608
Comparative genomic analysis of the Streptococcus dysgalactiae species group: gene content, molecular adaptation, and promoter evolution. PMID:21282711
Identification of a dopaminergic enhancer indicates complexity in vertebrate dopamine neuron phenotype specification. PMID:21276790
Vertebrate endothelial lipase: comparative studies of an ancient gene and protein in vertebrate evolution. PMID:21267636
S-adenosylmethionine decreases lipopolysaccharide-induced phosphodiesterase 4B2 and attenuates tumor necrosis factor expression via cAMP/protein kinase A pathway. PMID:21266552
Lineage-specific evolution of the vertebrate Otopetrin gene family revealed by comparative genomic analyses. PMID:21261979
Automated validation of genetic variants from large databases: ensuring that variant references refer to the same genomic locations. PMID:21258063
Nonsyndromic cleft lip and palate: CRISPLD genes and the folate gene pathway connection. PMID:21254358
Large duplications at reciprocal translocation breakpoints that might be the counterpart of large deletions and could arise from stalled replication bubbles. PMID:21252201
Comprehensive analysis of MGMT promoter methylation: correlation with MGMT expression and clinical response in GBM. PMID:21249131
Transcriptional repression and DNA looping associated with a novel regulatory element in the final exon of the lymphotoxin-β gene. PMID:21248773
Identification of human miRNA precursors that resemble box C/D snoRNAs. PMID:21247878
Next-generation sequencing for HLA typing of class I loci. PMID:21244689
Distinct regulatory programs establish widespread sex-specific alternative splicing in Drosophila melanogaster. PMID:21233220
Shape-based peak identification for ChIP-Seq. PMID:21226895
Quantification of gene transcripts with deep sequencing analysis of gene expression (DSAGE) using 1 to 2 µg total RNA. PMID:21225638
X-MATE: a flexible system for mapping short read data. PMID:21216778
Phylogeny and evolution of aldehyde dehydrogenase-homologous folate enzymes. PMID:21215736
Cyclin D1 is a selective modifier of androgen-dependent signaling and androgen receptor function. PMID:21212260
SeqWare Query Engine: storing and searching sequence data in the cloud. PMID:21210981
Alternative splicing enriched cDNA libraries identify breast cancer-associated transcripts. PMID:21210970
Tabix: fast retrieval of sequence features from generic TAB-delimited files. PMID:21208982
A systematic enhancer screen using lentivector transgenesis identifies conserved and non-conserved functional elements at the Olig1 and Olig2 locus. PMID:21206754
A pituitary-specific enhancer of the POMC gene with preferential activity in corticotrope cells. PMID:21193556
Evolution of gene regulation of pluripotency--the case for wiki tracks at genome browsers. PMID:21190561
Aromatase is a direct target of FOXL2: C134W in granulosa cell tumors via a single highly conserved binding site in the ovarian specific promoter. PMID:21188138
Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs. PMID:21187896
A systems genetic analysis of alcohol drinking by mice, rats and men: influence of brain GABAergic transmission. PMID:21185315
DiNAMIC: a method to identify recurrent DNA copy number aberrations in tumors. PMID:21183584
The Genomic HyperBrowser: inferential genomics at the sequence level. PMID:21182759
A rare myelin protein zero (MPZ) variant alters enhancer activity in vitro and in vivo. PMID:21179557
ASSIMILATOR: a new tool to inform selection of associated genetic variants for functional studies. PMID:21177990
Polycomb preferentially targets stalled promoters of coding and noncoding transcripts. PMID:21177970
Arxes: retrotransposed genes required for adipogenesis. PMID:21177646
seqMINER: an integrated ChIP-seq data interpretation platform. PMID:21177645
Genomic profiling of HMGN1 reveals an association with chromatin at regulatory regions. PMID:21173166
Relationships linking amplification level to gene over-expression in gliomas. PMID:21170331
Molecular evolution and functional divergence of the cytochrome P450 3 (CYP3) Family in Actinopterygii (ray-finned fish). PMID:21170327
SNPexp - A web tool for calculating and visualizing correlation between HapMap genotypes and gene expression levels. PMID:21167019
Molecular characterization of an allelic series of mutations in the mouse Nox3 gene. PMID:21161235
Setting up the JBrowse genome browser. PMID:21154710
Identifying a high fraction of the human genome to be under selective constraint using GERP++. PMID:21152010
Genomic safe harbors permit high β-globin transgene expression in thalassemia induced pluripotent stem cells. PMID:21151124
Five blood pressure loci identified by an updated genome-wide linkage scan: meta-analysis of the Family Blood Pressure Program. PMID:21151011
MU2A--reconciling the genome and transcriptome to determine the effects of base substitutions. PMID:21149339
Sequence-dependent histone variant positioning signatures. PMID:21143812
Serum response factor utilizes distinct promoter- and enhancer-based mechanisms to regulate cytoskeletal gene expression in macrophages. PMID:21135125
Mining Affymetrix microarray data for long non-coding RNAs: altered expression in the nucleus accumbens of heroin abusers. PMID:21128942
Combined linkage and linkage disequilibrium analysis of a motor speech phenotype within families ascertained for autism risk loci. PMID:21125004
Genome-wide association between branch point properties and alternative splicing. PMID:21124863
The reference human genome demonstrates high risk of type 1 diabetes and other disorders. PMID:21121051
Ensemble approach combining multiple methods improves human transcription start site prediction. PMID:21118509
Molecular mechanism by which the nucleoid occlusion factor, SlmA, keeps cytokinesis in check. PMID:21113127
A genetic variant near the PMAIP1/Noxa gene is associated with increased bleomycin sensitivity. PMID:21106707
Human SBK1 is dysregulated in multiple cancers and promotes survival of ovary cancer SK-OV-3 cells. PMID:21104019
Networking erythropoiesis. PMID:21098097
Genome-wide analysis of copy number variation in type 1 diabetes. PMID:21085585
Loss of heterozygosity and SOSTDC1 in adult and pediatric renal tumors. PMID:21080955
Engineering BAC reporter gene constructs for mouse transgenesis. PMID:21080280
Dual DNA methylation patterns in the CNS reveal developmentally poised chromatin and monoallelic expression of critical genes. PMID:21079792
HMMSplicer: a tool for efficient and sensitive discovery of known and novel splice junctions in RNA-Seq data. PMID:21079731
Expression of type II chorionic gonadotropin genes supports a role in the male reproductive system. PMID:21078876
Origin and evolution of a placental-specific microRNA family in the human genome. PMID:21067568
Localizing triplet periodicity in DNA and cDNA sequences. PMID:21059240
Non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association. PMID:21042586
Alternative pre-mRNA splicing regulation in cancer: pathways and programs unhinged. PMID:21041405
Molecular analysis of cataract families in India: new mutations in the CRYBB2 and GJA3 genes and rare polymorphisms. PMID:21031021
Ancient and recent adaptive evolution of primate non-homologous end joining genes. PMID:20975951
CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data. PMID:20972221
The GMOD Drupal bioinformatic server framework. PMID:20971988
REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila. PMID:20965965
FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data. PMID:20964841
In vitro screening for population variability in chemical toxicity. PMID:20952501
Generating and navigating proteome maps using mass spectrometry. PMID:20944666
Characterization of a mutation commonly associated with persistent stuttering: evidence for a founder mutation. PMID:20944643
Discovery and characterization of mammalian endogenous parvoviruses. PMID:20943964
Genome-wide distribution of macroH2A1 histone variants in mouse liver chromatin. PMID:20937776
The evolution and expression of the snaR family of small non-coding RNAs. PMID:20935053
Mutations in WDR62, encoding a centrosome-associated protein, cause microcephaly with simplified gyri and abnormal cortical architecture. PMID:20890278
Defining hypo-methylated regions of stem cell-specific promoters in human iPS cells derived from extra-embryonic amnions and lung fibroblasts. PMID:20885964
Clinical relevance of SKP2 alterations in metastatic melanoma. PMID:20883453
Homozygous deletion of the UGT2B17 gene is not associated with osteoporosis risk in elderly Caucasian women. PMID:20878390
Genome-wide significant associations for variants with minor allele frequency of 5% or less--an overview: A HuGE review. PMID:20876667
An effective method for detecting gene conversion events in whole genomes. PMID:20874409
IAP display: a simple method to identify mouse strain specific IAP insertions. PMID:20872285
A Gibbs sampling strategy applied to the mapping of ambiguous short-sequence tags. PMID:20871106
BMPER mutation in diaphanospondylodysostosis identified by ancestral autozygosity mapping and targeted high-throughput sequencing. PMID:20869035
Conserved proximal promoter elements control repulsive guidance molecule c/hemojuvelin (Hfe2) gene transcription in skeletal muscle. PMID:20858542
AVPR1A sequence variation in monogamous owl monkeys (Aotus azarai) and its implications for the evolution of platyrrhine social behavior. PMID:20838784
p53 activates the PANK1/miRNA-107 gene leading to downregulation of CDK6 and p130 cell cycle proteins. PMID:20833636
Differential detection of alternatively spliced variants of Ciz1 in normal and cancer cells using a custom exon-junction microarray. PMID:20831784
Asymmetric and non-uniform evolution of recently duplicated human genes. PMID:20825637
Candidate gene prioritization based on spatially mapped gene expression: an application to XLMR. PMID:20823330
A Pumilio-induced RNA structure switch in p27-3' UTR controls miR-221 and miR-222 accessibility. PMID:20818387
A rare novel deletion of the tyrosine hydroxylase gene in Parkinson disease. PMID:20809526
Array-based comparative genomic hybridization in ulcerative colitis neoplasia: single non-dysplastic biopsies distinguish progressors from non-progressors. PMID:20802465
OpenHelix: bioinformatics education outside of a different box. PMID:20798181
Prediction of regulatory networks in mouse abdominal wall. PMID:20797427
An N-terminally truncated envelope protein encoded by a human endogenous retrovirus W locus on chromosome Xq22.3. PMID:20735848
Independent susceptibility markers for atrial fibrillation on chromosome 4q25. PMID:20733104
DNA methylation prevents CTCF-mediated silencing of the oncogene BCL6 in B cell lymphomas. PMID:20733034
Exon-level transcriptome profiling in murine breast cancer reveals splicing changes specific to tumors with different metastatic abilities. PMID:20700505
Nicotinic α5 receptor subunit mRNA expression is associated with distant 5' upstream polymorphisms. PMID:20700147
Genomic signatures of germline gene expression. PMID:20686123
G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae. PMID:20676380
Enhancers of GnRH transcription embedded in an upstream gene use homeodomain proteins to specify hypothalamic expression. PMID:20667983
CPEB2, CPEB3 and CPEB4 are coordinately regulated by miRNAs recognizing conserved binding sites in paralog positions of their 3'-UTRs. PMID:20660482
Discovery and characterization of chromatin states for systematic annotation of the human genome. PMID:20657582
Analysis of candidate genes on chromosome 20q12-13.1 reveals evidence for BMI mediated association of PREX1 with type 2 diabetes in European Americans. PMID:20650312
The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. PMID:20644199
Integration and visualization of systems biology data in context of the genome. PMID:20642854
BigWig and BigBed: enabling browsing of large distributed datasets. PMID:20639541
Quantitative gene expression profiles in real time from expressed sequence tag databases. PMID:20635574
LocusZoom: regional visualization of genome-wide association scan results. PMID:20634204
Quantifying the mechanisms of domain gain in animal proteins. PMID:20633280
Computational analysis of whole-genome differential allelic expression data in human. PMID:20628616
Scapula development is governed by genetic interactions of Pbx1 with its family members and with Emx2 via their cooperative control of Alx1. PMID:20627960
Uncovering the complexity of transcriptomes with RNA-Seq. PMID:20625424
The evolution of tRNA genes in Drosophila. PMID:20624748
TRedD--a database for tandem repeats over the edit distance. PMID:20624712
Mammalian Rap1 controls telomere function and gene expression through binding to telomeric and extratelomeric sites. PMID:20622869
Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases. PMID:20620951
Low grade mosaic for a complex supernumerary ring chromosome 18 in an adult patient with multiple congenital anomalies. PMID:20618949
Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies. PMID:20615900
Segmental duplications in the human genome reveal details of pseudogene formation. PMID:20615899
Characterization of the human PANK2 promoter. PMID:20603201
Natural mutagenesis of human genomes by endogenous retrotransposons. PMID:20603005
Mobile interspersed repeats are major structural variants in the human genome. PMID:20602999
LINE-1 retrotransposition activity in human genomes. PMID:20602998
Comparative studies of mammalian acid lipases: Evidence for a new gene family in mouse and rat (Lipo). PMID:20598663
HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data. PMID:20598134
Identification of baboon microRNAs expressed in liver and lymphocytes. PMID:20594335
Mobile element scanning (ME-Scan) by targeted high-throughput sequencing. PMID:20591181
Targeted next-generation sequencing of DNA regions proximal to a conserved GXGXXG signaling motif enables systematic discovery of tyrosine kinase fusions in cancer. PMID:20587502
In Silico Enhanced Restriction Enzyme Based Methylation Analysis of the Human Glioblastoma Genome Using Agilent 244K CpG Island Microarrays. PMID:20582289
Transcobalamin II receptor polymorphisms are associated with increased risk for neural tube defects. PMID:20577008
Alternative splicing is frequent during early embryonic development in mouse. PMID:20573213
Savant: genome browser for high-throughput sequencing data. PMID:20562449
Large-scale expression analysis reveals distinct microRNA profiles at different stages of human neurodevelopment. PMID:20559549
Reconstruction of gene association network reveals a transmembrane protein required for adipogenesis and targeted by PPARγ. PMID:20552250
Multiplexed quantitative real-time PCR to detect 22q11.2 deletion in patients with congenital heart disease. PMID:20551144
CONAN: copy number variation analysis software for genome-wide association studies. PMID:20546565
Genomic SELEX: a discovery tool for genomic aptamers. PMID:20541015
Characteristics of transposable element exonization within human and mouse. PMID:20532223
A survey of genomic traces reveals a common sequencing error, RNA editing, and DNA editing. PMID:20531933
Next-generation genomics: an integrative approach. PMID:20531367
Transposable elements have rewired the core regulatory network of human embryonic stem cells. PMID:20526341
Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens. PMID:20525786
Transcription of the transforming growth factor beta activating integrin beta8 subunit is regulated by SP3, AP-1, and the p38 pathway. PMID:20519498
Gap5--editing the billion fragment sequence assembly. PMID:20513662
Comparative assessment of methods for aligning multiple genome sequences. PMID:20495551
Strong synaptic transmission impact by copy number variations in schizophrenia. PMID:20489179
Discovery of microRNAs and other small RNAs in solid tumors. PMID:20483914
Evolution of a distinct genomic domain in Drosophila: comparative analysis of the dot chromosome in Drosophila melanogaster and Drosophila virilis. PMID:20479145
Deletions of NRXN1 (neurexin-1) predispose to a wide spectrum of developmental disorders. PMID:20468056
Proximal human FOXP3 promoter transactivated by NF-kappaB and negatively controlled by feedback loop and SP3. PMID:20462637
Genome-wide association study of Lp-PLA(2) activity and mass in the Framingham Heart Study. PMID:20442857
GREAT improves functional interpretation of cis-regulatory regions. PMID:20436461
Genome-wide assessment of differential roles for p300 and CBP in transcription regulation. PMID:20435671
A retroviral vector common integration site between leupaxin and zinc finger protein 91 (ZFP91) observed in baboon hematopoietic repopulating cells. PMID:20434516
Mammalian carboxylesterase 3: comparative genomics and proteomics. PMID:20422440
MochiView: versatile software for genome browsing and DNA motif analysis. PMID:20409324
Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns. PMID:20409305
Horse carboxylesterases: evidence for six CES1 and four families of CES genes on chromosome 3. PMID:20403742
The value of position-specific priors in motif discovery using MEME. PMID:20380693
PU.1 binds to a distal regulatory element that is necessary for B cell-specific expression of CIITA. PMID:20363966
Three dysregulated miRNAs control kallikrein 10 expression and cell proliferation in ovarian cancer. PMID:20354523
Conservation of neutral substitution rate and substitutional asymmetries in mammalian genes. PMID:20333222
Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. PMID:20308636
Global and unbiased detection of splice junctions from RNA-seq data. PMID:20236510
Heads or tails: L1 insertion-associated 5' homopolymeric sequences. PMID:20226075
Strategies for enhanced annotation of a microarray probe set. PMID:20223738
Analysis of human small nucleolar RNAs (snoRNA) and the development of snoRNA modulator of gene expression vectors. PMID:20219969
Integrating multiple evidence sources to predict transcription factor binding in the human genome. PMID:20219943
A CTCF-independent role for cohesin in tissue-specific transcription. PMID:20219941
Trinucleotide repeats in human genome and exome. PMID:20215431
Redefining CpG islands using hidden Markov models. PMID:20212320
High-throughput sequence analysis of Ciona intestinalis SL trans-spliced mRNAs: alternative expression modes and gene function correlates. PMID:20212022
A conserved MRF4 promoter drives transgenic expression in Xenopus embryonic somites and adult muscle. PMID:20209434
Conserved regulatory motifs at phenylethanolamine N-methyltransferase (PNMT) are disrupted by common functional genetic variation: an integrated computational/experimental approach. PMID:20204374
Identification of a distant cis-regulatory element controlling pharyngeal arch-specific expression of zebrafish gdf6a/radar. PMID:20201106
Genome-wide analysis reveals novel genes influencing temporal lobe structure with relevance to neurodegeneration in Alzheimer's disease. PMID:20197096
Visualizing genomes: techniques and challenges. PMID:20195257
Experimental intrauterine growth restriction induces alterations in DNA methylation and gene expression in pancreatic islets of rats. PMID:20194508
SplicerAV: a tool for mining microarray expression data for changes in RNA processing. PMID:20184770
Heme controls ferroportin1 (FPN1) transcription involving Bach1, Nrf2 and a MARE/ARE sequence motif at position -7007 of the FPN1 promoter. PMID:20179090
The microRNA miR-124 controls gene expression in the sensory nervous system of Caenorhabditis elegans. PMID:20176573
Voxelwise genome-wide association study (vGWAS). PMID:20171287
Evolutionary dynamics of U12-type spliceosomal introns. PMID:20163699
Bovine Carboxylesterases: Evidence for Two CES1 and Five Families of CES Genes on Chromosome 18. PMID:20161341
A new class of mammalian carboxylesterase CES6. PMID:20161041
Solution structure of a unique G-quadruplex scaffold adopted by a guanosine-rich human intronic sequence. PMID:20152154
Beyond the HapMap Genotypic Data: Prospects of Deep Resequencing Projects. PMID:20151045
Greedy selection of species for ancestral state reconstruction on phylogenies: elimination is better than insertion. PMID:20140213
Mutations in Grxcr1 are the basis for inner ear dysfunction in the pirouette mouse. PMID:20137774
Impact of the 1000 genomes project on the next wave of pharmacogenomic discovery. PMID:20136363
MicroRNA regulation of IFN-beta protein expression: rapid and sensitive modulation of the innate immune response. PMID:20130213
Expression map of the human exome in CD34+ cells and blood cells: increased alternative splicing in cell motility and immune response genes. PMID:20126548
SOX2 is an oncogene activated by recurrent 3q26.3 amplifications in human lung squamous cell carcinomas. PMID:20126410
Cytosine methylation dysregulation in neonates following intrauterine growth restriction. PMID:20126273
Intronic elements in the Na+/I- symporter gene (NIS) interact with retinoic acid receptors and mediate initiation of transcription. PMID:20123735
Hit integration for identifying optimal spaced seeds. PMID:20122210
BEDTools: a flexible suite of utilities for comparing genomic features. PMID:20110278
Periostin shows increased evolutionary plasticity in its alternatively spliced region. PMID:20109226
Characterization of X-linked SNP genotypic variation in globally distributed human populations. PMID:20109212
Integrating the multiple dimensions of genomic and epigenomic landscapes of cancer. PMID:20108112
MicroRNAs: master regulators of ethanol abuse and toxicity? PMID:20102566
Genome-wide prediction of transcription factor binding sites using an integrated model. PMID:20096096
Genome-wide tissue-specific farnesoid X receptor binding in mouse liver and intestine. PMID:20091679
Highly punctuated patterns of population structure on the X chromosome and implications for African evolutionary history. PMID:20085712
Kinase expression and chromosomal rearrangements in papillary thyroid cancer tissues: investigations at the molecular and microscopic levels. PMID:20083851
The imprinted retrotransposon-like gene PEG11 (RTL1) is expressed as a full-length protein in skeletal muscle from Callipyge sheep. PMID:20072617
A reconfigured pattern of MLL occupancy within mitotic chromatin promotes rapid transcriptional reactivation following mitotic exit. PMID:20064463
Genome-wide identification of hypoxia-inducible factor binding sites and target genes by a probabilistic model integrating transcription-profiling data and in silico binding site prediction. PMID:20061373
Finding regulatory DNA motifs using alignment-free evolutionary conservation information. PMID:20047961
Evidence for bacterial origin of heat shock RNA-1. PMID:20040589
Analysis of complex disease association and linkage studies using the University of California Santa Cruz Genome Browser. PMID:20031585
A new measurement of sequence conservation. PMID:20028539
Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells. PMID:20026622
Mutations in the formin gene INF2 cause focal segmental glomerulosclerosis. PMID:20023659
Association of a functional microsatellite within intron 1 of the BMP5 gene with susceptibility to osteoarthritis. PMID:20021689
Algorithms for locating extremely conserved elements in multiple sequence alignments. PMID:20021665
Global demethylation of rat chondrosarcoma cells after treatment with 5-aza-2'-deoxycytidine results in increased tumorigenicity. PMID:20019818
Region-based analysis in genome-wide association study of Framingham Heart Study blood lipid phenotypes. PMID:20017993
Evidence of uneven selective pressure on different subsets of the conserved human genome; implications for the significance of intronic and intergenic DNA. PMID:20015390
Gene, region and pathway level analyses in whole-genome studies. PMID:20013942
A conserved activation element in BMP signaling during Drosophila development. PMID:20010841
Meta-analyses of genome-wide association studies identify multiple loci associated with pulmonary function. PMID:20010835
The histone variant macroH2A1 marks repressed autosomal chromatin, but protects a subset of its target genes from silencing. PMID:20008927
Genomic and functional analysis identifies CRKL as an oncogene amplified in lung cancer. PMID:19966867
GWAS or Gee Whiz, PSAS or Pshaw: elucidating the biologic and clinical significance of genetic variation in cardiovascular disease. PMID:19959124
YY1's DNA-binding motifs in mammalian olfactory receptor genes. PMID:19958529
The UCSC Genome Browser. PMID:19957273
Short Promoters in Viral Vectors Drive Selective Expression in Mammalian Inhibitory Neurons, but do not Restrict Activity to Specific Inhibitory Cell-Types. PMID:19949461
Consensus miRNA expression profiles derived from interplatform normalization of microarray data. PMID:19948767
Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA. PMID:19946276
DISPARE: DIScriminative PAttern REfinement for Position Weight Matrices. PMID:19941641
Microarray-based cytogenetic profiling reveals recurrent and subtype-associated genomic copy number aberrations in feline sarcomas. PMID:19941159
EGAN: exploratory gene association networks. PMID:19933825
Expression profiling of rainbow trout testis development identifies evolutionary conserved genes involved in spermatogenesis. PMID:19925684
Summary of contributions to GAW Group 15: family-based samples are useful in identifying common polymorphisms associated with complex traits. PMID:19924714
A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data. PMID:19923232
Replication of association between working memory and Reelin, a potential modifier gene in schizophrenia. PMID:19922905
ENCODE whole-genome data in the UCSC Genome Browser. PMID:19920125
Discovery and annotation of functional chromatin signatures in the human genome. PMID:19918365
Alu repeats increase local recombination rates. PMID:19917129
Genetic variation in the NBS1, MRE11, RAD50 and BLM genes and susceptibility to non-Hodgkin lymphoma. PMID:19917125
Discovery of microvascular miRNAs using public gene expression data: miR-145 is expressed in pericytes and is a regulator of Fli1. PMID:19917099
Endogenous control genes in complex vascular tissue samples. PMID:19900295
Regulation of major histocompatibility complex class II gene expression, genetic variation and disease. PMID:19890353
Information-theoretic gene-gene and gene-environment interaction analysis of quantitative traits. PMID:19889230
Relationship between CAD risk genotype in the chromosome 9p21 locus and gene expression. Identification of eight new ANRIL splice variants. PMID:19888323
Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression. PMID:19887574
iTriplet, a rule-based nucleic acid sequence motif finder. PMID:19874606
Nme protein family evolutionary history, a vertebrate perspective. PMID:19852809
A systematic approach to identify functional motifs within vertebrate developmental enhancers. PMID:19850031
A syndrome of short stature, microcephaly and speech delay is associated with duplications reciprocal to the common Sotos syndrome deletion. PMID:19844260
Next-generation gap. PMID:19844227
Chromosomal position mediates spinal cord expression of a dbx1a enhancer. PMID:19842185
Probe-level analysis of expression microarrays characterizes isoform-specific degradation during mouse oocyte maturation. PMID:19834616
Generation of aggrecan-CreERT2 knockin mice for inducible Cre activity in adult cartilage. PMID:19830818
An integrated approach for experimental target identification of hypoxia-induced miR-210. PMID:19826008
Differential roles for ETS, CREB, and EGR binding sites in mediating VEGF receptor 1 expression in vivo. PMID:19822898
Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing. PMID:19822575
High DNA melting temperature predicts transcription start site location in human and mouse. PMID:19820114
The smooth muscle cell-restricted KCNMB1 ion channel subunit is a direct transcriptional target of serum response factor and myocardin. PMID:19801679
Quadruplex MAPH: improvement of throughput in high-resolution copy number screening. PMID:19785739
A species-generalized probabilistic model-based definition of CpG islands. PMID:19777308
Many LINE1 elements contribute to the transcriptome of human somatic cells. PMID:19772661
A methodology for the analysis of differential coexpression across the human lifespan. PMID:19772654
Testicular cell adhesion molecule 1 (TCAM1) is not essential for fertility. PMID:19766163
A c-Myc regulatory subnetwork from human transposable element sequences. PMID:19763338
Human miRNA precursors with box H/ACA snoRNA features. PMID:19763159
Evaluating the accuracy of a functional SNP annotation system. PMID:19761565
Genome-wide colonization of gene regulatory elements by G4 DNA motifs. PMID:19759215
Prediction and identification of tumor-specific noncoding RNAs from human UniGene. PMID:19757216
The Otto Aufranc Award: Identification of a 4 Mb region on chromosome 17q21 linked to developmental dysplasia of the hip in one 18-member, multigeneration family. PMID:19756907
Identifying and characterizing a novel protein kinase STK35L1 and deciphering its orthologs and close-homologs in vertebrates. PMID:19756140
Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth. PMID:19747392
Meta-coexpression conservation analysis of microarray data: a "subset" approach provides insight into brain-derived neurotrophic factor regulation. PMID:19737418
Prediction and experimental validation of novel STAT3 target genes in human cancer cells. PMID:19730699
Mammalian carboxylesterase 5: comparative biochemistry and genomics. PMID:19727319
Transcriptional regulation of vascular endothelial growth factor C by oxidative and thermal stress is mediated by lens epithelium-derived growth factor/p75. PMID:19724686
The transcription factor D-Pax2 regulates crystallin production during eye development in Drosophila melanogaster. PMID:19718746
Collection of variation causing disease--the Human Variome Project. PMID:19706360
Partitioning the C. elegans genome by nucleosome modification, occupancy, and positioning. PMID:19705140
Global analysis of H3K4 methylation defines MLL family member targets and points to a role for MLL1-mediated H3K4 methylation in the regulation of transcriptional initiation by RNA polymerase II. PMID:19703992
Molecular biology, genetics and biochemistry of the repulsive guidance molecule family. PMID:19698085
Nucleosome positioning as a determinant of exon recognition. PMID:19684599
Long-range regulation is a major driving force in maintaining genome integrity. PMID:19682388
Computational analyses of mammalian lactate dehydrogenases: human, mouse, opossum and platypus LDHs. PMID:19679512
Long tandem repeats as a form of genomic copy number variation: structure and length polymorphism of a chromosome 5p repeat in control and schizophrenia populations. PMID:19672138
A genome-wide in vitro bacterial-infection screen reveals human variation in the host response associated with inflammatory disease. PMID:19664744
Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence. PMID:19662163
Comprehensive resequence analysis of a 97 kb region of chromosome 10q11.2 containing the MSMB gene associated with prostate cancer. PMID:19644707
MLGA: a cost-effective approach to the diagnosis of gene deletions in eye development anomalies. PMID:19641633
Repertoire of bovine miRNA and miRNA-like small regulatory RNAs expressed upon viral infection. PMID:19633723
Widespread cleavage of A-to-I hyperediting substrates. PMID:19622679
Transcriptome of embryonic and neonatal mouse cortex by high-throughput RNA sequencing. PMID:19617558
OligoRAP - an Oligo Re-Annotation Pipeline to improve annotation and estimate target specificity. PMID:19615117
Transcriptional programs: modelling higher order structure in transcriptional control. PMID:19607663
Integration of genetic and genomic methods for identification of genes and gene variants encoding QTLs in the nonhuman primate. PMID:19596448
Word-based characterization of promoters involved in human DNA repair pathways. PMID:19594877
Quantification of the yeast transcriptome by single-molecule sequencing. PMID:19581875
Methods for incorporating the hypermutability of CpG dinucleotides in detecting natural selection operating at the amino acid sequence level. PMID:19581348
JBrowse: a next-generation genome browser. PMID:19570905
k-link EST clustering: evaluating error introduced by chimeric sequences under different degrees of linkage. PMID:19570806
Variation in novel exons (RACEfrags) of the MECP2 gene in Rett syndrome patients and controls. PMID:19562714
A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry. PMID:19561019
Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. PMID:19546169
A novel method, digital genome scanning detects KRAS gene amplification in gastric cancers: involvement of overexpressed wild-type KRAS in downstream signaling and cancer cell growth. PMID:19545448
Mapping insertions, deletions and SNPs on Venter's chromosomes. PMID:19543403
The aryl hydrocarbon receptor: a perspective on potential roles in the immune system. PMID:19538249
Identifying putative promoter regions of Hermansky-Pudlak syndrome genes by means of phylogenetic footprinting. PMID:19523149
Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencing. PMID:19508715
Genomic features that predict allelic imbalance in humans suggest patterns of constraint on gene expression variation. PMID:19506001
The Sequence Alignment/Map format and SAMtools. PMID:19505943
Successful hematopoietic stem-cell transplantation in a patient with chronic granulomatous disease and McLeod phenotype sensitized to Kx and K antigens. PMID:19503108
A novel protein isoform of the multicopy human NAIP gene derives from intragenic Alu SINE promoters. PMID:19488400
Identifying novel constrained elements by exploiting biased substitution patterns. PMID:19478016
Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. PMID:19474294
Primate phylogenomics: developing numerous nuclear non-coding, non-repetitive markers for ecological and phylogenetic applications and analysis of evolutionary rate variation. PMID:19470178
rtracklayer: an R package for interfacing with genome browsers. PMID:19468054
Loss of the Mili-interacting Tudor domain-containing protein-1 activates transposons and alters the Mili-associated small RNA profile. PMID:19465913
Differential splicing using whole-transcript microarrays. PMID:19463149
Comprehensive analysis of the impact of SNPs and CNVs on human microRNAs and their regulatory genes. PMID:19458495
A novel L1 retrotransposon marker for HeLa cell line identification. PMID:19450234
Segmental duplications mediate novel, clinically relevant chromosome rearrangements. PMID:19443486
Tissue-specific regulatory network extractor (TS-REX): a database and software resource for the tissue and cell type-specific investigation of transcription factor-gene networks. PMID:19443447
Myoblast sensitivity and fibroblast insensitivity to osteogenic conversion by BMP-2 correlates with the expression of Bmpr-1a. PMID:19442313
Widespread genomic signatures of natural selection in hominid evolution. PMID:19424416
Predicting potential miRNA target sites within gene promoters. PMID:19423343
Improving gene-finding in Chlamydomonas reinhardtii:GreenGenie2. PMID:19422688
Sleeping beauty transposition from nonintegrating lentivirus. PMID:19417741
Recovering genome rearrangements in the mammalian phylogeny. PMID:19411607
Autism genome-wide copy number variation reveals ubiquitin and neuronal genes. PMID:19404257
A general integrative genomic feature transcription factor binding site prediction method applied to analysis of USF1 binding in cardiovascular disease. PMID:19403457
SNP discovery and haplotype analysis in the segmentally duplicated DRD5 coding region. PMID:19397556
The bovine lactation genome: insights into the evolution of mammalian milk. PMID:19393040
Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data. PMID:19390574
A consolidated catalogue and graphical annotation of dbSNP polymorphisms in the human tissue kallikrein (KLK) locus. PMID:19383304
The regulated retrotransposon transcriptome of mammalian cells. PMID:19377475
Transcriptional features of genomic regulatory blocks. PMID:19374772
Expression and alternative splicing of folate pathway genes in HapMap lymphoblastoid cell lines. PMID:19374514
In silico whole genome association scan for murine prepulse inhibition. PMID:19370154
Fine mapping linkage analysis identifies a novel susceptibility locus for myopia on chromosome 2q37 adjacent to but not overlapping MYP12. PMID:19365569
'Putting our heads together': insights into genomic conservation between human and canine intracranial tumors. PMID:19333554
The UCSC Cancer Genomics Browser. PMID:19333237
A common variant associated with dyslexia reduces expression of the KIAA0319 gene. PMID:19325871
Visualization of genomic data with the Hilbert curve. PMID:19297348
Agreement among type 2 diabetes linkage studies but a poor correlation with results from genome-wide association studies. PMID:19296077
Copy number variants in genetic susceptibility and severity of systemic lupus erythematosus. PMID:19287148
Localization of multiple pleiotropic genes for lipoprotein metabolism in baboons. PMID:19270339
Mouse models of Huntington disease: variations on a theme. PMID:19259385
Coherent but overlapping expression of microRNAs and their targets during vertebrate development. PMID:19240133
Novel autosomal recessive non-syndromic hearing impairment locus (DFNB71) maps to chromosome 8p22-21.3. PMID:19229252
Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation. PMID:19222862
The cerebellin 4 precursor gene is a direct target of SRY and SOX9 in mice. PMID:19211811
Di(2-ethylhexyl) phthalate is a highly potent agonist for the human constitutive androstane receptor splice variant CAR2. PMID:19211671
Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. PMID:19208812
Yin yang 1 regulates the expression of snail through a distal enhancer. PMID:19208738
Identifying hypothetical genetic influences on complex disease phenotypes. PMID:19208188
HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models. PMID:19208136
ModuleDigger: an itemset mining framework for the detection of cis-regulatory modules. PMID:19208131
SEPT9 mutations and a conserved 17q25 sequence in sporadic and hereditary brachial plexus neuropathy. PMID:19204161
A missense mutation in CASK causes FG syndrome in an Italian family. PMID:19200522
Baboon carboxylesterases 1 and 2: sequences, structures and phylogenetic relationships with human and other primate carboxylesterases. PMID:19187434
Tcf3 inhibits spinal cord neurogenesis by regulating sox4a expression. PMID:19176587
Recognition of atypical 5' splice sites by shifted base-pairing to U1 snRNA. PMID:19169258
AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context. PMID:19168913
Identification of an ancient Bmp4 mesoderm enhancer located 46 kb from the promoter. PMID:19159624
HapMap methylation-associated SNPs, markers of germline DNA methylation, positively correlate with regional levels of human meiotic recombination. PMID:19158364
Identification of direct T-box target genes in the developing zebrafish mesoderm. PMID:19158186
Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4+ T cells. PMID:19144320
MicroRNA regulation of DNA repair gene expression in hypoxic stress. PMID:19141645
bioDBnet: the biological database network. PMID:19129209
Asymmetrical distribution of non-conserved regulatory sequences at PHOX2B is reflected at the ENCODE loci and illuminates a possible genome-wide trend. PMID:19128492
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. PMID:19122651
A regulatory interplay between miR-27a and Runx1 during megakaryopoiesis. PMID:19114653
Prediction of regulatory elements in mammalian genomes using chromatin signatures. PMID:19094206
FastMap: fast eQTL mapping in homozygous populations. PMID:19091771
Genome-wide analysis of cancer/testis gene expression. PMID:19088187
GPAT: retrieval of genomic annotation from large genomic position datasets. PMID:19077303
Human chromosomal translocations at CpG sites and a theoretical basis for their lineage and stage specificity. PMID:19070581
Genotype-phenotype databases: challenges and solutions for the post-genomic era. PMID:19065136
FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease. PMID:19061490
Evolution of Drosophila ribosomal protein gene core promoters. PMID:19059316
Regulation of neural macroRNAs by the transcriptional repressor REST. PMID:19050060
c-REDUCE: incorporating sequence conservation to detect motifs that correlate with expression. PMID:19040743
ProSeeK: a web server for MLPA probe design. PMID:19040730
Analysis of exonic elastin variants in severe, early-onset chronic obstructive pulmonary disease. PMID:19029017
BMP-2 vs. BMP-4 expression and activity in glucocorticoid-arrested MC3T3-E1 osteoblasts: Smad signaling, not alkaline phosphatase activity, predicts rescue of mineralization. PMID:19021035
Does selection against transcriptional interference shape retroelement-free regions in mammalian genomes? PMID:19018283
Complexity reduction in context-dependent DNA substitution models. PMID:19017657
PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. PMID:18981473
NF-kappaB-YY1-miR-29 regulatory circuitry in skeletal myogenesis and rhabdomyosarcoma. PMID:18977326
Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PMID:18974828
Microarray analysis of Foxa2 mutant mouse embryos reveals novel gene expression and inductive roles for the gastrula organizer and its derivatives. PMID:18973680
Positional distribution of human transcription factor binding sites. PMID:18953043
VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts. PMID:18953038
Embryonic nervous system genes predominate in searches for dinucleotide simple sequence repeats flanked by conserved sequences. PMID:18952158
PharmGKB: understanding the effects of individual genetic variants. PMID:18949600
HGVbaseG2P: a central genetic association database. PMID:18948288
UCbase & miRfunc: a database of ultraconserved sequences and microRNA function. PMID:18945703
Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods. PMID:18936483
Nested Patch PCR enables highly multiplexed mutation discovery in candidate genes. PMID:18849522
Evolutionary signatures of common human cis-regulatory haplotypes. PMID:18846218
Practical applications of the bioinformatics toolbox for narrowing quantitative trait loci. PMID:18845850
CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens. PMID:18838390
Transcript- and tissue-specific imprinting of a tumour suppressor gene. PMID:18836209
Active Alu retrotransposons in the human genome. PMID:18836035
Haplotype sorting using human fosmid clone end-sequence pairs. PMID:18836033
MECP2 genomic structure and function: insights from ENCODE. PMID:18820302
Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif. PMID:18818370
Down-regulation of hepcidin in porphyria cutanea tarda. PMID:18809758
Missense mutation in exon 2 of SLC36A1 responsible for champagne dilution in horses. PMID:18802473
Ab initio identification of functionally interacting pairs of cis-regulatory elements. PMID:18799692
Identification of Arx transcriptional targets in the developing basal forebrain. PMID:18799476
The whole alignment and nothing but the alignment: the problem of spurious alignment flanks. PMID:18796526
Effect of single nucleotide polymorphisms on Affymetrix match-mismatch probe pairs. PMID:18795114
F-Seq: a feature density estimator for high-throughput sequence tags. PMID:18784119
Human MLPA Probe Design (H-MAPD): a probe design tool for both electrophoresis-based and bead-coupled human multiplex ligation-dependent probe amplification assays. PMID:18783624
The short-sequence designs of isochores from the human genome. PMID:18780784
Human-specific gain of function in a developmental enhancer. PMID:18772437
Regulation of the mouse Treacher Collins syndrome homolog (Tcof1) promoter through differential repression of constitutive expression. PMID:18771418
Runs of homozygosity in European populations. PMID:18760389
Interleukin-29 functions cooperatively with interferon to induce antiviral gene expression and inhibit hepatitis C virus replication. PMID:18757365
Sequencing and comparative analysis of a conserved syntenic segment in the Solanaceae. PMID:18723883
The Lawc protein is required for proper transcription by RNA polymerase II in Drosophila. PMID:18716797
Genomic screening identifies novel linkages and provides further evidence for a role of MYH9 in nonsyndromic cleft lip and palate. PMID:18716610
Full-length hdmX transcripts decrease following genotoxic stress. PMID:18711402
A human genome-wide library of local phylogeny predictions for whole-genome inference problems. PMID:18710563
Reduced purifying selection prevails over positive selection in human copy number variant evolution. PMID:18687881
Human endogenous retrovirus family HERV-K(HML-2) RNA transcripts are selectively packaged into retroviral particles produced by the human germ cell tumor line Tera-1 and originate mainly from a provirus on chromosome 22q11.21. PMID:18684837
Evolution of the mammalian transcription factor binding repertoire via transposable elements. PMID:18682548
A core paired-type and POU homeodomain-containing transcription factor program drives retinal bipolar cell gene expression. PMID:18667607
Expression patterns of transcribed human endogenous retrovirus HERV-K(HML-2) loci in human tissues and the need for a HERV Transcriptome Project. PMID:18664271
Is there an acceleration of the CpG transition rate during the mammalian radiation? PMID:18662928
Maps of cis-Regulatory Nodes in Megabase Long Genome Segments are an Inevitable Intermediate Step Toward Whole Genome Functional Mapping. PMID:18660850
Fine mapping of the GLC1K juvenile primary open-angle glaucoma locus and exclusion of candidate genes. PMID:18648523
Comparative transcriptomics of human multipotent stem cells during adipogenesis and osteoblastogenesis. PMID:18637193
11th Intelligent Systems for Molecular Biology 2003 (ISMB 2003). PMID:18629025
A common haplotype within the PON1 promoter region is associated with sporadic ALS. PMID:18618303
Genome-wide association scan identifies candidate polymorphisms associated with differential response to anti-TNF treatment in rheumatoid arthritis. PMID:18615156
A discontinuous hammerhead ribozyme embedded in a mammalian messenger RNA. PMID:18615019
Asymmetric histone modifications between the original and derived loci of human segmental duplications. PMID:18598352
Species-specific Differences among KCNMB3 BK beta3 auxiliary subunits: some beta3 N-terminal variants may be primate-specific subunits. PMID:18591419
Nucleosome positioning from tiling microarray data. PMID:18586706
Evolution of the redox function in mammalian apurinic/apyrimidinic endonuclease. PMID:18579163
Positive selection in alternatively spliced exons of human genes. PMID:18571144
GMODWeb: a web framework for the Generic Model Organism Database. PMID:18570664
MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays. PMID:18566192
Screening for PPAR Responsive Regulatory Modules in Cancer. PMID:18551184
TiGER: a database for tissue-specific gene expression and regulation. PMID:18541026
Genomic profiling identifies GATA6 as a candidate oncogene amplified in pancreatobiliary cancer. PMID:18535672
To gate or not to gate: are the delta subunits in the glutamate receptor family functional ion channels? PMID:18521762
Genotype, phenotype, and karyotype correlation in the XO mouse model of Turner Syndrome. PMID:18499648
A novel DNA sequence database for analyzing human demographic history. PMID:18493019
Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA. PMID:18485226
A transcriptional enhancer from the coding region of ADAMTS5. PMID:18478108
A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. PMID:18469162
CCAAT/enhancer binding protein-beta is a transcriptional regulator of peroxisome-proliferator-activated receptor-gamma coactivator-1alpha in the regenerating liver. PMID:18467525
Mutations of different molecular origins exhibit contrasting patterns of regional substitution rate variation. PMID:18463707
Confirming the phylogeny of mammals by use of large comparative sequence data sets. PMID:18453548
Oxytocin deficiency mediates hyperphagic obesity of Sim1 haploinsufficient mice. PMID:18451093
Characterization of clinically-attenuated Burkholderia mallei by whole genome sequencing: candidate strain for exclusion from Select Agent lists. PMID:18446194
What everybody should know about the rat genome and its online resources. PMID:18443589
Prediction and analysis of nucleosome exclusion regions in the human genome. PMID:18430246
Performance and scalability of discriminative metrics for comparative gene identification in 12 Drosophila genomes. PMID:18421375
Novel TCF-binding sites specify transcriptional repression by Wnt signalling. PMID:18418383
Chromatin decouples promoter threshold from dynamic range. PMID:18418379
Pituitary homeobox 2 regulates adrenal4 binding protein/steroidogenic factor-1 gene transcription in the pituitary gonadotrope through interaction with the intronic enhancer. PMID:18417734
The human ABC transporter pseudogene family: Evidence for transcription and gene-pseudogene interference. PMID:18405356
WAMIDEX: a web atlas of murine genomic imprinting and differential expression. PMID:18398312
GeneTrack--a genomic data processing and visualization framework. PMID:18388141
An integrative genomic and epigenomic approach for the study of transcriptional regulation. PMID:18365023
Probabilistic inference of transcription factor binding from multiple data sources. PMID:18364997
Endogenous retroviruses of the chicken genome. PMID:18361801
An analytical pipeline for genomic representations used for cytosine methylation studies. PMID:18353789
Disruption of contactin 4 in three subjects with autism spectrum disorder. PMID:18349135
Mapping of a new autosomal recessive non-syndromic hearing impairment locus (DFNB45) to chromosome 1q43-q44. PMID:18325041
The Innate Immune Database (IIDB). PMID:18321385
Goldsurfer2 (Gs2): a comprehensive tool for the analysis and visualization of genome wide association studies. PMID:18318908
Modeling transcriptome based on transcript-sampling data. PMID:18286206
Comparative gene mapping in cattle, Indian muntjac, and Chinese muntjac by fluorescence in situ hybridization. PMID:18283540
Oct4 dependence of chromatin structure within the extended Nanog locus in ES cells. PMID:18283123
Genomic identification of regulatory elements by evolutionary sequence comparison and functional analysis. PMID:18282510
Natural variation in four human collagen genes across an ethnically diverse population. PMID:18272325
Genome-wide analysis identifies interleukin-10 mRNA as target of tristetraprolin. PMID:18256032
Sequence variation in the human transcription factor gene POU5F1. PMID:18254969
MethCancerDB--aberrant DNA methylation in human cancer. PMID:18253128
A single SNP in an evolutionary conserved region within intron 86 of the HERC2 gene determines human blue-brown eye color. PMID:18252222
Mechanisms and consequences of small supernumerary marker chromosomes: from Barbara McClintock to modern genetic-counseling issues. PMID:18252220
High-resolution mapping and characterization of open chromatin across the genome. PMID:18243105
Segmental duplications and evolutionary plasticity at tumor chromosome break-prone regions. PMID:18230801
Genomic analysis of the chromosome 15q11-q13 Prader-Willi syndrome region and characterization of transcripts for GOLGA8E and WHCD1L1 from the proximal breakpoint region. PMID:18226259
Genomic profiling identifies TITF1 as a lineage-specific oncogene amplified in lung cancer. PMID:18212743
High-throughput biochemical analysis of in vivo location data reveals novel distinct classes of POU5F1(Oct4)/DNA complexes. PMID:18212089
Mortality risks in patients with constitutional autosomal chromosome deletions in Britain: a cohort study. PMID:18196273
Identification of novel homologous microRNA genes in the rhesus macaque genome. PMID:18186931
Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome. PMID:18173853
A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands. PMID:18172160
Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions. PMID:18096747
The UCSC Genome Browser Database: 2008 update. PMID:18086701
Variable transcriptional activity of endogenous retroviruses in human breast cancer. PMID:18077721
Germline rates of de novo meiotic deletions and duplications causing several genomic disorders. PMID:18059269
The genome browser at UCSC for locating genes, and much more! PMID:18058261
G9a histone methyltransferase contributes to imprinting in the mouse placenta. PMID:18039842
REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila. PMID:18039705
Extragenic accumulation of RNA polymerase II enhances transcription by RNA polymerase III. PMID:18039033
A code for transcription initiation in mammalian genomes. PMID:18032727
Features of 5'-splice-site efficiency derived from disease-causing mutations and comparative genomics. PMID:18032726
The "alternative" choice of constitutive exons throughout evolution. PMID:18020709
Genetic loci affecting body weight and fatness in a C57BL/6J x PWK/PhJ mouse intercross. PMID:18008102
The GLUT9 gene is associated with serum uric acid levels in Sardinia and Chianti cohorts. PMID:17997608
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. PMID:17994088
Orthologous microRNA genes are located in cancer-associated genomic regions in human and mouse. PMID:17989771
Genomic regulatory blocks underlie extensive microsynteny conservation in insects. PMID:17989259
Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes. PMID:17989253
Reliable prediction of regulator targets using 12 Drosophila genomes. PMID:17989251
Significant gene content variation characterizes the genomes of inbred mouse strains. PMID:17989247
TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates. PMID:17986453
28-way vertebrate alignment and conservation track in the UCSC Genome Browser. PMID:17984227
The full-ORF clone resource of the German cDNA Consortium. PMID:17974005
Fine-tuning enhancer models to predict transcriptional targets across multiple genomes. PMID:17973026
How accurately is ncRNA aligned within whole-genome multiple alignments? PMID:17963514
Bioinformatic identification of novel putative photoreceptor specific cis-elements. PMID:17953763
Genes involved in TGF beta1-driven epithelial-mesenchymal transition of renal epithelial cells are topologically related in the human interactome map. PMID:17953753
Regulatory pathway analysis by high-throughput in situ hybridization. PMID:17953485
Structural and functional analysis of the human TAF1/DYT3 multiple transcript system. PMID:17952504
CG dinucleotide clustering is a species-specific property of the genome. PMID:17932072
Waves of genomic hitchhikers shed light on the evolution of gamebirds (Aves: Galliformes). PMID:17925025
Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data. PMID:17910767
Framingham Heart Study genome-wide association: results for pulmonary function measures. PMID:17903307
Genome-wide association study of electrocardiographic and heart rate variability traits: the Framingham Heart Study. PMID:17903306
A genome-wide association study of breast and prostate cancer in the NHLBI's Framingham Heart Study. PMID:17903305
Genome-wide association with diabetes-related traits in the Framingham Heart Study. PMID:17903298
Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study. PMID:17903297
Genetic correlates of longevity and selected age-related phenotypes: a genome-wide association study in the Framingham Study. PMID:17903295
Genome-wide identification of estrogen receptor alpha-binding sites in mouse liver. PMID:17901129
PADB: published association database. PMID:17877839
Epidermal growth factor receptor (EGFR) is transcriptionally induced by the Y-box binding protein-1 (YB-1) and can be inhibited with Iressa in basal-like breast cancer, providing a potential target for therapy. PMID:17875215
Novel rapidly evolving hominid RNAs bind nuclear factor 90 and display tissue-restricted distribution. PMID:17855395
Detection of RNA structures in porcine EST data and related mammals. PMID:17845718
Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion. PMID:17785536
Tissue-dependent paired expression of miRNAs. PMID:17726050
Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PMID:17708682
Cloning and expression profiling of testis-expressed piRNA-like RNAs. PMID:17698640
A screen for suppressors of gross chromosomal rearrangements identifies a conserved role for PLP in preventing DNA lesions. PMID:17696614
Competing interactions between micro-RNAs determine neural progenitor survival and proliferation after ethanol exposure: evidence from an ex vivo model of the fetal cerebral cortical neuroepithelium. PMID:17687032
Translational regulation of human methionine synthase by upstream open reading frames. PMID:17683808
A periodic pattern of SNPs in the human genome. PMID:17673700
Genetics of Alzheimer's disease: a centennial review. PMID:17659183
Meta-analysis of primary target genes of peroxisome proliferator-activated receptors. PMID:17650321
Germ-line DNA copy number variation frequencies in a large North American population. PMID:17638019
Correlations of EGFR mutations and increases in EGFR and HER2 copy number to gefitinib response in a retrospective analysis of lung cancer patients. PMID:17626639
A novel testis ubiquitin-binding protein gene arose by exon shuffling in hominoids. PMID:17623810
Widely variable endogenous retroviral methylation levels in human placenta. PMID:17617638
Measuring the accuracy of genome-size multiple alignments. PMID:17594489
Functional analysis of the human N-acetyltransferase 1 major promoter: quantitation of tissue expression and identification of critical sequence elements. PMID:17591675
Genome position and gene amplification. PMID:17584934
Fast-evolving noncoding sequences in the human genome. PMID:17578567
Structured RNAs in the ENCODE selected regions of the human genome. PMID:17568003
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. PMID:17567995
The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci. PMID:17567993
Comparative genomics reveals functional transcriptional control sequences in the Prop1 gene. PMID:17557180
PrimerZ: streamlined primer design for promoters, exons and human SNPs. PMID:17537812
Systematic analysis of genetic alterations in tumors using Cancer Genome WorkBench (CGWB). PMID:17525135
A comprehensive computational characterization of conserved mammalian intronic sequences reveals conserved motifs associated with constitutive and alternative splicing. PMID:17525134
PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis. PMID:17517777
A first look at ARFome: dual-coding genes in mammalian genomes. PMID:17511511
Revealing signaling pathway deregulation by using gene expression signatures and regulatory motif analysis. PMID:17498287
Discovery and characterization of 91 novel transcripts expressed in cattle placenta. PMID:17488528
CARGO: a web portal to integrate customized biological information. PMID:17483515
Mortality and cancer incidence in males with Y polysomy in Britain: a cohort study. PMID:17457613
Discovery of tissue-specific exons using comprehensive human exon microarrays. PMID:17456239
In silico mining identifies IGFBP3 as a novel target of methylation in prostate cancer. PMID:17453001
Novel peptide identification from tandem mass spectra using ESTs and sequence database compression. PMID:17437027
Origin and evolution of human microRNAs from transposable elements. PMID:17435244
Evidence for de novo evolution of testis-expressed genes in the Drosophila yakuba/Drosophila erecta clade. PMID:17435230
A new platform linking chromosomal and sequence information. PMID:17406992
Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. PMID:17382889
Strong association of de novo copy number mutations with autism. PMID:17363630
Non-coding sequence retrieval system for comparative genomic analysis of gene regulatory elements. PMID:17362514
The strength of selection on ultraconserved elements in the human genome. PMID:17357075
Hawkeye: an interactive visual analytics tool for genome assemblies. PMID:17349036
microRNA expression in the prefrontal cortex of individuals with schizophrenia and schizoaffective disorder. PMID:17326821
Using genomic data to unravel the root of the placental mammal phylogeny. PMID:17322288
Genome display tool: visualizing features in complex data sets. PMID:17300731
A screen for retrotransposed imprinted genes reveals an association between X chromosome homology and maternal germ-line methylation. PMID:17291163
Identification of N-acetyltransferase 2 (NAT2) transcription start sites and quantitation of NAT2-specific mRNA in human tissues. PMID:17287389
AT-rich repeats associated with chromosome 22q11.2 rearrangement disorders shape human genome architecture on Yq12. PMID:17284672
Erythroid Krüppel-like factor directly activates the basic Krüppel-like factor gene in erythroid cells. PMID:17283065
Bmp2 transcription in osteoblast progenitors is regulated by a distant 3' enhancer located 156.3 kilobases from the promoter. PMID:17283059
Complex genomic rearrangement in CCS-LacZ transgenic mice. PMID:17269130
Novel expressed sequences identified in a model of androgen independent prostate cancer. PMID:17257419
Mandatory chromosomal segment balance in aneuploid tumor cells. PMID:17257397
Statistical significance of cis-regulatory modules. PMID:17241466
Isolation, sequencing, and functional analysis of the TATA-less murine ATPase II promoter and structural analysis of the ATPase II gene. PMID:17239457
Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips. PMID:17224057
Predicting tissue-specific enhancers in the human genome. PMID:17210927
MicroRNAs regulate the expression of the alternative splicing factor nPTB during muscle development. PMID:17210790
Palladin mutation causes familial pancreatic cancer and suggests a new cancer mechanism. PMID:17194196
A unique configuration of genome-wide DNA methylation patterns in the testis. PMID:17190809
Noncoding RNA synthesis and loss of Polycomb group repression accompanies the colinear activation of the human HOXA cluster. PMID:17185360
High-resolution mapping identifies a commonly amplified 11q13.3 region containing multiple genes flanked by segmental duplications. PMID:17171571
Noncoding RNAs database (ncRNAdb). PMID:17169980
The ENCODE Project at UC Santa Cruz. PMID:17166863
Evolution of the metazoan protein phosphatase 2C superfamily. PMID:17160364
Mammalian small nucleolar RNAs are mobile genetic elements. PMID:17154719
Variation resources at UC Santa Cruz. PMID:17151077
Transgenic analysis of Dlx regulation in fish tooth development reveals evolutionary retention of enhancer function despite organ loss. PMID:17146045
The UCSC genome browser database: update 2007. PMID:17142222
Characterization of the short RNAs bound by the P19 suppressor of RNA silencing in mouse embryonic stem cells. PMID:17135486
SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms. PMID:17135185
Genome-wide sequence and functional analysis of early replicating DNA in normal human fibroblasts. PMID:17134498
Genome assembly comparison identifies structural variants in the human genome. PMID:17115057
PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits. PMID:17099235
Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. PMID:17099229
Patterns of sequence conservation in presynaptic neural genes. PMID:17096848
BoCaTFBS: a boosted cascade learner to refine the binding sites suggested by ChIP-chip experiments. PMID:17078876
Exon-based mapping of microarray probes: recovering differential gene expression signal in underpowered hypoxia experiment. PMID:17071053
BAC constructs in transgenic reporter mouse lines control efficient and specific LacZ expression in hypertrophic chondrocytes under the complete Col10a1 promoter. PMID:17051351
Experimental validation of predicted mammalian erythroid cis-regulatory modules. PMID:17038566
Identification, genome mapping, and CTCF binding of potential insulators within the FXYD5-COX7A1 locus of human chromosome 19q13.12. PMID:17019650
Reconstructing contiguous regions of an ancestral genome. PMID:16983148
Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues. PMID:16982645
PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification. PMID:16973001
Characterization of binding sites of eukaryotic transcription factors. PMID:16970547
The human ortholog of the rodent testis-specific ABC transporter Abca17 is a ubiquitously expressed pseudogene (ABCA17P) and shares a common 5' end with ABCA3. PMID:16968533
Genome-wide DNA polymorphism analyses using VariScan. PMID:16968531
Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire. PMID:16963704
Genomic organization and evolution of the ULBP genes in cattle. PMID:16953885
In vivo requirement of the small subunit of U2AF for recognition of a weak 3' splice site. PMID:16940179
Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts. PMID:16925842
Histone H3 acetylation and H3 K4 methylation define distinct chromatin regions permissive for transgene expression. PMID:16914722
Oligonucleotide microarray analysis of genomic imbalance in children with mental retardation. PMID:16909388
An initial map of insertion and deletion (INDEL) variation in the human genome. PMID:16902084
NF-Y, AP2, Nrf1 and Sp1 regulate the fragile X-related gene 2 (FXR2). PMID:16886907
L1 antisense promoter drives tissue-specific transcription of human genes. PMID:16877819
Bioinformatics methods for identifying candidate disease genes. PMID:16848981
A distant upstream locus control region is critical for expression of the Kit receptor gene in mast cells. PMID:16847336
Genomic sites of human immunodeficiency virus type 2 (HIV-2) integration: similarities to HIV-1 in vitro and possible differences in vivo. PMID:16840312
SAP30L interacts with members of the Sin3A corepressor complex and targets Sin3A to the nucleolus. PMID:16820529
Comparative isoschizomer profiling of cytosine methylation: the HELP assay. PMID:16809668
Combining gene expression QTL mapping and phenotypic spectrum analysis to uncover gene regulatory relationships. PMID:16783639
A novel trinucleotide repeat expansion at chromosome 3q26.2 identified by a CAG/CTG repeat expansion detection array. PMID:16783570
Clusters of internally primed transcripts reveal novel long noncoding RNAs. PMID:16683026
Heterotachy in mammalian promoter evolution. PMID:16683025
SPA: a probabilistic algorithm for spliced alignment. PMID:16683023
Iterative gene prediction and pseudogene removal improves genome annotation. PMID:16651666
Identification and classification of conserved RNA secondary structures in the human genome. PMID:16628248
Evidence that bovine forebrain embryonic zinc finger-like gene influences immune response associated with mastitis resistance. PMID:16611727
Evolutionary expansion and divergence in the ZNF91 subfamily of primate-specific zinc finger genes. PMID:16606703
A comprehensive catalog of human KRAB-associated zinc finger genes: insights into the evolutionary history of a large family of transcriptional repressors. PMID:16606702
A statistical method for predicting splice variants between two groups of samples using GeneChip expression array data. PMID:16603076
An isochore map of human chromosomes. PMID:16597586
Regions of extreme synonymous codon selection in mammalian genes. PMID:16556911
A third approach to gene prediction suggests thousands of additional human transcribed regions. PMID:16543943
Haplotype analysis suggest common founders in carriers of the recurrent BRCA2 mutation, 3398delAAAAG, in French Canadian hereditary breast and/ovarian cancer families. PMID:16539696
A dopamine transporter gene functional variant associated with cocaine abuse in a Brazilian sample. PMID:16537431
Choosing the best heuristic for seeded alignment of DNA sequences. PMID:16533404
NovelFam3000--uncharacterized human protein domains conserved across model organisms. PMID:16533400
Recently mobilized transposons in the human and chimpanzee genomes. PMID:16532396
Gene expression profiling of naïve sheep genetically resistant and susceptible to gastrointestinal nematodes. PMID:16515715
Alternative promoter usage of the membrane glycoprotein CD36. PMID:16515687
dbRIP: a highly integrated database of retrotransposon insertion polymorphisms in humans. PMID:16511833
A reliable method to display authentic DNase I hypersensitive sites at long-ranges in single-copy genes from large genomes. PMID:16510851
SinicView: a visualization environment for comparisons of multiple nucleotide sequence alignment tools. PMID:16509994
Comparison of human (and other) genome browsers. PMID:16460652
Genomic analysis of a heterogeneous Mendelian phenotype: multiple novel alleles for inherited hearing loss in the Palestinian population. PMID:16460646
A general method for manipulating DNA sequences from any organism with optical tweezers. PMID:16452295
Acute myeloid leukemia is associated with retroviral gene transfer to hematopoietic progenitor cells in a rhesus macaque. PMID:16439674
Variable molecular clocks in hominoids. PMID:16432233
A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. PMID:16432200
Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration. PMID:16426464
Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan. PMID:16420694
A novel approach to identifying regulatory motifs in distantly related genomes. PMID:16420672
Identification of large-scale human-specific copy number differences by inter-species array comparative genomic hybridization. PMID:16395594
The UCSC Genome Browser Database: update 2006. PMID:16381938
QTL MatchMaker: a multi-species quantitative trait loci (QTL) database and query system for annotation of genes and QTL. PMID:16381937
The UCSC Archaeal Genome Browser. PMID:16381898
A computational screen for mammalian pseudouridylation guide H/ACA RNAs. PMID:16373490
Global landscape of recent inferred Darwinian selection for Homo sapiens. PMID:16371466
L1 integration in a transgenic mouse model. PMID:16365384
Evolution of alternative splicing after gene duplication. PMID:16365379
Genome-wide associations of gene expression variation in humans. PMID:16362079
Recently evolved genes identified from Drosophila yakuba and D. erecta accessory gland expressed sequence tags. PMID:16361246
Analysis of concordance of different haplotype block partitioning algorithms. PMID:16356172
A mouse atlas of gene expression: large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells. PMID:16352711
Abundant novel transcriptional units and unconventional gene pairs on human chromosome 22. PMID:16344557
The evolutionary dynamics of alpha-satellite. PMID:16344556
Primate-specific endogenous cis-antisense transcription in the human 5q31 protocadherin gene cluster. PMID:16341467
New approaches to the analysis of palindromic sequences from the human genome: evolution and polymorphism of an intronic site at the NF1 locus. PMID:16340004
A frameshift polymorphism in P2X5 elicits an allogeneic cytotoxic T lymphocyte response associated with remission of chronic myeloid leukemia. PMID:16322791
Mapping and characterization of the amplicon near APOA2 in 1q23 in human sarcomas by FISH and array CGH. PMID:16274472
Ancient and recent positive selection transformed opioid cis-regulation in humans. PMID:16274263
The International HapMap Project Web site. PMID:16251469
Genomic regions exhibiting positive selection identified from dense genotype data. PMID:16251465
Sequence features in regions of weak and strong linkage disequilibrium. PMID:16251462
Galaxy: a platform for interactive large-scale genome analysis. PMID:16169926
Epigenetic inactivation and aberrant transcription of CSMD1 in squamous cell carcinoma cell lines. PMID:16153303
Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates. PMID:16140992
Why do human diversity levels vary at a megabase scale? PMID:16140990
Fitting background-selection predictions to levels of nucleotide variation and divergence along the human autosomes. PMID:16140989
G2D: a tool for mining genes associated with disease. PMID:16115313
Alternative pre-mRNA processing regulates cell-type specific expression of the IL4l1 and NUP62 genes. PMID:16029492
Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences. PMID:16024817
Repression of c-kit and its downstream substrates by GATA-1 inhibits cell proliferation during erythroid maturation. PMID:16024808
Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. PMID:15998911
Genomic analysis of heat-shock factor targets in Drosophila. PMID:15998452
Analysis of the Macaca mulatta transcriptome and the sequence divergence between Macaca and human. PMID:15998449
Dcode.org anthology of comparative genomic tools. PMID:15980535
Identification of regulatory targets of tissue-specific transcription factors: application to retina-specific gene regulation. PMID:15967807
Satellog: a database for the identification and prioritization of satellite repeats in disease association studies. PMID:15949044
Polymorphisms in signal transducer and activator of transcription 3 and lung function in asthma. PMID:15935090
CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome. PMID:15911630
Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing. PMID:15899965
Clustering and conservation patterns of human microRNAs. PMID:15891114
Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing. PMID:15885146
Anatomy of a founder effect: myotonic dystrophy in Northeastern Quebec. PMID:15883838
Exploring relationships and mining data with the UCSC Gene Sorter. PMID:15867434
Promoter features related to tissue specificity as measured by Shannon entropy. PMID:15833120
Orphan nuclear receptor LRH-1 is required to maintain Oct4 expression at the epiblast stage of embryonic development. PMID:15831456
Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser. PMID:15826305
Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus. PMID:15804358
Genomic and gene expression profiling of minute alterations of chromosome arm 1p in small-cell lung carcinoma cells. PMID:15785753
Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example. PMID:15752422
The synthetic form of a novel chicken beta-defensin identified in silico is predominantly active against intestinal pathogens. PMID:15744537
Comparative genomics and diversifying selection of the clustered vertebrate protocadherin genes. PMID:15744052
Human endogenous retrovirus HERV-K14 families: status, variants, evolution, and mobilization of other cellular sequences. PMID:15709013
Automated genomic sequence analysis of the three collagen VI genes: applications to Ullrich congenital muscular dystrophy and Bethlem myopathy. PMID:15689448
Fast and reliable prediction of noncoding RNAs. PMID:15665081
CpG methylation directly regulates transcriptional activity of the human endogenous retrovirus family HERV-K(HML-2). PMID:15613316
The MAPPER database: a multi-genome catalog of putative transcription factor binding sites. PMID:15608292
FESD: a Functional Element SNPs Database in human. PMID:15608252
DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes. PMID:15608249
Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results. PMID:15608239
The Vertebrate Genome Annotation (Vega) database. PMID:15608237
The UCSC Proteome Browser. PMID:15608236
Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics. PMID:15601538
Comparison of splice sites in mammals and chicken. PMID:15590946
Mulan: multiple-sequence local alignment and visualization for studying function and evolution. PMID:15590941
ABC: software for interactive browsing of genomic multiple sequence alignment data. PMID:15588288
Reconstructing large regions of an ancestral mammalian genome in silico. PMID:15574820
Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome. PMID:15534692
A novel method for multiple alignment of sequences with repeated and shuffled elements. PMID:15520295
Natural genetic variation caused by transposable elements in humans. PMID:15514065
BMP receptor signaling is required for postnatal maintenance of articular cartilage. PMID:15492776
From ORFeome to biology: a functional genomics pipeline. PMID:15489336
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). PMID:15489334
Inverted repeat structure of the human genome: the X-chromosome contains a preponderance of large, highly homologous inverted repeats that contain testes genes. PMID:15466286
A locus for posterior polymorphous corneal dystrophy (PPCD3) maps to chromosome 10. PMID:15384081
Detecting single DNA copy number variations in complex genomes using one nanogram of starting DNA and BAC-array CGH. PMID:15284333
Replication study supports evidence for linkage to 9p24 in obsessive-compulsive disorder. PMID:15272418
Molecular structure of double-minute chromosomes bearing amplified copies of the epidermal growth factor receptor gene in gliomas. PMID:15269346
Clustering of DNA sequences in human promoters. PMID:15256515
Fine mapping of 10q and 18q for familial Alzheimer's disease in Caribbean Hispanics. PMID:15241431
VISTA: computational tools for comparative genomics. PMID:15215394
PromoSer: improvements to the algorithm, visualization and accessibility. PMID:15215378
A transcript finishing initiative for closing gaps in the human transcriptome. PMID:15197164
Interaction profile-based protein classification of death domain. PMID:15189571
ELXR: a resource for rapid exon-directed sequence analysis. PMID:15128450
The Ensembl Web site: mechanics of a genome browser. PMID:15123591
The Ensembl analysis pipeline. PMID:15123589
Visualization of multiple genome annotations and alignments with the K-BROWSER. PMID:15060015
Aligning multiple genomic sequences with the threaded blockset aligner. PMID:15060014
Automated whole-genome multiple alignment of rat, mouse, and human. PMID:15060011
Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat. PMID:15060007
Comparative recombination rates in the rat, mouse, and human genomes. PMID:15059993
Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes. PMID:15059991
Recent segmental duplications in the working draft assembly of the brown Norway rat. PMID:15059990
Assessment of clusters of transcription factor binding sites in relationship to human promoter, CpG islands and gene expression. PMID:15053842
WebQTL: web-based complex trait analysis. PMID:15043217
Combined subtractive cDNA cloning and array CGH: an efficient approach for identification of overexpressed genes in DNA amplicons. PMID:15018647
Fine mapping a gene for pediatric gastroesophageal reflux on human chromosome 13q14. PMID:15014979
Sequence organization and matrix attachment regions of the human serine protease inhibitor gene cluster at 14q32.1. PMID:15014966
zPicture: dynamic alignment and visualization tool for analyzing conservation profiles. PMID:14993211
Gene conversion and the evolution of protocadherin gene cluster diversity. PMID:14993203
Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. PMID:14993201
Presence of dUTPase in the various human endogenous retrovirus K (HERV-K) families. PMID:14745533
Packaging and reverse transcription of snRNAs by retroviruses may generate pseudogenes. PMID:14730028
Localization and characterization of mouse-human alignments within the human genome. Does evolutionary conservation suggest functional importance? PMID:14728497
EnsMart: a generic system for fast and flexible access to biological data. PMID:14707178
Mapping and initial analysis of human subtelomeric sequence assemblies. PMID:14707167
RTCGD: retroviral tagged cancer gene database. PMID:14681473
The UCSC Table Browser data retrieval tool. PMID:14681465
HERVd: the Human Endogenous RetroViruses Database: update. PMID:14681356
Multi-species sequence comparison: the next frontier in genome annotation. PMID:14659006
Identification and characterization of multi-species conserved sequences. PMID:14656959
The German cDNA network: cDNAs, functional genomics and proteomics. PMID:14649292
SVA elements are nonautonomous retrotransposons that cause disease in humans. PMID:14628287
Comparative genomics. PMID:14624258
Nucleotide frequency variation across human genes. PMID:14613976
Matrix attachment region (MAR) properties and abnormal expansion of AT island minisatellites in FRA16B fragile sites in leukemic CEM cells. PMID:14576323
An endogenous retroviral long terminal repeat is the dominant promoter for human beta1,3-galactosyltransferase 5 in the colon. PMID:14534330
Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. PMID:14500911
cDNA2Genome: a tool for mapping and annotating cDNAs. PMID:12964951
GANESH: software for customized annotation of genome regions. PMID:12952886
Genomewide linkage scan for schizophrenia susceptibility loci among Ashkenazi Jewish families shows evidence of linkage on chromosome 10q22. PMID:12929083
Insights from human/mouse genome comparisons. PMID:12925891
Refinement of a chimpanzee pericentric inversion breakpoint to a segmental duplication cluster. PMID:12914658
Single nucleotide polymorphisms (SNPs) that map to gaps in the human SNP map. PMID:12907734
Age-related macular degeneration--a genome scan in extended families. PMID:12900797
Dependence of mutational asymmetry on gene-expression levels in the human genome. PMID:12881777
ETOPE: Evolutionary test of predicted exons. PMID:12824366
PromoSer: A large-scale mammalian promoter and transcription start site identification service. PMID:12824364
FIE2: A program for the extraction of genomic DNA sequences around the start and translation initiation site of human genes. PMID:12824363
Connecting sequence and biology in the laboratory mouse. PMID:12819150
GeneLynx mouse: integrated portal to the mouse genome. PMID:12819149
Identification of promoter regions in the human genome by using a retroviral plasmid library-based functional reporter gene assay. PMID:12805274
Identification of a polymorphic gene, BCL2A1, encoding two novel hematopoietic lineage-specific minor histocompatibility antigens. PMID:12771180
Identification of conserved regulatory elements by comparative genome analysis. PMID:12760745
Gene expression profiling of the cellular transcriptional network regulated by alpha/beta interferon and its partial attenuation by the hepatitis C virus nonstructural 5A protein. PMID:12743294
Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes. PMID:12727901
Complex evolution of 7E olfactory receptor genes in segmental duplications. PMID:12727898
Comparative genomic tools and databases: providing insights into the human genome. PMID:12697725
MHC class I-like genes in cattle, MHCLA, with similarity to genes encoding NK cell stimulatory ligands. PMID:12679856
Gatm, a creatine synthesis enzyme, is imprinted in mouse placenta. PMID:12671064
GALA, a database for genomic sequence alignments and annotations. PMID:12671007
Rapid direct sequence analysis of the dystrophin gene. PMID:12632325
Molecular classification of familial non-BRCA1/BRCA2 breast cancer. PMID:12610208
PA26 is a candidate gene for heterotaxia in humans: identification of a novel PA26-related gene family in human and mouse. PMID:12607115
STRP screening sets for the human genome at 5 cM density. PMID:12600278
Discovery of the breast cancer gene BASE using a molecular approach to enrich for genes encoding membrane and secreted proteins. PMID:12538848
An integrated computational pipeline and database to support whole-genome sequence annotation. PMID:12537570
Human-mouse alignments with BLASTZ. PMID:12529312
Strategies and tools for whole-genome alignments. PMID:12529308
Distinguishing regulatory DNA from neutral sites. PMID:12529307
Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map. PMID:12529305
Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. PMID:12529302
Cross-species sequence comparisons: a review of methods and available resources. PMID:12529301
SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. PMID:12519986
The SNP Consortium website: past, present and future. PMID:12519964
The UCSC Genome Browser Database. PMID:12519945
SeqVISTA: a graphical tool for sequence feature visualization and comparison. PMID:12513700
POTE, a highly homologous gene family located on numerous chromosomes and expressed in prostate, ovary, testis, placenta, and prostate cancer. PMID:12475935
HapScope: a software system for automated and visual analysis of functionally annotated haplotypes. PMID:12466546
Distribution and characterization of regulatory elements in the human genome. PMID:12466286
Development and production of an oligonucleotide MuscleChip: use for validation of ambiguous ESTs. PMID:12456269
Identification of candidate genes regulating HDL cholesterol using a chromosomal region expression array. PMID:12421756
Visualizing the genome: techniques for presenting human genome data and annotations. PMID:12149135 -
BLAT--the BLAST-like alignment tool
PubMed citations: 4200.
4200 articles citing: BLAT--the BLAST-like alignment tool
Complete genome sequencing and investigation on the fiber-degrading potential of Bacillus amyloliquefaciens strain TL106 from the tibetan pig. PMID:35906551
Comparative repeatome analysis reveals new evidence on genome evolution in wild diploid Arachis (Fabaceae) species. PMID:35895167
Exceptional diversity and selection pressure on coronavirus host receptors in bats compared to other mammals. PMID:35892217
Screening of Genes Related to Sex Determination and Differentiation in Mandarin Fish (Siniperca chuatsi). PMID:35887035
REDfly: An Integrated Knowledgebase for Insect Regulatory Genomics. PMID:35886794
Identification of fusions with potential clinical significance in melanoma. PMID:35871080
Patient-Specific Assays Based on Whole-Genome Sequencing Data to Measure Residual Disease in Children With Acute Lymphoblastic Leukemia: A Proof of Concept Study. PMID:35865473
Phylogeographical Pattern and Population Evolution History of Indigenous Elymus sibiricus L. on Qinghai-Tibetan Plateau. PMID:35845670
Equilibrated evolution of the mixed auto-/allopolyploid haplotype-resolved genome of the invasive hexaploid Prussian carp. PMID:35835759
Turnover in Life-Strategies Recapitulates Marine Microbial Succession Colonizing Model Particles. PMID:35814698
Chromosome-level assembly and annotation of the blue catfish Ictalurus furcatus, an aquaculture species for hybrid catfish reproduction, epigenetics, and heterosis studies. PMID:35809049
Retrospective Natural History Study of RPGR-Related Cone- and Cone-Rod Dystrophies While Expanding the Mutation Spectrum of the Disease. PMID:35806195
Differential Transcriptional Responses in Two Old World Bemisia tabaci Cryptic Species Post Acquisition of Old and New World Begomoviruses. PMID:35805143
Bioinformatics Approaches for Determining the Functional Impact of Repetitive Elements on Non-coding RNAs. PMID:35796972
Computational Methods for the Discovery and Annotation of Viral Integrations. PMID:35796971
Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. PMID:35789323
Complex Feline Disease Mapping Using a Dense Genotyping Array. PMID:35782544
Introduction to the principles and methods underlying the recovery of metagenome-assembled genomes from metagenomic data. PMID:35765182
Along the Bos taurus genome, uncover candidate imprinting control regions. PMID:35764919
A chromosome-level genome of Brachymystax tsinlingensis provides resources and insights into salmonids evolution. PMID:35758619
A Novel miRNA Located in the HER2 Gene Shows an Inhibitory Effect on Wnt Signaling and Cell Cycle Progression. PMID:35747498
Population Scale Analysis of Centromeric Satellite DNA Reveals Highly Dynamic Evolutionary Patterns and Genomic Organization in Long-Tailed and Rhesus Macaques. PMID:35741082
The chromosome-level genome for Toxicodendron vernicifluum provides crucial insights into Anacardiaceae evolution and urushiol biosynthesis. PMID:35733792
Chromosomal Translocation t(5;12)(p13;q14) Leading to Fusion of High-mobility Group AT-hook 2 Gene With Intergenic Sequences From Chromosome Sub-Band 5p13.2 in Benign Myoid Neoplasms of the Breast: A Second Case. PMID:35732319
Blood-derived lncRNAs as biomarkers for cancer diagnosis: the Good, the Bad and the Beauty. PMID:35729321
Human follicular mites: Ectoparasites becoming symbionts. PMID:35724423
Expansion of a retrovirus lineage in the koala genome. PMID:35696585
Repetitive Elements, Sequence Turnover and Cyto-Nuclear Gene Transfer in Gymnosperm Mitogenomes. PMID:35692831
Taxonomy, comparative genomics and evolutionary insights of Penicillium ucsense: a novel species in series Oxalica. PMID:35678932
Comprehensive identification and characterization of the HERV-K (HML-9) group in the human genome. PMID:35676699
Deep Sequencing Analysis of Individual HIV-1 Proviruses Reveals Frequent Asymmetric Long Terminal Repeats. PMID:35674431
Genetic and genomic architecture of species-specific cuticular hydrocarbon variation in parasitoid wasps. PMID:35673870
Chromosome-scale assembly with a phased sex-determining region resolves features of early Z and W chromosome differentiation in a wild octoploid strawberry. PMID:35666193
Genome-wide specificity of plant genome editing by both CRISPR-Cas9 and TALEN. PMID:35665758
Semi-subterranean environment and soil metagenomic datasets of the Gyeongju Seokbinggo (stone ice storage) in South Korea. PMID:35664653
Intron losses and gains in the nematodes. PMID:35659725
First Chromosome-Scale Assembly and Deep Floral-Bud Transcriptome of a Male Kiwifruit. PMID:35651931
ANI analysis of poxvirus genomes reveals its potential application to viral species rank demarcation. PMID:35646390
Computationally designed hyperactive Cas9 enzymes. PMID:35641498
mebipred: identifying metal binding potential in protein sequence. PMID:35639953
Chromosome-level genome assembly of the black widow spider Latrodectus elegans illuminates composition and evolution of venom and silk proteins. PMID:35639632
Phyloepigenetics. PMID:35625482
Revealing diverse alternative splicing variants of the highly homologous SMN1 and SMN2 genes by targeted long-read sequencing. PMID:35612622
Chromosome-scale genome assembly of an important medicinal plant honeysuckle. PMID:35610245
Chromosome-level genome assembly of the diploid blueberry Vaccinium darrowii provides insights into its subtropical adaptation and cuticle synthesis. PMID:35605198
The assembled and annotated genome of the masked palm civet (Paguma larvata). PMID:35583674
Genome-Based Analysis of Aspergillus niger Aggregate Species from China and Their Potential for Fumonisin B2 and Ochratoxin A Production. PMID:35579721
Alignment-Free Analysis of Whole-Genome Sequences From Symbiodiniaceae Reveals Different Phylogenetic Signals in Distinct Regions. PMID:35557718
Comprehensive 16S rRNA and metagenomic data from the gut microbiome of aging and rejuvenation mouse models. PMID:35538082
Nitrogen fixation and other biogeochemically important features of Atacama Desert giant horsetail plant microbiomes inferred from metagenomic contig analysis. PMID:35533355
Genes and evolutionary fates of the amanitin biosynthesis pathway in poisonous mushrooms. PMID:35533275
CircMiMi: a stand-alone software for constructing circular RNA-microRNA-mRNA interactions across species. PMID:35524165
EBV genome variations enhance clinicopathological features of nasopharyngeal carcinoma in a non-endemic region. PMID:35485636
Evolution of coastal forests based on a full set of mangrove genomes. PMID:35484219
Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding. PMID:35482491
KmerKeys: a web resource for searching indexed genome assemblies and variants. PMID:35474383
A Chromosome-Level Reference Genome of Chinese Balloon Flower (Platycodon grandiflorus). PMID:35464833
Intraspecific de novo gene birth revealed by presence-absence variant genes in Caenorhabditis elegans. PMID:35464238
Recently Integrated Alu Elements in Capuchin Monkeys: A Resource for Cebus/Sapajus Genomics. PMID:35456378
Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF. PMID:35440598
Open reading frame dominance indicates protein-coding potential of RNAs. PMID:35438231
Scan of the endogenous retrovirus sequences across the swine genome and survey of their copy number variation and sequence diversity among various Chinese and Western pig breeds. PMID:35437972
Assessing the Effect of Smokeless Tobacco Consumption on Oral Microbiome in Healthy and Oral Cancer Patients. PMID:35433507
A draft genome of Drung cattle reveals clues to its chromosomal fusion and environmental adaptation. PMID:35418663
Putting small and big pieces together: a genome assembly approach reveals the largest Lamiid plastome in a woody vine. PMID:35415013
Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila. PMID:35413957
Using iRNA-seq analysis to predict gene expression regulatory level and activity in Zea mays tissues. PMID:35404453
Relationship between nitrifying microorganisms and other microorganisms residing in the maize rhizosphere. PMID:35394234
The Gastrodia menghaiensis (Orchidaceae) genome provides new insights of orchid mycorrhizal interactions. PMID:35392808
A high-quality assembly reveals genomic characteristics, phylogenetic status, and causal genes for leucism plumage of Indian peafowl. PMID:35383847
RNA aptamers specific for transmembrane p24 trafficking protein 6 and Clusterin for the targeted delivery of imaging reagents and RNA therapeutics to human β cells. PMID:35383192
Accurate detection of tumor-specific gene fusions reveals strongly immunogenic personal neo-antigens. PMID:35379963
A generalist-specialist trade-off between switchgrass cytotypes impacts climate adaptation and geographic range. PMID:35377798
Precise in vivo functional analysis of DNA variants with base editing using ACEofBASEs target prediction. PMID:35373735
Beyond Genes: Inclusion of Alternative Splicing and Alternative Polyadenylation to Assess the Genetic Architecture of Predisposition to Voluntary Alcohol Consumption in Brain of the HXB/BXH Recombinant Inbred Rat Panel. PMID:35368676
Linking genomic and epidemiologic information to advance the study of COVID-19. PMID:35354824
Metagenomic clustering reveals microbial contamination as an essential consideration in ultraconserved element design for phylogenomics with insect museum specimens. PMID:35342556
The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features. PMID:35333302
Global mapping of RNA homodimers in living cells. PMID:35332098
Original Leaf Colonisers Shape Fungal Decomposer Communities of Phragmites australis in Intermittent Habitats. PMID:35330286
Host-Species Variation and Environment Influence Endophyte Symbiosis and Mycotoxin Levels in Chinese Oxytropis Species. PMID:35324678
ADARs act as potent regulators of circular transcriptome in cancer. PMID:35314703
Ethylene Response Factor109 Attunes Immunity, Photosynthesis, and Iron Homeostasis in Arabidopsis Leaves. PMID:35310669
A point mutation in HIV-1 integrase redirects proviral integration into centromeric repeats. PMID:35304442
Targeted Sanger sequencing to recover key mutations in SARS-CoV-2 variant genome assemblies produced by next-generation sequencing. PMID:35294336
PanCancer analysis of somatic mutations in repetitive regions reveals recurrent mutations in snRNA U2. PMID:35288589
Comprehensive RNA dataset of tissue and plasma from patients with esophageal cancer or precursor lesions. PMID:35288573
Dissection of molecular and histological subtypes of papillary thyroid cancer using alternative splicing profiles. PMID:35277656
Exome sequencing identifies variants in infants with sacral agenesis. PMID:35274497
Integrated metagenomics identifies a crucial role for trimethylamine-producing Lachnoclostridium in promoting atherosclerosis. PMID:35273169
Chromosome-level genome assembly of a xerophytic plant, Haloxylon ammodendron. PMID:35266513
The evolution, evolvability and engineering of gene regulatory DNA. PMID:35264797
Comparative analysis of the Mercenaria mercenaria genome provides insights into the diversity of transposable elements and immune molecules in bivalve mollusks. PMID:35260071
Transposon insertions regulate genome-wide allele-specific expression and underpin flower colour variations in apple (Malus spp.). PMID:35258172
Transcriptome and proteome profiling reveals complex adaptations of Candida parapsilosis cells assimilating hydroxyaromatic carbon sources. PMID:35255079
ExceS-A: an exon-centric split aligner. PMID:35254744
Genome-Wide Methylation Profiling in the Thalamus of Scrapie Sheep. PMID:35252421
Landscape of adenosine-to-inosine RNA recoding across human tissues. PMID:35246538
Nanopore ReCappable sequencing maps SARS-CoV-2 5' capping sites and provides new insights into the structure of sgRNAs. PMID:35244721
Combined tumor and immune signals from genomes or transcriptomes predict outcomes of checkpoint inhibition in melanoma. PMID:35243413
Conservation of chromatin conformation in carnivores. PMID:35217621
Transcriptomic Analysis Suggests Auxin Regulation in Dorsal-Ventral Petal Asymmetry of Wild Progenitor Sinningia speciosa. PMID:35216188
Characterizing mobile element insertions in 5675 genomes. PMID:35212372
A Chromosome-Level Genome Assembly of the European Beech (Fagus sylvatica) Reveals Anomalies for Organelle DNA Integration, Repeat Content and Distribution of SNPs. PMID:35211148
Comparison of Immune Checkpoint Molecules PD-1 and PD-L1 in Paired Primary and Recurrent Glioma: Increasing Trend When Recurrence. PMID:35204029
Background splicing as a predictor of aberrant splicing in genetic disease. PMID:35188075
Genome Sequences of Two Strains of Prototheca wickerhamii Provide Insight Into the Protothecosis Evolution. PMID:35186789
Comparative genomics analysis of bHLH genes in cucurbits identifies a novel gene regulating cucurbitacin biosynthesis. PMID:35184192
Clonal lineage tracing reveals shared origin of conventional and plasmacytoid dendritic cells. PMID:35180378
Gene losses may contribute to subterranean adaptations in naked mole-rat and blind mole-rat. PMID:35172813
Placental methylome reveals a 22q13.33 brain regulatory gene locus associated with autism. PMID:35168652
Association of Tandem Repeat Number Variabilities in Subunit S of the Type I Restriction-Modification System with Macrolide Resistance in Mycoplasma pneumoniae. PMID:35160167
High Stability of the Epigenome in Drosophila Interspecific Hybrids. PMID:35143649
Multiple phylogenetically-diverse, differentially-virulent Burkholderia pseudomallei isolated from a single soil sample collected in Thailand. PMID:35143500
Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives. PMID:35139817
Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. PMID:35135349
WormBase in 2022-data, processes, and tools for analyzing Caenorhabditis elegans. PMID:35134929
Heterochiasmy and the establishment of gsdf as a novel sex determining gene in Atlantic halibut. PMID:35134055
A High-Density Genetic Map Enables Genome Synteny and QTL Mapping of Vegetative Growth and Leaf Traits in Gardenia. PMID:35132310
A Chromosome-Level Genome Assembly of Yellowtail Kingfish (Seriola lalandi). PMID:35126476
Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber. PMID:35115520
Genomic insight into the scale specialization of the biological control agent Novius pumilus (Weise, 1892). PMID:35100986
Dysgu: efficient structural variant calling using short or long reads. PMID:35100420
Evolution of DNA Methylation Across Ecdysozoa. PMID:35089376
Chromosome-Level Genome Assembly of a Human Fungal Pathogen Reveals Synteny among Geographically Distinct Species. PMID:35089059
Comparative assessment of genes driving cancer and somatic evolution in non-cancer tissues: an update of the Network of Cancer Genes (NCG) resource. PMID:35078504
Mitochondrial DNA variation across 56,434 individuals in gnomAD. PMID:35074858
Genome sequence data of the antagonistic soil-borne yeast Cyberlindnera sargentensis (SHA 17.2). PMID:35071701
Quantitative Trait Loci Mapping and Development of KASP Marker Smut Screening Assay Using High-Density Genetic Map and Bulked Segregant RNA Sequencing in Sugarcane (Saccharum spp.). PMID:35069651
Genomically Hardwired Regulation of Gene Activity Orchestrates Cellular Iron Homeostasis in Arabidopsis. PMID:35067184
A comparative analysis of complete chloroplast genomes of seven Ocotea species (Lauraceae) confirms low sequence divergence within the Ocotea complex. PMID:35064146
No link between population isolation and speciation rate in squamate reptiles. PMID:35058358
Characterisation of the Complete Mitochondrial Genome of Critically Endangered Mustela lutreola (Carnivora: Mustelidae) and Its Phylogenetic and Conservation Implications. PMID:35052465
Trade-off between sex and growth in diatoms: Molecular mechanisms and demographic implications. PMID:35044817
The Barley and Wheat Pan-Genomes. PMID:35037204
Circulating T-Cell Repertoires Correlate With the Tumor Response in Patients With Breast Cancer Receiving Neoadjuvant Chemotherapy. PMID:35025620
De novo mutations identified by whole-genome sequencing implicate chromatin modifications in obsessive-compulsive disorder. PMID:35020433
Long-read nanopore DNA sequencing can resolve complex intragenic duplication/deletion variants, providing information to enable preimplantation genetic diagnosis. PMID:35014072
Partitioning RNAs by length improves transcriptome reconstruction from short-read RNA-seq data. PMID:35013600
The metabolic core of the prokaryotic community from deep-sea sediments of the southern Gulf of Mexico shows different functional signatures between the continental slope and abyssal plain. PMID:34993013
Metatranscriptome Profiling of a Specialized Microbial Consortium during the Degradation of Nixtamalized Maize Pericarp. PMID:34985337
The Dark Side of Microbial Processes: Accumulation of Nitrate During Storage of Surface Water in the Dark and the Underlying Mechanism. PMID:34985332
CLUSTER guide RNAs enable precise and efficient RNA editing with endogenous ADAR enzymes in vivo. PMID:34980913
Dosage sensitivity and exon shuffling shape the landscape of polymorphic duplicates in Drosophila and humans. PMID:34969986
Genetic and Molecular Characterization of a Self-Compatible Brassica rapa Line Possessing a New Class II S Haplotype. PMID:34961286
Identification of starch candidate genes using SLAF-seq and BSA strategies and development of related SNP-CAPS markers in tetraploid potato. PMID:34932571
Genomic analysis of Elsinoë arachidis reveals its potential pathogenic mechanism and the biosynthesis pathway of elsinochrome toxin. PMID:34914789
Uncovering the Role of Gut Microbiota in Amino Acid Metabolic Disturbances in Heart Failure Through Metagenomic Analysis. PMID:34912870
Evaluation of accessible regions of Escherichia coli fimH mRNA through computational prediction and experimental investigation. PMID:34900163
Identification of Novel Regulatory Regions Induced by Intrauterine Growth Restriction in Rat Islets. PMID:34894232
Epigenetic Dysregulation of KCNK9 Imprinting and Triple-Negative Breast Cancer. PMID:34885139
Species-specific partial gene duplication in Arabidopsis thaliana evolved novel phenotypic effects on morphological traits under strong positive selection. PMID:34875081
Medium levels of transcription and replication related chromosomal instability are associated with poor clinical outcome. PMID:34873180
Transcriptome Analysis Reveals Higher Levels of Mobile Element-Associated Abnormal Gene Transcripts in Temporal Lobe Epilepsy Patients. PMID:34868252
ChiTaH: a fast and accurate tool for identifying known human chimeric sequences from high-throughput sequencing data. PMID:34859212
Error-prone, stress-induced 3' flap-based Okazaki fragment maturation supports cell survival. PMID:34855483
Rare and potentially pathogenic variants in hydroxycarboxylic acid receptor genes identified in breast cancer cases. PMID:34852802
Stability of DNA methylation and chromatin accessibility in structurally diverse maize genomes. PMID:34849810
MammaPrint and BluePrint comprehensively capture the cancer hallmarks in early-stage breast cancer patients. PMID:34841595
Baiting out a full length sequence from unmapped RNA-seq data. PMID:34837950
Chloranthus genome provides insights into the early diversification of angiosperms. PMID:34836973
Origins and Function of VL30 lncRNA Packaging in Small Extracellular Vesicles: Implications for Cellular Physiology and Pathology. PMID:34829970
Plastome sequencing reveals phylogenetic relationships among Comastoma and related taxa (Gentianaceae) from the Qinghai-Tibetan Plateau. PMID:34824809
Molecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae). PMID:34814832
Vertical Inheritance Facilitates Interspecies Diversification in Biosynthetic Gene Clusters and Specialized Metabolites. PMID:34809466
InsectBase 2.0: a comprehensive gene resource for insects. PMID:34792158
The U1 snRNP component RBP45d regulates temperature-responsive flowering in Arabidopsis. PMID:34791475
A Rapid Evolving microRNA Cluster Rewires Its Target Regulatory Networks in Drosophila. PMID:34777478
Massively parallel DNA target capture using long adapter single stranded oligonucleotide (LASSO) probes assembled through a novel DNA recombinase mediated methodology. PMID:34775678
PCR Primer Design for the Rapidly Evolving SARS-CoV-2 Genome. PMID:34773624
Genome-wide survey and characterization of transcription factors in the silk gland of the silkworm, Bombyx mori. PMID:34762712
Shotgun metagenomics evaluation of soil fertilization effect on the rhizosphere viral community of maize plants. PMID:34762236
Resolving the Microalgal Gene Landscape at the Strain Level: a Novel Hybrid Transcriptome of Emiliania huxleyi CCMP3266. PMID:34757817
Phylogeny of Crataegus (Rosaceae) based on 257 nuclear loci and chloroplast genomes: evaluating the impact of hybridization. PMID:34754629
CSC software corrects off-target mediated gRNA depletion in CRISPR-Cas9 essentiality screens. PMID:34753924
SeekFusion - A Clinically Validated Fusion Transcript Detection Pipeline for PCR-Based Next-Generation Sequencing of RNA. PMID:34745213
Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus. PMID:34737427
Benchmarking pipelines for subclonal deconvolution of bulk tumour sequencing data. PMID:34737285
Transposable elements that have recently been mobile in the human genome. PMID:34732136
Uncovering Bleomycin-Induced Genomic Alterations and Underlying Mechanisms in the Yeast Saccharomyces cerevisiae. PMID:34731050
Genome-Wide Identification of Tomato Xylem Sap Fitness Factors for Three Plant-Pathogenic Ralstonia Species. PMID:34726495
Phylogenomics of Salvia L. subgenus Calosphace (Lamiaceae). PMID:34721456
Nanopore sequencing of SARS-CoV-2: Comparison of short and long PCR-tiling amplicon protocols. PMID:34714886
RBPmap: A Tool for Mapping and Predicting the Binding Sites of RNA-Binding Proteins Considering the Motif Environment. PMID:34694603
MINTIA: a metagenomic INserT integrated assembly and annotation tool. PMID:34692239
Comparative genomics reveal shared genomic changes in syngnathid fishes and signatures of genetic convergence with placental mammals. PMID:34692118
MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data. PMID:34686194
An Emiliania huxleyi pan-transcriptome reveals basal strain specificity in gene expression patterns. PMID:34675226
High-quality genome assembly of an important biodiesel plant, Euphorbia lathyris L. PMID:34664644
Co-evolutionary Signals Identify Burkholderia pseudomallei Survival Strategies in a Hostile Environment. PMID:34662416
Whole-Genome Sequencing and Genome-Wide Studies of Spiny Head Croaker (Collichthys lucidus) Reveals Potential Insights for Well-Developed Otoliths in the Family Sciaenidae. PMID:34659355
RGD v2.0: a major update of the ruminant functional and evolutionary genomics database. PMID:34643708
Chromosomal-Level Genome Assembly of a True Bug, Aspongopus chinensis Dallas, 1851 (Hemiptera: Dinidoridae). PMID:34623414
Chemical Inhibition of Apurinic-Apyrimidinic Endonuclease 1 Redox and DNA Repair Functions Affects the Inflammatory Response via Different but Overlapping Mechanisms. PMID:34616737
High-Quality de novo Chromosome-Level Genome Assembly of a Single Bombyx mori With BmNPV Resistance by a Combination of PacBio Long-Read Sequencing, Illumina Short-Read Sequencing, and Hi-C Sequencing. PMID:34603381
RetroCHMP3 blocks budding of enveloped viruses without blocking cytokinesis. PMID:34597582
Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish. PMID:34594040
Transcriptional Landscapes of Long Non-coding RNAs and Alternative Splicing in Pyricularia oryzae Revealed by RNA-Seq. PMID:34589103
The Euscaphis japonica genome and the evolution of malvids. PMID:34587334
The genome of the naturally evolved obesity-prone Ossabaw miniature pig. PMID:34585119
Transcriptomic profile of leg muscle during early growth and development in Haiyang yellow chicken. PMID:34584942
The genomic basis of army ant chemosensory adaptations. PMID:34582590
De Novo Genome Assembly of the Electric Fish Brachyhypopomus occidentalis (Hypopomidae, Gymnotiformes). PMID:34581791
Chemistry and Bioinformatics Considerations in Using Next-Generation Sequencing Technologies to Inferring HIV Proviral DNA Genome-Intactness. PMID:34578455
Patterns of Coevolutionary Adaptations across Time and Space in Mouse Gammaretroviruses and Three Restrictive Host Factors. PMID:34578445
Metagenomic Analyses of Plant Growth-Promoting and Carbon-Cycling Genes in Maize Rhizosphere Soils with Distinct Land-Use and Management Histories. PMID:34573413
Prognostic Roles of BRAF, KIT, NRAS, IGF2R and SF3B1 Mutations in Mucosal Melanomas. PMID:34571863
Tiara: Deep learning-based classification system for eukaryotic sequences. PMID:34570171
Genome assembly of primitive cultivated potato Solanum stenotomum provides insights into potato evolution. PMID:34568923
Microbial Composition and Genes for Key Metabolic Attributes in the Gut Digesta of Sea Urchins Lytechinus variegatus and Strongylocentrotus purpuratus Using Shotgun Metagenomics. PMID:34563039
Protein-coding repeat polymorphisms strongly shape diverse human phenotypes. PMID:34554798
Characterization of the complete chloroplast genome of Hordeum jubatum (Poaceae: Pooideae: Triticeae) and phylogenetic analysis. PMID:34553047
Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. PMID:34547909
Genome-wide detection and classification of terpene synthase genes in Aquilaria agallochum. PMID:34539112
Genomic Epidemiology and Strain Taxonomy of Corynebacterium diphtheriae. PMID:34524891
Phylogeographic analysis delimits three evolutionary significant units of least chipmunks in North America and identifies unique genetic diversity within the imperiled Peñasco population. PMID:34522364
Genome and transcriptome assemblies of the kuruma shrimp, Marsupenaeus japonicus. PMID:34515781
Chromoanagenesis Event Underlies a de novo Pericentric and Multiple Paracentric Inversions in a Single Chromosome Causing Coffin-Siris Syndrome. PMID:34512724
A near complete genome for goat genetic and genomic research. PMID:34507524
Gender-Dependent Deregulation of Linear and Circular RNA Variants of HOMER1 in the Entorhinal Cortex of Alzheimer's Disease. PMID:34502114
Genomic insights into the origin, domestication and diversification of Brassica juncea. PMID:34493868
Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing. PMID:34493830
Genomic anatomy of male-specific microchromosomes in a gynogenetic fish. PMID:34491994
A chromosome-level genome of Antechinus flavipes provides a reference for an Australian marsupial genus with male death after mating. PMID:34486812
Recombination Marks the Evolutionary Dynamics of a Recently Endogenized Retrovirus. PMID:34480565
A Bayesian approach for accurate de novo transcriptome assembly. PMID:34480063
Zanthoxylum-specific whole genome duplication and recent activity of transposable elements in the highly repetitive paleotetraploid Z. bungeanum genome. PMID:34480029
Molecular and functional profiling identifies therapeutically targetable vulnerabilities in plasmablastic lymphoma. PMID:34465776
Chromosome-scale assembly of the Dendrobium chrysotoxum genome enhances the understanding of orchid evolution. PMID:34465765
Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome. PMID:34465761
Highly susceptible SARS-CoV-2 model in CAG promoter-driven hACE2-transgenic mice. PMID:34463644
Evidence for and localization of proposed causative variants in cattle and pig genomes. PMID:34461824
The Easter Egg Weevil (Pachyrhynchus) genome reveals syntenic patterns in Coleoptera across 200 million years of evolution. PMID:34460814
Computational analysis of sense-antisense chimeric transcripts reveals their potential regulatory features and the landscape of expression in human cells. PMID:34458728
Aptamer-mediated transcriptional gene silencing of Fox p 3 inhibits regulatory T cells and potentiates antitumor response. PMID:34457999
The first genome assembly of fungal pathogen Pyrenophora tritici-repentis race 1 isolate using Oxford Nanopore MinION sequencing. PMID:34454585
A Genome-Wide CRISPR/Cas9 Screen Reveals the Requirement of Host Sphingomyelin Synthase 1 for Infection with Pseudorabies Virus Mutant gD-Pass. PMID:34452438
Technology dictates algorithms: recent developments in read alignment. PMID:34446078
Transcriptional Regulation of RUNX1: An Informatics Analysis. PMID:34440349
Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case. PMID:34439964
Genome, transcriptome and secretome analyses of the antagonistic, yeast-like fungus Aureobasidium pullulans to identify potential biocontrol genes. PMID:34395586
Genome-Wide Association Study of Root and Shoot Related Traits in Spring Soybean (Glycine max L.) at Seedling Stages Using SLAF-Seq. PMID:34394134
Comparative transcriptomics provides a strategy for phylogenetic analysis and SSR marker development in Chaenomeles. PMID:34385515
nf-LO: A Scalable, Containerized Workflow for Genome-to-Genome Lift Over. PMID:34383887
Cancer cells are highly susceptible to accumulation of templated insertions linked to MMBIR. PMID:34379776
Nanopore sequencing of brain-derived full-length circRNAs reveals circRNA-specific exon usage, intron retention and microexons. PMID:34376658
Exome sequencing of child-parent trios with bladder exstrophy: Findings in 26 children. PMID:34355505
Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger. PMID:34354050
De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. PMID:34353948
Evidence that toxin resistance in poison birds and frogs is not rooted in sodium channel mutations and may rely on "toxin sponge" proteins. PMID:34351379
Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae. PMID:34336405
Genomic signatures of natural selection at phenology-related genes in a widely distributed tree species Fagus sylvatica L. PMID:34332553
Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms. PMID:34318308
Landscape of tissue-specific RNA Editome provides insight into co-regulated and altered gene expression in pigs (Sus-scrofa). PMID:34314293
A consensus and saturated genetic map provides insight into genome anchoring, synteny of Solanaceae and leaf- and fruit-related QTLs in wolfberry (Lycium Linn.). PMID:34303361
Accurate spliced alignment of long RNA sequencing reads. PMID:34302453
Large palindromes on the primate X Chromosome are preserved by natural selection. PMID:34290043
Early-life social experience affects offspring DNA methylation and later life stress phenotype. PMID:34285226
An actin-related protein that is most highly expressed in Drosophila testes is critical for embryonic development. PMID:34282725
Single Copy Oligonucleotide Fluorescence In Situ Hybridization Probe Design Platforms: Development, Application and Evaluation. PMID:34281175
Distinct Retrotransposon Evolution Profile in the Genome of Rabbit (Oryctolagus cuniculus). PMID:34270728
Large parental differences in chromatin organization in pancreatic beta cell line explaining diabetes susceptibility effects. PMID:34267199
Haplotype-resolved germline and somatic alterations in renal medullary carcinomas. PMID:34261517
Levenshtein Distance, Sequence Comparison and Biological Database Search. PMID:34257466
DNA transposons mediate duplications via transposition-independent and -dependent mechanisms in metazoans. PMID:34257290
An epigenetic switch regulates the ontogeny of AXL-positive/EGFR-TKi-resistant cells by modulating miR-335 expression. PMID:34254585
GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing. PMID:34253237
Target enrichment improves phylogenetic resolution in the genus Zanthoxylum (Rutaceae) and indicates both incomplete lineage sorting and hybridization events. PMID:34250543
Dynamic partitioning of search patterns for approximate pattern matching using search schemes. PMID:34235407
Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding. PMID:34226565
Protocol for HSDFinder: Identifying, annotating, categorizing, and visualizing duplicated genes in eukaryotic genomes. PMID:34223195
The complete mitochondrial genome of Osmanthus fragrans (Lamiales, Oleaceae) from China. PMID:34212096
High Resolution Haplotype Analyses of Classical HLA Genes in Families With Multiple Sclerosis Highlights the Role of HLA-DP Alleles in Disease Susceptibility. PMID:34211458
Metagenomic Insight into the Community Structure of Maize-Rhizosphere Bacteria as Predicted by Different Environmental Factors and Their Functioning within Plant Proximity. PMID:34209383
The Influence of Soil Fertilization on the Distribution and Diversity of Phosphorus Cycling Genes and Microbes Community of Maize Rhizosphere Using Shotgun Metagenomics. PMID:34209356
DNA-RNA Hybrid (R-Loop): From a Unified Picture of the Mammalian Telomere to the Genome-Wide Profile. PMID:34205454
Tracking HIV-1-Infected Cell Clones Using Integration Site-Specific qPCR. PMID:34202310
Plasmodium matutinum Causing Avian Malaria in Lovebirds (Agapornis roseicollis) Hosted in an Italian Zoo. PMID:34201448
NGS Methodologies and Computational Algorithms for the Prediction and Analysis of Plant Circular RNAs. PMID:34195961
Gene-rich UV sex chromosomes harbor conserved regulators of sexual development. PMID:34193417
Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome. PMID:34193290
SINE jumping contributes to large-scale polymorphisms in the pig genomes. PMID:34183049
Acute Effects on the Human Peripheral Blood Transcriptome of Decompression Sickness Secondary to Scuba Diving. PMID:34177613
A de novo transcriptional atlas in Danaus plexippus reveals variability in dosage compensation across tissues. PMID:34172835
A combinatorial cis-regulatory logic restricts color-sensing Rhodopsins to specific photoreceptor subsets in Drosophila. PMID:34161320
Mobile element insertions and associated structural variants in longitudinal breast cancer samples. PMID:34158539
Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation. PMID:34156172
Gene Expression Modification by an Autosomal Inversion Associated With Three Male Mating Morphs. PMID:34149796
Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination. PMID:34146097
Draft de novo Genome Assembly of the Elusive Jaguarundi, Puma yagouaroundi. PMID:34146095
Predicting future from past: The genomic basis of recurrent and rapid stickleback evolution. PMID:34144992
Genome-wide analysis of European sea bass provides insights into the evolution and functions of single-exon genes. PMID:34141239
LIQA: long-read isoform quantification and analysis. PMID:34140043
The nearly complete genome of Ginkgo biloba illuminates gymnosperm evolution. PMID:34135482
Molecular classification and diagnostics of upper urinary tract urothelial carcinoma. PMID:34129823
Complete chloroplast genome of Alternanthera philoxeroides by de novo sequencing. PMID:34124357
A porcine brain-wide RNA editing landscape. PMID:34112917
SNP detection and population structure evaluation of Salix gordejevii Y. L. Chang et Skv. in Hunshandake Sandland, Inner Mongolia, China. PMID:34108824
Contiguous erosion of the inactive X in human pluripotency concludes with global DNA hypomethylation. PMID:34107261
Enhancer Hijacking Drives Oncogenic BCL11B Expression in Lineage-Ambiguous Stem Cell Leukemia. PMID:34103329
SaQuant: a real-time PCR assay for quantitative assessment of Staphylococcus aureus. PMID:34103012
Cis-regulatory evolution spotlights species differences in the adaptive potential of gene expression plasticity. PMID:34099660
Wolfberry genomes and the evolution of Lycium (Solanaceae). PMID:34083720
Cotton D genome assemblies built with long-read data unveil mechanisms of centromere evolution and stress tolerance divergence. PMID:34082735
High-Density Genetic Map Construction and Identification of QTLs Controlling Leaf Abscission Trait in Poncirus trifoliata. PMID:34072027
Dog10K_Boxer_Tasha_1.0: A Long-Read Assembly of the Dog Reference Genome. PMID:34070911
Cross-Predicting Essential Genes between Two Model Eukaryotic Species Using Machine Learning. PMID:34064595
Identification of A-to-I RNA editing profiles and their clinical relevance in lung adenocarcinoma. PMID:34050895
TSSFinder-fast and accurate ab initio prediction of the core promoter in eukaryotic genomes. PMID:34050351
Multimodal analysis of cell-free DNA whole-genome sequencing for pediatric cancers with low mutational burden. PMID:34050156
Introgressing the Aegilops tauschii genome into wheat as a basis for cereal improvement. PMID:34045708
Hardware Acceleration of Genomics Data Analysis: Challenges and Opportunities. PMID:34037688
Genome Sequencing and Assembly Strategies and a Comparative Analysis of the Genomic Characteristics in Penaeid Shrimp Species. PMID:34012463
Long non-coding RNAs and their targets as potential biomarkers in breast cancer. PMID:33991433
Transcriptomic Analysis of Skin Color in Anole Lizards. PMID:33988681
Hapo-G, haplotype-aware polishing of genome assemblies with accurate reads. PMID:33987534
Tissue-specific activation of gene expression by the Synergistic Activation Mediator (SAM) CRISPRa system in mice. PMID:33986266
Polyploidy underlies co-option and diversification of biosynthetic triterpene pathways in the apple tribe. PMID:33986115
piRNA-mediated gene regulation and adaptation to sex-specific transposon expression in D. melanogaster male germline. PMID:33985970
Comparative Analyses of Gibbon Centromeres Reveal Dynamic Genus-Specific Shifts in Repeat Composition. PMID:33983366
Characterization of intermediate-sized insertions using whole-genome sequencing data and analysis of their functional impact on gene expression. PMID:33978893
Impact of cropping systems on the functional diversity of rhizosphere microbial communities associated with maize plant: a shotgun approach. PMID:33973044
Pests, diseases, and aridity have shaped the genome of Corymbia citriodora. PMID:33972666
The cytochrome P450 (CYP) superfamily in cnidarians. PMID:33972594
Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome. PMID:33971925
Reverse-transcribed SARS-CoV-2 RNA can integrate into the genome of cultured human cells and can be expressed in patient-derived tissues. PMID:33958444
The genome of a wild Medicago species provides insights into the tolerant mechanisms of legume forage to environmental stress. PMID:33957908
Elephant Genomes Reveal Accelerated Evolution in Mechanisms Underlying Disease Defenses. PMID:33944920
Comparative transcriptomic analysis highlights contrasting levels of resistance of Vitis vinifera and Vitis amurensis to Botrytis cinerea. PMID:33931625
Sex-Biased lncRNA Signature in Fetal Growth Restriction (FGR). PMID:33923632
Genetic Diversity and Population Structures in Chinese Miniature Pigs Revealed by SINE Retrotransposon Insertion Polymorphisms, a New Type of Genetic Markers. PMID:33921134
Targeting of the Essential acpP, ftsZ, and rne Genes in Carbapenem-Resistant Acinetobacter baumannii by Antisense PNA Precision Antibacterials. PMID:33921011
A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses. PMID:33920047
Identification and Characterization of Alternatively Spliced Transcript Isoforms of IRX4 in Prostate Cancer. PMID:33919200
Genome-Wide Analysis of Terpene Synthase Gene Family in Mentha longifolia and Catalytic Activity Analysis of a Single Terpene Synthase. PMID:33918244
Metagenomics Assessment of Soil Fertilization on the Chemotaxis and Disease Suppressive Genes Abundance in the Maize Rhizosphere. PMID:33917127
Universal nomenclature for oxytocin-vasotocin ligand and receptor families. PMID:33911268
Whole-genome sequencing with long reads reveals complex structure and origin of structural variation in human genetic variations and somatic mutations in cancer. PMID:33910608
Single cell transcriptome sequencing on the Nanopore platform with ScNapBar. PMID:33906975
Whole-genome sequencing of phenotypically distinct inflammatory breast cancers reveals similar genomic alterations to non-inflammatory breast cancers. PMID:33902690
Sp1 is a substrate of Keap1 and regulates the activity of CRL4AWDR23 ubiquitin ligase toward Nrf2. PMID:33895141
Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly. PMID:33893684
Increased expression of peptides from non-coding genes in cancer proteomics datasets suggests potential tumor neoantigens. PMID:33888849
The Chinese mitten crab genome provides insights into adaptive plasticity and developmental regulation. PMID:33888695
Radiation-related genomic profile of papillary thyroid carcinoma after the Chernobyl accident. PMID:33888599
Impact of different numbers of microsatellite markers on population genetic results using SLAF-seq data for Rhododendron species. PMID:33883608
Complete genome sequence analysis of the peanut pathogen Ralstonia solanacearum strain Rs-P.362200. PMID:33874906
Functional and Pathological Roles of AHCY. PMID:33869213
Benchmarking the Human Leukocyte Antigen Typing Performance of Three Assays and Seven Next-Generation Sequencing-Based Algorithms. PMID:33868290
ΔNp63 is a pioneer factor that binds inaccessible chromatin and elicits chromatin remodeling. PMID:33865440
Conserved long-range base pairings are associated with pre-mRNA processing of human genes. PMID:33863890
Effect of thermospermine on expression profiling of different gene using massive analysis of cDNA ends (MACE) and vascular maintenance in Arabidopsis. PMID:33854285
Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus Symbiodinium. PMID:33849527
A novel KCNQ4 gene variant (c.857A>G; p.Tyr286Cys) in an extended family with non‑syndromic deafness 2A. PMID:33846771
Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes. PMID:33836575
A study of transposable element-associated structural variations (TASVs) using a de novo-assembled Korean genome. PMID:33833373
Complete chloroplast genome of Zingiber mioga by de novo sequencing. PMID:33829093
Complete chloroplast genome and phylogenetic analysis of a wild grass, Hordeum roshevitzii Bowden. PMID:33829089
An EAV-HP insertion in the promoter region of SLCO1B3 has pleiotropic effects on chicken liver metabolism based on the transcriptome and proteome analysis. PMID:33828143
ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics. PMID:33827654
Diploid chromosome-scale assembly of the Muscadinia rotundifolia genome supports chromosome fusion and disease resistance gene expansion during Vitis and Muscadinia divergence. PMID:33824960
Chromosomal Inversion Polymorphisms in Two Sympatric Ascidian Lineages. PMID:33822040
Characterization of Haemophilus Parasuis Serovar 2 CL120103, a Moderately Virulent Strain in China. PMID:33817086
Fast lightweight accurate xenograft sorting. PMID:33810805
Whole-Genome Sequencing and Characterization of Buffalo Genetic Resources: Recent Advances and Future Challenges. PMID:33809937
Searching the Dark Genome for Alzheimer's Disease Risk Variants. PMID:33800766
The complete mitochondrial and plastid genomes of Rhododendron simsii, an important parent of widely cultivated azaleas. PMID:33796782
Plasmodium matutinum Transmitted by Culex pipiens as a Cause of Avian Malaria in Captive African Penguins (Spheniscus demersus) in Italy. PMID:33796578
The Physcomitrella patens chromatin adaptor PpMRG1 interacts with H3K36me3 and regulates light-responsive alternative splicing. PMID:33793927
Longitudinal study of the scalp microbiome suggests coconut oil to enrich healthy scalp commensals. PMID:33790324
Deciphering the transcriptomic regulation of heat stress responses in Nothofagus pumilio. PMID:33784314
Comprehensive identification of somatic nucleotide variants in human brain tissue. PMID:33781308
Primate innate immune responses to bacterial and viral pathogens reveals an evolutionary trade-off between strength and specificity. PMID:33771921
Long insert clone experimental evidence for assembly improvement and chimeric chromosomes detection in an allopentaploid beer yeast. PMID:33768233
The complete mitochondrial genome of Aconitum kusnezoffii Rchb. (Ranales, Ranunculaceae). PMID:33763576
Large-scale transcriptomics to dissect 2 years of the life of a fungal phytopathogen interacting with its host plant. PMID:33757516
Nanopore Sequencing Indicates That Tandem Amplification of Chromosome 20q11.21 in Human Pluripotent Stem Cells Is Driven by Break-Induced Replication. PMID:33757297
High-Fiber, Whole-Food Dietary Intervention Alters the Human Gut Microbiome but Not Fecal Short-Chain Fatty Acids. PMID:33727392
Alvis: a tool for contig and read ALignment VISualisation and chimera detection. PMID:33726674
A multi-omic characterization of temperature stress in a halotolerant Scenedesmus strain for algal biotechnology. PMID:33712730
X chromosome-dependent disruption of placental regulatory networks in hybrid dwarf hamsters. PMID:33710276
Hepatitis delta virus-like circular RNAs from diverse metazoans encode conserved hammerhead ribozymes. PMID:33708415
Revealing the active microbiome connected with the rhizosphere soil of maize plants in Ventersdorp, South Africa. PMID:33688297
Why are rare variants hard to impute? Coalescent models reveal theoretical limits in existing algorithms. PMID:33686438
riboCIRC: a comprehensive database of translatable circRNAs. PMID:33685493
Evaluating human autosomal loci for sexually antagonistic viability selection in two large biobanks. PMID:33683357
Comparative analysis of chloroplast genomes of kenaf cytoplasmic male sterile line and its maintainer line. PMID:33674697
Metagenomic profiling of rhizosphere microbial community structure and diversity associated with maize plant as affected by cropping systems. PMID:33666787
A Spontaneous rapZ Mutant Impairs Infectivity of Lytic Bacteriophage vB_EcoM_JS09 against Enterotoxigenic Escherichia coli. PMID:33658278
CRISPR-SE: a brute force search engine for CRISPR design. PMID:33655210
The genome of Magnolia biondii Pamp. provides insights into the evolution of Magnoliales and biosynthesis of terpenoids. PMID:33642574
Latent trait modeling of tau neuropathology in progressive supranuclear palsy. PMID:33635380
The complete mitochondrial genome of Glycyrrhiza uralensis Fisch. (Fabales, Leguminosae). PMID:33628894
Genome sequences of Tropheus moorii and Petrochromis trewavasae, two eco-morphologically divergent cichlid fishes endemic to Lake Tanganyika. PMID:33619328
Chromosome-scale assembly of the genome of Salix dunnii reveals a male-heterogametic sex determination system on chromosome 7. PMID:33609314
Rare KMT2A-ELL and Novel ZNF56-KMT2A Fusion Genes in Pediatric T-cell Acute Lymphoblastic Leukemia. PMID:33608309
Optimization of scleroglucan production by Sclerotium rolfsii by lowering pH during fermentation via oxalate metabolic pathway manipulation using CRISPR/Cas9. PMID:33602329
Curation of over 10 000 transcriptomic studies to enable data reuse. PMID:33599246
Improved contiguity of the threespine stickleback genome using long-read sequencing. PMID:33598708
Divergence in alternative polyadenylation contributes to gene regulatory differences between humans and chimpanzees. PMID:33595436
A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth-associated genes. PMID:33586292
Draft genome of the herbaceous bamboo Raddia distichophylla. PMID:33585868
Enrichment of Circular RNA Expression Deregulation at the Transition to Recurrent Spontaneous Seizures in Experimental Temporal Lobe Epilepsy. PMID:33584828
Benchmark study comparing liftover tools for genome conversion of epigenome sequencing data. PMID:33575605
A complex resistance locus in Solanum americanum recognizes a conserved Phytophthora effector. PMID:33574576
Simple sequence repeats drive genome plasticity and promote adaptive evolution in penaeid shrimp. PMID:33574498
A novel canine reference genome resolves genomic architecture and uncovers transcript complexity. PMID:33568770
Flagellar Perturbations Activate Adhesion through Two Distinct Pathways in Caulobacter crescentus. PMID:33563824
Carbon fixation and rhodopsin systems in microbial mats from hypersaline lakes Brava and Tebenquiche, Salar de Atacama, Chile. PMID:33561170
Soil fertilization affects the abundance and distribution of carbon and nitrogen cycling genes in the maize rhizosphere. PMID:33555438
BSGatlas: a unified Bacillus subtilis genome and transcriptome annotation atlas with enhanced information access. PMID:33539279
First finding of free-living representatives of Prokinetoplastina and their nuclear and mitochondrial genomes. PMID:33536456
Detecting High Scoring Local Alignments in Pangenome Graphs. PMID:33532821
Combined genomic, transcriptomic, and metabolomic analyses provide insights into chayote (Sechium edule) evolution and fruit development. PMID:33517348
Pervasive duplication of tumor suppressors in Afrotherians during the evolution of large bodies and reduced cancer risk. PMID:33513090
A microbial gene catalog of anaerobic digestion from full-scale biogas plants. PMID:33506264
Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass. PMID:33505029
Identification and sequencing of 59 highly polymorphic microhaplotypes for analysis of DNA mixtures. PMID:33502549
A Long-Term Conserved Satellite DNA That Remains Unexpanded in Several Genomes of Characiformes Fish Is Actively Transcribed. PMID:33502491
Draft Genome Assemblies and Annotations of Agrypnia vestita Walker, and Hesperophylax magnus Banks Reveal Substantial Repetitive Element Expansion in Tube Case-Making Caddisflies (Insecta: Trichoptera). PMID:33501983
The Compact Macronuclear Genome of the Ciliate Halteria grandinella: A Transcriptome-Like Genome with 23,000 Nanochromosomes. PMID:33500338
Pleiotropy and epistasis within and between signaling pathways defines the genetic architecture of fungal virulence. PMID:33493169
Unveiling the putative functional genes present in root-associated endophytic microbiome from maize plant using the shotgun approach. PMID:33486715
RUNX1/RUNX1T1 mediates alternative splicing and reorganises the transcriptional landscape in leukemia. PMID:33483506
A novel deletion in FLOWERING LOCUS T modulates flowering time in winter oilseed rape. PMID:33471161
Stenoparib, an Inhibitor of Cellular Poly(ADP-Ribose) Polymerase, Blocks Replication of the SARS-CoV-2 and HCoV-NL63 Human Coronaviruses In Vitro. PMID:33468703
InsectOR-Webserver for sensitive identification of insect olfactory receptor genes from non-model genomes. PMID:33465132
A novel terpene synthase controls differences in anti-aphrodisiac pheromone production between closely related Heliconius butterflies. PMID:33465061
The complete chloroplast genome sequence of Red Asparagus Lettuce (Lactuca sativa var. asparagine L. red) (Asteraceae), endemic to China. PMID:33458037
Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis. PMID:33452249
The Reliability of Metagenome-Assembled Genomes (MAGs) in Representing Natural Populations: Insights from Comparing MAGs against Isolate Genomes Derived from the Same Fecal Sample. PMID:33452027
Population genomics in the arboviral vector Aedes aegypti reveals the genomic architecture and evolution of endogenous viral elements. PMID:33432714
Uncovering deeply conserved motif combinations in rapidly evolving noncoding sequences. PMID:33430943
The complete mitochondrial genome of an endangered tree: Malania oleifera. PMID:33426292
WY195, a New Inducible Promoter From the Rubber Powdery Mildew Pathogen, Can Be Used as an Excellent Tool for Genetic Engineering. PMID:33424812
Significantly improving the quality of genome assemblies through curation. PMID:33420778
Therapy-induced Deletion in 11q23 Leading to Fusion of KMT2A With ARHGEF12 and Development of B Lineage Acute Lymphoplastic Leukemia in a Child Treated for Acute Myeloid Leukemia Caused by t(9;11)(p21;q23)/KMT2A-MLLT3. PMID:33419897
A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons. PMID:33419731
Evolution of regulatory networks associated with traits under selection in cichlids. PMID:33419455
Genome-Wide Characterization of RNA Editing Sites in Primary Gastric Adenocarcinoma through RNA-seq Data Analysis. PMID:33415135
Evaluating High-Throughput Sequencing Data of Microalgae Living in Melting Snow: Improvements and Limitations1. PMID:33414851
Survey of Maize Rhizosphere Microbiome Using Shotgun Metagenomics. PMID:33414318
Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias). PMID:33410870
Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp. PMID:33407428
HapSolo: an optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding. PMID:33407090
Genome survey sequencing and genetic diversity of cultivated Akebia trifoliata assessed via phenotypes and SSR markers. PMID:33400074
Improved metagenome binning and assembly using deep variational autoencoders. PMID:33398153
Metagenomics survey unravels diversity of biogas microbiomes with potential to enhance productivity in Kenya. PMID:33395690
A chromosome-level reference genome of non-heading Chinese cabbage [Brassica campestris (syn. Brassica rapa) ssp. chinensis]. PMID:33372175
Complete chloroplast genome of Physalis chenopodifolia Lam. (Solanaceae). PMID:33366468
Mutations altering acetylated residues in the CTD of HIV-1 integrase cause defects in proviral transcription at early times after integration of viral DNA. PMID:33351861
Conserved Imprinted Genes between Intra-Subspecies and Inter-Subspecies Are Involved in Energy Metabolism and Seed Development in Rice. PMID:33348666
Unique k-mer sequences for validating cancer-related substitution, insertion and deletion mutations. PMID:33345188
Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility. PMID:33335035
Whole-Genome Sequencing of Procyonids Reveals Distinct Demographic Histories in Kinkajou (Potos flavus) and Northern Raccoon (Procyon lotor). PMID:33331895
Frameshift Variant in Novel Adenosine-A1-Receptor Homolog Associated With Bovine Spastic Syndrome/Late-Onset Bovine Spastic Paresis in Holstein Sires. PMID:33329738
A Chromosome-Level Genome Assembly of the Anglerfish Lophius litulon. PMID:33329719
The genome and transcriptome analysis of snake gourd provide insights into its evolution and fruit development and ripening. PMID:33328440
High-Resolution Typing of Staphylococcus epidermidis Based on Core Genome Multilocus Sequence Typing To Investigate the Hospital Spread of Multidrug-Resistant Clones. PMID:33328176
AnnoLnc: A One-Stop Portal to Systematically Annotate Novel Human Long Noncoding RNAs. PMID:33326073
C-terminal truncated HBx initiates hepatocarcinogenesis by downregulating TXNIP and reprogramming glucose metabolism. PMID:33323975
Ancient microRNA profiles of a 14,300-year-old canid samples confirm taxonomic origin and give glimpses into tissue-specific gene regulation from the Pleistocene. PMID:33323528
Long-read assembly of the Brassica napus reference genome Darmor-bzh. PMID:33319912
Hormonal regulation of microRNA expression dynamics in the gut of the yellow fever mosquito Aedes aegypti. PMID:33317406
Hybrid sequencing resolves two germline ultra-complex chromosomal rearrangements consisting of 137 breakpoint junctions in a single carrier. PMID:33315133
The comparative genomic landscape of adaptive radiation in crater lake cichlid fishes. PMID:33305470
Scalable multiple whole-genome alignment and locally collinear block construction with SibeliaZ. PMID:33303762
Shotgun Sequencing Revealed the Microbiota of Zea mays Rhizosphere of a Former Grassland and an Intensively Cultivated Agricultural Land. PMID:33272993
Mitochondrial D-loop sequence variation and maternal lineage in the endangered Cleveland Bay horse. PMID:33270708
The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements. PMID:33267872
Hybrid capture of 964 nuclear genes resolves evolutionary relationships in the mimosoid legumes and reveals the polytomous origins of a large pantropical radiation. PMID:33253423
Major SCP/TAPS protein expansion in Lucilia cuprina is associated with novel tandem array organisation and domain architecture. PMID:33246493
Multiple wheat genomes reveal global variation in modern breeding. PMID:33239791
The barley pan-genome reveals the hidden legacy of mutation breeding. PMID:33239781
KRAB zinc finger protein diversification drives mammalian interindividual methylation variability. PMID:33239447
Intrinsic laws of k-mer spectra of genome sequences and evolution mechanism of genomes. PMID:33228538
Genomic and Transcriptomic Analysis for Identification of Genes and Interlinked Pathways Mediating Artemisinin Resistance in Leishmania donovani. PMID:33213096
Genome-enabled discovery of anthraquinone biosynthesis in Senna tora. PMID:33208749
Optimizing performance of GATK workflows using Apache Arrow In-Memory data framework. PMID:33208101
A High Quality Asian Genome Assembly Identifies Features of Common Missing Regions. PMID:33202901
Developmental Validation of a MPS Workflow with a PCR-Based Short Amplicon Whole Mitochondrial Genome Panel. PMID:33202822
A long-term study of AAV gene therapy in dogs with hemophilia A identifies clonal expansions of transduced liver cells. PMID:33199875
Conservative route to genome compaction in a miniature annelid. PMID:33199869
Development and validation of a 4-color multiplexing spinal muscular atrophy (SMA) genotyping assay on a novel integrated digital PCR instrument. PMID:33199817
BiSCoT: improving large eukaryotic genome assemblies with optical maps. PMID:33194395
Contributions of Adaptive Plant Architecture to Transgressive Salinity Tolerance in Recombinant Inbred Lines of Rice: Molecular Mechanisms Based on Transcriptional Networks. PMID:33193743
The Eruca sativa Genome and Transcriptome: A Targeted Analysis of Sulfur Metabolism and Glucosinolate Biosynthesis Pre and Postharvest. PMID:33193472
Catabolic Machinery of the Human Gut Microbes Bestow Resilience Against Vanillin Antimicrobial Nature. PMID:33193247
An Improved Sequencing-Based Bioinformatics Pipeline to Track the Distribution and Clonal Architecture of Proviral Integration Sites. PMID:33193242
Insertion variants missing in the human reference genome are widespread among human populations. PMID:33187521
Dedicated transcriptomics combined with power analysis lead to functional understanding of genes with weak phenotypic changes in knockout lines. PMID:33180766
Progressive Cactus is a multiple-genome aligner for the thousand-genome era. PMID:33177663
Genome sequence of Hydrangea macrophylla and its application in analysis of the double flower phenotype. PMID:33175097
Comprehensive profiling of extracellular RNA in HPV-induced cancers using an improved pipeline for small RNA-seq analysis. PMID:33173155
A Persisting Nontropical Focus of Burkholderia pseudomallei with Limited Genome Evolution over Five Decades. PMID:33172968
Molecular basis of resistance to organophosphate insecticides in the New World screw-worm fly. PMID:33168079
LSH mediates gene repression through macroH2A deposition. PMID:33159050
Neoantigen prediction in human breast cancer using RNA sequencing data. PMID:33155341
Towards a better understanding of the low recall of insertion variants with short-read based variant callers. PMID:33148192
A New Dinoflagellate Genome Illuminates a Conserved Gene Cluster Involved in Sunscreen Biosynthesis. PMID:33146374
Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication. PMID:33139952
Dynamic evolution of transposable elements, demographic history, and gene content of paleognathous birds. PMID:33124220
LncRBase V.2: an updated resource for multispecies lncRNAs and ClinicLSNP hosting genetic variants in lncRNAs for cancer patients. PMID:33112702
MDACP: A Pathogen Genome and Metagenome Analysis Cloud Platform. PMID:33110420
New methodology for repetitive sequences identification in human X and Y chromosomes. PMID:33101452
Temperate Bacteriophages (Prophages) in Pseudomonas aeruginosa Isolates Belonging to the International Cystic Fibrosis Clone (CC274). PMID:33101229
Progress in quickly finding orthologs as reciprocal best hits: comparing blast, last, diamond and MMseqs2. PMID:33099302
A chromosome-level genome assembly provides insights into ascorbic acid accumulation and fruit softening in guava (Psidium guajava). PMID:33098334
Dietary Phytase- and Lactic Acid-Treated Cereals Caused Greater Taxonomic Adaptations than Functional Adaptations in the Cecal Metagenome of Growing Pigs. PMID:33097516
The celery genome sequence reveals sequential paleo-polyploidizations, karyotype evolution and resistance gene reduction in apiales. PMID:33095976
Genome streamlining in a minute herbivore that manipulates its host plant. PMID:33095158
Metagenomes of Maize Rhizosphere Samples after Different Fertilization Treatments at Molelwane Farm, Located in North-West Province, South Africa. PMID:33093043
Extracellular microRNA 3' end modification across diverse body fluids. PMID:33092484
A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism. PMID:33090996
Genome sequencing increases diagnostic yield in clinically diagnosed Alagille syndrome patients with previously negative test results. PMID:33077891
Chromosome-level genome assembly of a parent species of widely cultivated azaleas. PMID:33077749
Global RNA editome landscape discovers reduced RNA editing in glioma: loss of editing of gamma-amino butyric acid receptor alpha subunit 3 (GABRA3) favors glioma migration and invasion. PMID:33062411
Draft Genome Sequences of Two Virulent Streptococcus equi subsp. zooepidemicus Swine Isolates from Pennsylvania. PMID:33060275
Identification of fruit size associated quantitative trait loci featuring SLAF based high-density linkage map of goji berry (Lycium spp.). PMID:33059596
A MicroRNA Expression Signature as Prognostic Marker for Oropharyngeal Squamous Cell Carcinoma. PMID:33057626
dbGuide: a database of functionally validated guide RNAs for genome editing in human and mouse cells. PMID:33051688
The mechanism of potato resistance to Globodera rostochiensis: comparison of root transcriptomes of resistant and susceptible Solanum phureja genotypes. PMID:33050888
Use of the Illumina EPIC methylation array for epigenomic research in the crab-eating macaque (Macaca fascicularis). PMID:33037870
Origin and adaptation to high altitude of Tibetan semi-wild wheat. PMID:33033250
pH-dependent transcriptional profile changes in iron-deficient Arabidopsis roots. PMID:33023472
Genome assembly and annotation of Meloidogyne enterolobii, an emerging parthenogenetic root-knot nematode. PMID:33020495
Genomic diversity generated by a transposable element burst in a rice recombinant inbred population. PMID:33020276
An All-In-One Transcriptome-Based Assay to Identify Therapy-Guiding Genomic Aberrations in Nonsmall Cell Lung Cancer Patients. PMID:33019710
HIV-1 viremia not suppressible by antiretroviral therapy can originate from large T cell clones producing infectious virus. PMID:33016926
A Novel Microduplication Spanning Exons 8-16 of ATP2C1 That Was Undetectable by Standard Sanger Sequencing in a Japanese Patient With Hailey-Hailey Disease. PMID:33015087
Bacterial Genome Wide Association Studies (bGWAS) and Transcriptomics Identifies Cryptic Antimicrobial Resistance Mechanisms in Acinetobacter baumannii. PMID:33014966
A database resource and online analysis tools for coronaviruses on a historical and global scale. PMID:33009914
High-quality nuclear genome for Sarcoptes scabiei-A critical resource for a neglected parasite. PMID:33001992
Haplotype-resolved genome analyses of a heterozygous diploid potato. PMID:32989320
Gene-Level, but Not Chromosome-Wide, Divergence between a Very Young House Fly Proto-Y Chromosome and Its Homologous Proto-X Chromosome. PMID:32986844
Interrogating Genomic-Scale Data to Resolve Recalcitrant Nodes in the Spider Tree of Life. PMID:32986823
Shotgun Metagenomic Survey of Maize Soil Rhizobiome. PMID:32972943
Comparative genomic analyses illuminate the distinct evolution of megabats within Chiroptera. PMID:32966557
The genome of Cleistogenes songorica provides a blueprint for functional dissection of dimorphic flower differentiation and drought adaptability. PMID:32964579
Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing. PMID:32962098
PacBio genome sequencing reveals new insights into the genomic organisation of the multi-copy ToxB gene of the wheat fungal pathogen Pyrenophora tritici-repentis. PMID:32957933
Viral Abundance and Diversity of Production Fluids in Oil Reservoirs. PMID:32957569
Ultrasensitive deletion detection links mitochondrial DNA replication, disease, and aging. PMID:32943091
Long-read sequencing and de novo genome assembly of marine medaka (Oryzias melastigma). PMID:32938378
A Novel Recurrent COL5A1 Genetic Variant Is Associated With a Dysplasia-Associated Arterial Disease Exhibiting Dissections and Fibromuscular Dysplasia. PMID:32938213
Identification of the SUT Gene Family in Pomegranate (Punica granatum L.) and Functional Analysis of PgL0145810.1. PMID:32927615
The Phoebe genome sheds light on the evolution of magnoliids. PMID:32922818
Control of Transcription Initiation by Biased Thermal Fluctuations on Repetitive Genomic Sequences. PMID:32916947
The UCSC SARS-CoV-2 Genome Browser. PMID:32908258
Cytogenetically visible inversions are formed by multiple molecular mechanisms. PMID:32906200
Environmental stability impacts the differential sensitivity of marine microbiomes to increases in temperature and acidity. PMID:32887943
Background-suppressed live visualization of genomic loci with an improved CRISPR system based on a split fluorophore. PMID:32887690
An integrative proteogenomics approach reveals peptides encoded by annotated lincRNA in the mouse kidney inner medulla. PMID:32866085
Construction of a High-Density Genetic Map Based on SLAF Markers and QTL Analysis of Leaf Size in Rice. PMID:32849702
New Plasmodium vivax Genomes From the China-Myanmar Border. PMID:32849480
Clusters of polymorphic transmembrane genes control resistance to schistosomes in snail vectors. PMID:32845238
Genomic content of chemosensory receptors in two sister blister beetles facilitates characterization of chemosensory evolution. PMID:32842954
In Silico Analysis of HSP70 Gene Family in Bovine Genome. PMID:32840700
Positive autoregulation of lag-1 in response to LIN-12 activation in cell fate decisions during C. elegans reproductive system development. PMID:32839181
Sequencing and assembly of the Egyptian buffalo genome. PMID:32813723
Metagenomic profiling of the community structure, diversity, and nutrient pathways of bacterial endophytes in maize plant. PMID:32803452
Genomic characterization of malignant progression in neoplastic pancreatic cysts. PMID:32796935
Multi-Omics Characterization of the 4T1 Murine Mammary Gland Tumor Model. PMID:32793490
Comparative genomics of muskmelon reveals a potential role for retrotransposons in the modification of gene expression. PMID:32792560
An Unbiased Molecular Approach Using 3'-UTRs Resolves the Avian Family-Level Tree of Life. PMID:32781465
An evolutionary driver of interspersed segmental duplications in primates. PMID:32778141
Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica). PMID:32775052
The Acer truncatum genome provides insights into nervonic acid biosynthesis. PMID:32772482
Fusion transcript detection using spatial transcriptomics. PMID:32753032
smsMap: mapping single molecule sequencing reads by locating the alignment starting positions. PMID:32753028
Whole-genome de novo assemblies reveal extensive structural variations and dynamic organelle-to-nucleus DNA transfers in African and Asian rice. PMID:32748498
Ancestral regulatory mechanisms specify conserved midbrain circuitry in arthropods and vertebrates. PMID:32747566
In Vivo Gene Therapy for Canine SCID-X1 Using Cocal-Pseudotyped Lentiviral Vector. PMID:32741228
Mapping and Quantification of Non-Coding RNA Originating from the rDNA in Human Glioma Cells. PMID:32731436
Analysis of conserved miRNAs in cynomolgus macaque genome using small RNA sequencing and homology searching. PMID:32728489
Contributions of de novo variants to systemic lupus erythematosus. PMID:32724065
Accurate Detection of HPV Integration Sites in Cervical Cancer Samples Using the Nanopore MinION Sequencer Without Error Correction. PMID:32714374
Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses. PMID:32706331
Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps. PMID:32703219
Six reference-quality genomes reveal evolution of bat adaptations. PMID:32699395
SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. PMID:32699345
Privately computing set-maximal matches in genomic data. PMID:32693838
DropSynth 2.0: high-fidelity multiplexed gene synthesis in emulsions. PMID:32692349
IC4R-2.0: Rice Genome Reannotation Using Massive RNA-seq Data. PMID:32683045
The genetic factors of bilaterian evolution. PMID:32672535
HIV-1 replication complexes accumulate in nuclear speckles and integrate into speckle-associated genomic domains. PMID:32665593
Intestinal Virome in Patients With Alcoholic Hepatitis. PMID:32654263
Genomic insights of body plan transitions from bilateral to pentameral symmetry in Echinoderms. PMID:32651448
Development of a Genome-Wide Oligonucleotide Microarray Platform for Detection of DNA Copy Number Aberrations in Feline Cancers. PMID:32645884
Shotgun metagenomic data of root endophytic microbiome of maize (Zea mays L.). PMID:32637499
High-density genetic map construction and identification of loci controlling flower-type traits in Chrysanthemum (Chrysanthemum × morifolium Ramat.). PMID:32637136
Termite Societies Promote the Taxonomic and Functional Diversity of Archaeal Communities in Mound Soils. PMID:32630446
Sequence Compression Benchmark (SCB) database-A comprehensive evaluation of reference-free compressors for FASTA-formatted sequences. PMID:32627830
A fully-automated method discovers loss of mouse-lethal and human-monogenic disease genes in 58 mammals. PMID:32614390
Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion. PMID:32605573
Ultraconserved Non-coding DNA Within Diptera and Hymenoptera. PMID:32601058
Suppression of adenosine-to-inosine (A-to-I) RNA editome by death associated protein 3 (DAP3) promotes cancer progression. PMID:32596459
High-Quality Genome Assembly of Chrysaora quinquecirrha Provides Insights Into the Adaptive Evolution of Jellyfish. PMID:32582283
Genetic Variants of the DSF Quorum Sensing System in Stenotrophomonas maltophilia Influence Virulence and Resistance Phenotypes Among Genotypically Diverse Clinical Isolates. PMID:32582100
Inducible aging in Hydra oligactis implicates sexual reproduction, loss of stem cells, and genome maintenance as major pathways. PMID:32578072
Shotgun metagenomic sequencing data of sunflower rhizosphere microbial community in South Africa. PMID:32577457
Differentially evolved drought stress indices determine the genetic variation of Brassica napus at seedling traits by genome-wide association mapping. PMID:32577311
Genome Report: Whole Genome Sequence and Annotation of the Parasitoid Jewel Wasp Nasonia giraulti Laboratory Strain RV2X[u]. PMID:32571804
CandiMeth: Powerful yet simple visualization and quantification of DNA methylation at candidate genes. PMID:32568373
Draft genome of the famous ornamental plant Paeonia suffruticosa. PMID:32551041
Capturing Differential Allele-Level Expression and Genotypes of All Classical HLA Loci and Haplotypes by a New Capture RNA-Seq Method. PMID:32547543
The Complete Chloroplast Genome Sequencing and Comparative Analysis of Reed Canary Grass (Phalaris arundinacea) and Hardinggrass (P. aquatica). PMID:32545897
Structural and Functional Annotation of Transposable Elements Revealed a Potential Regulation of Genes Involved in Rubber Biosynthesis by TE-Derived siRNA Interference in Hevea brasiliensis. PMID:32545790
Dissecting the genome of star fruit (Averrhoa carambola L.). PMID:32528706
DNA markers based on retrotransposon insertion polymorphisms can detect short DNA fragments for strawberry cultivar identification. PMID:32523405
Whole genome sequence analysis reveals genetic structure and X-chromosome haplotype structure in indigenous Chinese pigs. PMID:32523001
The genetic basis of sex determination in grapes. PMID:32518223
Type 2 and interferon inflammation strongly regulate SARS-CoV-2 related gene expression in the airway epithelium. PMID:32511326
Efficient Nuclease-Directed Integration of Lentivirus Vectors into the Human Ribosomal DNA Locus. PMID:32504545
Development and Application of a Core Genome Multilocus Sequence Typing Scheme for the Health Care-Associated Pathogen Pseudomonas aeruginosa. PMID:32493782
Genome sequence and comparative analysis of reindeer (Rangifer tarandus) in northern Eurasia. PMID:32488117
Insight into the Possible Formation Mechanism of the Intersex Phenotype of Lanzhou Fat-Tailed Sheep Using Whole-Genome Resequencing. PMID:32486017
AnthOligo: automating the design of oligonucleotides for capture/enrichment technologies. PMID:32484858
The third generation sequencing: the advanced approach to genetic diseases. PMID:32477917
Synergistic CRISPRa-Regulated Chondrogenic Extracellular Matrix Deposition Without Exogenous Growth Factors. PMID:32460686
Personalized and graph genomes reveal missing signal in epigenomic data. PMID:32450900
Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera. PMID:32442304
Gapless assembly of maize chromosomes using long-read technologies. PMID:32434565
A copy number variant is associated with a spectrum of pigmentation patterns in the rock pigeon (Columba livia). PMID:32433666
High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome. PMID:32432329
Allele-aware chromosome-level genome assembly and efficient transgene-free genome editing for the autotetraploid cultivated alfalfa. PMID:32427850
The Evolution of Human Cancer Gene Duplications across Mammals. PMID:32421773
A Fast and Memory-Efficient Spectral Library Search Algorithm Using Locality-Sensitive Hashing. PMID:32415809
Unique properties of a subset of human pluripotent stem cells with high capacity for self-renewal. PMID:32415101
Computational prediction and characterisation of miRNAs and their pathway genes in human schistosomiasis caused by Schistosoma haematobium. PMID:32401998
TGFam-Finder: a novel solution for target-gene family annotation in plants. PMID:32392385
Chromosome-level assembly of the horseshoe crab genome provides insights into its genome evolution. PMID:32385269
A Comparison of Two DNA Metagenomic Bioinformatic Pipelines While Evaluating the Microbial Diversity in Feces of Tanzanian Small Holder Dairy Cattle. PMID:32382536
Ampliconic Genes on the Great Ape Y Chromosomes: Rapid Evolution of Copy Number but Conservation of Expression Levels. PMID:32374870
Bioinformatic prediction of potential T cell epitopes for SARS-Cov-2. PMID:32372051
The Role of lncRNAs TAPIR-1 and -2 as Diagnostic Markers and Potential Therapeutic Targets in Prostate Cancer. PMID:32365858
Genotyping by multiplexed sequencing (GMS): A customizable platform for genomic selection. PMID:32357171
DNA Barcoding in Nonhuman Primates Reveals Important Limitations in Retrovirus Integration Site Analysis. PMID:32355868
Independent Whole-Genome Duplications Define the Architecture of the Genomes of the Devastating West African Cacao Black Pod Pathogen Phytophthora megakarya and Its Close Relative Phytophthora palmivora. PMID:32354704
Tissue memory CD4+ T cells expressing IL-7 receptor-alpha (CD127) preferentially support latent HIV-1 infection. PMID:32353080
The gene-rich genome of the scallop Pecten maximus. PMID:32352532
Aging-regulated anti-apoptotic long non-coding RNA Sarrah augments recovery from acute myocardial infarction. PMID:32341350
Comprehensive Analysis of HERV Transcriptome in HIV+ Cells: Absence of HML2 Activation and General Downregulation of Individual HERV Loci. PMID:32340287
ASFVdb: an integrative resource for genomic and proteomic analyses of African swine fever virus. PMID:32294195
Exploring the success of Brazilian endemic clone Pseudomonas aeruginosa ST277 and its association with the CRISPR-Cas system type I-C. PMID:32293244
A Chromosome-Scale Assembly of the Asian Honeybee Apis cerana Genome. PMID:32292419
Expansion and Conservation of Biosynthetic Gene Clusters in Pathogenic Pyrenophora spp. PMID:32283749
First Genome Sequence of the Gunnison's Prairie Dog (Cynomys gunnisoni), a Keystone Species and Player in the Transmission of Sylvatic Plague. PMID:32277812
Mutational landscape and genetic signatures of cell-free DNA in tumour-induced osteomalacia. PMID:32277576
Nuclear-mitochondrial DNA segments resemble paternally inherited mitochondrial DNA in humans. PMID:32269217
The UCSC repeat browser allows discovery and visualization of evolutionary conflict across repeat families. PMID:32266012
Comparison of SNP Calling Pipelines and NGS Platforms to Predict the Genomic Regions Harboring Candidate Genes for Nodulation in Cultivated Peanut. PMID:32265983
Draft genomes of two Atlantic bay scallop subspecies Argopecten irradians irradians and A. i. concentricus. PMID:32251283
De novo Assembly of Transcriptomes From a B73 Maize Line Introgressed With a QTL for Resistance to Gray Leaf Spot Disease Reveals a Candidate Allele of a Lectin Receptor-Like Kinase. PMID:32231673
Modified nucleotides may have enhanced early RNA catalysis. PMID:32229566
Accelerating next generation sequencing data analysis: an evaluation of optimized best practices for Genome Analysis Toolkit algorithms. PMID:32224843
Evidence of constraint in the 3D genome for trans-splicing in human cells. PMID:32221814
Inferring Tunicate Relationships and the Evolution of the Tunicate Hox Cluster with the Genome of Corella inflata. PMID:32211845
Comprehensive analysis of indels in whole-genome microsatellite regions and microsatellite instability across 21 cancer types. PMID:32209592
Can we use it? On the utility of de novo and reference-based assembly of Nanopore data for plant plastome sequencing. PMID:32208422
Genomic characterization of human brain metastases identifies drivers of metastatic lung adenocarcinoma. PMID:32203465
Small circRNAs with self-cleaving ribozymes are highly expressed in diverse metazoan transcriptomes. PMID:32198887
A Partially Phase-Separated Genome Sequence Assembly of the Vitis Rootstock 'Börner' (Vitis riparia × Vitis cinerea) and Its Exploitation for Marker Development and Targeted Mapping. PMID:32194587
Cis-regulatory analysis of Onecut1 expression in fate-restricted retinal progenitor cells. PMID:32192535
De novo assembly of the cattle reference genome with single-molecule sequencing. PMID:32191811
Genomic and transcriptomic analysis of Candida intermedia reveals the genetic determinants for its xylose-converting capacity. PMID:32190113
Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns. PMID:32188845
Grape-RNA: A Database for the Collection, Evaluation, Treatment, and Data Sharing of Grape RNA-Seq Datasets. PMID:32188014
New genome assembly of the barn owl (Tyto alba alba). PMID:32184981
AtXRN4 Affects the Turnover of Chosen miRNA*s in Arabidopsis. PMID:32182993
What Is in Umbilicaria pustulata? A Metagenomic Approach to Reconstruct the Holo-Genome of a Lichen. PMID:32163141
Humans Are Selectively Exposed to Pneumocystis jirovecii. PMID:32156824
Deficiency in the endocytic adaptor proteins PHETA1/2 impairs renal and craniofacial development. PMID:32152089
Large X-Linked Palindromes Undergo Arm-to-Arm Gene Conversion across Mus Lineages. PMID:32145018
The genome evolution and domestication of tropical fruit mango. PMID:32143734
Exploring the computational methods for protein-ligand binding site prediction. PMID:32140203
Pathogen to commensal? Longitudinal within-host population dynamics, evolution, and adaptation during a chronic >16-year Burkholderia pseudomallei infection. PMID:32134991
Expert curation of the human and mouse olfactory receptor gene repertoires identifies conserved coding regions split across two exons. PMID:32126975
Evolution and Diversity of the Wild Rice Oryza officinalis Complex, across Continents, Genome Types, and Ploidy Levels. PMID:32125373
Comparison of Arachis monticola with Diploid and Cultivated Tetraploid Genomes Reveals Asymmetric Subgenome Evolution and Improvement of Peanut. PMID:32099754
GSAlign: an efficient sequence alignment tool for intra-species genomes. PMID:32093618
Evolutionary Dynamics of the POTE Gene Family in Human and Nonhuman Primates. PMID:32085667
MAC: Merging Assemblies by Using Adjacency Algebraic Model and Classification. PMID:32082361
MtSSPdb: The Medicago truncatula Small Secreted Peptide Database. PMID:32079733
Silent Infection of B and CD8+ T Lymphocytes by Influenza A Virus in Children with Tonsillar Hypertrophy. PMID:32075928
Assembly of Mitochondrial Complex I Requires the Low-Complexity Protein AMC1 in Chlamydomonas reinhardtii. PMID:32075865
Enterovirus 71 Infection Shapes Host T Cell Receptor Repertoire and Presumably Expands VP1-Specific TCRβ CDR3 Cluster. PMID:32075096
Current Trends in Diagnostics of Viral Infections of Unknown Etiology. PMID:32074965
The draft genome of mandrill (Mandrillus sphinx): An Old World monkey. PMID:32051450
Transcriptional Signatures of Tau and Amyloid Neuropathology. PMID:32049030
An inferred fitness consequence map of the rice genome. PMID:32042156
ZEBrA: Zebra finch Expression Brain Atlas-A resource for comparative molecular neuroanatomy and brain evolution studies. PMID:32037563
The complete mitochondrial genome of Talpa aquitania (Talpidae; Insectivora), a mole species endemic to northern Spain and southern France. PMID:32034626
Comprehensive molecular characterization of mitochondrial genomes in human cancers. PMID:32024997
Unique k-mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling. PMID:32023871
Identification and characterization of ERV-W-like sequences in Platyrrhini species provides new insights into the evolutionary history of ERV-W in primates. PMID:32021657
REXTAL: Regional Extension of Assemblies Using Linked-Reads. PMID:32016171
Concentration-Dependent Recruitment of Mammalian Odorant Receptors. PMID:32015097
Parallel and nonparallel genomic responses contribute to herbicide resistance in Ipomoea purpurea, a common agricultural weed. PMID:32012153
O6-Methylguanine-DNA Methyltransferase (MGMT): Challenges and New Opportunities in Glioma Chemotherapy. PMID:32010632
High-Quality Genome Assembly of Eriocheir japonica sinensis Reveals Its Unique Genome Evolution. PMID:32010195
Whole-genome and time-course dual RNA-Seq analyses reveal chronic pathogenicity-related gene dynamics in the ginseng rusty root rot pathogen Ilyonectria robusta. PMID:32005849
Investigating RNA editing in deep transcriptome datasets with REDItools and REDIportal. PMID:31996844
The evolutionary arms race between transposable elements and piRNAs in Drosophila melanogaster. PMID:31992188
Genome Sequence of the Euryhaline Javafish Medaka, Oryzias javanicus: A Small Aquarium Fish Model for Studies on Adaptation to Salinity. PMID:31988161
Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing. PMID:31986137
Expanded complement of Niemann-Pick type C2-like protein genes in Clonorchis sinensis suggests functions beyond sterol binding and transport. PMID:31973758
The landscape of chimeric RNAs in non-diseased tissues and cells. PMID:31965184
Phylogenetic informativeness analyses to clarify past diversification processes in Cucurbitaceae. PMID:31949198
MRE11A Isoform Expression Associated with Outcome Following Radiotherapy in Muscle-Invasive Bladder Cancer does not Alter Cell Survival and DNA Double-Strand Break Repair Following Ionising Radiation. PMID:31942442
Cardiac mitochondrial function depends on BUD23 mediated ribosome programming. PMID:31939735
Enhanced genome assembly and a new official gene set for Tribolium castaneum. PMID:31937263
Water Deficit Transcriptomic Responses Differ in the Invasive Tamarix chinensis and T. ramosissima Established in the Southern and Northern United States. PMID:31936615
SWAV: a web-based visualization browser for sliding window analysis. PMID:31924845
Clonal kinetics and single-cell transcriptional profiling of CAR-T cells in patients undergoing CD19 CAR-T immunotherapy. PMID:31924795
Vanillin Production in Pseudomonas: Whole-Genome Sequencing of Pseudomonas sp. Strain 9.1 and Reannotation of Pseudomonas putida CalA as a Vanillin Reductase. PMID:31924622
Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding? PMID:31919520
ARID1A influences HDAC1/BRD4 activity, intrinsic proliferative capacity and breast cancer treatment response. PMID:31913353
Concordance of copy number abnormality detection using SNP arrays and Multiplex Ligation-dependent Probe Amplification (MLPA) in acute lymphoblastic leukaemia. PMID:31913349
An Automated Method To Predict Mouse Gene and Protein Sequences Using Variant Data. PMID:31911484
Chromosome-level genome assembly reveals the unique genome evolution of the swimming crab (Portunus trituberculatus). PMID:31904811
A shared genetic basis of mimicry across swallowtail butterflies points to ancestral co-option of doublesex. PMID:31900419
Targeted viral vector transduction of relaxin-3 neurons in the rat nucleus incertus using a novel cell-type specific promoter. PMID:31890981
Long walk to genomics: History and current approaches to genome sequencing and assembly. PMID:31890139
Atypical chromosome 22q11.2 deletions are complex rearrangements and have different mechanistic origins. PMID:31884517
Chromosome Translocation t(14;21)(q11;q22) Activates Both OLIG1 and OLIG2 in Pediatric T-cell Lymphoblastic Malignancies and May Signify Adverse Prognosis. PMID:31882550
Draft Genomes of Two Artocarpus Plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis). PMID:31878322
Chromosome-Level Comprehensive Genome of Mangrove Sediment-Derived Fungus Penicillium variabile HXQ-H-1. PMID:31878043
Integrative transcriptome analysis discloses the molecular basis of a heterogeneous fungal phytopathogen complex, Rhizoctonia solani AG-1 subgroups. PMID:31873088
Sex matters: Otolith shape and genomic variation in deacon rockfish (Sebastes diaconus). PMID:31871636
Towards Improved Molecular Identification Tools in Fine Fescue (Festuca L., Poaceae) Turfgrasses: Nuclear Genome Size, Ploidy, and Chloroplast Genome Sequencing. PMID:31867041
Identification and characterization of occult human-specific LINE-1 insertions using long-read sequencing technology. PMID:31853540
Genomes of early-diverging streptophyte algae shed light on plant terrestrialization. PMID:31844283
deSALT: fast and accurate long transcriptomic read alignment with de Bruijn graph-based index. PMID:31842925
ReVac: a reverse vaccinology computational pipeline for prioritization of prokaryotic protein vaccine candidates. PMID:31842745
SGID: a comprehensive and interactive database of the silkworm. PMID:31836898
Deciphering the microbiota data from termite mound soil in South Africa using shotgun metagenomics. PMID:31832528
From EST to structure models for functional inference of APP, BACE1, PSEN1, PSEN2 genes. PMID:31831959
Alignment-Free Sequence Analysis and Applications. PMID:31828235
Discovery of genomic variations by whole-genome resequencing of the North American Araucana chicken. PMID:31821332
A novel long noncoding RNA Linc-ASEN represses cellular senescence through multileveled reduction of p21 expression. PMID:31819156
Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus communis L.). PMID:31816089
Genetic Diversity and Signatures of Selection in 15 Chinese Indigenous Dog Breeds Revealed by Genome-Wide SNPs. PMID:31803243
Deciphering the high-quality genome sequence of coriander that causes controversial feelings. PMID:31799788
Genetic variation associated with infection and the environment in the accidental pathogen Burkholderia pseudomallei. PMID:31799430
QTL identification for seed weight and size based on a high-density SLAF-seq genetic map in peanut (Arachis hypogaea L.). PMID:31795931
Evaluation of Saccharomyces cerevisiae Wine Yeast Competitive Fitness in Enologically Relevant Environments by Barcode Sequencing. PMID:31792006
Alu insertion polymorphisms shared by Papio baboons and Theropithecus gelada reveal an intertwined common ancestry. PMID:31788036
Identification and Characterization of Cis-Regulatory Elements for Photoreceptor-Type-Specific Transcription in ZebraFish. PMID:31786786
Programmed DNA elimination of germline development genes in songbirds. PMID:31784533
Minimal in vivo requirements for developmentally regulated cardiac long intergenic non-coding RNAs. PMID:31784461
Comparative genomics of Mycoplasma pneumoniae isolated from children with pneumonia: South Korea, 2010-2016. PMID:31783732
Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop. PMID:31782791
Retroelement Insertion in a CRISPR/Cas9 Editing Site in the Early Embryo Intensifies Genetic Mosaicism. PMID:31781562
Genome sequence of the model rice variety KitaakeX. PMID:31775618
Annotated Draft Genomes of Two Caddisfly Species Plectrocnemia conspersa CURTIS and Hydropsyche tenuis NAVAS (Insecta: Trichoptera). PMID:31774498
A Conserved Noncoding Locus Regulates Random Monoallelic Xist Expression across a Topological Boundary. PMID:31759823
Sequencing and Functional Annotation of the Whole Genome of Shiraia bambusicola. PMID:31712259
Identification of Single Nucleotide Polymorphism in Red Clover (Trifolium pratense L.) Using Targeted Genomic Amplicon Sequencing and RNA-seq. PMID:31708937
Exploration of intermediate-sized INDELs by next-generation multigene panel testing in Han Chinese patients with breast cancer. PMID:31700649
A New Chloroplast DNA Extraction Protocol Significantly Improves the Chloroplast Genome Sequence Quality of Foxtail Millet (Setaria italica (L.) P. Beauv.). PMID:31700055
From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability. PMID:31694722
Optimized sequencing depth and de novo assembler for deeply reconstructing the transcriptome of the tea plant, an economically important plant species. PMID:31694521
UCSC Genome Browser enters 20th year. PMID:31691824
Genetic Variations of Ultraconserved Elements in the Human Genome. PMID:31689173
Evidence for adaptive introgression of exons across a hybrid swarm in deer. PMID:31684869
Multi-Tissue Transcriptomes Yield Information on High-Altitude Adaptation and Sex-Determination in Scutiger cf. sikimmensis. PMID:31683620
In-silico prediction of novel genes responsive to drought and salinity stress tolerance in bread wheat (Triticum aestivum). PMID:31671113
An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae. PMID:31667023
BBCancer: an expression atlas of blood-based biomarkers in the early diagnosis of cancers. PMID:31665503
Preventive antibiotic treatment of calves: emergence of dysbiosis causing propagation of obese state-associated and mobile multidrug resistance-carrying bacteria. PMID:31663669
The transcription factor ETS1 promotes apoptosis resistance of senescent cholangiocytes by epigenetically up-regulating the apoptosis suppressor BCL2L1. PMID:31659122
Structural variation of the complete chloroplast genome and plastid phylogenomics of the genus Asteropyrum (Ranunculaceae). PMID:31653891
Environmental transcriptomes of invasive dreissena, a model species in ecotoxicology and invasion biology. PMID:31653851
Comparative Genomics Analysis Reveals High Levels of Differential Retrotransposition among Primates from the Hominidae and the Cercopithecidae Families. PMID:31651947
SwiftOrtho: A fast, memory-efficient, multiple genome orthology classifier. PMID:31648300
A unicellular relative of animals generates a layer of polarized cells by actomyosin-dependent cellularization. PMID:31647412
Bovine Genome Database: new annotation tools for a new reference genome. PMID:31647100
Evolution of the new head by gradual acquisition of neural crest regulatory circuits. PMID:31645763
Chromosome-level genome assembly of golden pompano (Trachinotus ovatus) in the family Carangidae. PMID:31641137
Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods. PMID:31639029
Exploring the basis of 2-propenyl and 3-butenyl glucosinolate synthesis by QTL mapping and RNA-sequencing in Brassica juncea. PMID:31626668
Satellite DNA content of B chromosomes in the characid fish Characidium gomesi supports their origin from sex chromosomes. PMID:31624915
A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona. PMID:31621849
Genome-Wide Identification and Transcriptomic Analysis of MicroRNAs Across Various Amphioxus Organs Using Deep Sequencing. PMID:31616471
The Structure, Evolution, and Gene Expression Within the Caprine Leukocyte Receptor Complex. PMID:31616444
Genome-wide association mapping of date palm fruit traits. PMID:31615981
A new species in the major malaria vector complex sheds light on reticulated species evolution. PMID:31611571
FusionScan: accurate prediction of fusion genes from RNA-Seq data. PMID:31610622
Alternative mRNA Splicing in Three Venom Families Underlying a Possible Production of Divergent Venom Proteins of the Habu Snake, Protobothrops flavoviridis. PMID:31600994
A chromosome-level genome assembly of Pyropia haitanensis (Bangiales, Rhodophyta). PMID:31600851
Genome Assembly of the A-Group Wolbachia in Nasonia oneida Using Linked-Reads Technology. PMID:31596462
RNAIndel: discovering somatic coding indels from tumor RNA-Seq data. PMID:31593214
Realizing the potential of full-length transcriptome sequencing. PMID:31587638
A draft genome and transcriptome of common milkweed (Asclepias syriaca) as resources for evolutionary, ecological, and molecular studies in milkweeds and Apocynaceae. PMID:31579586
The sequencing and de novo assembly of the Larimichthys crocea genome using PacBio and Hi-C technologies. PMID:31575853
Pedigree-based estimation of human mobile element retrotransposition rates. PMID:31575651
The sequence and de novo assembly of Takifugu bimaculatus genome using PacBio and Hi-C technologies. PMID:31570724
RNA ligation precedes the retrotransposition of U6/LINE-1 chimeric RNA. PMID:31548405
BPSL1626: Reverse and Structural Vaccinology Reveal a Novel Candidate for Vaccine Design against Burkholderia pseudomallei. PMID:31544878
The evolution study on Oryza rufipogon. dw by whole-genome sequencing. PMID:31544797
Rapid Detection of Genetic Engineering, Structural Variation, and Antimicrobial Resistance Markers in Bacterial Biothreat Pathogens by Nanopore Sequencing. PMID:31534162
A Puzzling Anomaly in the 4-Mer Composition of the Giant Pandoravirus Genomes Reveals a Stringent New Evolutionary Selection Process. PMID:31534042
Α de novo 3.8-Mb inversion affecting the EDA and XIST genes in a heterozygous female calf with generalized hypohidrotic ectodermal dysplasia. PMID:31533624
Gene expression vs. sequence divergence: comparative transcriptome sequencing among natural Rhinolophus ferrumequinum populations with different acoustic phenotypes. PMID:31528181
Dosage regulation, and variation in gene expression and copy number of human Y chromosome ampliconic genes. PMID:31525193
A purely bioinformatic pipeline for the prediction of mammalian odorant receptor gene enhancers. PMID:31521109
Predisposition to childhood acute lymphoblastic leukemia caused by a constitutional translocation disrupting ETV6. PMID:31519648
Comparative Transcriptomics Provides Insights into Reticulate and Adaptive Evolution of a Butterfly Radiation. PMID:31518398
The statistical power of k-mer based aggregative statistics for alignment-free detection of horizontal gene transfer. PMID:31508512
Genome-Wide Variant Identification and High-Density Genetic Map Construction Using RADseq for Platycladus orientalis (Cupressaceae). PMID:31506321
Butterfly Mimicry Polymorphisms Highlight Phylogenetic Limits of Gene Reuse in the Evolution of Diverse Adaptations. PMID:31504750
Phytochrome Coordinates with a hnRNP to Regulate Alternative Splicing via an Exonic Splicing Silencer. PMID:31501299
Large miRNA survival analysis reveals a prognostic four-biomarker signature for triple negative breast cancer. PMID:31487369
Burkholderia pseudomallei, the causative agent of melioidosis, is rare but ecologically established and widely dispersed in the environment in Puerto Rico. PMID:31487287
The improved assembly of 7DL chromosome provides insight into the structure and evolution of bread wheat. PMID:31471988
Molecular Dating of the Emergence of Anaerobic Rumen Fungi and the Impact of Laterally Acquired Genes. PMID:31455637
Profiling the Functional Diversity of Termite Mound Soil Bacteria as Revealed by Shotgun Sequencing. PMID:31450818
CNEr: A toolkit for exploring extreme noncoding conservation. PMID:31449516
Conserved Pseudoknots in lncRNA MEG3 Are Essential for Stimulation of the p53 Pathway. PMID:31444106
Novel Locus Associated with Symmetrical Lupoid Onychodystrophy in the Bearded Collie. PMID:31443497
A SNP-Based High-Density Genetic Map of Leaf and Fruit Related Quantitative Trait Loci in Wolfberry (Lycium Linn.). PMID:31440266
Long-read sequencing and haplotype linkage analysis enabled preimplantation genetic testing for patients carrying pathogenic inversions. PMID:31439719
A high-quality genome assembly for the endangered golden snub-nosed monkey (Rhinopithecus roxellana). PMID:31437279
Rapidly evolving protointrons in Saccharomyces genomes revealed by a hungry spliceosome. PMID:31437148
Utilization of Tissue Ploidy Level Variation in de Novo Transcriptome Assembly of Pinus sylvestris. PMID:31427456
A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution. PMID:31409808
Heterogeneous Nuclear Ribonucleoprotein H1 Coordinates with Phytochrome and the U1 snRNP Complex to Regulate Alternative Splicing in Physcomitrella patens. PMID:31409629
Long noncoding RNAs are involved in multiple immunological pathways in response to vaccination. PMID:31399544
Horizontally transmitted symbiont populations in deep-sea mussels are genetically isolated. PMID:31395952
Metagenomics analysis of cocoa bean fermentation microbiome identifying species diversity and putative functional capabilities. PMID:31388591
BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single-cell analysis. PMID:31387612
Development of molecular markers associated with resistance to Meloidogyne incognita by performing quantitative trait locus analysis and genome-wide association study in sweetpotato. PMID:31377774
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. PMID:31375807
Exploring the molecular basis of neuronal excitability in a vocal learner. PMID:31375088
Uncovering missed indels by leveraging unmapped reads. PMID:31366961
Endogenous Retrovirus-Derived Long Noncoding RNA Enhances Innate Immune Responses via Derepressing RELA Expression. PMID:31363026
Challenges in funding and developing genomic software: roots and remedies. PMID:31358028
The genome of Peromyscus leucopus, natural host for Lyme disease and other emerging infections. PMID:31355335
An expanded landscape of human long noncoding RNA. PMID:31350901
Dicyemid Mesozoans: A Unique Parasitic Lifestyle and a Reduced Genome. PMID:31347665
Impact of sequencing depth and technology on de novo RNA-Seq assembly. PMID:31337347
Genome and transcriptome characterization of the glycoengineered Nicotiana benthamiana line ΔXT/FT. PMID:31324144
The genome assembly of asparagus bean, Vigna unguiculata ssp. sesquipedialis. PMID:31316072
Centromere Satellite Repeats Have Undergone Rapid Changes in Polyploid Wheat Subgenomes. PMID:31311836
Stress, novel sex genes, and epigenetic reprogramming orchestrate socially controlled sex change. PMID:31309157
Musa balbisiana genome reveals subgenome evolution and functional divergence. PMID:31308504
A high-quality genome of Eragrostis curvula grass provides insights into Poaceae evolution and supports new strategies to enhance forage quality. PMID:31308395
The tea plant reference genome and improved gene annotation using long-read and paired-end sequencing data. PMID:31308375
De novo genome assembly of the endangered Acer yangbiense, a plant species with extremely small populations endemic to Yunnan Province, China. PMID:31307060
Chromosome-Level Alpaca Reference Genome VicPac3.1 Improves Genomic Insight Into the Biology of New World Camelids. PMID:31293619
Genetic Diversity, Virulence, Race Profiling, and Comparative Genomic Analysis of the Fusarium oxysporum f. sp. conglutinans Strains Infecting Cabbages in China. PMID:31293534
Srrm234, but not canonical SR and hnRNP proteins, drive inclusion of Dscam exon 9 variable exons. PMID:31292260
Distribution of endogenous gammaretroviruses and variants of the Fv1 restriction gene in individual mouse strains and strain subgroups. PMID:31291374
Retroposed copies of RET gene: a somatically acquired event in medullary thyroid carcinoma. PMID:31288802
Extensive intraspecific gene order and gene structural variations in upland cotton cultivars. PMID:31278252
Closing target trimming and CTTdocker programs for discovering hidden superfamily loci in genomes. PMID:31265455
Box, stalked, and upside-down? Draft genomes from diverse jellyfish (Cnidaria, Acraspeda) lineages: Alatina alata (Cubozoa), Calvadosia cruxmelitensis (Staurozoa), and Cassiopea xamachana (Scyphozoa). PMID:31257419
HLA alleles and haplotypes observed in 263 US families. PMID:31256909
Arctic charr brain transcriptome strongly affected by summer seasonal growth but only subtly by feed deprivation. PMID:31248377
Draft Genome of the Rice Coral Montipora capitata Obtained from Linked-Read Sequencing. PMID:31243452
Long-read sequencing unveils IGH-DUX4 translocation into the silenced IGH allele in B-cell acute lymphoblastic leukemia. PMID:31243274
The genome assembly and annotation of yellowhorn (Xanthoceras sorbifolium Bunge). PMID:31241155
Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system. PMID:31238873
Improved detection of influenza A virus from blue-winged teals by sequencing directly from swab material. PMID:31236242
New Era in Plant Alternative Splicing Analysis Enabled by Advances in High-Throughput Sequencing (HTS) Technologies. PMID:31231413
Bioinformatic pipelines for whole transcriptome sequencing data exploitation in leukemia patients with complex structural variants. PMID:31223530
Deep sequencing of a recurrent oligodendroglioma and the derived xenografts reveals new insights into the evolution of human oligodendroglioma and candidate driver genes. PMID:31217899
Transcriptome Changes during Major Developmental Transitions Accompanied with Little Alteration of DNA Methylome in Two Pleurotus Species. PMID:31212970
Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts. PMID:31193391
BarkBase: Epigenomic Annotation of Canine Genomes. PMID:31181663
Factors other than hTau overexpression that contribute to tauopathy-like phenotype in rTg4510 mice. PMID:31171783
Genome sequencing provides insights into the evolution and antioxidant activity of Chinese bayberry. PMID:31170907
High-Throughput Genotyping of CRISPR/Cas Edited Cells in 96-Well Plates. PMID:31164571
The Biodiversity and Geochemistry of Cryoconite Holes in Queen Maud Land, East Antarctica. PMID:31159414
Variable Baseline Papio cynocephalus Endogenous Retrovirus (PcEV) Expression Is Upregulated in Acutely SIV-Infected Macaques and Correlated to STAT1 Expression in the Spleen. PMID:31156613
Effect of marker segregation distortion on high density linkage map construction and QTL mapping in Soybean (Glycine max L.). PMID:31152165
Comment on "A comprehensive overview and evaluation of circular RNA detection tools". PMID:31150384
Altered microRNA expression profiles in large offspring syndrome and Beckwith-Wiedemann syndrome. PMID:31144574
HNCDB: An Integrated Gene and Drug Database for Head and Neck Cancer. PMID:31139565
Phylogenomic Approaches to DNA Barcoding of Herbal Medicines: Developing Clade-Specific Diagnostic Characters for Berberis. PMID:31139202
Methanethiol and Dimethylsulfide Cycling in Stiffkey Saltmarsh. PMID:31134039
A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism. PMID:31133004
Microhomologies are prevalent at Cas9-induced larger deletions. PMID:31127293
Comprehensive Multiple eQTL Detection and Its Application to GWAS Interpretation. PMID:31123039
Leaf Transcriptome Assembly of Protium copal (Burseraceae) and Annotation of Terpene Biosynthetic Genes. PMID:31121954
Parallel Molecular Evolution in Pathways, Genes, and Sites in High-Elevation Hummingbirds Revealed by Comparative Transcriptomics. PMID:31114863
Pairwise alignment of nucleotide sequences using maximal exact matches. PMID:31113356
Transcript and metabolite changes during the early phase of abscisic acid-mediated induction of crassulacean acid metabolism in Talinum triangulare. PMID:31111894
How dynamic could be the 45S rDNA cistron? An intriguing variability in a grasshopper species revealed by integration of chromosomal and genomic data. PMID:31111199
Stenotrophomonas maltophilia Differential Gene Expression in Synthetic Cystic Fibrosis Sputum Reveals Shared and Cystic Fibrosis Strain-Specific Responses to the Sputum Environment. PMID:31109991
A global to local genomics analysis of Clostridioides difficile ST1/RT027 identifies cryptic transmission events in a northern Arizona healthcare network. PMID:31107202
Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight. PMID:31104630
Draft genome of the big-headed turtle Platysternon megacephalum. PMID:31097710
CiliaCarta: An integrated and validated compendium of ciliary genes. PMID:31095607
Islands of retroelements are major components of Drosophila centromeres. PMID:31086362
Splice-Aware Multiple Sequence Alignment of Protein Isoforms. PMID:31080963
Retrotransposons evolution and impact on lncRNA and protein coding genes in pigs. PMID:31080521
Genomic changes in the biological control agent Cryptolaemus montrouzieri associated with introduction. PMID:31080510
Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity. PMID:31080084
Slow Delivery Immunization Enhances HIV Neutralizing Antibody and Germinal Center Responses via Modulation of Immunodominance. PMID:31080066
Insertion of a chimeric retrotransposon sequence in mouse Axin1 locus causes metastable kinky tail phenotype. PMID:31073336
A high-density genetic map developed by specific-locus amplified fragment (SLAF) sequencing and identification of a locus controlling anthocyanin pigmentation in stalk of Zicaitai (Brassica rapa L. ssp. chinensis var. purpurea). PMID:31064320
Exploiting selection at linked sites to infer the rate and strength of adaptation. PMID:31061475
Dietary Energy Level Promotes Rumen Microbial Protein Synthesis by Improving the Energy Productivity of the Ruminal Microbiome. PMID:31057531
Temporal genomic contrasts reveal rapid evolutionary responses in an alpine mammal during recent climate change. PMID:31050681
The genomes of pecan and Chinese hickory provide insights into Carya evolution and nut nutrition. PMID:31049561
Mitochondrial autoimmunity and MNRR1 in breast carcinogenesis. PMID:31046734
Functional adaptations in the cecal and colonic metagenomes associated with the consumption of transglycosylated starch in a pig model. PMID:31046662
SeqTailor: a user-friendly webserver for the extraction of DNA or protein sequences from next-generation sequencing data. PMID:31045209
Linkage-based genome assembly improvement of oil palm (Elaeis guineensis). PMID:31036825
Germline-restricted chromosome (GRC) is widespread among songbirds. PMID:31036668
Dauer signalling pathway model for Haemonchus contortus. PMID:31036054
Accurate high throughput alignment via line sweep-based seed processing. PMID:31028275
Instability of the Pseudoautosomal Boundary in House Mice. PMID:31028113
Agricultural Origins of a Highly Persistent Lineage of Vancomycin-Resistant Enterococcus faecalis in New Zealand. PMID:31028029
Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance. PMID:31026256
Details in the evaluation of circular RNA detection tools: Reply to Chen and Chuang. PMID:31022173
Chromosome-Level Assembly of the Chinese Seabass (Lateolabrax maculatus) Genome. PMID:31019525
TransLiG: a de novo transcriptome assembler that uses line graph iteration. PMID:31014374
Subtype classification and functional annotation of L1Md retrotransposon promoters. PMID:31007728
BHap: a novel approach for bacterial haplotype reconstruction. PMID:31004480
Shedding Light on a Secretive Tertiary urodelean Relict: Hynobiid salamanders (Paradactylodon persicus s.l.) from Iran, Illuminated by Phylogeographic, Developmental and Transcriptomic Data. PMID:31003559
Diversity, Virulence, and Antimicrobial Resistance in Isolates From the Newly Emerging Klebsiella pneumoniae ST101 Lineage. PMID:31001209
Whole genomes and transcriptomes reveal adaptation and domestication of pistachio. PMID:30999938
Screening for mutations in selected miRNA genes in hypogonadotropic hypogonadism patients. PMID:30999277
Visualizing flow in an intact CSF network using optical coherence tomography: implications for human congenital hydrocephalus. PMID:30996265
Genome Sequence of an Arthroconidial Yeast, Saprochaete fungicola CBS 625.85. PMID:30975801
Whole genome sequencing reveals complexity in both HPV sequences present and HPV integrations in HPV-positive oropharyngeal squamous cell carcinomas. PMID:30975103
iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture. PMID:30967549
Low-cost assembly of a cacao crop genome is able to resolve complex heterozygous bubbles. PMID:30962937
Draft genome of the river water buffalo. PMID:30962899
Carbapenem-Susceptible OXA-23-Producing Proteus mirabilis in the French Community. PMID:30962345
Genome-wide de novo L1 Retrotransposition Connects Endonuclease Activity with Replication. PMID:30955886
A quick guide for student-driven community genome annotation. PMID:30943207
MGS-Fast: Metagenomic shotgun data fast annotation using microbial gene catalogs. PMID:30942867
Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds. PMID:30936435
Analysis of 100 high-coverage genomes from a pedigreed captive baboon colony. PMID:30926611
SplicedFamAlign: CDS-to-gene spliced alignment and identification of transcript orthology groups. PMID:30925859
Deep-learning augmented RNA-seq analysis of transcript splicing. PMID:30923373
The Genome and mRNA Transcriptome of the Cosmopolitan Calanoid Copepod Acartia tonsa Dana Improve the Understanding of Copepod Genome Size Evolution. PMID:30918947
Placenta Transcriptome Profiling in Intrauterine Growth Restriction (IUGR). PMID:30917529
Improving in-silico normalization using read weights. PMID:30914698
Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA. PMID:30902979
Cryo-EM structure of a light chain-derived amyloid fibril from a patient with systemic AL amyloidosis. PMID:30894526
Anaerotruncus massiliensis sp. nov., a succinate-producing bacterium isolated from human stool from an obese patient after bariatric surgery. PMID:30891246
Amplification Dynamics of Platy-1 Retrotransposons in the Cebidae Platyrrhine Lineage. PMID:30888417
Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton. PMID:30886425
Long-read based assembly and synteny analysis of a reference Drosophila subobscura genome reveals signatures of structural evolution driven by inversions recombination-suppression effects. PMID:30885123
Circular RNAs in human and vertebrate neural retinas. PMID:30874468
A reference-grade wild soybean genome. PMID:30872580
Memory and relatedness of transcriptional activity in mammalian cell lineages. PMID:30872573
Chromothripsis during telomere crisis is independent of NHEJ, and consistent with a replicative origin. PMID:30872351
Sex-Biased Gene Expression and Dosage Compensation on the Artemia franciscana Z-Chromosome. PMID:30865260
Characterization of mammalian Lipocalin UTRs in silico: Predictions for their role in post-transcriptional regulation. PMID:30840684
Genome-wide analysis reveals the genomic features of the turkey vulture (Cathartes aura) as a scavenger. PMID:30834967
Genome Sequence of Flavor-Producing Yeast Saprochaete suaveolens NRRL Y-17571. PMID:30834381
A Modifying Autoantigen in Graves' Disease. PMID:30822352
Evolutionary Implications of the microRNA- and piRNA Complement of Lepidodermella squamata (Gastrotricha). PMID:30813358
Development of High-Density SNP Markers and Their Application in Evaluating Genetic Diversity and Population Structure in Elaeis guineensis. PMID:30809240
Draft genomic and transcriptome resources for marine chelicerate Tachypleus tridentatus. PMID:30806641
Magic roundabout is an endothelial-specific ohnolog of ROBO1 which neo-functionalized to an essential new role in angiogenesis. PMID:30802244
Unraveling the complex genome of Saccharum spontaneum using Polyploid Gene Assembler. PMID:30768175
Ribosomal DNA harbors an evolutionarily conserved clock of biological aging. PMID:30765617
Ipa1 Is an RNA Polymerase II Elongation Factor that Facilitates Termination by Maintaining Levels of the Poly(A) Site Endonuclease Ysh1. PMID:30759400
A cell cycle-coordinated Polymerase II transcription compartment encompasses gene expression before global genome activation. PMID:30741925
Comprehensive structural variation genome map of individuals carrying complex chromosomal rearrangements. PMID:30735495
The sequence and de novo assembly of Oxygymnocypris stewartii genome. PMID:30720802
RNA sequencing discloses the genome‑wide profile of long noncoding RNAs in dilated cardiomyopathy. PMID:30720098
Ultrafast search of all deposited bacterial and viral genomic data. PMID:30718882
Evolution-guided evaluation of the inverted terminal repeats of the synthetic transposon Sleeping Beauty. PMID:30718656
Molecular Classification and Comparative Taxonomics of Foveal and Peripheral Cells in Primate Retina. PMID:30712875
Gene editing of the multi-copy H2A.B gene and its importance for fertility. PMID:30704500
Complete Chloroplast Genome Sequences of Kaempferia Galanga and Kaempferia Elegans: Molecular Structures and Comparative Analysis. PMID:30699955
Genomic content of a novel yeast species Hanseniaspora gamundiae sp. nov. from fungal stromata (Cyttaria) associated with a unique fermented beverage in Andean Patagonia, Argentina. PMID:30699175
The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches. PMID:30698687
Environmental filtering of bacterial functional diversity along an aridity gradient. PMID:30696918
Genome structure and evolution of Antirrhinum majus L. PMID:30692677
Genome sequence of Malania oleifera, a tree with great value for nervonic acid production. PMID:30689848
Intact HIV-1 proviruses accumulate at distinct chromosomal positions during prolonged antiretroviral therapy. PMID:30688658
Genomewide Association Study of Fracture Nonunion Using Electronic Health Records. PMID:30680360
Taxonomic profiling and populational patterns of bacterial bile salt hydrolase (BSH) genes based on worldwide human gut microbiome. PMID:30674356
Prediction of functional microRNA targets by integrative modeling of microRNA binding and target expression data. PMID:30670076
Inflammation in Traumatic Brain Injury: Roles for Toxic A1 Astrocytes and Microglial-Astrocytic Crosstalk. PMID:30661228
Dynamic Interactions Between the Genome and an Endogenous Retrovirus: Tirant in Drosophila simulans Wild-Type Strains. PMID:30658967
Genomes of Three Closely Related Caribbean Amazons Provide Insight for Species History and Conservation. PMID:30654561
pblat: a multithread blat algorithm speeding up aligning sequences to genomes. PMID:30646844
A Sequence-Based Novel Approach for Quality Evaluation of Third-Generation Sequencing Reads. PMID:30646604
Comparative bioinformatic analysis suggests that specific dauer-like signalling pathway components regulate Toxocara canis development and migration in the mammalian host. PMID:30642380
Chromosome level comparative analysis of Brassica genomes. PMID:30632049
AtFusionDB: a database of fusion transcripts in Arabidopsis thaliana. PMID:30624648
SQuIRE reveals locus-specific regulation of interspersed repeat expression. PMID:30624635
Improved Genome Sequence of Wild Emmer Wheat Zavitan with the Aid of Optical Maps. PMID:30622124
Simulation of heterogeneous tumour genomes with HeteroGenesis and in silico whole exome sequencing. PMID:30615054
Gorillas have been infected with the HERV-K (HML-2) endogenous retrovirus much more recently than humans and chimpanzees. PMID:30610173
The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens. PMID:30606230
NCLcomparator: systematically post-screening non-co-linear transcripts (circular, trans-spliced, or fusion RNAs) identified from various detectors. PMID:30606103
A benchmark study of sequence alignment methods for protein clustering. PMID:30598070
Panproteome-wide analysis of antibody responses to whole cell pneumococcal vaccination. PMID:30592459
RGAAT: A Reference-based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes. PMID:30583062
Multiple forms of selection shape reproductive isolation in a primate hybrid zone. PMID:30582763
QTL Mapping Combined With Bulked Segregant Analysis Identify SNP Markers Linked to Leaf Shape Traits in Pisum sativum Using SLAF Sequencing. PMID:30568674
A Method for RNA Structure Prediction Shows Evidence for Structure in lncRNAs. PMID:30560136
Seasonality Drives Microbial Community Structure, Shaping both Eukaryotic and Prokaryotic Host⁻Viral Relationships in an Arctic Marine Ecosystem. PMID:30558156
Transcriptome reprogramming during severe dehydration contributes to physiological and metabolic changes in the resurrection plant Haberlea rhodopensis. PMID:30541446
The draft genomes of five agriculturally important African orphan crops. PMID:30535374
UM-HACC-2A: MYB-NFIB fusion-positive human adenoid cystic carcinoma cell line. PMID:30527239
Comparative genomics of 84 Pectobacterium genomes reveals the variations related to a pathogenic lifestyle. PMID:30526490
The genomic landscape of molecular responses to natural drought stress in Panicum hallii. PMID:30523281
Off- and on-target effects of genome editing in mouse embryos. PMID:30518723
The Transcriptomic Landscape of Yaks Reveals Molecular Pathways for High Altitude Adaptation. PMID:30517636
High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. PMID:30504855
Integrated Genomic, Epigenomic, and Expression Analyses of Ovarian Cancer Cell Lines. PMID:30485824
Profiling microRNA expression in Atlantic killifish (Fundulus heteroclitus) gill and responses to arsenic and hyperosmotic stress. PMID:30476744
Evaluation and application of RNA-Seq by MinION. PMID:30462165
De novo assembly and comparative transcriptome analysis: novel insights into terpenoid biosynthesis in Chamaemelum nobile L. PMID:30430213
Whole genome sequencing of Trypanosoma cruzi field isolates reveals extensive genomic variability and complex aneuploidy patterns within TcII DTU. PMID:30424726
Heterochromatin-Enriched Assemblies Reveal the Sequence and Organization of the Drosophila melanogaster Y Chromosome. PMID:30420487
SynerClust: a highly scalable, synteny-aware orthologue clustering tool. PMID:30418868
Defining TP53 pioneering capabilities with competitive nucleosome binding assays. PMID:30409772
A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC/CBD acid synthase loci. PMID:30409771
The UCSC Genome Browser database: 2019 update. PMID:30407534
imGLAD: accurate detection and quantification of target organisms in metagenomes. PMID:30405973
Assessing the impact of exact reads on reducing the error rate of read mapping. PMID:30400807
De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing. PMID:30398473
Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient. PMID:30397261
Potential of Oryza officinalis to augment the cold tolerance genetic mechanisms of Oryza sativa by network complementation. PMID:30397229
RNAcentral: a hub of information for non-coding RNA sequences. PMID:30395267
Wingless promotes EGFR signaling in follicle stem cells to maintain self-renewal. PMID:30389852
Evolutionary conservation of Y Chromosome ampliconic gene families despite extensive structural variation. PMID:30381290
Genomic distribution of a novel Pyrenophora tritici-repentis ToxA insertion element. PMID:30379913
Whole-Genome Alignment and Comparative Annotation. PMID:30379572
Non-invasive genotyping with a massively parallel sequencing panel for the detection of SNPs in HPA-axis genes. PMID:30374157
Phenotypic characterization and whole genome analysis of extended-spectrum beta-lactamase-producing bacteria isolated from dogs in Germany. PMID:30365516
gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data. PMID:30365027
Characterization of the satellitome in lower vascular plants: the case of the endangered fern Vandenboschia speciosa. PMID:30357311
Structural and Comparative Analysis of the Complete Chloroplast Genome of Pyrus hopeiensis-"Wild Plants with a Tiny Population"-and Three Other Pyrus Species. PMID:30347837
Comparison of Healthy and Dandruff Scalp Microbiome Reveals the Role of Commensals in Scalp Health. PMID:30338244
A Comparative Assessment of Human and Chimpanzee iPSC-derived Cardiomyocytes with Primary Heart Tissues. PMID:30333510
High-resolution chromosome painting with repetitive and single-copy oligonucleotides in Arachis species identifies structural rearrangements and genome differentiation. PMID:30333010
Identification of Arbuscular Mycorrhiza Fungi Responsive microRNAs and Their Regulatory Network in Maize. PMID:30332850
REDfly: the transcriptional regulatory element database for Drosophila. PMID:30329093
The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history. PMID:30325307
Firefly genomes illuminate parallel origins of bioluminescence in beetles. PMID:30324905
Phylogenetic analysis of the cytochrome P450 (CYP450) nucleotide sequences of the horse and predicted CYP450s of the white rhinoceros (Ceratotherium simum) and other mammalian species. PMID:30324017
Unicellular Origin of the Animal MicroRNA Machinery. PMID:30318349
Rapid preimplantation genetic screening using a handheld, nanopore-based DNA sequencer. PMID:30316437
The somatic piRNA pathway controls germline transposition over generations. PMID:30312469
"Out of the Can": A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina pilchardus. PMID:30304855
Genome-scale fitness profile of Caulobacter crescentus grown in natural freshwater. PMID:30297849
Whole-genome comparison of endogenous retrovirus segregation across wild and domestic host species populations. PMID:30297425
Genomic Characterization and Probiotic Potency of Bacillus sp. DU-106, a Highly Effective Producer of L-Lactic Acid Isolated From Fermented Yogurt. PMID:30294310
Repurposing of promoters and enhancers during mammalian evolution. PMID:30287902
CRISPRlnc: a manually curated database of validated sgRNAs for lncRNAs. PMID:30285246
MetaPGN: a pipeline for construction and graphical visualization of annotated pangenome networks. PMID:30277499
Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms. PMID:30272673
Progress of analytical tools and techniques for human gut microbiome research. PMID:30267313
Structure and evolution of double minutes in diagnosis and relapse brain tumors. PMID:30267146
Considerations for Optimization of High-Throughput Sequencing Bioinformatics Pipelines for Virus Detection. PMID:30262776
Chromosome Y-encoded antigens associate with acute graft-versus-host disease in sex-mismatched stem cell transplant. PMID:30262602
Opaque-2 Regulates a Complex Gene Network Associated with Cell Differentiation and Storage Functions of Maize Endosperm. PMID:30262552
Genetic mapping of anthocyanin accumulation-related genes in pepper fruits using a combination of SLAF-seq and BSA. PMID:30261055
De novo clustering of long reads by gene from transcriptomics data. PMID:30260405
Rare variants in the splicing regulatory elements of EXOC3L4 are associated with brain glucose metabolism in Alzheimer's disease. PMID:30255815
Fine mapping and candidate gene screening of the downy mildew resistance gene RPF1 in Spinach. PMID:30244393
The Grayling Genome Reveals Selection on Gene Expression Regulation after Whole-Genome Duplication. PMID:30239729
Factors Influencing Gene Family Size Variation Among Related Species in a Plant Family, Solanaceae. PMID:30239695
Roquin targets mRNAs in a 3'-UTR-specific manner by different modes of regulation. PMID:30232334
Genomic analysis of MHC-based mate choice in the monogamous California mouse. PMID:30214134
QTL Mapping and Marker Identification for Sex-Determining: Indicating XY Sex Determination System in the Swimming Crab (Portunus trituberculatus). PMID:30210528
The genetic basis and cell of origin of mixed phenotype acute leukaemia. PMID:30209392
Improving nanopore read accuracy with the R2C2 method enables the sequencing of highly multiplexed full-length single-cell cDNA. PMID:30201725
Comparative genomics and transcriptomics of Chrysolophus provide insights into the evolution of complex plumage coloration. PMID:30192940
Pairs of Adjacent Conserved Noncoding Elements Separated by Conserved Genomic Distances Act as Cis-Regulatory Units. PMID:30184074
Draft genome of Dugesia japonica provides insights into conserved regulatory elements of the brain restriction gene nou-darake in planarians. PMID:30181897
Regulatory processes that control haploid expression of salmon sperm mRNAs. PMID:30176937
A novel panel of short mononucleotide repeats linked to informative polymorphisms enabling effective high volume low cost discrimination between mismatch repair deficient and proficient tumours. PMID:30157243
Comparative analysis of whole flower transcriptomes in the Zingiberales. PMID:30155368
Whole genome shotgun sequencing revealed highly polymorphic genome regions and genes in Escherichia coli O157:H7 isolates collected from a single feedlot. PMID:30153286
Repeated translocation of a gene cassette drives sex-chromosome turnover in strawberries. PMID:30148831
Complete sequence of kenaf (Hibiscus cannabinus) mitochondrial genome and comparative analysis with the mitochondrial genomes of other plants. PMID:30143661
Draft genome of Glyptosternon maculatum, an endemic fish from Tibet Plateau. PMID:30124856
Characterization of the β-defensin genes in giant panda. PMID:30120296
The landscape of the A-to-I RNA editome from 462 human genomes. PMID:30104667
Potent HIV-1-Specific CD8 T Cell Responses Induced in Mice after Priming with a Multiepitopic DNA-TMEP and Boosting with the HIV Vaccine MVA-B. PMID:30104537
The chromosome-level genome assemblies of two rattans (Calamus simplicifolius and Daemonorops jenkinsiana). PMID:30101322
Xenotropic Mouse Gammaretroviruses Isolated from Pre-Leukemic Tissues Include a Recombinant. PMID:30096897
Comparative genetic and genomic analysis of the novel fusellovirus Sulfolobus spindle-shaped virus 10. PMID:30094064
Ancient convergent losses of Paraoxonase 1 yield potential risks for modern marine mammals. PMID:30093596
Evolutionary stability of topologically associating domains is associated with conserved gene regulation. PMID:30086749
Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave. PMID:30081833
No Evidence for Recent Selection at FOXP2 among Diverse Human Populations. PMID:30078708
Transcriptional profiling of HERV-K(HML-2) in amyotrophic lateral sclerosis and potential implications for expression of HML-2 proteins. PMID:30068350
Naked mole-rat transcriptome signatures of socially suppressed sexual maturation and links of reproduction to aging. PMID:30068345
Expanding the Mutation Spectrum in ABCA4: Sixty Novel Disease Causing Variants and Their Associated Phenotype in a Large French Stargardt Cohort. PMID:30060493
Genome sequence of Jatropha curcas L., a non-edible biodiesel plant, provides a resource to improve seed-related traits. PMID:30059608
Development of Target Sequence Capture and Estimation of Genomic Relatedness in a Mixed Oak Stand. PMID:30057586
Mobile elements contribute to the uniqueness of human genome with 15,000 human-specific insertions and 14 Mbp sequence increase. PMID:30052927
The habu genome reveals accelerated evolution of venom protein genes. PMID:30050104
Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks. PMID:30046115
Evolution of gene dosage on the Z-chromosome of schistosome parasites. PMID:30044216
Trichoplax genomes reveal profound admixture and suggest stable wild populations without bisexual reproduction. PMID:30042472
Comparative Genomics of Escherichia coli Sequence Type 219 Clones From the Same Patient: Evolution of the IncI1 blaCMY-Carrying Plasmid in Vivo. PMID:30038606
Genome Plasticity in Cultured Leishmania donovani: Comparison of Early and Late Passages. PMID:30018594
Relationship Between Sequence Homology, Genome Architecture, and Meiotic Behavior of the Sex Chromosomes in North American Voles. PMID:30002081
miR-196b target screen reveals mechanisms maintaining leukemia stemness with therapeutic potential. PMID:29997117
Coinfections identified from metagenomic analysis of cervical lymph nodes from tularemia patients. PMID:29996780
The Genetics of a Behavioral Speciation Phenotype in an Island System. PMID:29996514
De Novo Mutation in Genes Regulating Neural Stem Cell Fate in Human Congenital Hydrocephalus. PMID:29983323
Efficient and precise editing of endogenous transcripts with SNAP-tagged ADARs. PMID:29967493
The genetic architecture of genome-wide recombination rate variation in allopolyploid wheat revealed by nested association mapping. PMID:29952048
Whole body transcriptomes and new insights into the biology of the tick Ixodes ricinus. PMID:29941016
Efficacy and safety of a clinically relevant foamy vector design in human hematopoietic repopulating cells. PMID:29935087
High-quality assembly of the reference genome for scarlet sage, Salvia splendens, an economically important ornamental plant. PMID:29931210
Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract. PMID:29925834
SNP hot-spots in the clam parasite QPX. PMID:29925308
Long-read sequencing and de novo genome assembly of Ammopiptanthus nanus, a desert shrub. PMID:29917074
The genome of Rhizophagus clarus HR1 reveals a common genetic basis for auxotrophy among arbuscular mycorrhizal fungi. PMID:29914365
In silico read normalization using set multi-cover optimization. PMID:29912280
Detecting de Novo Homoeologous Recombination Events in Cultivated Brassica napus Using a Genome-Wide SNP Array. PMID:29907649
Association mapping from sequencing reads using k-mers. PMID:29897334
Transcriptional analyses provide new insight into the late-stage immune response of a diseased Caribbean coral. PMID:29892394
Hydrogen-Fueled Microbial Pathways in Biogas Upgrading Systems Revealed by Genome-Centric Metagenomics. PMID:29892275
A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits. PMID:29892093
Blazing Signature Filter: a library for fast pairwise similarity comparisons. PMID:29890950
Investigating the Molecular Genetic Basis of Cytoplasmic Sex Determination Caused by Wolbachia Endosymbionts in Terrestrial Isopods. PMID:29890648
Genetic variation affecting exon skipping contributes to brain structural atrophy in Alzheimer's disease. PMID:29888056
Population resequencing reveals candidate genes associated with salinity adaptation of the Pacific oyster Crassostrea gigas. PMID:29875442
The Genomic Architecture of a Rapid Island Radiation: Recombination Rate Variation, Chromosome Structure, and Genome Assembly of the Hawaiian Cricket Laupala. PMID:29875253
phylotaR: An Automated Pipeline for Retrieving Orthologous DNA Sequences from GenBank in R. PMID:29874797
A survey of microRNA single nucleotide polymorphisms identifies novel breast cancer susceptibility loci in a case-control, population-based study of African-American women. PMID:29871690
Genomic Variations in Probiotic Lactobacillus plantarum P-8 in the Human and Rat Gut. PMID:29867805
Massive NGS data analysis reveals hundreds of potential novel gene fusions in human cell lines. PMID:29860514
Gene family innovation, conservation and loss on the animal stem lineage. PMID:29848444
Size and Content of the Sex-Determining Region of the Y Chromosome in Dioecious Mercurialis annua, a Plant with Homomorphic Sex Chromosomes. PMID:29844299
Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi. PMID:29843602
The small RNA complement of adult Schistosoma haematobium. PMID:29813122
SMARTIV: combined sequence and structure de-novo motif discovery for in-vivo RNA binding data. PMID:29800452
Whole-genome sequencing reveals genomic signatures associated with the inflammatory microenvironments in Chinese NSCLC patients. PMID:29799009
Bidirectional regulation of adenosine-to-inosine (A-to-I) RNA editing by DEAH box helicase 9 (DHX9) in cancer. PMID:29796672
A High Quality Genome for Mus spicilegus, a Close Relative of House Mice with Unique Social and Ecological Adaptations. PMID:29794166
Comparative transcriptome analysis of the invasive weed Mikania micrantha with its native congeners provides insights into genetic basis underlying successful invasion. PMID:29793434
The Eukaryotic Proteome Is Shaped by E3 Ubiquitin Ligases Targeting C-Terminal Degrons. PMID:29779948
Association of Polygenic Risk Scores for Multiple Cancers in a Phenome-wide Study: Results from The Michigan Genomics Initiative. PMID:29779563
Curation of microarray oligonucleotides and corresponding ESTs/cDNAs used for gene expression analysis in zebra finches. PMID:29776372
Genome Sequencing and Analysis of the Peanut B-Genome Progenitor (Arachis ipaensis). PMID:29774047
Methylation guide RNA evolution in archaea: structure, function and genomic organization of 110 C/D box sRNA families across six Pyrobaculum species. PMID:29771354
Single-step Precision Genome Editing in Yeast Using CRISPR-Cas9. PMID:29770349
Mutant phenotypes for thousands of bacterial genes of unknown function. PMID:29769716
Population genomic data reveal genes related to important traits of quail. PMID:29762663
Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes. PMID:29761466
Molecular Cytogenetics Guides Massively Parallel Sequencing of a Radiation-Induced Chromosome Translocation in Human Cells. PMID:29749794
Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs. PMID:29747566
Identification of candidate genes for gelatinization temperature, gel consistency and pericarp color by GWAS in rice based on SLAF-sequencing. PMID:29746484
Genome sequence of the progenitor of wheat A subgenome Triticum urartu. PMID:29743678
Improved de novo genomic assembly for the domestic donkey. PMID:29740610
Targeting legume loci: A comparison of three methods for target enrichment bait design in Leguminosae phylogenomics. PMID:29732266
Applications and efficiencies of the first cat 63K DNA array. PMID:29728693
Cigarette smoke and chewing tobacco alter expression of different sets of miRNAs in oral keratinocytes. PMID:29728663
Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis. PMID:29722876
A new strategy to infer circularity applied to four new complete frog mitogenomes. PMID:29721275
Improved strategy for the curation and classification of kinases, with broad applicability to other eukaryotic protein groups. PMID:29717207
Reconstruction of a replication-competent ancestral murine endogenous retrovirus-L. PMID:29716624
The genetic architecture of floral traits in the woody plant Prunus mume. PMID:29703940
CAS-viewer: web-based tool for splicing-guided integrative analysis of multi-omics cancer data. PMID:29697367
Metaproteogenomic Profiling of Microbial Communities Colonizing Actively Venting Hydrothermal Chimneys. PMID:29696004
Unsupervised, Statistically Based Systems Biology Approach for Unraveling the Genetics of Complex Traits: A Demonstration with Ethanol Metabolism. PMID:29689131
Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species. PMID:29689044
Chromosome-scale assembly of the Monopterus genome. PMID:29688346
Comparative genomics of the wheat fungal pathogen Pyrenophora tritici-repentis reveals chromosomal variations and genome plasticity. PMID:29685100
Parallel evolution of Batesian mimicry supergene in two Papilio butterflies, P. polytes and P. memnon. PMID:29675466
Successful application of human-based methyl capture sequencing for methylome analysis in non-human primate models. PMID:29669513
The evolution of CpG density and lifespan in conserved primate and mammalian promoters. PMID:29661983
A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants. PMID:29661190
Insights into the Function of Long Noncoding RNAs in Sepsis Revealed by Gene Co-Expression Network Analysis. PMID:29657277
HNRNPA1 promotes recognition of splice site decoys by U2AF2 in vivo. PMID:29650551
Replication-incompetent gammaretroviral and lentiviral vector-based insertional mutagenesis screens identify prostate cancer progression genes. PMID:29643985
L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis. PMID:29643204
The Origins and Vulnerabilities of Two Transmissible Cancers in Tasmanian Devils. PMID:29634948
Genome-wide association identifies a novel locus for delirium risk. PMID:29631748
Detection and genotyping of human papillomavirus (HPV) in HIV-infected women and its relationship with HPV/HIV co-infection. PMID:29620669
G-Anchor: a novel approach for whole-genome comparative mapping utilizing evolutionary conserved DNA sequences. PMID:29618053
Draft genome of the Peruvian scallop Argopecten purpuratus. PMID:29617765
De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution. PMID:29615780
The constitutive differential transcriptome of a brain circuit for vocal learning. PMID:29614959
Homo sapiens-Specific Binding Site Variants within Brain Exclusive Enhancers Are Subject to Accelerated Divergence across Human Population. PMID:29608725
Unexpected conservation of the RNA splicing apparatus in the highly streamlined genome of Galdieria sulphuraria. PMID:29606099
Deep learning improves antimicrobial peptide recognition. PMID:29590297
HOXB7 overexpression in lung cancer is a hallmark of acquired stem-like phenotype. PMID:29576613
Long-lived rodents reveal signatures of positive selection in genes associated with lifespan. PMID:29570707
Analysis of lineage-specific Alu subfamilies in the genome of the olive baboon, Papio anubis. PMID:29560044
FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods. PMID:29559002
Candidate genes for first flower node identified in pepper using combined SLAF-seq and BSA. PMID:29558466
Long Non-Coding RNAs Responsive to Salt and Boron Stress in the Hyper-Arid Lluteño Maize from Atacama Desert. PMID:29558449
High-density genetic map construction and comparative genome analysis in asparagus bean. PMID:29555986
DNA Conformation Induces Adaptable Binding by Tandem Zinc Finger Proteins. PMID:29551271
High-throughput analysis of satellite DNA in the grasshopper Pyrgomorpha conica reveals abundance of homologous and heterologous higher-order repeats. PMID:29549528
The diversity of ice algal communities on the Greenland Ice Sheet as revealed by oligotyping. PMID:29547098
Rapid Multiplex Small DNA Sequencing on the MinION Nanopore Sequencing Platform. PMID:29540443
Novel FR-900493 Analogues That Inhibit the Outgrowth of Clostridium difficile Spores. PMID:29503973
Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow. PMID:29500430
P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads. PMID:29499650
Landscape of the spliced leader trans-splicing mechanism in Schistosoma mansoni. PMID:29497070
Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours. PMID:29489755
A Genetic Screen Identifies PRP18a, a Putative Second Step Splicing Factor Important for Alternative Splicing and a Normal Phenotype in Arabidopsis thaliana. PMID:29487188
Evolution of pyrrolizidine alkaloid biosynthesis in Apocynaceae: revisiting the defence de-escalation hypothesis. PMID:29479722
A translational silencing function of MCPIP1/Regnase-1 specified by the target site context. PMID:29471506
Genome-wide identification and analysis of A-to-I RNA editing events in bovine by transcriptome sequencing. PMID:29470549
Whole-Genome Analysis Illustrates Global Clonal Population Structure of the Ubiquitous Dermatophyte Pathogen Trichophyton rubrum. PMID:29467168
Cooption of heat shock regulatory system for anhydrobiosis in the sleeping chironomid Polypedilum vanderplanki. PMID:29463761
Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat. PMID:29459707
Identification of piRNA Binding Sites Reveals the Argonaute Regulatory Landscape of the C. elegans Germline. PMID:29456082
Recently integrated Alu insertions in the squirrel monkey (Saimiri) lineage and application for population analyses. PMID:29449901
The Integrated Genomic Landscape of Thymic Epithelial Tumors. PMID:29438696
Genome sequence and description of Haloferax massiliense sp. nov., a new halophilic archaeon isolated from the human gut. PMID:29435649
Identification of an (AC)n microsatellite in the Six1 gene promoter and its effect on production traits in Pietrain × Duroc × Landrace × Yorkshire pigs. PMID:29432614
5-Azacytidine prevents relapse and produces long-term complete remissions in leukemia xenografts treated with Moxetumomab pasudotox. PMID:29432154
Metatranscriptome Sequencing Reveals Insights into the Gene Expression and Functional Potential of Rumen Wall Bacteria. PMID:29410661
Evolution of the Quorum network and the mobilome (plasmids and bacteriophages) in clinical strains of Acinetobacter baumannii during a decade. PMID:29410443
Comparing fixed sampling with minimizer sampling when using k-mer indexes to find maximal exact matches. PMID:29389989
Preferential use of unmutated immunoglobulin heavy variable region genes in Boxer dogs with chronic lymphocytic leukemia. PMID:29385200
MUMmer4: A fast and versatile genome alignment system. PMID:29373581
Whole-genome assembly of the coral reef Pearlscale Pygmy Angelfish (Centropyge vrolikii). PMID:29367590
Genetical genomics of growth in a chicken model. PMID:29361907
HERV-W group evolutionary history in non-human primates: characterization of ERV-W orthologs in Catarrhini and related ERV groups in Platyrrhini. PMID:29351742
Population size may shape the accumulation of functional mutations following domestication. PMID:29351740
HybPhyloMaker: Target Enrichment Data Analysis From Raw Reads to Species Trees. PMID:29348708
Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D. PMID:29346625
Uncovering Genomic Regions Associated with Trypanosoma Infections in Wild Populations of the Tsetse Fly Glossina fuscipes. PMID:29343494
SLAF-based high-density genetic map construction and QTL mapping for major economic traits in sea urchin Strongylocentrotus intermedius. PMID:29339742
Contribution of transposable elements and distal enhancers to evolution of human-specific features of interphase chromatin architecture in embryonic stem cells. PMID:29335803
seq-seq-pan: building a computational pan-genome data structure on whole genome alignment. PMID:29334898
The genome sequence of the commercially cultivated mushroom Agrocybe aegerita reveals a conserved repertoire of fruiting-related genes and a versatile suite of biopolymer-degrading enzymes. PMID:29334897
Analysis of the Aedes albopictus C6/36 genome provides insight into cell line utility for viral propagation. PMID:29329394
Analysis of DNA Methylation in Young People: Limited Evidence for an Association Between Victimization Stress and Epigenetic Variation in Blood. PMID:29325449
POU6f1 Mediates Neuropeptide-Dependent Plasticity in the Adult Brain. PMID:29305536
Rapid genome shrinkage in a self-fertile nematode reveals sperm competition proteins. PMID:29302007
Multiplexed gene synthesis in emulsions for exploring protein functional landscapes. PMID:29301959
De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus. PMID:29297306
Scaling bioinformatics applications on HPC. PMID:29297287
A New Standard for Crustacean Genomes: The Highly Contiguous, Annotated Genome Assembly of the Clam Shrimp Eulimnadia texana Reveals HOX Gene Order and Identifies the Sex Chromosome. PMID:29294012
Global transcriptional landscape and promoter mapping of the gut commensal Bifidobacterium breve UCC2003. PMID:29281966
Detection of de novo single nucleotide variants in offspring of atomic-bomb survivors close to the hypocenter by whole-genome sequencing. PMID:29279608
The Hidden Genomic and Transcriptomic Plasticity of Giant Marker Chromosomes in Cancer. PMID:29279323
An integrated and comparative approach towards identification, characterization and functional annotation of candidate genes for drought tolerance in sorghum (Sorghum bicolor (L.) Moench). PMID:29273003
Overexpressed HSF1 cancer signature genes cluster in human chromosome 8q. PMID:29268782
Construction of an SNP-based high-density linkage map for flax (Linum usitatissimum L.) using specific length amplified fragment sequencing (SLAF-seq) technology. PMID:29267332
Genome-wide analysis of SSR and ILP markers in trees: diversity profiling, alternate distribution, and applications in duplication. PMID:29263331
The coding and noncoding transcriptome of Neurospora crassa. PMID:29258423
Genome assembly of the Pink Ipê (Handroanthus impetiginosus, Bignoniaceae), a highly valued, ecologically keystone Neotropical timber forest tree. PMID:29253216
Oncogenic Role of THOR, a Conserved Cancer/Testis Long Non-coding RNA. PMID:29245011
Efficient transgenesis and annotated genome sequence of the regenerative flatworm model Macrostomum lignano. PMID:29242515
The landscape of miRNA editing in animals and its impact on miRNA biogenesis and targeting. PMID:29233923
Whole-genome sequencing and SNV genotyping of 'Nebbiolo' (Vitis vinifera L.) clones. PMID:29229917
DNAAF1 links heart laterality with the AAA+ ATPase RUVBL1 and ciliary intraflagellar transport. PMID:29228333
CNVcaller: highly efficient and widely applicable software for detecting copy number variations in large populations. PMID:29220491
RetrogeneDB-a database of plant and animal retrocopies. PMID:29220443
Transcription profiling and identification of infection-related genes in Phytophthora cactorum. PMID:29218408
Age-related gene expression changes, and transcriptome wide association study of physical and cognitive aging traits, in the Lothian Birth Cohort 1936. PMID:29207374
Consideration of non-canonical splice sites improves gene prediction on the Arabidopsis thaliana Niederzenz-1 genome sequence. PMID:29202864
Contrasting patterns of evolutionary constraint and novelty revealed by comparative sperm proteomic analysis in Lepidoptera. PMID:29197336
Voluntary exposure to a toxin: the genetic influence on ethanol consumption. PMID:29196862
3C-PCR: a novel proximity ligation-based approach to phase chromosomal rearrangement breakpoints with distal allelic variants. PMID:29196799
A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles. PMID:29195078
Long-read sequence assembly of the firefly Pyrocoelia pectoralis genome. PMID:29186486
HLA genotyping by next-generation sequencing of complementary DNA. PMID:29179676
The full transcription map of mouse papillomavirus type 1 (MmuPV1) in mouse wart tissues. PMID:29176795
ABCA4 midigenes reveal the full splice spectrum of all reported noncanonical splice site variants in Stargardt disease. PMID:29162642
Fast batch searching for protein homology based on compression and clustering. PMID:29162030
Human Accelerated Regions and Other Human-Specific Sequence Variations in the Context of Evolution and Their Relevance for Brain Development. PMID:29149249
Age, estrogen, and immune response in breast adenocarcinoma and adjacent normal tissue. PMID:29147603
Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus). PMID:29145861
The deep conservation of the Lepidoptera Z chromosome suggests a non-canonical origin of the W. PMID:29133797
The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA. PMID:29127278
Comparative Transcriptome and DNA methylation analyses of the molecular mechanisms underlying skin color variations in Crucian carp (Carassius carassius L.). PMID:29121864
The complete chloroplast genome of Primulina and two novel strategies for development of high polymorphic loci for population genetic and phylogenetic studies. PMID:29115917
The UCSC Genome Browser database: 2018 update. PMID:29106570
Stable Core Gut Microbiota across the Freshwater-to-Saltwater Transition for Farmed Atlantic Salmon. PMID:29101198
K-mer clustering algorithm using a MapReduce framework: application to the parallelization of the Inchworm module of Trinity. PMID:29100493
Stress amplifies sex differences in primate prefrontal profiles of gene expression. PMID:29096718
Genome-wide discovery of long intergenic noncoding RNAs and their epigenetic signatures in the rat. PMID:29093522
A distinct hematopoietic stem cell population for rapid multilineage engraftment in nonhuman primates. PMID:29093179
Variant Review with the Integrative Genomics Viewer. PMID:29092934
Comparative analysis of genome sequences of the conifer tree pathogen, Heterobasidion annosum s.s. PMID:29085779
High rate of translocation-based gene birth on the Drosophila Y chromosome. PMID:29078298
Differences in the genetic control of early egg development and reproduction between C. elegans and its parthenogenetic relative D. coronatus. PMID:29075433
Keeping it complicated: Mitochondrial genome plasticity across diplonemids. PMID:29074957
Detecting large deletions at base pair level by combining split read and paired read data. PMID:29072143
Detection and quantification of mitochondrial DNA deletions from next-generation sequence data. PMID:29072135
sRNAnalyzer-a flexible and customizable small RNA sequencing data analysis pipeline. PMID:29069500
An optimized approach for annotation of large eukaryotic genomic sequences using genetic algorithm. PMID:29065853
Metatranscriptomic and metagenomic description of the bacterial nitrogen metabolism in waste water wet oxidation effluents. PMID:29062974
Spontaneous circadian rhythms in a cold-adapted natural isolate of Aureobasidium pullulans. PMID:29062053
Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination. PMID:29052505
The genome draft of coconut (Cocos nucifera). PMID:29048487
Genome structure of Rosa multiflora, a wild ancestor of cultivated roses. PMID:29045613
Complete mitochondrial genome sequences of the northern spotted owl (Strix occidentalis caurina) and the barred owl (Strix varia; Aves: Strigiformes: Strigidae) confirm the presence of a duplicated control region. PMID:29038757
Frequency-dependent selection in vaccine-associated pneumococcal population dynamics. PMID:29038424
MG-RAST version 4-lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis. PMID:29028869
Frequency-dependent selection in vaccine-associated pneumococcal population dynamics. PMID:29038424
MG-RAST version 4-lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis. PMID:29028869
HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing. PMID:29026435
Dynamic landscape and regulation of RNA editing in mammals. PMID:29022589
The draft genome assembly of Rhododendron delavayi Franch. var. delavayi. PMID:29020749
Comprehensive benchmarking of SNV callers for highly admixed tumor data. PMID:29020110
DNA sequencing at 40: past, present and future. PMID:29019985
A Massively Parallel Sequence Similarity Search for Metagenomic Sequencing Data. PMID:29019934
The First Genetic Map in Sweet Osmanthus (Osmanthus fragrans Lour.) Using Specific Locus Amplified Fragment Sequencing. PMID:29018460
High-throughput analysis unveils a highly shared satellite DNA library among three species of fish genus Astyanax. PMID:29018237
Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer. PMID:28988769
Genome-wide Mapping of Off-Target Events in Single-Stranded Oligodeoxynucleotide-Mediated Gene Repair Experiments. PMID:28988714
Genome-wide mapping of large deletions and their population-genetic properties in dairy cattle. PMID:28985340
Optimal choice of word length when comparing two Markov sequences using a χ 2-statistic. PMID:28984181
Convergent evolution of Y chromosome gene content in flies. PMID:28978907
qPrimerDB: a thermodynamics-based gene-specific qPCR primer database for 147 organisms. PMID:28977518
A Genetic Screen for Pre-mRNA Splicing Mutants of Arabidopsis thaliana Identifies Putative U1 snRNP Components RBM25 and PRP39a. PMID:28971960
A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3). PMID:28971018
Federation in genomics pipelines: techniques and challenges. PMID:28968781
EST-BASED ANALYSIS OF GENE EXPRESSION IN THE HUMAN COCHLEA. PMID:28967002
Evolution of Alu Subfamily Structure in the Saimiri Lineage of New World Monkeys. PMID:28957461
Accurate clinical genetic testing for autoinflammatory diseases using the next-generation sequencing platform MiSeq. PMID:28956000
VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy. PMID:28931371
Comprehensive analysis of lncRNAs and mRNAs in skeletal muscle of rainbow trout (Oncorhynchus mykiss) exposed to estradiol. PMID:28924252
Root transcriptomic responses of grafted grapevines to heterogeneous nitrogen availability depend on rootstock genotype. PMID:28922755
Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. PMID:28922347
Genomic structure and evolution of the mating type locus in the green seaweed Ulva partita. PMID:28916791
Assessment of T-cell receptor repertoire and clonal expansion in peripheral T-cell lymphoma using RNA-seq data. PMID:28900149
Approaches for in silico finishing of microbial genome sequences. PMID:28898352
Acidophilic green algal genome provides insights into adaptation to an acidic environment. PMID:28893987
Evaluation of single-cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis. PMID:28887541
Perilipin-2 modulates dietary fat-induced microbial global gene expression profiles in the mouse intestine. PMID:28877764
A miRNA catalogue and ncRNA annotation of the short-living fish Nothobranchius furzeri. PMID:28874118
Assembly and analysis of a qingke reference genome demonstrate its close genetic relation to modern cultivated barley. PMID:28871634
Quantitative sequence characterization for repetitive DNA content in the supernumerary chromosome of the migratory locust. PMID:28868580
Efficient genome-wide association in biobanks using topic modeling identifies multiple novel disease loci. PMID:28861588
Transcriptome analysis reveals the host selection fitness mechanisms of the Rhizoctonia solani AG1IA pathogen. PMID:28860554
Persistent histone modifications at the BDNF and Cdk-5 promoters following extinction of nicotine-seeking in rats. PMID:28857504
A Glimpse into the Satellite DNA Library in Characidae Fish (Teleostei, Characiformes). PMID:28855916
Transposable Element Misregulation Is Linked to the Divergence between Parental piRNA Pathways in Drosophila Hybrids. PMID:28854624
De novo assembly and characterization of breast cancer transcriptomes identifies large numbers of novel fusion-gene transcripts of potential functional significance. PMID:28851357
Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters. PMID:28851275
Genome Plasticity and Polymorphisms in Critical Genes Correlate with Increased Virulence of Dutch Outbreak-Related Coxiella burnetii Strains. PMID:28848533
Analysis of 62 hybrid assembled human Y chromosomes exposes rapid structural changes and high rates of gene conversion. PMID:28846694
Population genetic structure of Guiana dolphin (Sotalia guianensis) from the southwestern Atlantic coast of Brazil. PMID:28837691
An integrated expression atlas of miRNAs and their promoters in human and mouse. PMID:28829439
Searching for signatures across microbial communities: Metagenomic analysis of soil samples from mangrove and other ecosystems. PMID:28821820
Improvement of the Threespine Stickleback Genome Using a Hi-C-Based Proximity-Guided Assembly. PMID:28821183
Reliable Detection of Herpes Simplex Virus Sequence Variation by High-Throughput Resequencing. PMID:28812996
Transcriptome Association Identifies Regulators of Wheat Spike Architecture. PMID:28807930
Draft de novo transcriptome assembly and proteome characterization of the electric lobe of Tetronarce californica: a molecular tool for the study of cholinergic neurotransmission in the electric organ. PMID:28806931
A transcriptome atlas of rabbit revealed by PacBio single-molecule long-read sequencing. PMID:28794490
Recombinant Origins of Pathogenic and Nonpathogenic Mouse Gammaretroviruses with Polytropic Host Range. PMID:28794032
SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes. PMID:28778180
Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula. PMID:28778149
Evaluating allopolyploid origins in strawberries (Fragaria) using haplotypes generated from target capture sequencing. PMID:28778145
High-Coverage Whole-Exome Sequencing Identifies Candidate Genes for Suicide in Victims with Major Depressive Disorder. PMID:28769055
Presence of a Shared 5'-Leader Sequence in Ancestral Human and Mammalian Retroviruses and Its Transduction into Feline Leukemia Virus. PMID:28768854
Elevated auxin biosynthesis and transport underlie high vein density in C4 leaves. PMID:28761000
Structural basis of head to head polyketide fusion by CorB. PMID:28757960
The house spider genome reveals an ancient whole-genome duplication during arachnid evolution. PMID:28756775
Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis. PMID:28750650
A systems approach to a spatio-temporal understanding of the drought stress response in maize. PMID:28747711
Whole-Genome Sequencing and Concordance Between Antimicrobial Susceptibility Genotypes and Phenotypes of Bacterial Isolates Associated with Bovine Respiratory Disease. PMID:28739600
Transcription through the eye of a needle: daily and annual cyclic gene expression variation in Douglas-fir needles. PMID:28738815
Differentiating Botulinum Neurotoxin-Producing Clostridia with a Simple, Multiplex PCR Assay. PMID:28733282
Gene expression patterns of chicken neuregulin 3 in association with copy number variation and frameshift deletion. PMID:28732471
Dynamics of genomic innovation in the unicellular ancestry of animals. PMID:28726632
Regulation of amino-acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica. PMID:28725468
Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells. PMID:28722025
Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks. PMID:28721231
Microbiome overview in swine lungs. PMID:28719637
Regulation of the activity of the promoter of RNA-induced silencing, C3PO. PMID:28714243
Splicing Activation by Rbfox Requires Self-Aggregation through Its Tyrosine-Rich Domain. PMID:28708999
LINE-1 Hypermethylation in Serum Cell-Free DNA of Relapsing Remitting Multiple Sclerosis Patients. PMID:28707075
Indoleacrylic Acid Produced by Commensal Peptostreptococcus Species Suppresses Inflammation. PMID:28704649
The effects of sampling on the efficiency and accuracy of k-mer indexes: Theoretical and empirical comparisons using the human genome. PMID:28686614
Interpreting whole genome and exome sequencing data of individual gastric cancer samples. PMID:28683819
Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer. PMID:28678784
Genome Sequences of Marine Shrimp Exopalaemon carinicauda Holthuis Provide Insights into Genome Size Evolution of Caridea. PMID:28678163
Expression of a SOX1 overlapping transcript in neural differentiation and cancer models. PMID:28674729
Automated tools for comparative sequence analysis of genic regions using the GenePalette application. PMID:28673819
A massively parallel strategy for STR marker development, capture, and genotyping. PMID:28666376
A Highly Dense Genetic Map for Ginkgo biloba Constructed Using Sequence-Based Markers. PMID:28663754
Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments. PMID:28652936
In Vivo Murine-Matured Human CD3+ Cells as a Preclinical Model for T Cell-Based Immunotherapies. PMID:28649577
Genomic introgression mapping of field-derived multiple-anthelmintic resistance in Teladorsagia circumcincta. PMID:28644839
McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data. PMID:28637810
Flavivirus and Filovirus EvoPrinters: New alignment tools for the comparative analysis of viral evolution. PMID:28622346
Mapping and Preliminary Analysis of ABORTED MICROSPORES (AMS) as the Candidate Gene Underlying the Male Sterility (MS-5) Mutant in Melon (Cucumis melo L.). PMID:28611814
Gene silencing by RNA interference in Sarcoptes scabiei: a molecular tool to identify novel therapeutic targets. PMID:28601087
Whole genome sequencing of an ExPEC that caused fatal pneumonia at a pig farm in Changchun, China. PMID:28599670
Androgen receptor and miR-206 regulation in prostate cancer. PMID:28598253
CottonFGD: an integrated functional genomics database for cotton. PMID:28595571
Sequencing, de novo assembling, and annotating the genome of the endangered Chinese crocodile lizard Shinisaurus crocodilurus. PMID:28595343
A comprehensive overview and evaluation of circular RNA detection tools. PMID:28594838
A simple and economical method for improving whole genome alignment. PMID:28589863
Specific-Locus Amplified Fragment Sequencing Reveals Spontaneous Single-Nucleotide Mutations in Rice OsMsh6 Mutants. PMID:28589142
Identification of Proteases and Protease Inhibitors in Allergenic and Non-Allergenic Pollen. PMID:28587253
Analysis of LINE-1 Elements in DNA from Postmortem Brains of Individuals with Schizophrenia. PMID:28585566
Crop wild relative populations of Beta vulgaris allow direct mapping of agronomically important genes. PMID:28585529
Allelic variants of OsHKT1;1 underlie the divergence between indica and japonica subspecies of rice (Oryza sativa) for root sodium content. PMID:28582424
High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. PMID:28581499
The evolution and population diversity of human-specific segmental duplications. PMID:28580430
Analysis of Copy Number Variation in the Abp Gene Regions of Two House Mouse Subspecies Suggests Divergence during the Gene Family Expansions. PMID:28575204
The Agassiz's desert tortoise genome provides a resource for the conservation of a threatened species. PMID:28562605
Repeated divergent selection on pigmentation genes in a rapid finch radiation. PMID:28560331
A Review on Recent Computational Methods for Predicting Noncoding RNAs. PMID:28553651
An episomal vector-based CRISPR/Cas9 system for highly efficient gene knockout in human pluripotent stem cells. PMID:28539611
GCN2 phosphorylates HIV-1 integrase and decreases HIV-1 replication by limiting viral integration. PMID:28536474
Association Mapping of Yield and Yield-related Traits Under Reproductive Stage Drought Stress in Rice (Oryza sativa L.). PMID:28523639
Reading LINEs within the cocaine addicted brain. PMID:28523221
MET Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma. PMID:28522754
Identification of Sex-determining Loci in Pacific White Shrimp Litopeneaus vannamei Using Linkage and Association Analysis. PMID:28508952
Linkage disequilibrium matches forensic genetic records to disjoint genomic marker sets. PMID:28507140
An independent component analysis confounding factor correction framework for identifying broad impact expression quantitative trait loci. PMID:28505156
Expansion of the redox-sensitive proteome coincides with the plastid endosymbiosis. PMID:28504699
Genome-Wide SNP Markers Based on SLAF-Seq Uncover Breeding Traces in Rapeseed (Brassica napus L.). PMID:28503182
Short Read Mapping: An Algorithmic Tour. PMID:28502990
Detection of viromes of RNA viruses using the next generation sequencing libraries prepared by three methods. PMID:28501627
High-Density Genetic Map Construction and Gene Mapping of Basal Branching Habit and Flowers per Leaf Axil in Sesame. PMID:28496450
Target enrichment sequencing in cultivated peanut (Arachis hypogaea L.) using probes designed from transcript sequences. PMID:28492983
GeSeq - versatile and accurate annotation of organelle genomes. PMID:28486635
Chromosome-level genome assembly and transcriptome of the green alga Chromochloris zofingiensis illuminates astaxanthin production. PMID:28484037
Heritable L1 retrotransposition in the mouse primordial germline and early embryo. PMID:28483779
High-density genetic map construction and QTLs identification for plant height in white jute (Corchorus capsularis L.) using specific locus amplified fragment (SLAF) sequencing. PMID:28482802
Soft Sweeps Are the Dominant Mode of Adaptation in the Human Genome. PMID:28482049
Draft genome sequence of the Tibetan medicinal herb Rhodiola crenulata. PMID:28475810
Comparative study of viromes from freshwater samples of the Ile-Balkhash region of Kazakhstan captured through metagenomic analysis. PMID:28466051
Geno- and phenotypic characteristics of a transfected Babesia bovis 6-Cys-E knockout clonal line. PMID:28464956
Evolutionary history of glucose-6-phosphatase encoding genes in vertebrate lineages: towards a better understanding of the functions of multiple duplicates. PMID:28464795
A-to-I RNA Editing in the Earliest-Diverging Eumetazoan Phyla. PMID:28453786
A new GTF2I-BRAF fusion mediating MAPK pathway activation in pilocytic astrocytoma. PMID:28448514
Draft genome of the lined seahorse, Hippocampus erectus. PMID:28444302
Mutational screening of SLC39A5, LEPREL1 and LRPAP1 in a cohort of 187 high myopia patients. PMID:28442722
Whole genome sequencing predicts novel human disease models in rhesus macaques. PMID:28438488
HirBin: high-resolution identification of differentially abundant functions in metagenomes. PMID:28431529
Large-scale collection of full-length cDNA and transcriptome analysis in Hevea brasiliensis. PMID:28431015
The draft genome of Ruellia speciosa (Beautiful Wild Petunia: Acanthaceae). PMID:28431014
Next generation mapping reveals novel large genomic rearrangements in prostate cancer. PMID:28423598
Typing and Characterization of Bacteria Using Bottom-up Tandem Mass Spectrometry Proteomics. PMID:28420677
Contrasting evolutionary genome dynamics between domesticated and wild yeasts. PMID:28416820
gb4gv: a genome browser for geminivirus. PMID:28413726
TRE5-A retrotransposition profiling reveals putative RNA polymerase III transcription complex binding sites on the Dictyostelium extrachromosomal rDNA element. PMID:28406973
LTR-Retrotransposons from Bdelloid Rotifers Capture Additional ORFs Shared between Highly Diverse Retroelement Types. PMID:28398238
A comprehensive hybridization model allows whole HERV transcriptome profiling using high density microarray. PMID:28390408
Copy number increases of transposable elements and protein-coding genes in an invasive fish of hybrid origin. PMID:28390096
HALC: High throughput algorithm for long read error correction. PMID:28381259
Kart: a divide-and-conquer algorithm for NGS read alignment. PMID:28379292
Comparative genomic identification and validation of β-defensin genes in the Ovis aries genome. PMID:28376793
Construction of a high-density genetic map and the X/Y sex-determining gene mapping in spinach based on large-scale markers developed by specific-locus amplified fragment sequencing (SLAF-seq). PMID:28376721
A genetic screen implicates a CWC16/Yju2/CCDC130 protein and SMU1 in alternative splicing in Arabidopsis thaliana. PMID:28373290
Draft genome of the sea cucumber Apostichopus japonicus and genetic polymorphism among color variants. PMID:28369350
Generation of mature T cells from human hematopoietic stem and progenitor cells in artificial thymic organoids. PMID:28369043
Genome-wide sequencing of longan (Dimocarpus longan Lour.) provides insights into molecular basis of its polyphenol-rich characteristics. PMID:28368449
In silico analysis of the sequence features responsible for alternatively spliced introns in the model green alga Chlamydomonas reinhardtii. PMID:28364390
MIPE: A metagenome-based community structure explorer and SSU primer evaluation tool. PMID:28350876
Large scale genomic analysis shows no evidence for pathogen adaptation between the blood and cerebrospinal fluid niches during bacterial meningitis. PMID:28348877
Redefining the differences in gene content between Yersinia pestis and Yersinia pseudotuberculosis using large-scale comparative genomics. PMID:28348813
Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes. PMID:28347275
Different expression patterns of sperm motility-related genes in testis of diploid and tetraploid cyprinid fish†. PMID:28340181
Transcriptomic Complexity of Aspergillus terreus Velvet Gene Family under the Influence of Butyrolactone I. PMID:28335447
Efficient CNV breakpoint analysis reveals unexpected structural complexity and correlation of dosage-sensitive genes with clinical severity in genomic disorders. PMID:28334874
The mouse genome displays highly dynamic populations of KRAB-zinc finger protein genes and related genetic units. PMID:28334004
Time-course expression QTL-atlas of the global transcriptional response of wheat to Fusarium graminearum. PMID:28332274
Targeted Enrichment for Pathogen Detection and Characterization in Three Felid Species. PMID:28330894
MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach. PMID:28327976
GENE-IS: Time-Efficient and Accurate Analysis of Viral Integration Events in Large-Scale Gene Therapy Data. PMID:28325279
Alterations in Gastric Microbiota After H. Pylori Eradication and in Different Histological Stages of Gastric Carcinogenesis. PMID:28322295
Genomic innovations linked to infection strategies across emerging pathogenic chytrid fungi. PMID:28322291
Computational Model Reveals Limited Correlation between Germinal Center B-Cell Subclone Abundancy and Affinity: Implications for Repertoire Sequencing. PMID:28321219
An Analysis of Adenovirus Genomes Using Whole Genome Software Tools. PMID:28293072
The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity. PMID:28284188
A Frameshift Mutation in KIT is Associated with White Spotting in the Arabian Camel. PMID:28282952
The birth of a human-specific neural gene by incomplete duplication and gene fusion. PMID:28279197
Aboriginal mitogenomes reveal 50,000 years of regionalism in Australia. PMID:28273067
Defining the diverse spectrum of inversions, complex structural variation, and chromothripsis in the morbid human genome. PMID:28260531
SAG-QC: quality control of single amplified genome information by subtracting non-target sequences based on sequence compositions. PMID:28259144
Chromatin states shape insertion profiles of the piggyBac, Tol2 and Sleeping Beauty transposons and murine leukemia virus. PMID:28252665
Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads. PMID:28250805
RNA-Sequencing data supports the existence of novel VEGFA splicing events but not of VEGFAxxxb isoforms. PMID:28246395
An atlas of human long non-coding RNAs with accurate 5' ends. PMID:28241135
Mutational landscape reflects the biological continuum of plasma cell dyscrasias. PMID:28234344
Overexpression of hsa-miR-939 follows by NGFR down-regulation and apoptosis reduction. PMID:28229962
PEMapper and PECaller provide a simplified approach to whole-genome sequencing. PMID:28223510
A user guide to the Brassica 60K Illumina Infinium™ SNP genotyping array. PMID:28220206
Pneumococcal prophages are diverse, but not without structure or history. PMID:28218261
Convergent Evolution of the Osmoregulation System in Decapod Shrimps. PMID:28204969
An annotated draft genome for Radix auricularia (Gastropoda, Mollusca). PMID:28204581
Transcriptome analysis around the onset of strawberry fruit ripening uncovers an important role of oxidative phosphorylation in ripening. PMID:28195221
Functional preservation and variation in the cone opsin genes of nocturnal tarsiers. PMID:28193820
ETS Proto-oncogene 1 Transcriptionally Up-regulates the Cholangiocyte Senescence-associated Protein Cyclin-dependent Kinase Inhibitor 2A. PMID:28184004
Small genomic insertions form enhancers that misregulate oncogenes. PMID:28181482
Evolutionary mechanism and biological functions of 8-mers containing CG dinucleotide in yeast. PMID:28181048
Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits. PMID:28179367
Comparative genomics of canine hemoglobin genes reveals primacy of beta subunit delta in adult carnivores. PMID:28178945
PALADIN: protein alignment for functional profiling whole metagenome shotgun data. PMID:28158639
The first complete chloroplast genome sequences of Ulmus species by de novo sequencing: Genome comparative and taxonomic position analysis. PMID:28158318
RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing. PMID:28149701
Survey of (Meta)genomic Approaches for Understanding Microbial Community Dynamics. PMID:28148977
Improved annotation with de novo transcriptome assembly in four social amoeba species. PMID:28143409
Integrated high-density consensus genetic map of Pyrus and anchoring of the 'Bartlett' v1.0 (Pyrus communis) genome. PMID:28130382
Global and regional dissemination and evolution of Burkholderia pseudomallei. PMID:28112723
High Level of Nonsynonymous Changes in Common Bean Suggests That Selection under Domestication Increased Functional Diversity at Target Traits. PMID:28111584
Photosynthesis in C3-C4 intermediate Moricandia species. PMID:28110276
Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments. PMID:28105025
Rfx2 Stabilizes Foxj1 Binding at Chromatin Loops to Enable Multiciliated Cell Gene Expression. PMID:28103240
Loss of AXIN1 drives acquired resistance to WNT pathway blockade in colorectal cancer cells carrying RSPO3 fusions. PMID:28100566
An improved genome assembly uncovers prolific tandem repeats in Atlantic cod. PMID:28100185
The genome sequence of Barbarea vulgaris facilitates the study of ecological biochemistry. PMID:28094805
Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus. PMID:28092920
Identification of some main Streptococcus iniae associated proteins: relationship. PMID:28091882
Identification of misexpressed genetic elements in hybrids between Drosophila-related species. PMID:28091568
Transcriptomic analysis of diplomonad parasites reveals a trans-spliced intron in a helicase gene in Giardia. PMID:28090405
A SNP-Enabled Assessment of Genetic Diversity, Evolutionary Relationships and the Identification of Candidate Genes in Chrysanthemum. PMID:28082602
Comparative Analysis of Vertebrate Diurnal/Circadian Transcriptomes. PMID:28076377
Accurate Breakpoint Mapping in Apparently Balanced Translocation Families with Discordant Phenotypes Using Whole Genome Mate-Pair Sequencing. PMID:28072833
A molecular genetic toolbox for Yarrowia lipolytica. PMID:28066508
Cloning and Characterization of TaTGW-7A Gene Associated with Grain Weight in Wheat via SLAF-seq-BSA. PMID:28066462
Transcriptome profiles reveal gene regulation of peanut (Arachis hypogaea L.) nodulation. PMID:28059169
MPD: multiplex primer design for next-generation targeted sequencing. PMID:28056760
Cytosine methylation at CpCpG sites triggers accumulation of non-CpG methylation in gene bodies. PMID:28053115
Evolution of transcript modification by N6-methyladenosine in primates. PMID:28052920
ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data. PMID:28049418
A second generation SNP and SSR integrated linkage map and QTL mapping for the Chinese mitten crab Eriocheir sinensis. PMID:28045132
A Point Mutation in a lincRNA Upstream of GDNF Is Associated to a Canine Insensitivity to Pain: A Spontaneous Model for Human Sensory Neuropathies. PMID:28033318
Immunodominance of Antibody Recognition of the HIV Envelope V2 Region in Ig-Humanized Mice. PMID:28011932
SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and sequence assembly. PMID:28011768
Bioinformatic tools for analysis of CLIP ribonucleoprotein data. PMID:28008714
Genomic Basis of Adaptive Evolution: The Survival of Amur Ide (Leuciscus waleckii) in an Extremely Alkaline Environment. PMID:28007977
A pipeline for local assembly of minisatellite alleles from single-molecule sequencing data. PMID:27998939
Complete plastid genome of Eriobotrya japonica (Thunb.) Lindl and comparative analysis in Rosaceae. PMID:27995013
Identification of a novel 15.5 kb SHOX deletion associated with marked intrafamilial phenotypic variability and analysis of its molecular origin. PMID:27994182
A comprehensive benchmark of RNA-RNA interaction prediction tools for all domains of life. PMID:27993777
Comparative metagenomics reveals taxonomically idiosyncratic yet functionally congruent communities in periodontitis. PMID:27991530
Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics. PMID:27980708
The intron-enriched HERV-K(HML-10) family suppresses apoptosis, an indicator of malignant transformation. PMID:27980690
Hotair Is Dispensible for Mouse Development. PMID:27977683
DNA Methylation Identifies Loci Distinguishing Hereditary Nonpolyposis Colorectal Cancer Without Germ-Line MLH1/MSH2 Mutation from Sporadic Colorectal Cancer. PMID:27977020
The seahorse genome and the evolution of its specialized morphology. PMID:27974754
RPAN: rice pan-genome browser for ∼3000 rice genomes. PMID:27940610
LTR-mediated retroposition as a mechanism of RNA-based duplication in metazoans. PMID:27934698
Acquired RAS or EGFR mutations and duration of response to EGFR blockade in colorectal cancer. PMID:27929064
A chromosome-level genome assembly of the Asian arowana, Scleropages formosus. PMID:27922628
A human microprotein that interacts with the mRNA decapping complex. PMID:27918561
Whole exome association of rare deletions in multiplex oral cleft families. PMID:27910131
The UCSC Genome Browser database: 2017 update. PMID:27899642
MEGARes: an antimicrobial resistance database for high throughput sequencing. PMID:27899569
RNA-Sequencing for profiling goat milk transcriptome in colostrum and mature milk. PMID:27884183
Metagenomics of Two Severe Foodborne Outbreaks Provides Diagnostic Signatures and Signs of Coinfection Not Attainable by Traditional Methods. PMID:27881416
Draft genome of the living fossil Ginkgo biloba. PMID:27871309
Whole-Genome Sequencing of Cytogenetically Balanced Chromosome Translocations Identifies Potentially Pathological Gene Disruptions and Highlights the Importance of Microhomology in the Mechanism of Formation. PMID:27862604
A novel codon-based de Bruijn graph algorithm for gene construction from unassembled transcriptomes. PMID:27855707
AnnoLnc: a web server for systematically annotating novel human lncRNAs. PMID:27852242
A New Chicken Genome Assembly Provides Insight into Avian Genome Structure. PMID:27852011
Identification of new TRIP12 variants and detailed clinical evaluation of individuals with non-syndromic intellectual disability with or without autism. PMID:27848077
Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme. PMID:27843499
Genetic architecture of the maize kernel row number revealed by combining QTL mapping using a high-density genetic map and bulked segregant RNA sequencing. PMID:27842488
Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma. PMID:27829365
LSCplus: a fast solution for improving long read accuracy by short read alignment. PMID:27829364
Circular RNAs and their associations with breast cancer subtypes. PMID:27829232
Is the Evolution of Salmonella enterica subsp. enterica Linked to Restriction-Modification Systems? PMID:27822532
Postnatal regulation of MAMDC4 in the porcine intestinal epithelium is influenced by bacterial colonization. PMID:27821716
The endotracheal tube microbiome associated with Pseudomonas aeruginosa or Staphylococcus epidermidis. PMID:27812037
Systems-wide analysis of manganese deficiency-induced changes in gene activity of Arabidopsis roots. PMID:27804982
Computational workflow for the fine-grained analysis of metagenomic samples. PMID:27801291
Identifying Cancer Driver Genes Using Replication-Incompetent Retroviral Vectors. PMID:27792127
TRPM8 genetic variations associated with COPD risk in the Chinese Han population. PMID:27789940
EumicrobeDBLite: a lightweight genomic resource and analytic platform for draft oomycete genomes. PMID:27785876
Transcriptomic resources and marker validation for diploid and polyploid Veronica (Plantaginaceae) from New Zealand and Europe. PMID:27785388
Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries. PMID:27756200
Endogenous Multiple Exon Skipping and Back-Splicing at the DMD Mutation Hotspot. PMID:27754374
Morphological and Transcriptomic Analysis of a Beetle Chemosensory System Reveals a Gnathal Olfactory Center. PMID:27751175
Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance. PMID:27734962
Genomics Study of Mycobacterium tuberculosis Strains from Different Ethnic Populations in Taiwan. PMID:27721649
Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling. PMID:27717381
A De Novo Genome Sequence Assembly of the Arabidopsis thaliana Accession Niederzenz-1 Displays Presence/Absence Variation and Strong Synteny. PMID:27711162
High expression of new genes in trochophore enlightening the ontogeny and evolution of trochozoans. PMID:27698463
Targeted next-generation sequencing for TP53, RAS, BRAF, ALK and NF1 mutations in anaplastic thyroid cancer. PMID:27696251
Feralisation targets different genomic loci to domestication in the chicken. PMID:27686863
Comprehensive analysis of microRNA signature of mouse pancreatic acini: overexpression of miR-21-3p in acute pancreatitis. PMID:27686613
A Bacillus anthracis Genome Sequence from the Sverdlovsk 1979 Autopsy Specimens. PMID:27677796
Sex-Biased Transcriptome of Schistosoma mansoni: Host-Parasite Interaction, Genetic Determinants and Epigenetic Regulators Are Associated with Sexual Differentiation. PMID:27677173
Butyricimonas phoceensis sp. nov., a new anaerobic species isolated from the human gut microbiota of a French morbidly obese patient. PMID:27668083
C3 cotyledons are followed by C4 leaves: intra-individual transcriptome analysis of Salsola soda (Chenopodiaceae). PMID:27660482
Differing Alterations of Two Esca Associated Fungi, Phaeoacremonium aleophilum and Phaeomoniella chlamydospora on Transcriptomic Level, to Co-Cultured Vitis vinifera L. calli. PMID:27658052
Digital Gene Expression Profiling to Explore Differentially Expressed Genes Associated with Terpenoid Biosynthesis during Fruit Development in Litsea cubeba. PMID:27657027
The Effects of Signal Erosion and Core Genome Reduction on the Identification of Diagnostic Markers. PMID:27651357
Comparative genomic analysis between newly sequenced Brucella suis Vaccine Strain S2 and the Virulent Brucella suis Strain 1330. PMID:27645563
Exploring the transcriptome of Staphylococcus aureus in its natural niche. PMID:27641137
Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes. PMID:27633831
A novel TP53-KPNA3 translocation defines a de novo treatment-resistant clone in osteosarcoma. PMID:27626065
PGD: a pangolin genome hub for the research community. PMID:27616775
Contribution of type W human endogenous retroviruses to the human genome: characterization of HERV-W proviral insertions and processed pseudogenes. PMID:27613107
The genome of the largest bony fish, ocean sunfish (Mola mola), provides insights into its fast growth rate. PMID:27609345
Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler. PMID:27595578
The cancer-associated CTCFL/BORIS protein targets multiple classes of genomic repeats, with a distinct binding and functional preference for humanoid-specific SVA transposable elements. PMID:27588042
Prevalence and Abundance of Florfenicol and Linezolid Resistance Genes in Soils Adjacent to Swine Feedlots. PMID:27573068
Metagenomics uncovers gaps in amplicon-based detection of microbial diversity. PMID:27572438
Draft genome sequence of Cicer reticulatum L., the wild progenitor of chickpea provides a resource for agronomic trait improvement. PMID:27567261
Genome-wide characterization of microsatellites in Triticeae species: abundance, distribution and evolution. PMID:27561724
Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216(T). PMID:27559429
High-quality genome assembly of channel catfish, Ictalurus punctatus. PMID:27549802
Intron gain by tandem genomic duplication: a novel case in a potato gene encoding RNA-dependent RNA polymerase. PMID:27547574
Cardiometabolic risk loci share downstream cis- and trans-gene regulation across tissues and diseases. PMID:27540175
RES-Scanner: a software package for genome-wide identification of RNA-editing sites. PMID:27538485
Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63. PMID:27535938
Uncovering Earth's virome. PMID:27533034
Evaluation of Normalization Methods for RNA-Seq Gene Expression Estimation. PMID:27532058
Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq). PMID:27531712
De novo transcriptome assembly and analysis of differentially expressed genes of two barley genotypes reveal root-zone-specific responses to salt exposure. PMID:27527578
Satellite DNA content illuminates the ancestry of a supernumerary (B) chromosome. PMID:27522227
Proline Coordination with Fatty Acid Synthesis and Redox Metabolism of Chloroplast and Mitochondria. PMID:27512016
Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians. PMID:27502555
Association of variations in HLA class II and other loci with susceptibility to EGFR-mutated lung adenocarcinoma. PMID:27501781
The Genomic Scrapheap Challenge; Extracting Relevant Data from Unmapped Whole Genome Sequencing Reads, Including Strain Specific Genomic Segments, in Rats. PMID:27501045
Distinct interacting core taxa in co-occurrence networks enable discrimination of polymicrobial oral diseases with similar symptoms. PMID:27499042
Pinpointing the vesper bat transposon revolution using the Miniopterus natalensis genome. PMID:27489570
Norovirus Whole-Genome Sequencing by SureSelect Target Enrichment: a Robust and Sensitive Method. PMID:27487952
Meiotic pairing and gene expression disturbance in germ cells from an infertile boar with a balanced reciprocal autosome-autosome translocation. PMID:27484982
Differences in molecular evolutionary rates among microRNAs in the human and chimpanzee genomes. PMID:27474039
Identification of new branch points and unconventional introns in Saccharomyces cerevisiae. PMID:27473169
Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations. PMID:27473065
Characterization of the T-cell receptor beta chain repertoire in tumor-infiltrating lymphocytes. PMID:27465739
TALEN-Mediated Mutagenesis and Genome Editing. PMID:27464798
SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence. PMID:27458203
On the origin and evolutionary consequences of gene body DNA methylation. PMID:27457936
Transcriptome Profiling of Huanglongbing (HLB) Tolerant and Susceptible Citrus Plants Reveals the Role of Basal Resistance in HLB Tolerance. PMID:27446161
The mitochondrial genome map of Nelumbo nucifera reveals ancient evolutionary features. PMID:27444405
Variant discovery and breakpoint region prediction for studying the human 22q11.2 deletion using BAC clone and whole genome sequencing analysis. PMID:27436579
Reciprocal genomic evolution in the ant-fungus agricultural symbiosis. PMID:27436133
Deciphering the Wisent Demographic and Adaptive Histories from Individual Whole-Genome Sequences. PMID:27436010
RNA editing generates cellular subsets with diverse sequence within populations. PMID:27418407
Comorbid Analysis of Genes Associated with Autism Spectrum Disorders Reveals Differential Evolutionary Constraints. PMID:27414027
Microbiota Dysbiosis Controls the Neuroinflammatory Response after Stroke. PMID:27413153
Analyses of Compact Trichinella Kinomes Reveal a MOS-Like Protein Kinase with a Unique N-Terminal Domain. PMID:27412987
Transcriptome analysis of woodland strawberry (Fragaria vesca) response to the infection by Strawberry vein banding virus (SVBV). PMID:27411713
CrispRVariants charts the mutation spectrum of genome engineering experiments. PMID:27404876
Identification and Validation of SNP Markers Linked to Dwarf Traits Using SLAF-Seq Technology in Lagerstroemia. PMID:27404662
The next generation of target capture technologies - large DNA fragment enrichment and sequencing determines regional genomic variation of high complexity. PMID:27393338
Identification of Multiple Forms of RNA Transcripts Associated with Human-Specific Retrotransposed Gene Copies. PMID:27389689
Comparative Analysis of Human B Cell Epitopes Based on BCG Genomes. PMID:27382565
Structure and evolution of the gorilla and orangutan growth hormone loci. PMID:27376725
Natural Allelic Variations in Highly Polyploidy Saccharum Complex. PMID:27375658
Freshwater Metaviromics and Bacteriophages: A Current Assessment of the State of the Art in Relation to Bioinformatic Challenges. PMID:27375355
A high-density SNP genotyping array for Brassica napus and its ancestral diploid species based on optimised selection of single-locus markers in the allotetraploid genome. PMID:27364915
Tessaracoccus massiliensis sp. nov., a new bacterial species isolated from the human gut. PMID:27358740
The multicellularity genes of dictyostelid social amoebas. PMID:27357338
Development of Molecular Markers for Determining Continental Origin of Wood from White Oaks (Quercus L. sect. Quercus). PMID:27352242
Origins of the 2009 H1N1 influenza pandemic in swine in Mexico. PMID:27350259
Genome-Wide Survey of Gut Fungi (Harpellales) Reveals the First Horizontally Transferred Ubiquitin Gene from a Mosquito Host. PMID:27343289
CAP protein superfamily members in Toxocara canis. PMID:27342979
Retrozymes are a unique family of non-autonomous retrotransposons with hammerhead ribozymes that propagate in plants through circular RNAs. PMID:27339130
Overexpression of CHOP in Myelinating Cells Does Not Confer a Significant Phenotype under Normal or Metabolic Stress Conditions. PMID:27335410
PEP_scaffolder: using (homologous) proteins to scaffold genomes. PMID:27334475
Identification of polymorphic and off-target probe binding sites on the Illumina Infinium MethylationEPIC BeadChip. PMID:27330998
Microsatellite markers used for genome-wide association mapping of partial resistance to Sclerotinia sclerotiorum in a world collection of Brassica napus. PMID:27330402
TBR1 regulates autism risk genes in the developing neocortex. PMID:27325115
Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families. PMID:27322404
Genome puzzle master (GPM): an integrated pipeline for building and editing pseudomolecules from fragmented sequences. PMID:27318200
Identification of Coilin Mutants in a Screen for Enhanced Expression of an Alternatively Spliced GFP Reporter Gene in Arabidopsis thaliana. PMID:27317682
BLAT2DOLite: An Online System for Identifying Significant Relationships between Genetic Sequences and Diseases. PMID:27315278
Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis. PMID:27309962
RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes. PMID:27307617
Evaluation of microRNA alignment techniques. PMID:27284164
Para-allopatry in hybridizing fire-bellied toads (Bombina bombina and B. variegata): Inference from transcriptome-wide coalescence analyses. PMID:27282112
Aberrant PD-L1 expression through 3'-UTR disruption in multiple cancers. PMID:27281199
The Simple Chordate Ciona intestinalis Has a Reduced Complement of Genes Associated with Fanconi Anemia. PMID:27279728
A Chromosome 7 Pericentric Inversion Defined at Single-Nucleotide Resolution Using Diagnostic Whole Genome Sequencing in a Patient with Hand-Foot-Genital Syndrome. PMID:27272187
Metagenomic Reconstruction of Key Anaerobic Digestion Pathways in Municipal Sludge and Industrial Wastewater Biogas-Producing Systems. PMID:27252693
Global assessment of imprinted gene expression in the bovine conceptus by next generation sequencing. PMID:27245094
Tricking Arthrinium malaysianum into Producing Industrially Important Enzymes Under 2-Deoxy D-Glucose Treatment. PMID:27242677
gEVE: a genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomes. PMID:27242033
Draft Genome Sequence of Mycobacterium interjectum Strain ATCC 51457T. PMID:27231376
Draft Genome Sequence of Mycobacterium houstonense Strain ATCC 49403T. PMID:27231371
Sixteen kiwi (Apteryx spp) transcriptomes provide a wealth of genetic markers and insight into sex chromosome evolution in birds. PMID:27230888
JUMPg: An Integrative Proteogenomics Pipeline Identifying Unannotated Proteins in Human Brain and Cancer Cells. PMID:27225868
Expression Patterns and Functional Novelty of Ribonuclease 1 in Herbivorous Megalobrama amblycephala. PMID:27213364
Identification of human RNA editing sites: A historical perspective. PMID:27208508
Characterisation of Candida within the Mycobiome/Microbiome of the Lower Respiratory Tract of ICU Patients. PMID:27206014
Zinc Finger Domain of the PRDM9 Gene on Chromosome 1 Exhibits High Diversity in Ruminants but Its Paralog PRDM7 Contains Multiple Disruptive Mutations. PMID:27203728
Pleiotropic effect of thyroid hormones on gene expression in fish as exemplified from the blue bream Ballerus ballerus (Cyprinidae): Results of transcriptomic analysis. PMID:27193715
Viruses are a dominant driver of protein adaptation in mammals. PMID:27187613
An automated approach for global identification of sRNA-encoding regions in RNA-Seq data from Mycobacterium tuberculosis. PMID:27174874
A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination. PMID:27172201
Development of new PCR multiplex system by the simultaneous detection of 10 miniSTRs, SE33, Penta E, Penta D, and four Y-STRs. PMID:27166705
Next-generation sequencing-based detection of germline L1-mediated transductions. PMID:27161561
A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution. PMID:27158781
Genomic analysis of mouse VL30 retrotransposons. PMID:27158269
DNA methylation changes facilitated evolution of genes derived from Mutator-like transposable elements. PMID:27154274
Efficient privacy-preserving string search and an application in genomics. PMID:27153731
Informed kmer selection for de novo transcriptome assembly. PMID:27153653
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. PMID:27153593
Targeted Capture Sequencing in Whitebark Pine Reveals Range-Wide Demographic and Adaptive Patterns Despite Challenges of a Large, Repetitive Genome. PMID:27148310
Impact of Hypocaloric Hyperproteic Diet on Gut Microbiota in Overweight or Obese Patients with Nonalcoholic Fatty Liver Disease: A Pilot Study. PMID:27142672
Mitochondrial Genome and Nuclear Markers Provide New Insight into the Evolutionary History of Macaques. PMID:27135608
Redundans: an assembly pipeline for highly heterozygous genomes. PMID:27131372
Mechanical cell competition kills cells via induction of lethal p53 levels. PMID:27109213
Using Synthetic Mouse Spike-In Transcripts to Evaluate RNA-Seq Analysis Tools. PMID:27100792
Application of whole genome shotgun sequencing for detection and characterization of genetically modified organisms and derived products. PMID:27100228
LINE-1-like retrotransposons contribute to RNA-based gene duplication in dicots. PMID:27098918
Bitpacking techniques for indexing genomes: I. Hash tables. PMID:27095998
The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts. PMID:27089831
Prediction of Toxin Genes from Chinese Yellow Catfish Based on Transcriptomic and Proteomic Sequencing. PMID:27089325
UNDR ROVER - a fast and accurate variant caller for targeted DNA sequencing. PMID:27083325
CDROM: Classification of Duplicate gene RetentiOn Mechanisms. PMID:27080514
Stress-induced gene expression and behavior are controlled by DNA methylation and methyl donor availability in the dentate gyrus. PMID:27078100
High-Density Genetic Mapping Identifies New Major Loci for Tolerance to Low-Phosphorus Stress in Soybean. PMID:27065041
Genomic Aberrations in Crizotinib Resistant Lung Adenocarcinoma Samples Identified by Transcriptome Sequencing. PMID:27045755
Toward Understanding the Genetic Basis of Yak Ovary Reproduction: A Characterization and Comparative Analyses of Estrus Ovary Transcriptiome in Yak and Cattle. PMID:27044040
Reactive Oxygen Species Play a Role in the Infection of the Necrotrophic Fungi, Rhizoctonia solani in Wheat. PMID:27031952
Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants. PMID:27029936
Multivariate models from RNA-Seq SNVs yield candidate molecular targets for biomarker discovery: SNV-DA. PMID:27029813
Placenta-Enriched LincRNAs MIR503HG and LINC00629 Decrease Migration and Invasion Potential of JEG-3 Cell Line. PMID:27023770
Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites. PMID:27023428
Using a Candidate Gene-Based Genetic Linkage Map to Identify QTL for Winter Survival in Perennial Ryegrass. PMID:27010567
The real cost of sequencing: scaling computation to keep pace with data generation. PMID:27009100
Learning to cope with stress modulates anterior cingulate cortex stargazin expression in monkeys and mice. PMID:27003116
Mapping of a Novel Race Specific Resistance Gene to Phytophthora Root Rot of Pepper (Capsicum annuum) Using Bulked Segregant Analysis Combined with Specific Length Amplified Fragment Sequencing Strategy. PMID:26992080
RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to metagenomes. PMID:26984526
Unlocking the genetic diversity of Creole wheats. PMID:26976656
BBBomics-Human Blood Brain Barrier Transcriptomics Hub. PMID:26973449
Noncontiguous finished genome sequence and description of Paenibacillus ihumii sp. nov. strain AT5. PMID:26958346
Population Structure and Antimicrobial Resistance Profiles of Streptococcus suis Serotype 2 Sequence Type 25 Strains. PMID:26954687
Comparative Developmental Transcriptomics Reveals Rewiring of a Highly Conserved Gene Regulatory Network during a Major Life History Switch in the Sea Urchin Genus Heliocidaris. PMID:26943850
Identification of mRNA isoform switching in breast cancer. PMID:26939613
Comparative genomic analyses reveal broad diversity in botulinum-toxin-producing Clostridia. PMID:26939550
A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y. PMID:26934921
Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict. PMID:26934590
Integrated metabolomics and metagenomics analysis of plasma and urine identified microbial metabolites associated with coronary heart disease. PMID:26932197
The Genetic Linkage Map of the Medicinal Mushroom Agaricus subrufescens Reveals Highly Conserved Macrosynteny with the Congeneric Species Agaricus bisporus. PMID:26921302
Host Mitochondrial Association Evolved in the Human Parasite Toxoplasma gondii via Neofunctionalization of a Gene Duplicate. PMID:26920761
Transcriptome Analysis in Domesticated Species: Challenges and Strategies. PMID:26917953
HsfA2 Controls the Activity of Developmentally and Stress-Regulated Heat Stress Protection Mechanisms in Tomato Male Reproductive Tissues. PMID:26917685
Discovery of a new repeat family in the Callithrix jacchus genome. PMID:26916108
γ-Crystallins of the chicken lens: remnants of an ancient vertebrate gene family in birds. PMID:26913478
Genetic features of Mycobacterium tuberculosis modern Beijing sublineage. PMID:26905026
Comparison of Acceleration Techniques for Selected Low-Level Bioinformatics Operations. PMID:26904094
The genome of the miiuy croaker reveals well-developed innate immune and sensory systems. PMID:26902509
Resolving rates of mutation in the brain using single-neuron genomics. PMID:26901440
Natural variation in non-coding regions underlying phenotypic diversity in budding yeast. PMID:26898953
Ensembl comparative genomics resources. PMID:26896847
BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data. PMID:26894997
Genomic and transcriptomic comparison of nucleotide variations for insights into bruchid resistance of mungbean (Vigna radiata [L.] R. Wilczek). PMID:26887961
Genetic mapping and molecular marker development for Pi65(t), a novel broad-spectrum resistance gene to rice blast using next-generation sequencing. PMID:26883042
TOPORS, a Dual E3 Ubiquitin and Sumo1 Ligase, Interacts with 26 S Protease Regulatory Subunit 4, Encoded by the PSMC1 Gene. PMID:26872363
Expansion and stress responses of AP2/EREBP superfamily in Brachypodium distachyon. PMID:26869021
Identification of Targets of CUG-BP, Elav-Like Family Member 1 (CELF1) Regulation in Embryonic Heart Muscle. PMID:26866591
Sequence Diversity, Intersubgroup Relationships, and Origins of the Mouse Leukemia Gammaretroviruses of Laboratory and Wild Mice. PMID:26865715
Comparative assessment of methods for the fusion transcripts detection from RNA-Seq data. PMID:26862001
Bacterioplankton Dynamics within a Large Anthropogenically Impacted Urban Estuary. PMID:26858690
New insights into the Plasmodium vivax transcriptome using RNA-Seq. PMID:26858037
Genome ARTIST: a robust, high-accuracy aligner tool for mapping transposon insertions and self-insertions. PMID:26855675
Genomes of Strongylocentrotus franciscanus and Lytechinus variegatus: are there any genomic explanations for the two order of magnitude difference in the lifespan of sea urchins? PMID:26851889
Homozygosity mapping identified a novel protein truncating mutation (p.Ser100Leufs*24) of the BBS9 gene in a consanguineous Pakistani family with Bardet Biedl syndrome. PMID:26846096
Reconstruction of the insulin-like signalling pathway of Haemonchus contortus. PMID:26842675
Mapping the Flavor Contributing Traits on "Fengwei Melon" (Cucumis melo L.) Chromosomes Using Parent Resequencing and Super Bulked-Segregant Analysis. PMID:26840947
Long Read Alignment with Parallel MapReduce Cloud Platform. PMID:26839887
A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae). PMID:26828929
Rapid Identification of Candidate Genes for Seed Weight Using the SLAF-Seq Method in Brassica napus. PMID:26824525
Genome Sequence and Analysis of Peptoclostridium difficile Strain ZJCDC-S82. PMID:26823648
Discovering All Transcriptome Single-Nucleotide Polymorphisms and Scanning for Selection Signatures in Ducks (Anas platyrhynchos). PMID:26819540
Genome-Wide Analysis of Transposon and Retroviral Insertions Reveals Preferential Integrations in Regions of DNA Flexibility. PMID:26818075
Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs. PMID:26814032
Statistical evaluation of methods for identification of differentially abundant genes in comparative metagenomics. PMID:26810311
Sp1 and Sp3 Are the Transcription Activators of Human ek1 Promoter in TSA-Treated Human Colon Carcinoma Cells. PMID:26807725
The Mouse Solitary Odorant Receptor Gene Promoters as Models for the Study of Odorant Receptor Gene Choice. PMID:26794459
H-NS Facilitates Sequence Diversification of Horizontally Transferred DNAs during Their Integration in Host Chromosomes. PMID:26789284
Landscape and evolutionary dynamics of terminal repeat retrotransposons in miniature in plant genomes. PMID:26781660
The Phenotypic and Genetic Underpinnings of Flower Size in Polemoniaceae. PMID:26779209
Expression of a Novel D4 Dopamine Receptor in the Lamprey Brain. Evolutionary Considerations about Dopamine Receptors. PMID:26778974
An evaluation of the accuracy and speed of metagenome analysis tools. PMID:26778510
PTESFinder: a computational method to identify post-transcriptional exon shuffling (PTES) events. PMID:26758031
Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality. PMID:26757703
Microvirga massiliensis sp. nov., the human commensal with the largest genome. PMID:26749561
Improving microRNA target prediction by modeling with unambiguously identified microRNA-target pairs from CLIP-ligation studies. PMID:26743510
Genetical Genomics of Behavior: A Novel Chicken Genomic Model for Anxiety Behavior. PMID:26733665
Effects of Gene Duplication, Positive Selection, and Shifts in Gene Expression on the Evolution of the Venom Gland Transcriptome in Widow Spiders. PMID:26733576
Enhanced diagnostic yield in Meckel-Gruber and Joubert syndrome through exome sequencing supplemented with split-read mapping. PMID:26729329
Schistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seq. PMID:26719891
Transposable element detection from whole genome sequence data. PMID:26719777
Application of a Novel "Pan-Genome"-Based Strategy for Assigning RNAseq Transcript Reads to Staphylococcus aureus Strains. PMID:26717500
TauCstF-64 Mediates Correct mRNA Polyadenylation and Splicing of Activator and Repressor Isoforms of the Cyclic AMP-Responsive Element Modulator (CREM) in Mouse Testis. PMID:26700942
Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes. PMID:26699716
Mutational Landscapes of Sequential Prostate Metastases and Matched Patient Derived Xenografts during Enzalutamide Therapy. PMID:26695660
Investigation of a Quadruplex-Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp. PMID:26695179
Engineering an allosteric transcription factor to respond to new ligands. PMID:26689263
Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis. PMID:26668163
Timing and Scope of Genomic Expansion within Annelida: Evidence from Homeoboxes in the Genome of the Earthworm Eisenia fetida. PMID:26659921
No association between HPV positive breast cancer and expression of human papilloma viral transcripts. PMID:26658849
Whole Genome Sequencing Defines the Genetic Heterogeneity of Familial Pancreatic Cancer. PMID:26658419
Improvement of genome assembly completeness and identification of novel full-length protein-coding genes by RNA-seq in the giant panda genome. PMID:26658305
The MG-RAST metagenomics database and portal in 2015. PMID:26656948
Kiwifruit Information Resource (KIR): a comparative platform for kiwifruit genomics. PMID:26656885
De Novo Transcriptome Sequencing of the Orange-Fleshed Sweet Potato and Analysis of Differentially Expressed Genes Related to Carotenoid Biosynthesis. PMID:26649293
High-density genetic map construction and gene mapping of pericarp color in wax gourd using specific-locus amplified fragment (SLAF) sequencing. PMID:26647294
Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation. PMID:26645680
De novo assembly of the dual transcriptomes of a polymorphic raptor species and its malarial parasite. PMID:26645667
A human 3'UTR clone collection to study post-transcriptional gene regulation. PMID:26645212
The Haemonchus contortus kinome--a resource for fundamental molecular investigations and drug discovery. PMID:26644012
ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly. PMID:26643039
Transcript Quantification by RNA-Seq Reveals Differentially Expressed Genes in the Red and Yellow Fruits of Fragaria vesca. PMID:26636322
Integrated 'Omics', Targeted Metabolite and Single-cell Analyses of Arctic Snow Algae Functionality and Adaptability. PMID:26635781
Defining the Schistosoma haematobium kinome enables the prediction of essential kinases as anti-schistosome drug targets. PMID:26635209
Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection. PMID:26627243
Fusion transcript loci share many genomic features with non-fusion loci. PMID:26626734
Using Next Generation Sequencing for Multiplexed Trait-Linked Markers in Wheat. PMID:26625271
Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement. PMID:26617401
The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling. PMID:26615215
Genome-wide association study of 8 carcass traits in Jinghai Yellow chickens using specific-locus amplified fragment sequencing technology. PMID:26614681
The first draft genome of the aquatic model plant Lemna minor opens the route for future stress physiology research and biotechnological applications. PMID:26609323
Advanced Applications of RNA Sequencing and Challenges. PMID:26609224
Identification of Genetic Variation between Obligate Plant Pathogens Pseudoperonospora cubensis and P. humuli Using RNA Sequencing and Genotyping-By-Sequencing. PMID:26599440
The UCSC Genome Browser database: 2016 update. PMID:26590259
Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets. PMID:26587879
Stable recombination hotspots in birds. PMID:26586757
Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis. PMID:26586576
The role of biofilms as environmental reservoirs of antibiotic resistance. PMID:26583011
Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data. PMID:26582927
HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes. PMID:26578596
Unique transposon landscapes are pervasive across Drosophila melanogaster genomes. PMID:26578579
Novel mutations in the genes TGM1 and ALOXE3 underlying autosomal recessive congenital ichthyosis. PMID:26578203
misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads. PMID:26573684
Meta-Analysis of DNA Tumor-Viral Integration Site Selection Indicates a Role for Repeats, Gene Expression and Epigenetics. PMID:26569308
Dp412e: a novel human embryonic dystrophin isoform induced by BMP4 in early differentiated cells. PMID:26568816
The X Chromosome of Hemipteran Insects: Conservation, Dosage Compensation and Sex-Biased Expression. PMID:26556591
Legume information system (LegumeInfo.org): a key component of a set of federated data resources for the legume family. PMID:26546515
Draft Genome Sequence of Mycobacterium neworleansense Strain ATCC 49404T. PMID:26543131
Spatio-temporal regulation of circular RNA expression during porcine embryonic brain development. PMID:26541409
Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin. PMID:26539826
Reversible Burst of Transcriptional Changes during Induction of Crassulacean Acid Metabolism in Talinum triangulare. PMID:26530316
Differential expression analysis of human endogenous retroviruses based on ENCODE RNA-seq data. PMID:26530187
Exocarp Properties and Transcriptomic Analysis of Cucumber (Cucumis sativus) Fruit Expressing Age-Related Resistance to Phytophthora capsici. PMID:26528543
Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae. PMID:26528397
Functionally conserved enhancers with divergent sequences in distant vertebrates. PMID:26519295
Lentiviral vector-mediated insertional mutagenesis screen identifies genes that influence androgen independent prostate cancer progression and predict clinical outcome. PMID:26512949
The essential gene set of a photosynthetic organism. PMID:26508635
A novel gammaretroviral shuttle vector insertional mutagenesis screen identifies SHARPIN as a breast cancer metastasis gene and prognostic biomarker. PMID:26506596
Fixing Formalin: A Method to Recover Genomic-Scale DNA Sequence Data from Formalin-Fixed Museum Specimens Using High-Throughput Sequencing. PMID:26505622
Genome-wide evolutionary and functional analysis of the Equine Repetitive Element 1: an insertion in the myostatin promoter affects gene expression. PMID:26503543
Discovery and characterization of Alu repeat sequences via precise local read assembly. PMID:26503250
mBLAST: Keeping up with the sequencing explosion for (meta)genome analysis. PMID:26500804
Rapid Short-Read Sequencing and Aneuploidy Detection Using MinION Nanopore Technology. PMID:26500254
A catalogue of novel bovine long noncoding RNA across 18 tissues. PMID:26496443
Hypomorphic mutations in TRNT1 cause retinitis pigmentosa with erythrocytic microcytosis. PMID:26494905
Characterization and fine mapping of a novel barley Stage Green-Revertible Albino Gene (HvSGRA) by Bulked Segregant Analysis based on SSR assay and Specific Length Amplified Fragment Sequencing. PMID:26494145
Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes. PMID:26475107
An Exon-Capture System for the Entire Class Ophiuroidea. PMID:26474846
Genome and transcriptome delineation of two major oncogenic pathways governing invasive ductal breast cancer development. PMID:26474389
Novel RNA variants in colorectal cancers. PMID:26474385
Small RNA Sequencing Uncovers New miRNAs and moRNAs Differentially Expressed in Normal and Primary Myelofibrosis CD34+ Cells. PMID:26468945
Phylogenetic and genomic diversity in isolates from the globally distributed Acinetobacter baumannii ST25 lineage. PMID:26462752
Jitterbug: somatic and germline transposon insertion detection at single-nucleotide resolution. PMID:26459856
SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data. PMID:26454280
MEPD: medaka expression pattern database, genes and more. PMID:26450962
NCLscan: accurate identification of non-co-linear transcripts (fusion, trans-splicing and circular RNA) with a good balance between sensitivity and precision. PMID:26442529
Data in support of genome-wide identification of lineage-specific genes within Caenorhabditis elegans. PMID:26442285
Assembly and characterization of novel Alu inserts detected from next-generation sequencing data. PMID:26442170
Spatial and temporal dynamics of virus occurrence in two freshwater lakes captured through metagenomic analysis. PMID:26441894
Whole Blood Gene Expression Profiles of Patients with a Past Aneurysmal Subarachnoid Hemorrhage. PMID:26439625
Entropy-scaling search of massive biological data. PMID:26436140
Generation of a de novo transcriptome from equine lamellar tissue. PMID:26432030
Ovarian Transcriptome Analysis of Portunus trituberculatus Provides Insights into Genes Expressed during Phase III and IV Development. PMID:26431399
Survey of Programs Used to Detect Alternative Splicing Isoforms from Deep Sequencing Data In Silico. PMID:26421304
A novel locus of resistance to severe malaria in a region of ancient balancing selection. PMID:26416757
A catalog of the mouse gut metagenome. PMID:26414350
Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks. PMID:26392177
Construction of a dense genetic linkage map and mapping quantitative trait loci for economic traits of a doubled haploid population of Pyropia haitanensis (Bangiales, Rhodophyta). PMID:26391981
Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River. PMID:26388969
A comprehensive epigenome map of Plasmodium falciparum reveals unique mechanisms of transcriptional regulation and identifies H3K36me2 as a global mark of gene suppression. PMID:26388940
RNA-Seq analysis identifies key genes associated with haustorial development in the root hemiparasite Santalum album. PMID:26388878
FARE-CAFE: a database of functional and regulatory elements of cancer-associated fusion events. PMID:26384373
A novel retroviral mutagenesis screen identifies prognostic genes in RUNX1 mediated myeloid leukemogenesis. PMID:26384344
Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data. PMID:26382944
Identification of Ramie Genes in Response to Pratylenchus coffeae Infection Challenge by Digital Gene Expression Analysis. PMID:26378527
The genome of the vervet (Chlorocebus aethiops sabaeus). PMID:26377836
Gene activity in primary T cells infected with HIV89.6: intron retention and induction of genomic repeats. PMID:26377088
Complex Population Structure and Virulence Differences among Serotype 2 Streptococcus suis Strains Belonging to Sequence Type 28. PMID:26375680
Genetic mapping uncovers cis-regulatory landscape of RNA editing. PMID:26373807
A draft genome sequence of an invasive mosquito: an Italian Aedes albopictus. PMID:26369436
Living without DAT: Loss and compensation of the dopamine transporter gene in sauropsids (birds and reptiles). PMID:26364979
Accelerated rates of protein evolution in barley grain and pistil biased genes might be legacy of domestication. PMID:26362289
A new amino acid substitution (Ala-205-Phe) in acetolactate synthase (ALS) confers broad spectrum resistance to ALS-inhibiting herbicides. PMID:26353912
Discovering New Biology through Sequencing of RNA. PMID:26353759
Tentacle: distributed quantification of genes in metagenomes. PMID:26351566
Draft genome of a commonly misdiagnosed multidrug resistant pathogen Candida auris. PMID:26346253
The Genome of the "Great Speciator" Provides Insights into Bird Diversification. PMID:26338191
Combinatorial DNA Rearrangement Facilitates the Origin of New Genes in Ciliates. PMID:26338187
Exploiting single-molecule transcript sequencing for eukaryotic gene prediction. PMID:26328666
High-resolution analysis of the human T-cell receptor repertoire. PMID:26324409
RASER: reads aligner for SNPs and editing sites of RNA. PMID:26323713
Sequence Analysis and Characterization of Active Human Alu Subfamilies Based on the 1000 Genomes Pilot Project. PMID:26319576
Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties. PMID:26315624
Rapid evolution of chemosensory receptor genes in a pair of sibling species of orchid bees (Apidae: Euglossini). PMID:26314297
SCR96, a small cysteine-rich secretory protein of Phytophthora cactorum, can trigger cell death in the Solanaceae and is important for pathogenicity and oxidative stress tolerance. PMID:26307454
Fecal Recovery of Ingested Cellular DNA: Implications for Noninvasive Detection of Upper Gastrointestinal Neoplasms. PMID:26297132
Comprehensive analyses of genomes, transcriptomes and metabolites of neem tree. PMID:26290780
Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe. PMID:26283343
Construction of a high-density genetic map using specific length amplified fragment markers and identification of a quantitative trait locus for anthracnose resistance in walnut (Juglans regia L.). PMID:26283231
Local sequence assembly reveals a high-resolution profile of somatic structural variations in 97 cancer genomes. PMID:26283183
Comparative genome analysis of Mycoplasma pneumoniae. PMID:26275904
ApiAP2 Factors as Candidate Regulators of Stochastic Commitment to Merozoite Production in Theileria annulata. PMID:26273826
Assessing Recent Selection and Functionality at Long Noncoding RNA Loci in the Mouse Genome. PMID:26272717
Identification, Phylogeny, and Function of fabp2 Paralogs in Two Non-Model Teleost Fish Species. PMID:26272429
High Resolution Consensus Mapping of Quantitative Trait Loci for Fiber Strength, Length and Micronaire on Chromosome 25 of the Upland Cotton (Gossypium hirsutum L.). PMID:26262992
Comprehensive assembly of novel transcripts from unmapped human RNA-Seq data and their association with cancer. PMID:26253570
The Evolution of Bony Vertebrate Enhancers at Odds with Their Coding Sequence Landscape. PMID:26253316
Draft De Novo Transcriptome of the Rat Kangaroo Potorous tridactylus as a Tool for Cell Biology. PMID:26252667
Draft Genome Sequence of Mycobacterium bohemicum Strain DSM 44277T. PMID:26251499
Genetic signatures of adaptation revealed from transcriptome sequencing of Arctic and red foxes. PMID:26250829
High speed BLASTN: an accelerated MegaBLAST search tool. PMID:26250111
The complete mitochondrial genome sequence of the green microalga Lobosphaera (Parietochloris) incisa reveals a new type of palindromic repetitive repeat. PMID:26238519
A reanalysis of mouse ENCODE comparative gene expression data. PMID:26236466
Identification of heat-responsive genes in carnation (Dianthus caryophyllus L.) by RNA-seq. PMID:26236320
A high-density genetic map for P genome of Agropyron Gaertn. based on specific-locus amplified fragment sequencing (SLAF-seq). PMID:26232919
Analysis of paired end Pol II ChIP-seq and short capped RNA-seq in MCF-7 cells. PMID:26229744
Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampei. PMID:26228545
SuRankCo: supervised ranking of contigs in de novo assemblies. PMID:26224355
The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment. PMID:26214836
Characterization of an APC Promoter 1B deletion in a Patient Diagnosed with Familial Adenomatous Polyposis via Whole Genome Shotgun Sequencing. PMID:26213617
Transcriptional profiling of predator-induced phenotypic plasticity in Daphnia pulex. PMID:26213557
Quantitative Trait Loci Associated with the Tocochromanol (Vitamin E) Pathway in Barley. PMID:26208213
GESPA: classifying nsSNPs to predict disease association. PMID:26206375
Draft Genome Sequence of Mycobacterium lentiflavum CSUR P1491. PMID:26205866
Genomic variations of the mevalonate pathway in porokeratosis. PMID:26202976
Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos. PMID:26201400
Scrutinizing the immune defence inventory of Camponotus floridanus applying total transcriptome sequencing. PMID:26198742
Characterization of fossilized relatives of the White Spot Syndrome Virus in genomes of decapod crustaceans. PMID:26187050
Functional Analysis of Chicken IRF7 in Response to dsRNA Analog Poly(I:C) by Integrating Overexpression and Knockdown. PMID:26186542
The sequenced rat brain transcriptome--its use in identifying networks predisposing alcohol consumption. PMID:26183165
The molecular evolution of spiggin nesting glue in sticklebacks. PMID:26173374
BatAlign: an incremental method for accurate alignment of sequencing reads. PMID:26170239
Vy-PER: eliminating false positive detection of virus integration events in next generation sequencing data. PMID:26166306
BSPAT: a fast online tool for DNA methylation co-occurrence pattern analysis based on high-throughput bisulfite sequencing data. PMID:26163275
Salix purpurea Stimulates the Expression of Specific Bacterial Xenobiotic Degradation Genes in a Soil Contaminated with Hydrocarbons. PMID:26161539
Genome Modeling System: A Knowledge Management Platform for Genomics. PMID:26158448
GenomePeek-an online tool for prokaryotic genome and metagenome analysis. PMID:26157610
An Efficient Strategy Developed for Next-Generation Sequencing of Endosymbiont Genomes Performed Using Crude DNA Isolated from Host Tissues: A Case Study of Blattabacterium cuenoti Inhabiting the Fat Bodies of Cockroaches. PMID:26156552
Cell periphery-related proteins as major genomic targets behind the adaptive evolution of an industrial Saccharomyces cerevisiae strain to combined heat and hydrolysate stress. PMID:26156140
Read count-based method for high-throughput allelic genotyping of transposable elements and structural variants. PMID:26153459
Transcriptome Sequencing of Lima Bean (Phaseolus lunatus) to Identify Putative Positive Selection in Phaseolus and Legumes. PMID:26151849
VISA--Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing. PMID:26150117
An improved understanding of cancer genomics through massively parallel sequencing. PMID:26146607
High-throughput RNA sequencing reveals structural differences of orthologous brain-expressed genes between western lowland gorillas and humans. PMID:26132897
Nmf9 Encodes a Highly Conserved Protein Important to Neurological Function in Mice and Flies. PMID:26131556
Natural variation of the expression pattern of the segmentation gene even-skipped in melanogaster. PMID:26129990
Trends in IT Innovation to Build a Next Generation Bioinformatics Solution to Manage and Analyse Biological Big Data Produced by NGS Technologies. PMID:26125026
BlastXtract2: Improving early exploration of (meta) genomes. PMID:26124555
BGD: a database of bat genomes. PMID:26110276
Endogenous Small RNA Mediates Meiotic Silencing of a Novel DNA Transposon. PMID:26109355
Annotation of the Protein Coding Regions of the Equine Genome. PMID:26107351
Re-analysis of RNA-seq transcriptome data reveals new aspects of gene activity in Arabidopsis root hairs. PMID:26106402
Np9, a cellular protein of retroviral ancestry restricted to human, chimpanzee and gorilla, binds and regulates ubiquitin ligase MDM2. PMID:26103464
Analysis of Multiple Brachyspira hyodysenteriae Genomes Confirms That the Species Is Relatively Conserved but Has Potentially Important Strain Variation. PMID:26098837
A piRNA-like small RNA interacts with and modulates p-ERM proteins in human somatic cells. PMID:26095918
RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications. PMID:26084484
piRNA-like small RNAs mark extended 3'UTRs present in germ and somatic cells. PMID:26076733
Cypiripi: exact genotyping of CYP2D6 using high-throughput sequencing data. PMID:26072492
Construction of a linkage map based on retrotransposon insertion polymorphisms in sweetpotato via high-throughput sequencing. PMID:26069444
Draft Genome Sequence of Stenotrophomonas maltophilia Strain UV74 Reveals Extensive Variability within Its Genomic Group. PMID:26067959
Whole transcriptome analysis reveals changes in expression of immune-related genes during and after bleaching in a reef-building coral. PMID:26064625
Structural basis for retroviral integration into nucleosomes. PMID:26061770
Transcriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae). PMID:26059236
Spider Transcriptomes Identify Ancient Large-Scale Gene Duplication Event Potentially Important in Silk Gland Evolution. PMID:26058392
The radish genome and comprehensive gene expression profile of tuberous root formation and development. PMID:26056784
Strong spurious transcription likely contributes to DNA insert bias in typical metagenomic clone libraries. PMID:26056565
TRUFA: A User-Friendly Web Server for de novo RNA-seq Analysis Using Cluster Computing. PMID:26056424
dbHiMo: a web-based epigenomics platform for histone-modifying enzymes. PMID:26055100
The distribution and evolution of Arabidopsis thaliana cis natural antisense transcripts. PMID:26054753
Recurrent somatic mutations in regulatory regions of human cancer genomes. PMID:26053494
Comprehensive Analysis of Disease-Related Genes in Chronic Lymphocytic Leukemia by Multiplex PCR-Based Next Generation Sequencing. PMID:26053404
Identification of Pathogen Signatures in Prostate Cancer Using RNA-seq. PMID:26053031
High-throughput monitoring of integration site clonality in preclinical and clinical gene therapy studies. PMID:26052530
Reference genome of wild goat (capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication. PMID:26044654
Mapping a Type 1 FHB resistance on chromosome 4AS of Triticum macha and deployment in combination with two Type 2 resistances. PMID:26040404
Large-Scale SNP Discovery and Genotyping for Constructing a High-Density Genetic Map of Tea Plant Using Specific-Locus Amplified Fragment Sequencing (SLAF-seq). PMID:26035838
Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms. PMID:26028266
Genetic regulation of bone metabolism in the chicken: similarities and differences to Mammalian systems. PMID:26023928
Draft Genome Sequence of the Archiascomycetous Yeast Saitoella complicata. PMID:26021914
JAFFA: High sensitivity transcriptome-focused fusion gene detection. PMID:26019724
Towards computational improvement of DNA database indexing and short DNA query searching. PMID:26019584
Unravelling the genome of Holy basil: an "incomparable" "elixir of life" of traditional Indian medicine. PMID:26017011
The First High-Density Genetic Map Construction in Tree Peony (Paeonia Sect. Moutan) using Genotyping by Specific-Locus Amplified Fragment Sequencing. PMID:26010095
Diversity of acid stress resistant variants of Listeria monocytogenes and the potential role of ribosomal protein S21 encoded by rpsU. PMID:26005439
Complete Genome Sequence of Streptococcus thermophilus SMQ-301, a Model Strain for Phage-Host Interactions. PMID:25999573
ImmuSort, a database on gene plasticity and electronic sorting for immune cells. PMID:25988315
Combining Next Generation Sequencing with Bulked Segregant Analysis to Fine Map a Stem Moisture Locus in Sorghum (Sorghum bicolor L. Moench). PMID:25984727
Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies. PMID:25983555
GraP: platform for functional genomics analysis of Gossypium raimondii. PMID:25982315
Lineage specific evolution of the VNTR composite retrotransposon central domain and its role in retrotransposition of gibbon LAVA elements. PMID:25981446
TUT7 controls the fate of precursor microRNAs by using three different uridylation mechanisms. PMID:25979828
Genome-Wide Transcriptional Profiling of Clostridium perfringens SM101 during Sporulation Extends the Core of Putative Sporulation Genes and Genes Determining Spore Properties and Germination Characteristics. PMID:25978838
Flatworms have lost the right open reading frame kinase 3 gene during evolution. PMID:25976756
Dynamic and Widespread lncRNA Expression in a Sponge and the Origin of Animal Complexity. PMID:25976353
Chromosome-Specific Painting in Cucumis Species Using Bulked Oligonucleotides. PMID:25971668
Bio301: A Web-Based EST Annotation Pipeline That Facilitates Functional Comparison Studies. PMID:25969743
Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons. PMID:25968644
Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells. PMID:25963125
Lactococcus garvieae: a small bacteria and a big data world. PMID:25960872
Design and bioinformatics analysis of genome-wide CLIP experiments. PMID:25958398
Transposable Elements and DNA Methylation Create in Embryonic Stem Cells Human-Specific Regulatory Sequences Associated with Distal Enhancers and Noncoding RNAs. PMID:25956794
Differential Gene Expression Profiling of Dystrophic Dog Muscle after MuStem Cell Transplantation. PMID:25955839
Transcriptional profiling provides insights into metronomic cyclophosphamide-activated, innate immune-dependent regression of brain tumor xenografts. PMID:25952672
Analysis of pollen-specific alternative splicing in Arabidopsis thaliana via semi-quantitative PCR. PMID:25945312
Gender-specific postnatal demethylation and establishment of epigenetic memory. PMID:25934504
Genome-wide amplification of proviral sequences reveals new polymorphic HERV-K(HML-2) proviruses in humans and chimpanzees that are absent from genome assemblies. PMID:25927962
Genome assembly using Nanopore-guided long and error-free DNA reads. PMID:25927464
Identification of a gene controlling variation in the salt tolerance of rapeseed (Brassica napus L.). PMID:25921693
Elucidating the composition and conservation of the autophagy pathway in photosynthetic eukaryotes. PMID:25915714
G&T-seq: parallel sequencing of single-cell genomes and transcriptomes. PMID:25915121
The genomes of two key bumblebee species with primitive eusocial organization. PMID:25908251
Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution. PMID:25893780
Evaluation and application of the strand-specific protocol for next-generation sequencing. PMID:25893191
BAP1 mutation is a frequent somatic event in peritoneal malignant mesothelioma. PMID:25889843
Transcriptome characterization of three wild Chinese Vitis uncovers a large number of distinct disease related genes. PMID:25888081
A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. PMID:25886949
RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets. PMID:25886935
The ReproGenomics Viewer: an integrative cross-species toolbox for the reproductive science community. PMID:25883147
Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizards. PMID:25880916
Inferring bona fide transfrags in RNA-Seq derived-transcriptome assemblies of non-model organisms. PMID:25880035
CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers. PMID:25879410
Numerous transitions of sex chromosomes in Diptera. PMID:25879221
Germline and somatic imprinting in the nonhuman primate highlights species differences in oocyte methylation. PMID:25862382
Whole-genome sequencing of Bacillus subtilis XF-1 reveals mechanisms for biological control and multiple beneficial properties in plants. PMID:25860123
Identification and functional analysis of genome mutations in a fluoride-resistant Streptococcus mutans strain. PMID:25856576
Comparative genome analyses of Serratia marcescens FS14 reveals its high antagonistic potential. PMID:25856195
Transcriptome-wide identification of adenosine-to-inosine editing using the ICE-seq method. PMID:25855956
SANSparallel: interactive homology search against Uniprot. PMID:25855811
ALDB: a domestic-animal long noncoding RNA database. PMID:25853886
Comparative whole-genome analysis of clinical isolates reveals characteristic architecture of Mycobacterium tuberculosis pangenome. PMID:25853708
Structural variation discovery in the cancer genome using next generation sequencing: computational solutions and perspectives. PMID:25849937
Acid sensitivity of the spinal dorsal root ganglia C-fiber nociceptors innervating the guinea pig esophagus. PMID:25846134
Transcriptional dynamics of Phytophthora infestans during sequential stages of hemibiotrophic infection of tomato. PMID:25845484
A Comprehensive Transcriptomic and Proteomic Analysis of Hydra Head Regeneration. PMID:25841488
Flexible, fast and accurate sequence alignment profiling on GPGPU with PaSWAS. PMID:25830241
Influence of a non-hospital medical care facility on antimicrobial resistance in wastewater. PMID:25821977
A thesaurus of genetic variation for interrogation of repetitive genomic regions. PMID:25820428
An Rtf2 Domain-Containing Protein Influences Pre-mRNA Splicing and Is Essential for Embryonic Development in Arabidopsis thaliana. PMID:25819795
LOTUS-DB: an integrative and interactive database for Nelumbo nucifera study. PMID:25819075
SNPfisher: tools for probing genetic variation in laboratory-reared zebrafish. PMID:25813542
Population structure and antimicrobial resistance of invasive serotype IV group B Streptococcus, Toronto, Ontario, Canada. PMID:25811284
Analysis of the tomato leaf transcriptome during successive hemibiotrophic stages of a compatible interaction with the oomycete pathogen Phytophthora infestans. PMID:25808779
Genome-wide identification, characterization and evolutionary analysis of long intergenic noncoding RNAs in cucumber. PMID:25799544
De novo origin of VCY2 from autosome to Y-transposed amplicon. PMID:25799347
Transcriptome assembly, gene annotation and tissue gene expression atlas of the rainbow trout. PMID:25793877
Disentangling the relationship of the Australian marsupial orders using retrotransposon and evolutionary network analyses. PMID:25786431
Identification of agonists for a group of human odorant receptors. PMID:25784876
Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives. PMID:25780758
Genome-wide characterization of developmental stage- and tissue-specific transcription factors in wheat. PMID:25766308
The distribution and mutagenesis of short coding INDELs from 1,128 whole exomes. PMID:25765891
The exonuclease Nibbler regulates age-associated traits and modulates piRNA length in Drosophila. PMID:25754031
Development of a high-resolution NGS-based HLA-typing and analysis pipeline. PMID:25753671
A CRISPR/Cas9 vector system for tissue-specific gene disruption in zebrafish. PMID:25752963
Pervasive variation of transcription factor orthologs contributes to regulatory network evolution. PMID:25748510
Drosophila muller f elements maintain a distinct set of genomic properties over 40 million years of evolution. PMID:25740935
The genome and transcriptome of the zoonotic hookworm Ancylostoma ceylanicum identify infection-specific gene families. PMID:25730766
Genome sequence-independent identification of RNA editing sites. PMID:25730491
Evidence for suppression of immunity as a driver for genomic introgressions and host range expansion in races of Albugo candida, a generalist parasite. PMID:25723966
Bridger: a new framework for de novo transcriptome assembly using RNA-seq data. PMID:25723335
RNA-Seq: Improving Our Understanding of Retinal Biology and Disease. PMID:25722474
Multicolor CRISPR labeling of chromosomal loci in human cells. PMID:25713381
Rock, paper, scissors: harnessing complementarity in ortholog detection methods improves comparative genomic inference. PMID:25711833
IRcall and IRclassifier: two methods for flexible detection of intron retention events from RNA-Seq data. PMID:25707295
A transcriptome derived female-specific marker from the invasive Western mosquitofish (Gambusia affinis). PMID:25707007
Whole transcriptome analysis using next-generation sequencing of sterile-cultured Eisenia andrei for immune system research. PMID:25706644
Identification of functional variants for cleft lip with or without cleft palate in or near PAX7, FGFR2, and NOG by targeted sequencing of GWAS loci. PMID:25704602
Cigarette smoke mediates epigenetic repression of miR-217 during esophageal adenocarcinogenesis. PMID:25703328
A large genomic deletion leads to enhancer adoption by the lamin B1 gene: a second path to autosomal dominant adult-onset demyelinating leukodystrophy (ADLD). PMID:25701871
Identification and Expression Analysis of Ribosome Biogenesis Factor Co-orthologs in Solanum lycopersicum. PMID:25698879
A complex genome-microRNA interplay in human mitochondria. PMID:25695052
Molecular description of eye defects in the zebrafish Pax6b mutant, sunrise, reveals a Pax6b-dependent genetic network in the developing anterior chamber. PMID:25692557
Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill. PMID:25689026
Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii. PMID:25683379
A multi-megabase copy number gain causes maternal transmission ratio distortion on mouse chromosome 2. PMID:25679959
Whole-genome sequencing reveals absence of recent gene flow and separate demographic histories for Anopheles punctulatus mosquitoes in Papua New Guinea. PMID:25677924
Global diversity lines - a five-continent reference panel of sequenced Drosophila melanogaster strains. PMID:25673134
RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. PMID:25666585
Nicotinic receptors in non-human primates: Analysis of genetic and functional conservation with humans. PMID:25661700
Comparative genomics of grass EST libraries reveals previously uncharacterized splicing events in crop plants. PMID:25652661
Expression and regulation of long noncoding RNAs in TLR4 signaling in mouse macrophages. PMID:25652569
A single nucleotide polymorphism associated with isolated cleft lip and palate, thyroid cancer and hypothyroidism alters the activity of an oral epithelium and thyroid enhancer near FOXE1. PMID:25652407
Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data. PMID:25650807
The fate of recent duplicated genes following a fourth-round whole genome duplication in a tetraploid fish, common carp (Cyprinus carpio). PMID:25645996
Developmental genetic mechanisms of C4 syndrome based on transcriptome analysis of C3 cotyledons and C4 assimilating shoots in Haloxylon ammodendron. PMID:25643361
Next-generation sequencing of duplication CNVs reveals that most are tandem and some create fusion genes at breakpoints. PMID:25640679
Identification of a recently active mammalian SINE derived from ribosomal RNA. PMID:25637222
Single-nucleotide polymorphism identification and genotyping in Camelina sativa. PMID:25620879
New cryptic karyotypic differences between cattle (Bos taurus) and goat (Capra hircus). PMID:25612562
Novel exons and splice variants in the human antibody heavy chain identified by single cell and single molecule sequencing. PMID:25611855
Evaluation of de novo transcriptome assemblies from RNA-Seq data. PMID:25608678
Vector design influences hepatic genotoxicity after adeno-associated virus gene therapy. PMID:25607839
Novel transcription factor variants through RNA-sequencing: the importance of being "alternative". PMID:25590302
The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau. PMID:25583503
Genetic mapping of the nulliplex-branch gene (gb_nb1) in cotton using next-generation sequencing. PMID:25575840
Studying genome heterogeneity within the arbuscular mycorrhizal fungal cytoplasm. PMID:25573960
Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure. PMID:25573196
A RESTful API for accessing microbial community data for MG-RAST. PMID:25569221
Three CCT domain-containing genes were identified to regulate heading date by candidate gene-based association mapping and transformation in rice. PMID:25563494
Extragenic suppressor mutations in ΔripA disrupt stability and function of LpxA. PMID:25551578
Comprehensive transcriptome analysis reveals accelerated genic evolution in a Tibet fish, Gymnodiptychus pachycheilus. PMID:25543049
Integrated analysis of whole genome and transcriptome sequencing reveals diverse transcriptomic aberrations driven by somatic genomic changes in liver cancers. PMID:25526364
Tissue-specific transcriptomics, chromosomal localization, and phylogeny of chemosensory and odorant binding proteins from the red flour beetle Tribolium castaneum reveal subgroup specificities for olfaction or more general functions. PMID:25523483
Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India. PMID:25520706
Conserved syntenic clusters of protein coding genes are missing in birds. PMID:25518852
Smoking-Associated Site-Specific Differential Methylation in Buccal Mucosa in the COPDGene Study. PMID:25517428
Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms. PMID:25517076
Recent advances in candidate-gene and whole-genome approaches to the discovery of anthelmintic resistance markers and the description of drug/receptor interactions. PMID:25516826
Genome-wide analysis of alternative splicing in Volvox carteri. PMID:25516378
Transcriptional consequence and impaired gametogenesis with high-grade aneuploidy in Arabidopsis thaliana. PMID:25514186
T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data. PMID:25510498
Gene prediction and annotation in Penstemon (Plantaginaceae): A workflow for marker development from extremely low-coverage genome sequencing. PMID:25506519
Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC. PMID:25503521
Potassium stress growth characteristics and energetics in the haloarchaeon Haloarcula marismortui. PMID:25503059
Dynamic evolution of the alpha (α) and beta (β) keratins has accompanied integument diversification and the adaptation of birds into novel lifestyles. PMID:25496280
CLAST: CUDA implemented large-scale alignment search tool. PMID:25495907
Construction of a high-density genetic map based on large-scale markers developed by specific length amplified fragment sequencing (SLAF-seq) and its application to QTL analysis for isoflavone content in Glycine max. PMID:25494922
Comparative genomics reveals molecular features unique to the songbird lineage. PMID:25494627
Genome-wide mapping in a house mouse hybrid zone reveals hybrid sterility loci and Dobzhansky-Muller interactions. PMID:25487987
Integrative workflows for metagenomic analysis. PMID:25478562
Evolutionary origins and dynamics of octoploid strawberry subgenomes revealed by dense targeted capture linkage maps. PMID:25477420
Triticeae resources in Ensembl Plants. PMID:25432969
Faster sequence homology searches by clustering subsequences. PMID:25432166
The UCSC Genome Browser database: 2015 update. PMID:25428374
BreaKmer: detection of structural variation in targeted massively parallel sequencing data using kmers. PMID:25428359
MitoCOGs: clusters of orthologous genes from mitochondria and implications for the evolution of eukaryotes. PMID:25421434
Anti-centrosome antibodies in breast cancer are the expression of autoimmunity. PMID:25420961
Complete genome sequence and comparative genome analysis of Klebsiella oxytoca HKOPL1 isolated from giant panda feces. PMID:25417012
Type I Interferon Regulates the Expression of Long Non-Coding RNAs. PMID:25414701
microDuMIP: target-enrichment technique for microarray-based duplex molecular inversion probes. PMID:25414325
Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation. PMID:25411636
Diversification of bacterial genome content through distinct mechanisms over different timescales. PMID:25407023
RADIA: RNA and DNA integrated analysis for somatic mutation detection. PMID:25405470
Fast and sensitive protein alignment using DIAMOND. PMID:25402007
Species-specific exon loss in human transcriptomes. PMID:25398629
Definition of the cattle killer cell Ig-like receptor gene family: comparison with aurochs and human counterparts. PMID:25398326
Comparative genomic analysis shows that avian pathogenic Escherichia coli isolate IMT5155 (O2:K1:H5; ST complex 95, ST140) shares close relationship with ST95 APEC O1:K1 and human ExPEC O18:K1 strains. PMID:25397580
Detection theory in identification of RNA-DNA sequence differences using RNA-sequencing. PMID:25396741
Evolution of an expanded mannose receptor gene family. PMID:25390371
Transcriptome of the invasive brown marmorated stink bug, Halyomorpha halys (Stål) (Heteroptera: Pentatomidae). PMID:25386688
Anchored multiplex PCR for targeted next-generation sequencing. PMID:25384085
Mutational spectrum of myeloid malignancies with inv(3)/t(3;3) reveals a predominant involvement of RAS/RTK signaling pathways. PMID:25381062
The genome of a Mongolian individual reveals the genetic imprints of Mongolians on modern human populations. PMID:25377941
Profiling the RNA editomes of wild-type C. elegans and ADAR mutants. PMID:25373143
MetaGeniE: characterizing human clinical samples using deep metagenomic sequencing. PMID:25365329
The mutational landscape in pediatric acute lymphoblastic leukemia deciphered by whole genome sequencing. PMID:25355294
Ensembl 2015. PMID:25352552
Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number. PMID:25348403
Host and viral determinants for MxB restriction of HIV-1 infection. PMID:25348155
Evaluation of a hybrid approach using UBLAST and BLASTX for metagenomic sequences annotation of specific functional genes. PMID:25347677
Intron evolution in Neurospora: the role of mutational bias and selection. PMID:25342722
Discovery of invariant T cells by next-generation sequencing of the human TCR α-chain repertoire. PMID:25339678
Single-cell analyses of transcriptional heterogeneity during drug tolerance transition in cancer cells by RNA sequencing. PMID:25339441
The functional potential of microbial communities in hydraulic fracturing source water and produced water from natural gas extraction characterized by metagenomic sequencing. PMID:25338024
PAIDB v2.0: exploration and analysis of pathogenicity and resistance islands. PMID:25336619
Disease variants in genomes of 44 centenarians. PMID:25333069
Genes involved in floral meristem in tomato exhibit drastically reduced genetic diversity and signature of selection. PMID:25325924
Postzygotic single-nucleotide mosaicisms in whole-genome sequences of clinically unremarkable individuals. PMID:25312340
Divergence of gene body DNA methylation and evolution of plant duplicate genes. PMID:25310342
A PTCH1 homolog transcriptionally activated by p53 suppresses Hedgehog signaling. PMID:25296753
A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature. PMID:25273102
High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis. PMID:25271953
Population history and genomic signatures for high-altitude adaptation in Tibetan pigs. PMID:25270331
Transposable element dynamics and PIWI regulation impacts lncRNA and gene expression diversity in Drosophila ovarian cell cultures. PMID:25267525
NSIT: novel sequence identification tool. PMID:25264906
Long non-coding RNAs differentially expressed between normal versus primary breast tumor tissues disclose converse changes to breast cancer-related protein-coding genes. PMID:25264628
Transcriptome sequencing and analysis of Plasmodium gallinaceum reveals polymorphisms and selection on the apical membrane antigen-1. PMID:25261185
Long distance linkage disequilibrium and limited hybridization suggest cryptic speciation in atlantic cod. PMID:25259573
Single-cell analyses of regulatory network perturbations using enhancer-targeting TALEs suggest novel roles for PU.1 during haematopoietic specification. PMID:25252941
Piecing the puzzle together: a revisit to transcript reconstruction problem in RNA-seq. PMID:25252653
Effective extraction and assembly methods for simultaneously obtaining plastid and mitochondrial genomes. PMID:25251391
circBase: a database for circular RNAs. PMID:25234927
Neutral nuclear variation in Baboons (genus Papio) provides insights into their evolutionary and demographic histories. PMID:25234435
LncRBase: an enriched resource for lncRNA information. PMID:25233092
Tangram: a comprehensive toolbox for mobile element insertion detection. PMID:25228379
Estimating overannotation across prokaryotic genomes using BLAST+, UBLAST, LAST and BLAT. PMID:25228073
Hyb-Seq: Combining target enrichment and genome skimming for plant phylogenomics. PMID:25225629
Improved rat genome gene prediction by integration of ESTs with RNA-Seq information. PMID:25217576
Comparative genome sequencing reveals genomic signature of extreme desiccation tolerance in the anhydrobiotic midge. PMID:25216354
De novo genome assembly of the economically important weed horseweed using integrated data from multiple sequencing platforms. PMID:25209985
Estimating the nucleotide diversity in Ceratodon purpureus (Ditrichaceae) from 218 conserved exon-primed, intron-spanning nuclear loci. PMID:25202534
Identification of species-specific nuclear insertions of mitochondrial DNA (numts) in gorillas and their potential as population genetic markers. PMID:25194325
Evidence for the persistence of an active endogenous retrovirus (ERVE) in humans. PMID:25192754
The expression profile of acid-sensing ion channel (ASIC) subunits ASIC1a, ASIC1b, ASIC2a, ASIC2b, and ASIC3 in the esophageal vagal afferent nerve subtypes. PMID:25190475
Genetic analysis of a consanguineous Pakistani family with Leber congenital amaurosis identifies a novel mutation in GUCY2D gene. PMID:25189253
Clone mapper: an online suite of tools for RNAi experiments in Caenorhabditis elegans. PMID:25187039
P2Y(12) receptor on the verge of a neuroinflammatory breakdown. PMID:25180027
Merging of multi-string BWTs with applications. PMID:25172922
Complete Genome Sequences of IncI1 Plasmids Carrying Extended-Spectrum β-Lactamase Genes. PMID:25169863
Comprehensive analysis of alternative splicing in Digitalis purpurea by strand-specific RNA-Seq. PMID:25167195
Lambda: the local aligner for massive biological data. PMID:25161219
A genome-wide map of hyper-edited RNA reveals numerous new sites. PMID:25158696
Genomic organization, transcriptomic analysis, and functional characterization of avian α- and β-keratins in diverse feather forms. PMID:25152353
Identification of oncogenic mutations and gene fusions in the follicular variant of papillary thyroid carcinoma. PMID:25148236
Potential for genomic instability associated with retrotranspositionally-incompetent L1 loci. PMID:25143528
Multiple groups of endogenous epsilon-like retroviruses conserved across primates. PMID:25142585
IRBIS: a systematic search for conserved complementarity. PMID:25142064
Profile hidden Markov models for the detection of viruses within metagenomic sequence data. PMID:25140992
Parallel evolution of tetrodotoxin resistance in three voltage-gated sodium channel genes in the garter snake Thamnophis sirtalis. PMID:25135948
Small RNAs as important regulators for the hybrid vigour of super-hybrid rice. PMID:25129133
The Babesia bovis gene and promoter model: an update from full-length EST analysis. PMID:25124460
Small RNAs as important regulators for the hybrid vigour of super-hybrid rice. PMID:25129133
The Babesia bovis gene and promoter model: an update from full-length EST analysis. PMID:25124460
HapMuC: somatic mutation calling using heterozygous germ line variants near candidate mutations. PMID:25123903
A comprehensive survey of non-canonical splice sites in the human transcriptome. PMID:25123659
Comparative transcriptome atlases reveal altered gene expression modules between two Cleomaceae C3 and C4 plant species. PMID:25122153
SNP identification by transcriptome sequencing and candidate gene-based association analysis for heat tolerance in the bay scallop Argopecten irradians. PMID:25121601
Gene-based SNP discovery and genetic mapping in pea. PMID:25119872
Plant vigour at establishment and following defoliation are both associated with responses to drought in perennial ryegrass (Lolium perenne L.). PMID:25104762
GHOSTX: an improved sequence homology search algorithm using a query suffix array and a database suffix array. PMID:25099887
Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data. PMID:25091138
Identification and validation of genetic variants that influence transcription factor and cell signaling protein levels. PMID:25087611
A Bead-based Normalization for Uniform Sequencing depth (BeNUS) protocol for multi-samples sequencing exemplified by HLA-B. PMID:25087472
Endogenous retrovirus insertion in the KIT oncogene determines white and white spotting in domestic cats. PMID:25085922
Haploinsufficiency of insulin gene enhancer protein 1 (ISL1) is associated with d-transposition of the great arteries. PMID:25077177
Gene Assembly from Chip-Synthesized Oligonucleotides. PMID:25077042
Corset: enabling differential gene expression analysis for de novo assembled transcriptomes. PMID:25063469
The nuclear hormone receptor family member NR5A2 controls aspects of multipotent progenitor cell formation and acinar differentiation during pancreatic organogenesis. PMID:25063451
Highly variable recombinational landscape modulates efficacy of natural selection in birds. PMID:25062920
Diversity in the preimmune immunoglobulin repertoire of SHR lines susceptible and resistant to end-organ injury. PMID:25056448
Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs. PMID:25056316
Repair of oxidative DNA base damage in the host genome influences the HIV integration site sequence preference. PMID:25051054
Genome-wide Association Study of Integrated Meat Quality-related Traits of the Duroc Pig Breed. PMID:25049955
Loss of oncogenic Notch1 with resistance to a PI3K inhibitor in T-cell leukaemia. PMID:25043004
The common marmoset genome provides insight into primate biology and evolution. PMID:25038751
Systematic identification and characterization of RNA editing in prostate tumors. PMID:25036877
NCI-60 whole exome sequencing and pharmacological CellMiner analyses. PMID:25032700
Epstein-Barr virus EBNA1 protein regulates viral latency through effects on let-7 microRNA and dicer. PMID:25031339
Cryptococcus gattii in North American Pacific Northwest: whole-population genome analysis provides insights into species evolution and dispersal. PMID:25028429
An integrated genomic and metabolomic framework for cell wall biology in rice. PMID:25023612
Quickly finding orthologs as reciprocal best hits with BLAT, LAST, and UBLAST: how much do we miss? PMID:25013894
A novel reannotation strategy for dissecting DNA methylation patterns of human long intergenic non-coding RNAs in cancers. PMID:25013169
First Complete Genome Sequence of Staphylococcus xylosus, a Meat Starter Culture and a Host to Propagate Staphylococcus aureus Phages. PMID:25013142
Apomictic and sexual germline development differ with respect to cell cycle, transcriptional, hormonal and epigenetic regulation. PMID:25010342
De novo transcriptome sequencing and sequence analysis of the malaria vector Anopheles sinensis (Diptera: Culicidae). PMID:25000941
A comprehensive set of transcript sequences of the heavy metal hyperaccumulator Noccaea caerulescens. PMID:24999345
An integrated catalog of reference genes in the human gut microbiome. PMID:24997786
Complete genome assembly and characterization of an outbreak strain of the causative agent of swine erysipelas--Erysipelothrix rhusiopathiae SY1027. PMID:24993343
Genome editing assessment using CRISPR Genome Analyzer (CRISPR-GA). PMID:24990609
Genome sequencing of four Aureobasidium pullulans varieties: biotechnological potential, stress tolerance, and description of new species. PMID:24984952
Genotyping cancer-associated genes in chordoma identifies mutations in oncogenes and areas of chromosomal loss involving CDKN2A, PTEN, and SMARCB1. PMID:24983247
A comprehensive analysis of piRNAs from adult human testis and their relationship with genes and mobile elements. PMID:24981367
Synthesis of 53 tissue and cell line expression QTL datasets reveals master eQTLs. PMID:24973796
MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing. PMID:24972667
Is the alcohol deprivation effect genetically mediated? Studies with HXB/BXH recombinant inbred rat strains. PMID:24961585
Genome assembly and annotation of a Drosophila simulans strain from Madagascar. PMID:24961367
BLAT-based comparative analysis for transposable elements: BLATCAT. PMID:24959585
Variable recombination dynamics during the emergence, transmission and 'disarming' of a multidrug-resistant pneumococcal clone. PMID:24957517
The draft assembly of the radically organized Stylonychia lemnae macronuclear genome. PMID:24951568
The Chlamydomonas genome project: a decade on. PMID:24950814
Fine-scale population epigenetic structure in relation to gastrointestinal parasite load in red grouse (Lagopus lagopus scotica). PMID:24943398
A method for detecting long non-coding RNAs with tiled RNA expression microarrays. PMID:24937006
The role of photorespiration during the evolution of C4 photosynthesis in the genus Flaveria. PMID:24935935
Efficient DNA fingerprinting based on the targeted sequencing of active retrotransposon insertion sites using a bench-top high-throughput sequencing platform. PMID:24935865
Multicilin drives centriole biogenesis via E2f proteins. PMID:24934224
AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references. PMID:24932000
Genome and transcriptome of the porcine whipworm Trichuris suis. PMID:24929829
The American cranberry: first insights into the whole genome of a species adapted to bog habitat. PMID:24927653
Shared and unique proteins in human, mouse and rat saliva proteomes: Footprints of functional adaptation. PMID:24926433
MorusDB: a resource for mulberry genomics and genome biology. PMID:24923822
Evolutionary origin and methylation status of human intronic CpG islands that are not present in mouse. PMID:24923327
Unfixed endogenous retroviral insertions in the human population. PMID:24920817
Rewiring Host Lipid Metabolism by Large Viruses Determines the Fate of Emiliania huxleyi, a Bloom-Forming Alga in the Ocean. PMID:24920329
The genome of Eucalyptus grandis. PMID:24919147
Evidence for soft selective sweeps in the evolution of pneumococcal multidrug resistance and vaccine escape. PMID:24916661
A reference genome for common bean and genome-wide analysis of dual domestications. PMID:24908249
ABRA: improved coding indel detection via assembly-based realignment. PMID:24907369
Identification of potential therapeutic targets in a model of neuropathic pain. PMID:24904634
Novel principles of gamma-retroviral insertional transcription activation in murine leukemia virus-induced end-stage tumors. PMID:24886479
GAP-Seq: a method for identification of DNA palindromes. PMID:24885769
A novel approach to identify driver genes involved in androgen-independent prostate cancer. PMID:24885513
Predicting the fungal CUG codon translation with Bagheera. PMID:24885275
Identification of G protein-coupled receptors in Schistosoma haematobium and S. mansoni by comparative genomics. PMID:24884876
XSAnno: a framework for building ortholog models in cross-species transcriptome comparisons. PMID:24884593
Heterochromatin controls γH2A localization in Neurospora crassa. PMID:24879124
Aptaligner: automated software for aligning pseudorandom DNA X-aptamers from next-generation sequencing data. PMID:24866698
GenomeVISTA--an integrated software package for whole-genome alignment and visualization. PMID:24860159
Characterization of natural antisense transcript, sclerotia development and secondary metabolism by strand-specific RNA sequencing of Aspergillus flavus. PMID:24849659
The ctenophore genome and the evolutionary origins of neural systems. PMID:24847885
APOBEC3A deaminates transiently exposed single-strand DNA during LINE-1 retrotransposition. PMID:24843014
Objective and comprehensive evaluation of bisulfite short read mapping tools. PMID:24839440
RBPmap: a web server for mapping binding sites of RNA-binding proteins. PMID:24829458
A naturally occurring, noncanonical GTP aptamer made of simple tandem repeats. PMID:24824832
Alignment-Annotator web server: rendering and annotating sequence alignments. PMID:24813445
Detection of gene rearrangements in targeted clinical next-generation sequencing. PMID:24813172
DICER1 is essential for survival of postmitotic rod photoreceptor cells in mice. PMID:24812086
The three major types of CRISPR-Cas systems function independently in CRISPR RNA biogenesis in Streptococcus thermophilus. PMID:24811454
Assessment and improvement of Indian-origin rhesus macaque and Mauritian-origin cynomolgus macaque genome annotations using deep transcriptome sequencing data. PMID:24810475
The tobacco genome sequence and its comparison with those of tomato and potato. PMID:24807620
Transcription-independent functions of an RNA polymerase II subunit, Rpb2, during genome rearrangement in the ciliate, Oxytricha trifallax. PMID:24793090
Development and characterization of a new 12-plex ChrX miniSTR system. PMID:24789265
A genome-wide analysis of genetic diversity in Trypanosoma cruzi intergenic regions. PMID:24784238
Toxoplasma effector MAF1 mediates recruitment of host mitochondria and impacts the host response. PMID:24781109
Mouse mammary tumor virus-based vector transduces non-dividing cells, enters the nucleus via a TNPO3-independent pathway and integrates in a less biased fashion than other retroviruses. PMID:24779422
Genome-Wide Analysis of Heat-Sensitive Alternative Splicing in Physcomitrella patens. PMID:24777346
Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum. PMID:24773339
Origins and functional evolution of Y chromosomes across mammals. PMID:24759410
A house finch (Haemorhous mexicanus) spleen transcriptome reveals intra- and interspecific patterns of gene expression, alternative splicing and genetic diversity in passerines. PMID:24758272
Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. PMID:24755901
The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. PMID:24755649
The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes. PMID:24749011
Bayesian estimation of nonsynonymous/synonymous rate ratios for pairwise sequence comparisons. PMID:24748652
Describing sequencing results of structural chromosome rearrangements with a suggested next-generation cytogenetic nomenclature. PMID:24746958
Genome Sequence of Fusarium graminearum Isolate CS3005. PMID:24744326
Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation. PMID:24743168
The impacts of read length and transcriptome complexity for de novo assembly: a simulation study. PMID:24736633
Widespread use of non-productive alternative splice sites in Saccharomyces cerevisiae. PMID:24722551
A hybrid qPCR/SNP array approach allows cost efficient assessment of KIR gene copy numbers in large samples. PMID:24720548
Comparative metagenomic analysis of human gut microbiome composition using two different bioinformatic pipelines. PMID:24719854
Bioinformatics for next generation sequencing data. PMID:24710047
Measuring turnover of SIV DNA in resting CD4+ T cells using pyrosequencing: implications for the timing of HIV eradication therapies. PMID:24710023
Trapping DNA replication origins from the human genome. PMID:24705160
No evidence of clonal dominance after transplant of HOXB4-expanded cord blood cells in a nonhuman primate model. PMID:24704161
The draft genome sequence of European pear (Pyrus communis L. 'Bartlett'). PMID:24699266
A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing. PMID:24682209
Comparative genomics of Taphrina fungi causing varying degrees of tumorous deformity in plants. PMID:24682155
CDKN2D-WDFY2 is a cancer-specific fusion gene recurrent in high-grade serous ovarian carcinoma. PMID:24675677
Plant systems biology: insights, advances and challenges. PMID:24671625
RNA-seq analysis identifies an intricate regulatory network controlling cluster root development in white lupin. PMID:24666749
Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. PMID:24653211
The Xenopus alcohol dehydrogenase gene family: characterization and comparative analysis incorporating amphibian and reptilian genomes. PMID:24649825
Towards an integrative model of C4 photosynthetic subtypes: insights from comparative transcriptome analysis of NAD-ME, NADP-ME, and PEP-CK C4 species. PMID:24642845
Patterns of divergence of a large family of nodule cysteine-rich peptides in accessions of Medicago truncatula. PMID:24635121
RepARK--de novo creation of repeat libraries from whole-genome NGS reads. PMID:24634442
AlgaePath: comprehensive analysis of metabolic pathways using transcript abundance data from next-generation sequencing in green algae. PMID:24628857
Genome-wide signals of positive selection in human evolution. PMID:24619126
Orione, a web-based framework for NGS analysis in microbiology. PMID:24618473
Deep RNA sequencing reveals hidden features and dynamics of early gene transcription in Paramecium bursaria chlorella virus 1. PMID:24608750
Detection of chromosomal breakpoints in patients with developmental delay and speech disorders. PMID:24603971
BambooGDB: a bamboo genome database with functional annotation and an analysis platform. PMID:24602877
doublesex is a mimicry supergene. PMID:24598547
Systematic design and functional analysis of artificial microRNAs. PMID:24598260
Cell cycle, oncogenic and tumor suppressor pathways regulate numerous long and macro non-protein-coding RNAs. PMID:24594072
MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. PMID:24589583
Genomic networks of hybrid sterility. PMID:24586194
Estimating differential expression from multiple indicators. PMID:24586062
Benchmarking of methods for genomic taxonomy. PMID:24574292
On the optimal trimming of high-throughput mRNA sequence data. PMID:24567737
OMACC: an Optical-Map-Assisted Contig Connector for improving de novo genome assembly. PMID:24564959
A tool for mapping Single Nucleotide Polymorphisms using Graphics Processing Units. PMID:24564714
Genome sequencing of high-penicillin producing industrial strain of Penicillium chrysogenum. PMID:24564352
A base composition analysis of natural patterns for the preprocessing of metagenome sequences. PMID:24564274
De novo sequencing, assembly, and analysis of the root transcriptome of Persea americana (Mill.) in response to Phytophthora cinnamomi and flooding. PMID:24563685
Improving transcriptome construction in non-model organisms: integrating manual and automated gene definition in Emiliania huxleyi. PMID:24559402
Evolution of primate α and θ defensins revealed by analysis of genomes. PMID:24557891
Molecular evolution and functional divergence of the metallothionein gene family in vertebrates. PMID:24557429
Mirror movement-like defects in startle behavior of zebrafish dcc mutants are caused by aberrant midline guidance of identified descending hindbrain neurons. PMID:24553931
Single cell genomics of uncultured, health-associated Tannerella BU063 (Oral Taxon 286) and comparison to the closely related pathogen Tannerella forsythia. PMID:24551246
Suppression of cell wall-related genes associated with stunting of Oryza glaberrima infected with Rice tungro spherical virus. PMID:24550897
Analysis of the floral transcriptome of Tarenaya hassleriana (Cleomaceae), a member of the sister group to the Brassicaceae: towards understanding the base of morphological diversity in Brassicales. PMID:24548348
Haploinsufficiency of Sf3b1 leads to compromised stem cell function but not to myelodysplasia. PMID:24535406
Evolution of gene structural complexity: an alternative-splicing-based model accounts for intron-containing retrogenes. PMID:24520158
The streamlined genome of Phytomonas spp. relative to human pathogenic kinetoplastids reveals a parasite tailored for plants. PMID:24516393
A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection. PMID:24512684
Genotyping of BCL11A and HBS1L-MYB SNPs associated with fetal haemoglobin levels: a SNaPshot minisequencing approach. PMID:24502199
Large inverted duplications in the human genome form via a fold-back mechanism. PMID:24497845
The Cryptococcus neoformans transcriptome at the site of human meningitis. PMID:24496797
Differential locus expansion distinguishes Toxoplasmatinae species and closely related strains of Toxoplasma gondii. PMID:24496792
Improved search heuristics find 20,000 new alignments between human and mouse genomes. PMID:24493737
Single Nucleotide Polymorphism (SNP) Detection and Genotype Calling from Massively Parallel Sequencing (MPS) Data. PMID:24489615
The imprinted NPAP1 gene in the Prader-Willi syndrome region belongs to a POM121-related family of retrogenes. PMID:24482533
Finding the missing honey bee genes: lessons learned from a genome upgrade. PMID:24479613
Current challenges in the bioinformatics of single cell genomics. PMID:24478987
Absence of Genomic Ikaros/IKZF1 Deletions in Pediatric B-Precursor Acute Lymphoblastic Leukemia. PMID:24478816
C2orf62 and TTC17 are involved in actin organization and ciliogenesis in zebrafish and human. PMID:24475127
Comprehensive transcriptome assembly of Chickpea (Cicer arietinum L.) using sanger and next generation sequencing platforms: development and applications. PMID:24465857
New microRNAs in Drosophila--birth, death and cycles of adaptive evolution. PMID:24465220
Functional divergence and evolutionary turnover in mammalian phosphoproteomes. PMID:24465218
Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. PMID:24463464
Genetic dysregulation in recurrent respiratory papillomatosis. PMID:24449512
Characterization of genetic diversity in the nematode Pristionchus pacificus from population-scale resequencing data. PMID:24443445
Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut. PMID:24438450
Construction of a public CHO cell line transcript database using versatile bioinformatics analysis pipelines. PMID:24427317
Somatic RHOA mutation in angioimmunoblastic T cell lymphoma. PMID:24413737
Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment. PMID:24413732
A bioinformatician's guide to the forefront of suffix array construction algorithms. PMID:24413184
Genome-wide eQTLs and heritability for gene expression traits in unrelated individuals. PMID:24405759
SlopMap: a software application tool for quick and flexible identification of similar sequences using exact k-mer matching. PMID:24404406
Genome-wide analysis of light-regulated alternative splicing mediated by photoreceptors in Physcomitrella patens. PMID:24398233
Computational approaches in detecting non- coding RNA. PMID:24396270
Low-bandwidth and non-compute intensive remote identification of microbes from raw sequencing reads. PMID:24391826
NCYM, a Cis-antisense gene of MYCN, encodes a de novo evolved protein that inhibits GSK3β resulting in the stabilization of MYCN in human neuroblastomas. PMID:24391509
Assessing the state of substitution models describing noncoding RNA evolution. PMID:24391153
Identification of Hematopoietic Stem Cell Engraftment Genes in Gene Therapy Studies. PMID:24383045
Evolutionary genetics and implications of small size and twinning in callitrichine primates. PMID:24379383
Soil microbial community responses to a decade of warming as revealed by comparative metagenomics. PMID:24375144
Epigenetic regulation of the DLK1-MEG3 microRNA cluster in human type 2 diabetic islets. PMID:24374217
The genome of Romanomermis culicivorax: revealing fundamental changes in the core developmental genetic toolkit in Nematoda. PMID:24373391
An integrative bioinformatics pipeline for the genomewide identification of novel porcine microRNA genes. PMID:24371181
A penile spine/vibrissa enhancer sequence is missing in modern and extinct humans but is retained in multiple primates with penile spines and sensory vibrissae. PMID:24367647
Comprehensive analysis of transcriptome variation uncovers known and novel driver events in T-cell acute lymphoblastic leukemia. PMID:24367274
A guide to bioinformatics for immunologists. PMID:24363654
Obligate mutualism within a host drives the extreme specialization of a fig wasp genome. PMID:24359812
Comparative transcriptome analysis of two rice varieties in response to rice stripe virus and small brown planthoppers during early interaction. PMID:24358146
Inferring the choreography of parental genomes during fertilization from ultralarge-scale whole-transcriptome analysis. PMID:24352427
Rapid diversification of FoxP2 in teleosts through gene duplication in the teleost-specific whole genome duplication event. PMID:24349554
Evaluation of assembly strategies using RNA-seq data associated with grain development of wheat (Triticum aestivum L.). PMID:24349528
Genetic screen of African Americans with Fuchs endothelial corneal dystrophy. PMID:24348007
Targeted-capture massively-parallel sequencing enables robust detection of clinically informative mutations from formalin-fixed tumours. PMID:24336498
A detailed gene expression study of the Miscanthus genus reveals changes in the transcriptome associated with the rejuvenation of spring rhizomes. PMID:24320546
The high polyphenol content of grapevine cultivar tannat berries is conferred primarily by genes that are not shared with the reference genome. PMID:24319081
Fusion of TTYH1 with the C19MC microRNA cluster drives expression of a brain-specific DNMT3B isoform in the embryonal brain tumor ETMR. PMID:24316981
Transparency tools in gene patenting for informing policy and practice. PMID:24316644
ASPic-GeneID: a lightweight pipeline for gene prediction and alternative isoforms detection. PMID:24308000
TIGRA: a targeted iterative graph routing assembler for breakpoint assembly. PMID:24307552
Amplification and thrifty single-molecule sequencing of recurrent somatic structural variations. PMID:24307551
Biochemical and molecular characterization of Treponema phagedenis-like spirochetes isolated from a bovine digital dermatitis lesion. PMID:24304812
Detection limit of intragenic deletions with targeted array comparative genomic hybridization. PMID:24304607
The GATA transcription factor/MTA-1 homolog egr-1 promotes longevity and stress resistance in Caenorhabditis elegans. PMID:24304470
Metagenomic Analysis of the Dynamic Changes in the Gut Microbiome of the Participants of the MARS-500 Experiment, Simulating Long Term Space Flight. PMID:24303207
Genome-block expression-assisted association studies discover malaria resistance genes in Anopheles gambiae. PMID:24297936
megaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering. PMID:24285304
Dissection of the octoploid strawberry genome by deep sequencing of the genomes of Fragaria species. PMID:24282021
Genome sequence and analysis of methylotrophic yeast Hansenula polymorpha DL1. PMID:24279325
Minke whale genome and aquatic adaptation in cetaceans. PMID:24270359
Analysis of western lowland gorilla (Gorilla gorilla gorilla) specific Alu repeats. PMID:24262036
Exploration of the gene fusion landscape of glioblastoma using transcriptome sequencing and copy number data. PMID:24261984
UnSplicer: mapping spliced RNA-Seq reads in compact genomes and filtering noisy splicing. PMID:24259430
MEGANTE: a web-based system for integrated plant genome annotation. PMID:24253915
Data compression for sequencing data. PMID:24252160
A new family of predicted Krüppel-like factor genes and pseudogenes in placental mammals. PMID:24244731
Cross-platform prediction of gene expression signatures. PMID:24244455
Systems approaches to modeling chronic mucosal inflammation. PMID:24228254
Spatial-temporal targeting of lung-specific mesenchyme by a Tbx4 enhancer. PMID:24225400
Efficient cellular fractionation improves RNA sequencing analysis of mature and nascent transcripts from human tissues. PMID:24225116
Global transcriptome analysis of Lactococcus garvieae strains in response to temperature. PMID:24223997
Optimal scaling of digital transcriptomes. PMID:24223126
Assembly errors cause false tandem duplicate regions in the chicken (Gallus gallus) genome sequence. PMID:24213641
Hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data. PMID:24211736
Evaluation of alignment algorithms for discovery and identification of pathogens using RNA-Seq. PMID:24204709
Variant splicing and influence of ionizing radiation on human endogenous retrovirus K (HERV-K) transcripts in cancer cell lines. PMID:24204631
Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability. PMID:24201445
Rhizosphere microbiome assemblage is affected by plant development. PMID:24196324
A comprehensive promoter landscape identifies a novel promoter for CD133 in restricted tissues, cancers, and stem cells. PMID:24194746
Genomic divergence between nine- and three-spined sticklebacks. PMID:24188282
Systematic evaluation of spliced alignment programs for RNA-seq data. PMID:24185836
GWIPS-viz: development of a ribo-seq genome browser. PMID:24185699
Global analysis of DNA methylation variation in adipose tissue from twins reveals links to disease-associated variants in distal regulatory elements. PMID:24183450
Transcriptome interrogation of human myometrium identifies differentially expressed sense-antisense pairs of protein-coding and long non-coding RNA genes in spontaneous labor at term. PMID:24168098
Large-scale detection of in vivo transcription errors. PMID:24167253
Ensembl Genomes 2013: scaling up access to genome-wide data. PMID:24163254
Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars. PMID:24162736
An evolutionary screen highlights canonical and noncanonical candidate antiviral genes within the primate TRIM gene family. PMID:24158625
An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays. PMID:24142994
Draft genome of the kiwifruit Actinidia chinensis. PMID:24136039
Identification of novel microRNAs in primates by using the synteny information and small RNA deep sequencing data. PMID:24135875
Sense-antisense gene pairs: sequence, transcription, and structure are not conserved between human and mouse. PMID:24133500
Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency. PMID:24131564
The spliced leader trans-splicing mechanism in different organisms: molecular details and possible biological roles. PMID:24130571
Fungal alternative splicing is associated with multicellular complexity and virulence: a genome-wide multi-species study. PMID:24122896
Comprehensive analysis of human endogenous retrovirus group HERV-W locus transcription in multiple sclerosis brain lesions by high-throughput amplicon sequencing. PMID:24109235
Revealing of Mycobacterium marinum transcriptome by RNA-seq. PMID:24098731
ToPS: a framework to manipulate probabilistic models of sequence data. PMID:24098098
Development of SSR markers by next-generation sequencing of Korean landraces of chamoe (Cucumis melo var. makuwa). PMID:24096890
Transcriptome analyses of a Chinese hazelnut species Corylus mandshurica. PMID:24093758
An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome. PMID:24083400
Hominoid fission of chromosome 14/15 and the role of segmental duplications. PMID:24077392
Reliable identification of genomic variants from RNA-seq data. PMID:24075185
A SNP profiling panel for sample tracking in whole-exome sequencing studies. PMID:24070238
BlastGraph: a comparative genomics tool based on BLAST and graph algorithms. PMID:24068035
Advancing our understanding of the human microbiome using QIIME. PMID:24060131
Construction of a high-density genetic map for sesame based on large scale marker development by specific length amplified fragment (SLAF) sequencing. PMID:24060091
The landscape of somatic mutations in Down syndrome-related myeloid disorders. PMID:24056718
The tiger genome and comparative analysis with lion and snow leopard genomes. PMID:24045858
Transcript assembly and quantification by RNA-Seq reveals differentially expressed genes between soft-endocarp and hard-endocarp hawthorns. PMID:24039819
Acquired genetic mechanisms of a multiresistant bacterium isolated from a treatment plant receiving wastewater from antibiotic production. PMID:24038701
Admixture mapping of prostate cancer in African Americans participating in the North Carolina-Louisiana Prostate Cancer Project (PCaP). PMID:24037755
CruzDB: software for annotation of genomic intervals with UCSC genome-browser database. PMID:24037212
Horizontal transfer of DNA from the mitochondrial to the plastid genome and its subsequent evolution in milkweeds (apocynaceae). PMID:24029811
Substantial loss of conserved and gain of novel MicroRNA families in flatworms. PMID:24025793
Complete genome analysis of a Haemophilus parasuis serovar 12 strain from China. PMID:24023711
RNA-Seq reveals infection-related gene expression changes in Phytophthora capsici. PMID:24019970
Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area. PMID:24015321
Comparative sex chromosome genomics in snakes: differentiation, evolutionary strata, and lack of global dosage compensation. PMID:24015111
Lizards and LINEs: selection and demography affect the fate of L1 retrotransposons in the genome of the green anole (Anolis carolinensis). PMID:24013105
L_RNA_scaffolder: scaffolding genomes with transcripts. PMID:24010822
Divergent evolutionary and expression patterns between lineage specific new duplicate genes and their parental paralogs in Arabidopsis thaliana. PMID:24009676
Genome sequences of six wheat-infecting fusarium species isolates. PMID:24009115
Web Apollo: a web-based genomic annotation editing platform. PMID:24000942
Breakpoint features of genomic rearrangements in neuroblastoma with unbalanced translocations and chromothripsis. PMID:23991058
The shared genomic architecture of human nucleolar organizer regions. PMID:23990606
The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus. PMID:23985341
Endonuclease-containing Penelope retrotransposons in the bdelloid rotifer Adineta vaga exhibit unusual structural features and play a role in expansion of host gene families. PMID:23981484
Genome sequencing and analysis of BCG vaccine strains. PMID:23977002
The perfect neuroimaging-genetics-computation storm: collision of petabytes of data, millions of hardware devices and thousands of software tools. PMID:23975276
MATCHCLIP: locate precise breakpoints for copy number variation using CIGAR string by matching soft clipped reads. PMID:23967014
Assembler for de novo assembly of large genomes. PMID:23966565
GnpIS: an information system to integrate genetic and genomic data from plants and fungi. PMID:23959375
Fine mapping of V(D)J recombinase mediated rearrangements in human lymphoid malignancies. PMID:23957733
De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana. PMID:23957668
Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms. PMID:23955599
HIV latency and integration site placement in five cell-based models. PMID:23953889
Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies. PMID:23941359
Comprehensive genomic characterization of campylobacter genus reveals some underlying mechanisms for its genomic diversification. PMID:23940551
Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations. PMID:23937694
Mena/VASP and αII-Spectrin complexes regulate cytoplasmic actin networks in cardiomyocytes and protect from conduction abnormalities and dilated cardiomyopathy. PMID:23937664
Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. PMID:23934149
Accuracy and coverage assessment of Oryctolagus cuniculus (rabbit) genes encoding immunoglobulins in the whole genome sequence assembly (OryCun2.0) and localization of the IGH locus to chromosome 20. PMID:23925440
Analysis of unannotated equine transcripts identified by mRNA sequencing. PMID:23922931
Optimizing information in Next-Generation-Sequencing (NGS) reads for improving de novo genome assembly. PMID:23922726
Genomic treasure troves: complete genome sequencing of herbarium and insect museum specimens. PMID:23922691
Improving transcriptome assembly through error correction of high-throughput sequence reads. PMID:23904992
Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis. PMID:23904502
Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling. PMID:23899370
Insertional mutagenesis using Tnt1 retrotransposon in potato. PMID:23898040
PECONPI: a novel software for uncovering pathogenic copy number variations in non-syndromic sensorineural hearing loss and other genetically heterogeneous disorders. PMID:23897863
A computational workflow to identify allele-specific expression and epigenetic modification in maize. PMID:23891706
The transcriptional response of Arabidopsis leaves to Fe deficiency. PMID:23888164
Integrative genomic analysis of the human immune response to influenza vaccination. PMID:23878721
Genome survey sequencing and genetic background characterization of Gracilariopsis lemaneiformis (Rhodophyta) based on next-generation sequencing. PMID:23875008
A systems-genetics approach and data mining tool to assist in the discovery of genes underlying complex traits in Oryza sativa. PMID:23874666
High-throughput miRNA and mRNA sequencing of paired colorectal normal, tumor and metastasis tissues and bioinformatic modeling of miRNA-1 therapeutic applications. PMID:23874421
Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome. PMID:23873082
Transcriptome analyses of the human retina identify unprecedented transcript diversity and 3.5 Mb of novel transcribed sequence via significant alternative splicing and novel genes. PMID:23865674
MisPred: a resource for identification of erroneous protein sequences in public databases. PMID:23864220
Populus euphratica: the transcriptomic response to drought stress. PMID:23857471
Detection of Human Endogenous Retrovirus K (HERV-K) Transcripts in Human Prostate Cancer Cell Lines. PMID:23847768
Genomics analysis of potassium channel genes in songbirds reveals molecular specializations of brain circuits for the maintenance and production of learned vocalizations. PMID:23845108
nhmmer: DNA homology search with profile HMMs. PMID:23842809
Microbial and viral metagenomes of a subtropical freshwater reservoir subject to climatic disturbances. PMID:23842651
EGN: a wizard for construction of gene and genome similarity networks. PMID:23841456
Exome sequencing identifies secondary mutations of SETBP1 and JAK3 in juvenile myelomonocytic leukemia. PMID:23832011
Endogenous gammaretrovirus acquisition in Mus musculus subspecies carrying functional variants of the XPR1 virus receptor. PMID:23824809
An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. PMID:23817568
IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels. PMID:23813001
Mapping gene activity of Arabidopsis root hairs. PMID:23800126
Separating homeologs by phasing in the tetraploid wheat transcriptome. PMID:23800085
Integrated molecular analysis of clear-cell renal cell carcinoma. PMID:23797736
MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures. PMID:23793516
Reversal of an ancient sex chromosome to an autosome in Drosophila. PMID:23792562
Genome-wide survey of cold stress regulated alternative splicing in Arabidopsis thaliana with tiling microarray. PMID:23776682
Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis. PMID:23773524
Combined methylation mapping of 5mC and 5hmC during early embryonic stages in bovine. PMID:23773395
Genetic heterogeneity revealed by sequence analysis of Mycobacterium tuberculosis isolates from extra-pulmonary tuberculosis patients. PMID:23773324
Integrated analysis of microRNA and mRNA expression: adding biological significance to microRNA target predictions. PMID:23771142
The development of 7E chromosome-specific molecular markers for Thinopyrum elongatum based on SLAF-seq technology. PMID:23762296
Automated design of paralogue ratio test assays for the accurate and rapid typing of copy number variation. PMID:23742985
Landscape of DNA virus associations across human malignant cancers: analysis of 3,775 cases using RNA-Seq. PMID:23740984
Spliced DNA sequences in the Paramecium germline: their properties and evolutionary potential. PMID:23737328
Genome-wide characterization of adaptation and speciation in tiger swallowtail butterflies using de novo transcriptome assemblies. PMID:23737327
Mutually exclusive alterations in secondary metabolism are critical for the uptake of insoluble iron compounds by Arabidopsis and Medicago truncatula. PMID:23735511
Genome-wide detection of condition-sensitive alternative splicing in Arabidopsis roots. PMID:23735510
Bellerophon: a hybrid method for detecting interchromosomal rearrangements at base pair resolution using next-generation sequencing data. PMID:23734783
The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. PMID:23731509
Dual host-virus arms races shape an essential housekeeping protein. PMID:23723737
Integrated analysis of recurrent properties of cancer genes to identify novel drivers. PMID:23718799
VirusFinder: software for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data. PMID:23717618
Compensation of the metabolic costs of antibiotic resistance by physiological adaptation in Escherichia coli. PMID:23716056
Phase-defined complete sequencing of the HLA genes by next-generation sequencing. PMID:23714642
Combined sequence-based and genetic mapping analysis of complex traits in outbred rats. PMID:23708188
WebAUGUSTUS--a web service for training AUGUSTUS and predicting genes in eukaryotes. PMID:23700307
Enrichment of processed pseudogene transcripts in L1-ribonucleoprotein particles. PMID:23696454
Neuropilin-2 promotes extravasation and metastasis by interacting with endothelial α5 integrin. PMID:23689123
Genome-wide, whole mount in situ analysis of transcriptional regulators in zebrafish embryos. PMID:23684812
Human GGT2 does not autocleave into a functional enzyme: A cautionary tale for interpretation of microarray data on redox signaling. PMID:23682772
ReviSTER: an automated pipeline to revise misaligned reads to simple tandem repeats. PMID:23677944
WebScipio: Reconstructing alternative splice variants of eukaryotic proteins. PMID:23677611
Draft genome sequence of the Tibetan antelope. PMID:23673643
Optimizing de novo assembly of short-read RNA-seq data for phylogenomics. PMID:23672450
Inactivation of the RB family prevents thymus involution and promotes thymic function by direct control of Foxn1 expression. PMID:23669396
Transcriptome of the Lymantria dispar (gypsy moth) larval midgut in response to infection by Bacillus thuringiensis. PMID:23658687
Genomic diversity and fitness of E. coli strains recovered from the intestinal and urinary tracts of women with recurrent urinary tract infection. PMID:23658245
Reprever: resolving low-copy duplicated sequences using template driven assembly. PMID:23658221
DDBJ read annotation pipeline: a cloud computing-based pipeline for high-throughput analysis of next-generation sequencing data. PMID:23657089
High occurrence of functional new chimeric genes in survey of rice chromosome 3 short arm genome sequences. PMID:23651622
Population genomics of post-vaccine changes in pneumococcal epidemiology. PMID:23644493
Simultaneous transcriptome analysis of Sorghum and Bipolaris sorghicola by using RNA-seq in combination with de novo transcriptome assembly. PMID:23638091
Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PMID:23637635
Somatic alterations contributing to metastasis of a castration-resistant prostate cancer. PMID:23636849
Metagenomic evidence for sulfur lithotrophy by Epsilonproteobacteria as the major energy source for primary productivity in a sub-aerial arctic glacial deposit, Borup Fiord Pass. PMID:23626586
The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. PMID:23624526
Phylogenomics of strongylocentrotid sea urchins. PMID:23617542
Widespread divergence of the CEACAM/PSG genes in vertebrates and humans suggests sensitivity to selection. PMID:23613906
Mechanisms of intron loss and gain in the fission yeast Schizosaccharomyces. PMID:23613904
Analysis and design of RNA sequencing experiments for identifying RNA editing and other single-nucleotide variants. PMID:23598527
Regional modulation of a stochastically expressed factor determines photoreceptor subtypes in the Drosophila retina. PMID:23597484
Computational solutions for omics data. PMID:23594911
Development of peptide nucleic acid probes for detection of the HER2 oncogene. PMID:23593123
Resequencing and comparative genomics of Stagonospora nodorum: sectional gene absence and effector discovery. PMID:23589517
CD34(+) expansion with Delta-1 and HOXB4 promotes rapid engraftment and transfusion independence in a Macaca nemestrina cord blood transplant model. PMID:23587923
Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo. PMID:23583100
Overexpression of full-length centrobin rescues limb malformation but not male fertility of the hypodactylous (hd) rats. PMID:23577170
Monocular inhibition reveals temporal and spatial changes in gene expression in the primary visual cortex of marmoset. PMID:23576954
The use of RelocaTE and unassembled short reads to produce high-resolution snapshots of transposable element generated diversity in rice. PMID:23576519
Construction of customized sub-databases from NCBI-nr database for rapid annotation of huge metagenomic datasets using a combined BLAST and MEGAN approach. PMID:23573212
Comprehensively identifying and characterizing the missing gene sequences in human reference genome with integrated analytic approaches. PMID:23572138
OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds. PMID:23571760
Defining the functional potential and active community members of a sediment microbial community in a high-arctic hypersaline subzero spring. PMID:23563939
Metagenomic study of the viruses of African straw-coloured fruit bats: detection of a chiropteran poxvirus and isolation of a novel adenovirus. PMID:23562481
Tumor-associated copy number changes in the circulation of patients with prostate cancer identified through whole-genome sequencing. PMID:23561577
Transcriptome analysis of the differentially expressed genes in the male and female shrub willows (Salix suchowensis). PMID:23560075
Probabilistic error correction for RNA sequencing. PMID:23558750
Genome-wide characterization and linkage mapping of simple sequence repeats in mei (Prunus mume Sieb. et Zucc.). PMID:23555708
Probabilistic inference of biochemical reactions in microbial communities from metagenomic sequences. PMID:23555216
Transduction-specific ATLAS reveals a cohort of highly active L1 retrotransposons in human populations. PMID:23553801
PRICE: software for the targeted assembly of components of (Meta) genomic sequence data. PMID:23550143
TRACER: a resource to study the regulatory architecture of the mouse genome. PMID:23547943
Sex-biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. PMID:23547111
Development and characterization of cDNA resources for the common marmoset: one of the experimental primate models. PMID:23543116
The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits. PMID:23542700
Contrasting patterns of transposable element and satellite distribution on sex chromosomes (XY1Y2) in the dioecious plant Rumex acetosa. PMID:23542206
The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits. PMID:23542700
Contrasting patterns of transposable element and satellite distribution on sex chromosomes (XY1Y2) in the dioecious plant Rumex acetosa. PMID:23542206
Sequencing of the Dutch elm disease fungus genome using the Roche/454 GS-FLX Titanium System in a comparison of multiple genomics core facilities. PMID:23542132
Genome sequence of ground tit Pseudopodoces humilis and its adaptation to high altitude. PMID:23537097
Construction of a plant-transformation-competent BIBAC library and genome sequence analysis of polyploid Upland cotton (Gossypium hirsutum L.). PMID:23537070
The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. PMID:23537068
Prediction of constitutive A-to-I editing sites from human transcriptomes in the absence of genomic sequences. PMID:23537002
The first symbiont-free genome sequence of marine red alga, Susabi-nori (Pyropia yezoensis). PMID:23536760
Contradiction between plastid gene transcription and function due to complex posttranscriptional splicing: an exemplary study of ycf15 function and evolution in angiosperms. PMID:23527231
SLAF-seq: an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing. PMID:23527008
Genetic-genomic replication to identify candidate mouse atherosclerosis modifier genes. PMID:23525445
The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. PMID:23525075
Genomics of Loa loa, a Wolbachia-free filarial parasite of humans. PMID:23525074
The Reference Genome of the Halophytic Plant Eutrema salsugineum. PMID:23518688
Microhomology-mediated mechanisms underlie non-recurrent disease-causing microdeletions of the FOXL2 gene or its regulatory domain. PMID:23516377
Association of intron loss with high mutation rate in Arabidopsis: implications for genome size evolution. PMID:23516254
Mobilomics in Saccharomyces cerevisiae strains. PMID:23514613
Whole transcriptome analysis using next-generation sequencing of model species Setaria viridis to support C4 photosynthesis research. PMID:23512102
PSimScan: algorithm and utility for fast protein similarity search. PMID:23505522
Analysis of metagenomic data containing high biodiversity levels. PMID:23505458
Retrotransposition of gene transcripts leads to structural variation in mammalian genomes. PMID:23497673
Exaptation of transposable elements into novel cis-regulatory elements: is the evidence always strong? PMID:23486611
Targeted genome enrichment for efficient purification of endosymbiont DNA from host DNA. PMID:23482460
Bacterial DNA sifted from the Trichoplax adhaerens (Animalia: Placozoa) genome project reveals a putative rickettsial endosymbiont. PMID:23475938
Global regulation of alternative splicing by adenosine deaminase acting on RNA (ADAR). PMID:23474544
An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data. PMID:23471004
Transforming growth factor beta receptor 2 (TGFBR2) changes sialylation in the microsatellite unstable (MSI) Colorectal cancer cell line HCT116. PMID:23468914
Modeling host genetic regulation of influenza pathogenesis in the collaborative cross. PMID:23468633
Evolutionary Genomics of Salmonella enterica Subspecies. PMID:23462113
RCPedia: a database of retrocopied genes. PMID:23457042
Estimating the population mutation rate from a de novo assembled Bactrian camel genome and cross-species comparison with dromedary ESTs. PMID:23454912
Comparative analysis of microRNA promoters in Arabidopsis and rice. PMID:23453017
Additional annotation enhances potential for biologically-relevant analysis of the Illumina Infinium HumanMethylation450 BeadChip array. PMID:23452981
Bioinformatic Tools Identify Chromosome-Specific DNA Probes and Facilitate Risk Assessment by Detecting Aneusomies in Extra-embryonic Tissues. PMID:23450259
Nucleotide resolution analysis of TMPRSS2 and ERG rearrangements in prostate cancer. PMID:23447416
Circular RNAs are a large class of animal RNAs with regulatory potency. PMID:23446348
RECOT: a tool for the coordinate transformation of next-generation sequencing reads for comparative genomics and transcriptomics. PMID:23442262
Genome sequencing identifies two nearly unchanged strains of persistent Listeria monocytogenes isolated at two different fish processing plants sampled 6 years apart. PMID:23435887
Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution. PMID:23433480
Transcriptome analysis of Inbred Long Sleep and Inbred Short Sleep mice. PMID:23433184
Genome sequence-based species delimitation with confidence intervals and improved distance functions. PMID:23432962
Transcriptome analyses reveal protein and domain families that delineate stage-related development in the economically important parasitic nematodes, Ostertagia ostertagi and Cooperia oncophora. PMID:23432754
Alternative polyadenylation in glioblastoma multiforme and changes in predicted RNA binding protein profiles. PMID:23421905
Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta. PMID:23419129
TNPO3 protects HIV-1 replication from CPSF6-mediated capsid stabilization in the host cell cytoplasm. PMID:23414560
Genetic diversity, linkage disequilibrium and selection signatures in chinese and Western pigs revealed by genome-wide SNP markers. PMID:23409110
TriageTools: tools for partitioning and prioritizing analysis of high-throughput sequencing data. PMID:23408855
The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes. PMID:23382650
Draft genome sequence of the rubber tree Hevea brasiliensis. PMID:23375136
Genomic diversity and evolution of the head crest in the rock pigeon. PMID:23371554
HDAM: a resource of human disease associated mutations from next generation sequencing studies. PMID:23369322
Genome-wide identification, characterization, and expression analysis of lineage-specific genes within zebrafish. PMID:23368736
A multispecies polyadenylation site model. PMID:23368518
Gene copy-number polymorphism caused by retrotransposition in humans. PMID:23359205
Comparative genome structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens. PMID:23357949
Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. PMID:23354103
Cloning, annotation and developmental expression of the chicken intestinal MUC2 gene. PMID:23349743
Trivalent live attenuated influenza-simian immunodeficiency virus vaccines: efficacy and evolution of cytotoxic T lymphocyte escape in macaques. PMID:23345519
Genome reannotation of the lizard Anolis carolinensis based on 14 adult and embryonic deep transcriptomes. PMID:23343042
A survey of tools for variant analysis of next-generation genome sequencing data. PMID:23341494
Identification of biologically relevant enhancers in human erythroid cells. PMID:23341446
Deep sequencing of RNA from ancient maize kernels. PMID:23326310
A structural-based strategy for recognition of transcription factor binding sites. PMID:23320072
Birth, decay, and reconstruction of an ancient TRIMCyp gene fusion in primate genomes. PMID:23319649
Comparative genomics of a plant-pathogenic fungus, Pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence. PMID:23316438
Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. PMID:23314698
A heterozygous moth genome provides insights into herbivory and detoxification. PMID:23313953
A large-scale in vivo analysis reveals that TALENs are significantly more mutagenic than ZFNs generated using context-dependent assembly. PMID:23303782
Lack of evidence for existence of noncanonical RNA editing. PMID:23302925
Henipavirus pathogenesis in human respiratory epithelial cells. PMID:23302882
Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. PMID:23299411
The cytochrome P450 genesis locus: the origin and evolution of animal cytochrome P450s. PMID:23297357
Meta-analytical biomarker search of EST expression data reveals three differentially expressed candidates. PMID:23282184
A specific family of interspersed repeats (SINEs) facilitates meiotic synapsis in mammals. PMID:23276256
rDNA-directed integration by an HIV-1 integrase--I-PpoI fusion protein. PMID:23275537
Spreading of heterochromatin is limited to specific families of maize retrotransposons. PMID:23271981
The genome of Prunus mume. PMID:23271652
A genomic scale map of genetic diversity in Trypanosoma cruzi. PMID:23270511
Identification of stanniocalcin 2 as a novel aryl hydrocarbon receptor target gene. PMID:23269473
A versatile genome-scale PCR-based pipeline for high-definition DNA FISH. PMID:23263692
Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). PMID:23263233
Genomic pathology of SLE-associated copy-number variation at the FCGR2C/FCGR3B/FCGR2B locus. PMID:23261299
Structural analysis of the genome of breast cancer cell line ZR-75-30 identifies twelve expressed fusion genes. PMID:23260012
Mutation spectrum of Drosophila CNVs revealed by breakpoint sequencing. PMID:23259534
Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. PMID:23257886
TrueSight: a new algorithm for splice junction detection using RNA-seq. PMID:23254332
An integrated approach of comparative genomics and heritability analysis of pig and human on obesity trait: evidence for candidate genes on human chromosome 2. PMID:23253381
Genome-wide analysis of DNA methylation differences in muscle and fat from monozygotic twins discordant for type 2 diabetes. PMID:23251491
Next-generation sequencing meets genetic diagnostics: development of a comprehensive workflow for the analysis of BRCA1 and BRCA2 genes. PMID:23249957
Latent regulatory potential of human-specific repetitive elements. PMID:23246434
Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi. PMID:23236275
ENU mutagenesis reveals that Notchless homolog 1 (Drosophila) affects Cdkn1a and several members of the Wnt pathway during murine pre-implantation development. PMID:23231322
The first genetic map of the American cranberry: exploration of synteny conservation and quantitative trait loci. PMID:23224333
Flexible and efficient genome tiling design with penalized uniqueness score. PMID:23216884
Using chimaeric expression sequence tag as the reference to identify three-dimensional chromosome contacts. PMID:23213109
Comprehensive human transcription factor binding site map for combinatory binding motifs discovery. PMID:23209563
A forward genetic screen reveals that calcium-dependent protein kinase 3 regulates egress in Toxoplasma. PMID:23209419
Integrated genomic analyses identify ARID1A and ARID1B alterations in the childhood cancer neuroblastoma. PMID:23202128
Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing. PMID:23197571
The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology. PMID:23193278
The evolution of the class A scavenger receptors. PMID:23181696
The chemical interactome space between the human host and the genetically defined gut metabotypes. PMID:23178670
Steric antisense inhibition of AMPA receptor Q/R editing reveals tight coupling to intronic editing sites and splicing. PMID:23172291
Activity-regulated RNA editing in select neuronal subfields in hippocampus. PMID:23172290
Identification, characterization and distribution of transposable elements in the flax (Linum usitatissimum L.) genome. PMID:23171245
Comparative analysis of genome sequences covering the seven cronobacter species. PMID:23166675
Deep sequencing reveals differences in the transcriptional landscapes of fibers from two cultivated species of cotton. PMID:23166598
Transcriptome sequencing and annotation for the Jamaican fruit bat (Artibeus jamaicensis). PMID:23166587
A high density recombination map of the pig reveals a correlation between sex-specific recombination and GC content. PMID:23152986
Strong signatures of selection in the domestic pig genome. PMID:23151514
The genome of the pear (Pyrus bretschneideri Rehd.). PMID:23149293
A streamlined method for detecting structural variants in cancer genomes by short read paired-end sequencing. PMID:23144753
ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data. PMID:23143107
Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. PMID:23136377
Comparative genomics of neuroglobin reveals its early origins. PMID:23133533
Variants affecting exon skipping contribute to complex traits. PMID:23133393
Current analysis platforms and methods for detecting copy number variation. PMID:23132758
Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat. PMID:23124323
Reanalysis of RNA-sequencing data reveals several additional fusion genes with multiple isoforms. PMID:23119097
A fish-specific transposable element shapes the repertoire of p53 target genes in zebrafish. PMID:23118857
Toward understanding the genetic basis of adaptation to high-elevation life in poikilothermic species: a comparative transcriptomic analysis of two ranid frogs, Rana chensinensis and R. kukunoris. PMID:23116153
Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes. PMID:23114024
The τCstF-64 polyadenylation protein controls genome expression in testis. PMID:23110235
Comparative evaluation of intron prediction methods and detection of plant genome annotation using intron length distributions. PMID:23105930
STAR: ultrafast universal RNA-seq aligner. PMID:23104886
Genome update of Botrytis cinerea strains B05.10 and T4. PMID:23104368
Sex-biased transcriptome evolution in Drosophila. PMID:23097318
CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex. PMID:23085716
A hybrid distance measure for clustering expressed sequence tags originating from the same gene family. PMID:23071763
Gene and genome parameters of mammalian liver circadian genes (LCGs). PMID:23071677
The Paramecium germline genome provides a niche for intragenic parasitic DNA: evolutionary dynamics of internal eliminated sequences. PMID:23071448
SPLOOCE: a new portal for the analysis of human splicing variants. PMID:23064119
Computational tools for viral metagenomics and their application in clinical research. PMID:23062738
Next-generation sequencing coupled with a cell-free display technology for high-throughput production of reliable interactome data. PMID:23056904
Selective constraint on copy number variation in human piwi-interacting RNA Loci. PMID:23056369
RNA-Seq Assembly - Are We There Yet? PMID:23056003
A statistical framework for accurate taxonomic assignment of metagenomic sequencing reads. PMID:23049702
A multi-omic map of the lipid-producing yeast Rhodosporidium toruloides. PMID:23047670
Conserved epigenetic sensitivity to early life experience in the rat and human hippocampus. PMID:23045659
Next-generation sequencing and de novo assembly, genome organization, and comparative genomic analyses of the genomes of two Helicobacter pylori isolates from duodenal ulcer patients in India. PMID:23045484
MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data. PMID:23044549
Hundreds of conserved non-coding genomic regions are independently lost in mammals. PMID:23042682
Discovery and characterization of human exonic transcriptional regulatory elements. PMID:23029400
Pan-genomic analysis provides insights into the genomic variation and evolution of Salmonella Paratyphi A. PMID:23028950
Tethering of the conserved piggyBac transposase fusion protein CSB-PGBD3 to chromosomal AP-1 proteins regulates expression of nearby genes in humans. PMID:23028371
A novel rhabdovirus associated with acute hemorrhagic fever in central Africa. PMID:23028323
Noncoder: a web interface for exon array-based detection of long non-coding RNAs. PMID:23012263
Genetic structure of community acquired methicillin-resistant Staphylococcus aureus USA300. PMID:23009684
ncRNAclassifier: a tool for detection and classification of transposable element sequences in RNA hairpins. PMID:23009561
The minimal active human SVA retrotransposon requires only the 5'-hexamer and Alu-like domains. PMID:23007156
High-resolution genotyping and mapping of recombination and gene conversion in the protozoan Theileria parva using whole genome sequencing. PMID:22998600
Rat Mcs1b is concordant to the genome-wide association-identified breast cancer risk locus at human 5q11.2 and MIER3 is a candidate cancer susceptibility gene. PMID:22993404
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. PMID:22988817
Genome sequencing and genetic breeding of a bioethanol Saccharomyces cerevisiae strain YJS329. PMID:22978491
Comparative genomics of eukaryotic small nucleolar RNAs reveals deep evolutionary ancestry amidst ongoing intragenomic mobility. PMID:22978381
Highly improved homopolymer aware nucleotide-protein alignments with 454 data. PMID:22971057
AbsIDconvert: an absolute approach for converting genetic identifiers at different granularities. PMID:22967011
Finding differentially expressed regions of arbitrary length in quantitative genomic data based on marked point process model. PMID:22962492
MetaCluster 5.0: a two-round binning approach for metagenomic data for low-abundance species in a noisy sample. PMID:22962452
Activity-dependent human brain coding/noncoding gene regulatory networks. PMID:22960213
RON is not a prognostic marker for resectable pancreatic cancer. PMID:22958871
Long noncoding RNAs are rarely translated in two human cell lines. PMID:22955977
Ruler arrays reveal haploid genomic structural variation. PMID:22952647
The GENCODE pseudogene resource. PMID:22951037
Genotypic and phenotypic evaluation of the evolution of high-level daptomycin nonsusceptibility in vancomycin-resistant Enterococcus faecium. PMID:22948885
SKIP is a component of the spliceosome linking alternative splicing and the circadian clock in Arabidopsis. PMID:22942380
Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms. PMID:22941634
Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize. PMID:22937793
An alu-based phylogeny of lemurs (infraorder: Lemuriformes). PMID:22937148
Mechanisms of dietary response in mice and primates: a role for EGR1 in regulating the reaction to human-specific nutritional content. PMID:22937124
A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence. PMID:22936249
Tissue-restricted transcription from a conserved intragenic CpG island in the Klf1 gene in mice. PMID:22933519
Integrase-deficient lentiviral vectors mediate efficient gene transfer to human vascular smooth muscle cells with minimal genotoxic risk. PMID:22931362
Identification and analysis of pig chimeric mRNAs using RNA sequencing data. PMID:22925561
Rapid phylogenetic and functional classification of short genomic fragments with signature peptides. PMID:22925230
Characterization of the standard and recommended CODIS markers. PMID:22925064
Dynamic regulation of HIV-1 mRNA populations analyzed by single-molecule enrichment and long-read sequencing. PMID:22923523
The diversity of class II transposable elements in mammalian genomes has arisen from ancestral phylogenetic splits during ancient waves of proliferation through the genome. PMID:22923465
The human transcriptome: an unfinished story. PMID:22916334
Eco-geographical diversification of bitter taste receptor genes (TAS2Rs) among subspecies of chimpanzees (Pan troglodytes). PMID:22916235
Identification and functional analysis of three isoforms of bovine BST-2. PMID:22911799
Personal receptor repertoires: olfaction as a model. PMID:22908908
The UCSC genome browser and associated tools. PMID:22908213
CaPSID: a bioinformatics platform for computational pathogen sequence identification in human genomes and transcriptomes. PMID:22901030
Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales. PMID:22900609
Mating of the stichotrichous ciliate Oxytricha trifallax induces production of a class of 27 nt small RNAs derived from the parental macronucleus. PMID:22900016
Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data. PMID:22891638
FoxO-dependent regulation of diacylglycerol kinase α gene expression. PMID:22890845
Genetic changes during a laboratory adaptive evolution process that allowed fast growth in glucose to an Escherichia coli strain lacking the major glucose transport system. PMID:22884033
SAP--a sequence mapping and analyzing program for long sequence reads alignment and accurate variants discovery. PMID:22880129
Integrative transcriptome analysis suggest processing of a subset of long non-coding RNAs to small RNAs. PMID:22871084
Ultra-high resolution HLA genotyping and allele discovery by highly multiplexed cDNA amplicon pyrosequencing. PMID:22866951
A genomic approach to investigate expression profiles in Slovenian patients with gastric cancer. PMID:22866164
Identification of 34 novel proinflammatory proteins in a genome-wide macrophage functional screen. PMID:22860121
The natural history of class I primate alcohol dehydrogenases includes gene duplication, gene loss, and gene conversion. PMID:22859968
Spatio-temporal regulation of ADAR editing during development in porcine neural tissues. PMID:22858680
Evolutionary patterns of RNA-based gene duplicates in Caenorhabditis nematodes coincide with their genomic features. PMID:22853807
Complementary proteome and transcriptome profiling in phosphate-deficient Arabidopsis roots reveals multiple levels of gene regulation. PMID:22843991
Newly evolved introns in human retrogenes provide novel insights into their evolutionary roles. PMID:22839428
Short-read reading-frame predictors are not created equal: sequence error causes loss of signal. PMID:22839106
Newly evolved introns in human retrogenes provide novel insights into their evolutionary roles. PMID:22839428
Short-read reading-frame predictors are not created equal: sequence error causes loss of signal. PMID:22839106
Sequencing of the smallest Apicomplexan genome from the human pathogen Babesia microti. PMID:22833609
Reverse engineering biomolecular systems using -omic data: challenges, progress and opportunities. PMID:22833495
YAHA: fast and flexible long-read alignment with optimal breakpoint detection. PMID:22829624
FAST-SeqS: a simple and efficient method for the detection of aneuploidy by massively parallel sequencing. PMID:22815955
Novel RNAi-mediated approach to G protein-coupled receptor deorphanization: proof of principle and characterization of a planarian 5-HT receptor. PMID:22815820
Comparative genomic and transcriptional analyses of CRISPR systems across the genus Pyrobaculum. PMID:22811677
Restricted gene flow among hospital subpopulations of Enterococcus faecium. PMID:22807567
The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. PMID:22801500
Large-scale transcriptome analysis of retroelements in the migratory locust, Locusta migratoria. PMID:22792363
Diversity of Antisense and Other Non-Coding RNAs in Archaea Revealed by Comparative Small RNA Sequencing in Four Pyrobaculum Species. PMID:22783241
Compressive genomics. PMID:22781691
Ultrafast clustering algorithms for metagenomic sequence analysis. PMID:22772836
Functional assignment of metagenomic data: challenges and applications. PMID:22772835
Oomycete Transcriptomics Database: a resource for oomycete transcriptomes. PMID:22768977
A pronounced evolutionary shift of the pseudoautosomal region boundary in house mice. PMID:22763584
Hybrid error correction and de novo assembly of single-molecule sequencing reads. PMID:22750884
Comparative transcriptome analysis between planarian Dugesia japonica and other platyhelminth species. PMID:22747887
Bovine polledness--an autosomal dominant trait with allelic heterogeneity. PMID:22737241
Large-scale collection and annotation of gene models for date palm (Phoenix dactylifera, L.). PMID:22736259
Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L. (Pinaceae). PMID:22731878
Expressed pseudogenes in the transcriptional landscape of human cancers. PMID:22726445
Developing the anemone Aiptasia as a tractable model for cnidarian-dinoflagellate symbiosis: the transcriptome of aposymbiotic A. pallida. PMID:22726260
Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development. PMID:22724064
Characteristics of nucleosomes and linker DNA regions on the genome of the basidiomycete Mixia osmundae revealed by mono- and dinucleosome mapping. PMID:22724063
A tumour suppressor network relying on the polyamine-hypusine axis. PMID:22722845
The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools. PMID:22720753
Skipping of exons by premature termination of transcription and alternative splicing within intron-5 of the sheep SCF gene: a novel splice variant. PMID:22719917
A SEL1L mutation links a canine progressive early-onset cerebellar ataxia to the endoplasmic reticulum-associated protein degradation (ERAD) machinery. PMID:22719266
Field monitoring of avian influenza viruses: whole-genome sequencing and tracking of neuraminidase evolution using 454 pyrosequencing. PMID:22718944
The molecular mechanism of action of the CR6261-Azichromycin combination found through computational analysis. PMID:22693576
UniPrimer: A Web-Based Primer Design Tool for Comparative Analyses of Primate Genomes. PMID:22693428
Novel domain combinations in proteins encoded by chimeric transcripts. PMID:22689780
SEQuel: improving the accuracy of genome assemblies. PMID:22689760
Dissect: detection and characterization of novel structural alterations in transcribed sequences. PMID:22689759
Xenome--a tool for classifying reads from xenograft samples. PMID:22689758
MFEprimer-2.0: a fast thermodynamics-based program for checking PCR primer specificity. PMID:22689644
Multi-locus phylogeographic and population genetic analysis of Anolis carolinensis: historical demography of a genomic model species. PMID:22685573
An Alu-based phylogeny of gibbons (hylobatidae). PMID:22683814
High accuracy mutation detection in leukemia on a selected panel of cancer genes. PMID:22675565
Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PMID:22675423
Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis. PMID:22674328
Genomic variation in natural populations of Drosophila melanogaster. PMID:22673804
A high-resolution map of the Nile tilapia genome: a resource for studying cichlids and other percomorphs. PMID:22672252
Regulated Expression of Chromobox Homolog 5 Revealed in Tumors of Apc(Min) (/+) ROSA11 Gene Trap Mice. PMID:22670227
The iPlant Collaborative: Cyberinfrastructure for Plant Biology. PMID:22645531
Mutation at the human D1S80 minisatellite locus. PMID:22645469
Transcriptome analysis of a North American songbird, Melospiza melodia. PMID:22645122
Epigenetics in the human brain. PMID:22643929
GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts. PMID:22641850
VarioWatch: providing large-scale and comprehensive annotations on human genomic variants in the next generation sequencing era. PMID:22618869
Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome. PMID:22615578
Molecular diagnostics for congenital hearing loss including 15 deafness genes using a next generation sequencing platform. PMID:22607986
Rapid transcriptional pulsing dynamics of high expressing retroviral transgenes in embryonic stem cells. PMID:22606340
jpHMM: recombination analysis in viruses with circular genomes such as the hepatitis B virus. PMID:22600739
Functional analysis of synonymous substitutions predicted to affect splicing of the CFTR gene. PMID:22591852
Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts. PMID:22588898
Metagenomics - a guide from sampling to data analysis. PMID:22587947
On the analysis of the illumina 450k array data: probes ambiguously mapped to the human genome. PMID:22586432
SIS: a program to generate draft genome sequence scaffolds for prokaryotes. PMID:22583530
Reference genome sequence of the model plant Setaria. PMID:22580951
Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. PMID:22580950
GHOSTM: a GPU-accelerated homology search tool for metagenomics. PMID:22574135
Meta-analysis of genetic association studies on bipolar disorder. PMID:22573399
Extended survival of glioblastoma patients after chemoprotective HSC gene therapy. PMID:22572881
Microarray analysis of LTR retrotransposon silencing identifies Hdac1 as a regulator of retrotransposon expression in mouse embryonic stem cells. PMID:22570599
Transcript profiling identifies dynamic gene expression patterns and an important role for Nrf2/Keap1 pathway in the developing mouse esophagus. PMID:22567161
BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data. PMID:22563071
Bioinformatic clonality analysis of next-generation sequencing-derived viral vector integration sites. PMID:22559057
Digital gene expression analysis based on integrated de novo transcriptome assembly of sweet potato [Ipomoea batatas (L.) Lam]. PMID:22558397
Experimental verification of a predicted intronic microRNA in human NGFR gene with a potential pro-apoptotic function. PMID:22558167
Elephant transcriptome provides insights into the evolution of eutherian placentation. PMID:22546564
Orangutan Alu quiescence reveals possible source element: support for ancient backseat drivers. PMID:22541534
A context-based approach to identify the most likely mapping for RNA-seq experiments. PMID:22537048
KISSPLICE: de-novo calling alternative splicing events from RNA-seq data. PMID:22537044
PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text. PMID:22537006
Tachyon search speeds up retrieval of similar sequences by several orders of magnitude. PMID:22531216
Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle. PMID:22529356
A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy. PMID:22524439
lobSTR: A short tandem repeat profiler for personal genomes. PMID:22522390
A beginner's guide to eukaryotic genome annotation. PMID:22510764
Mapping of gene expression reveals CYP27A1 as a susceptibility gene for sporadic ALS. PMID:22509407
A genome resource to address mechanisms of developmental programming: determination of the fetal sheep heart transcriptome. PMID:22508961
The Chlamydia psittaci genome: a comparative analysis of intracellular pathogens. PMID:22506068
Fast and accurate taxonomic assignments of metagenomic sequences using MetaBin. PMID:22496776
Search for an aetiological virus candidate in chronic lymphocytic leukaemia by extensive transcriptome analysis. PMID:22489537
Characterisation of bovine leukocyte Ig-like receptors. PMID:22485161
Exploring the switchgrass transcriptome using second-generation sequencing technology. PMID:22479570
Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies. PMID:22475018
Whole genome expression differences in human left and right atria ascertained by RNA sequencing. PMID:22474228
Identification of allele-specific alternative mRNA processing via transcriptome sequencing. PMID:22467206
A quantitative atlas of polyadenylation in five mammals. PMID:22454233
Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer. PMID:22443449
Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants. PMID:22417298
Bisquinolinium compounds induce quadruplex-specific transcriptome changes in HeLa S3 cell lines. PMID:22414013
Identification and properties of 1,119 candidate lincRNA loci in the Drosophila melanogaster genome. PMID:22403033
High Levels of Sequence Diversity in the 5' UTRs of Human-Specific L1 Elements. PMID:22400009
Genomic analysis of the hydrocarbon-producing, cellulolytic, endophytic fungus Ascocoryne sarcoides. PMID:22396667
Using BLAT to find sequence similarity in closely related genomes. PMID:22389010
Molecular cloning of large alternative transcripts based on comparative phylogenetic analysis and exploration of an EST database. PMID:22387390
Expression quantitative trait Loci for extreme host response to influenza a in pre-collaborative cross mice. PMID:22384400
Organizational heterogeneity of vertebrate genomes. PMID:22384143
FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads. PMID:22379138
Rapid identification of non-human sequences in high-throughput sequencing datasets. PMID:22377895
Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. PMID:22373417
ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information. PMID:22373054
Interrogation of alternative splicing events in duplicated genes during evolution. PMID:22369477
Profiling ascidian promoters as the primordial type of vertebrate promoter. PMID:22369359
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. PMID:22368243
Hospital and community ampicillin-resistant Enterococcus faecium are evolutionarily closely linked but have diversified through niche adaptation. PMID:22363425
Joint analysis of multiple metagenomic samples. PMID:22359490
Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions. PMID:22355574
Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PMID:22347999
Virus identification in unknown tropical febrile illness cases using deep sequencing. PMID:22347512
Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster. PMID:22347367
A differential sequencing-based analysis of the C. elegans noncoding transcriptome. PMID:22345127
Effect of periodontal pathogens on the metatranscriptome of a healthy multispecies biofilm model. PMID:22328675
CAPRG: sequence assembling pipeline for next generation sequencing of non-model organisms. PMID:22319566
SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data. PMID:22293517
The chimpanzee GH locus: composition, organization, and evolution. PMID:22290452
A cost-effective and universal strategy for complete prokaryotic genomic sequencing proposed by computer simulation. PMID:22289569
R-SAP: a multi-threading computational pipeline for the characterization of high-throughput RNA-sequencing data. PMID:22287631
Deep-sequencing of endothelial cells exposed to hypoxia reveals the complexity of known and novel microRNAs. PMID:22282338
Detection of base substitution-type somatic mosaicism of the NLRP3 gene with >99.9% statistical confidence by massively parallel sequencing. PMID:22279087
Adrenal androgen production in catarrhine primates and the evolution of adrenarche. PMID:22271526
A recurrent translocation is mediated by homologous recombination between HERV-H elements. PMID:22260357
Evidence for transcript networks composed of chimeric RNAs in human cells. PMID:22238572
Entry of human T-cell leukemia virus type 1 is augmented by heparin sulfate proteoglycans bearing short heparin-like structures. PMID:22238310
Investigation of the origin and spread of a Mammalian transposable element based on current sequence diversity. PMID:22222953
A nucleosomal surface defines an integration hotspot for the Saccharomyces cerevisiae Ty1 retrotransposon. PMID:22219511
Common promoter elements in odorant and vomeronasal receptor genes. PMID:22216168
Functional RNA interference (RNAi) screen identifies system A neutral amino acid transporter 2 (SNAT2) as a mediator of arsenic-induced endoplasmic reticulum stress. PMID:22215663
Genome-wide expression profiling of schizophrenia using a large combined cohort. PMID:22212594
SCOREM: statistical consolidation of redundant expression measures. PMID:22210887
Probe mapping across multiple microarray platforms. PMID:22199380
RNASEQR--a streamlined and accurate RNA-seq sequence analysis program. PMID:22199257
Phenotype-specific effect of chromosome 1q21.1 rearrangements and GJA5 duplications in 2436 congenital heart disease patients and 6760 controls. PMID:22199024
Molecular mechanisms of EGF signaling-dependent regulation of pipe, a gene crucial for dorsoventral axis formation in Drosophila. PMID:22198544
Analysis of expression sequence tags from a full-length-enriched cDNA library of developing sesame seeds (Sesamum indicum). PMID:22195973
Genome-wide signatures of 'rearrangement hotspots' within segmental duplications in humans. PMID:22194928
Transcriptome analyses to investigate the pathogenesis of RNA splicing factor retinitis pigmentosa. PMID:22183372
A deep sequencing approach to comparatively analyze the transcriptome of lifecycle stages of the filarial worm, Brugia malayi. PMID:22180794
Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12. PMID:22180530
The mosquito Aedes aegypti has a large genome size and high transposable element load but contains a low proportion of transposon-specific piRNAs. PMID:22171608
Neuroglobin-deficiency exacerbates Hif1A and c-FOS response, but does not affect neuronal survival during severe hypoxia in vivo. PMID:22164238
MicroRNA-driven developmental remodeling in the brain distinguishes humans from other primates. PMID:22162950
Polymorphic NumtS trace human population relationships. PMID:22160368
Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. PMID:22158310
Complete resequencing and reannotation of the Lactobacillus plantarum WCFS1 genome. PMID:22156394
Hematopoietic stem cell expansion facilitates multilineage engraftment in a nonhuman primate cord blood transplantation model. PMID:22155723
STELLAR: fast and exact local alignments. PMID:22151882
The repertoire of G protein-coupled receptors in the human parasite Schistosoma mansoni and the model organism Schmidtea mediterranea. PMID:22145649
Identification of a genomic reservoir for new TRIM genes in primate genomes. PMID:22144910
Estimated comparative integration hotspots identify different behaviors of retroviral gene transfer vectors. PMID:22144885
RecountDB: a database of mapped and count corrected transcribed sequences. PMID:22139942
Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster. PMID:22135405
Dr.VIS: a database of human disease-related viral integration sites. PMID:22135288
Revealing the missing expressed genes beyond the human reference genome by RNA-Seq. PMID:22133125
Miniature inverted-repeat transposable elements (MITEs) have been accumulated through amplification bursts and play important roles in gene expression and species diversity in Oryza sativa. PMID:22096216
Characterizing complex structural variation in germline and somatic genomes. PMID:22094265
High-resolution analysis of intrahost genetic diversity in dengue virus serotype 1 infection identifies mixed infections. PMID:22090119
Integrative deep sequencing of the mouse lung transcriptome reveals differential expression of diverse classes of small RNAs in response to respiratory virus infection. PMID:22086488
Effects of genome-wide copy number variation on expression in mammalian cells. PMID:22085887
CADRE: the Central Aspergillus Data REpository 2012. PMID:22080563
Evolutionary history and functional characterization of the amphibian xenosensor CAR. PMID:22074953
Drosophila duplication hotspots are associated with late-replicating regions of the genome. PMID:22072977
Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species. PMID:22067447
Identification, characterization, and comparative genomic distribution of the HERV-K (HML-2) group of human endogenous retroviruses. PMID:22067224
Approaches to Fungal Genome Annotation. PMID:22059117
Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. PMID:22057054
A Rickettsia genome overrun by mobile genetic elements provides insight into the acquisition of genes characteristic of an obligate intracellular lifestyle. PMID:22056929
RNA-Seq improves annotation of protein-coding genes in the cucumber genome. PMID:22047402
A living fossil in the genome of a living fossil: Harbinger transposons in the coelacanth genome. PMID:22045999
RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. PMID:22039206
Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance. PMID:22038251
Analysis of transcriptome complexity through RNA sequencing in normal and failing murine hearts. PMID:22034492
Identification of gene fusion transcripts by transcriptome sequencing in BRCA1-mutated breast cancers and cell lines. PMID:22032724
Ascaris suum draft genome. PMID:22031327
Silencing, positive selection and parallel evolution: busy history of primate cytochromes C. PMID:22028846
Graph accordance of next-generation sequence assemblies. PMID:22025481
The draft genome of the carcinogenic human liver fluke Clonorchis sinensis. PMID:22023798
Regional selection acting on the OFD1 gene family. PMID:22022562
Very few RNA and DNA sequence differences in the human transcriptome. PMID:22022455
MicroRNA expression and regulation in human, chimpanzee, and macaque brains. PMID:22022286
Endophytic life strategies decoded by genome and transcriptome analyses of the mutualistic root symbiont Piriformospora indica. PMID:22022265
The draft genome and transcriptome of Cannabis sativa. PMID:22014239
Conditional CD8+ T cell escape during acute simian immunodeficiency virus infection. PMID:22013056
De novo sequence assembly of Albugo candida reveals a small genome relative to other biotrophic oomycetes. PMID:21995639
The UCSC Genome Browser. PMID:21975940
Methylation of L1Hs promoters is lower on the inactive X, has a tendency of being higher on autosomes in smaller genomes and shows inter-individual variability at some loci. PMID:21972244
Kaviar: an accessible system for testing SNV novelty. PMID:21965822
Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris. PMID:21964414
Accurate identification of A-to-I RNA editing in human by transcriptome sequencing. PMID:21960545
Post-transcriptional exon shuffling events in humans can be evolutionarily conserved and abundant. PMID:21948523
Alu pair exclusions in the human genome. PMID:21943335
Genome of a novel isolate of Paracoccus denitrificans capable of degrading N,N-dimethylformamide. PMID:21914898
Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization. PMID:21914852
Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. PMID:21909094
A comparative physical map reveals the pattern of chromosomal evolution between the turkey (Meleagris gallopavo) and chicken (Gallus gallus) genomes. PMID:21906286
Next-generation transcriptome assembly. PMID:21897427
The human gut virome: inter-individual variation and dynamic response to diet. PMID:21880779
In silico reconstruction of viral genomes from small RNAs improves virus-derived small interfering RNA profiling. PMID:21880776
Protein-binding microarray analysis of tumor suppressor AP2α target gene specificity. PMID:21876733
A comprehensive map of mobile element insertion polymorphisms in humans. PMID:21876680
Whole-genome sequencing of multiple Arabidopsis thaliana populations. PMID:21874002
Activation of the glucocorticoid receptor is associated with poor prognosis in estrogen receptor-negative breast cancer. PMID:21868756
Parallelized short read assembly of large genomes using de Bruijn graphs. PMID:21867511
Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli. PMID:21864382
Discovery of lost diversity of paternal horse lineages using ancient DNA. PMID:21863017
Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds. PMID:21863010
Transcriptional profiling of human liver identifies sex-biased genes associated with polygenic dyslipidemia and coronary artery disease. PMID:21858147
Molecular genetic analyses of polytene chromosome region 72A-D in Drosophila melanogaster reveal a gene desert in 72D. PMID:21853143
Three periods of regulatory innovation during vertebrate evolution. PMID:21852499
Comparative deep transcriptional profiling of four developing oilseeds. PMID:21851431
Addressing inter-gene heterogeneity in maximum likelihood phylogenomic analysis: yeasts revisited. PMID:21850235
The head-regeneration transcriptome of the planarian Schmidtea mediterranea. PMID:21846378
Evidence-based annotation of transcripts and proteins in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. PMID:21840973
A boundary element between Tsix and Xist binds the chromatin insulator Ctcf and contributes to initiation of X-chromosome inactivation. PMID:21840866
TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. PMID:21835007
The genome sequence of the North-European cucumber (Cucumis sativus L.) unravels evolutionary adaptation mechanisms in plants. PMID:21829493
An unbiased genome-wide analysis of zinc-finger nuclease specificity. PMID:21822255
The fat body transcriptomes of the yellow fever mosquito Aedes aegypti, pre- and post- blood meal. PMID:21818341
Cross-species protein sequence and gene structure prediction with fine-tuned Webscipio 2.0 and Scipio. PMID:21798037
Identification of genomic indels and structural variations using split reads. PMID:21787423
Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly. PMID:21785424
The complexity of Rhipicephalus (Boophilus) microplus genome characterised through detailed analysis of two BAC clones. PMID:21777481
Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). PMID:21775302
Gene gain and loss during evolution of obligate parasitism in the white rust pathogen of Arabidopsis thaliana. PMID:21750662
Massive changes in genome architecture accompany the transition to self-fertility in the filamentous fungus Neurospora tetrasperma. PMID:21750257
Mutational analysis of 12 patients with the phenotype of Ehlers-Danlos syndrome type VIB shows no linkage to the zinc transporter gene SLC39A13. PMID:21739577
Microbial diversity in the midguts of field and lab-reared populations of the European corn borer Ostrinia nubilalis. PMID:21738787
Gene expression in Trypanosoma brucei: lessons from high-throughput RNA sequencing. PMID:21737348
Phosphorylation network rewiring by gene duplication. PMID:21734643
Deep sequencing of the human TCRγ and TCRβ repertoires suggests that TCRβ rearranges after αβ and γδ T cell commitment. PMID:21734177
Genome assembly has a major impact on gene content: a comparison of annotation in two Bos taurus assemblies. PMID:21731731
Poly (A)+ transcriptome assessment of ERBB2-induced alterations in breast cell lines. PMID:21731642
Evolution of the V, D, and J gene segments used in the primate gammadelta T-cell receptor reveals a dichotomy of conservation and diversity. PMID:21730193
Exome-wide DNA capture and next generation sequencing in domestic and wild species. PMID:21729323
Reproductive tissue-specific expression profiling and genetic variation across a 19 gene bovine β-defensin cluster. PMID:21713586
Evolution of C4 photosynthesis in the genus Flaveria: how many and which genes does it take to make C4? PMID:21705644
Evolutionary conserved microRNAs are ubiquitously expressed compared to tick-specific miRNAs in the cattle tick Rhipicephalus (Boophilus) microplus. PMID:21699734
Nuclear outsourcing of RNA interference components to human mitochondria. PMID:21695135
Genome of multidrug-resistant uropathogenic Escherichia coli strain NA114 from India. PMID:21685291
Meta-IDBA: a de Novo assembler for metagenomic data. PMID:21685107
Transcriptome analysis of sarracenia, an insectivorous plant. PMID:21676972
Comparative analysis of the ATRX promoter and 5' regulatory region reveals conserved regulatory elements which are linked to roles in neurodevelopment, alpha-globin regulation and testicular function. PMID:21676266
CREST maps somatic structural variation in cancer genomes with base-pair resolution. PMID:21666668
Human teneurin-1 is a direct target of the homeobox transcription factor EMX2 at a novel alternate promoter. PMID:21651764
Towards the human colorectal cancer microbiome. PMID:21647227
A novel mitofusin 2 mutation causes canine fetal-onset neuroaxonal dystrophy. PMID:21643798
Computational analysis of drought stress-associated miRNAs and miRNA co-regulation network in Physcomitrella patens. PMID:21641561
Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. PMID:21633356
Genome-wide identification of conserved regulatory function in diverged sequences. PMID:21628450
Refinement of primate copy number variation hotspots identifies candidate genomic regions evolving under positive selection. PMID:21627829
Evaluating the fidelity of de novo short read metagenomic assembly using simulated data. PMID:21625384
De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). PMID:21623354
Computational methods for transcriptome annotation and quantification using RNA-seq. PMID:21623353
Finding cancer-associated miRNAs: methods and tools. PMID:21607762
piRNA profiling during specific stages of mouse spermatogenesis. PMID:21602304
Inhibition of RNA interference and modulation of transposable element expression by cell death in Drosophila. PMID:21596898
Bioinformatics challenges for personalized medicine. PMID:21596790
Comprehensive assessment of sequence variation within the copy number variable defensin cluster on 8p23 by target enriched in-depth 454 sequencing. PMID:21592371
The first sequenced carnivore genome shows complex host-endogenous retrovirus relationships. PMID:21589882
Sequence-specific error profile of Illumina sequencers. PMID:21576222
RAPSearch: a fast protein similarity search tool for short reads. PMID:21575167
Full-length transcriptome assembly from RNA-Seq data without a reference genome. PMID:21572440
BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing. PMID:21565797
Functional divergences of GAPDH isoforms during early development in two perciform fish species. PMID:21559871
Enhancing genome assemblies by integrating non-sequence based data. PMID:21554765
Sequence alignment as hypothesis testing. PMID:21554016
Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing. PMID:21551146
TparvaDB: a database to support Theileria parva vaccine development. PMID:21546359
CORE: a phylogenetically-curated 16S rDNA database of the core oral microbiome. PMID:21544197
Methods and strategies for gene structure curation in WormBase. PMID:21543339
Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing. PMID:21542930
De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics. PMID:21536722
Identification of piRNAs in the central nervous system. PMID:21515829
Genomes of two chronological isolates (Helicobacter pylori 2017 and 2018) of the West African Helicobacter pylori strain 908 obtained from a single patient. PMID:21515762
Getting a full dose? Reconsidering sex chromosome dosage compensation in the silkworm, Bombyx mori. PMID:21508430
Mitochondrial genome sequences illuminate maternal lineages of conservation concern in a rare carnivore. PMID:21507265
FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes. PMID:21505035
The sequence, structure and evolutionary features of HOTAIR in mammals. PMID:21496275
Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual. PMID:21493686
Transcriptome sequencing demonstrates that human papillomavirus is not active in cutaneous squamous cell carcinoma. PMID:21490616
The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. PMID:21478890
A high-resolution linkage map for comparative genome analysis and QTL fine mapping in Asian seabass, Lates calcarifer. PMID:21457569
A vertebrate case study of the quality of assemblies derived from next-generation sequences. PMID:21453517
Rice-Map: a new-generation rice genome browser. PMID:21450055
Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite. PMID:21439036
Fast local fragment chaining using sum-of-pair gap costs. PMID:21418573
Targeted deep resequencing of the human cancer genome using next-generation technologies. PMID:21415896
A method for visualization of "omic" datasets for sphingolipid metabolism to predict potentially interesting differences. PMID:21415121
Rhythms and synchronization patterns in gene expression in the Aedes aegypti mosquito. PMID:21414217
Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos). PMID:21410945
Chromosome conformation capture uncovers potential genome-wide interactions between human conserved non-coding sequences. PMID:21408183
Metatranscriptomic approach to analyze the functional human gut microbiota. PMID:21408168
Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PMID:21408061
Evolution of synonymous codon usage in Neurospora tetrasperma and Neurospora discreta. PMID:21402862
Disease and phenotype data at Ensembl. PMID:21400687
A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues. PMID:21383968
Genome sequence of Neisseria meningitidis serogroup B strain H44/76. PMID:21378179
Discovery and annotation of small proteins using genomics, proteomics, and computational approaches. PMID:21367939
Abundant human DNA contamination identified in non-primate genome databases. PMID:21358816
Distinct influences of tandem repeats and retrotransposons on CENH3 nucleosome positioning. PMID:21352520
FoSTeS, MMBIR and NAHR at the human proximal Xp region and the mechanisms of human Xq isochromosome formation. PMID:21349920
PositionMatcher: A Fast Custom-Annotation Tool for Short DNA Sequences. PMID:21347141
Genome-wide linkage analysis of global gene expression in loin muscle tissue identifies candidate genes in pigs. PMID:21346809
Annotating genes and genomes with DNA sequences extracted from biomedical articles. PMID:21325301
Support vector machines-based identification of alternative splicing in Arabidopsis thaliana from whole-genome tiling arrays. PMID:21324185
Neuronal genes for subcutaneous fat thickness in human and pig are identified by local genomic sequencing and combined SNP association study. PMID:21311593
Zygomycetes, microsporidia, and the evolutionary ancestry of sex determination. PMID:21307298
Quantitative trait loci involved in sex determination and body growth in the gilthead sea bream (Sparus aurata L.) through targeted genome scan. PMID:21304996
Considering transposable element diversification in de novo annotation approaches. PMID:21304975
Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. PMID:21304686
Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. PMID:21304684
Phylogenetic comparison of F-Box (FBX) gene superfamily within the plant kingdom reveals divergent evolutionary histories indicative of genomic drift. PMID:21297981
The effects of EBV transformation on gene expression levels and methylation profiles. PMID:21289059
Genomic sequencing and analysis of a Chinese hamster ovary cell line using Illumina sequencing technology. PMID:21269493
Seventy million years of concerted evolution of a homoeologous chromosome pair, in parallel, in major Poaceae lineages. PMID:21266659
S-adenosylmethionine decreases lipopolysaccharide-induced phosphodiesterase 4B2 and attenuates tumor necrosis factor expression via cAMP/protein kinase A pathway. PMID:21266552
Narrowing a region on rat chromosome 13 that protects against hypertension in Dahl SS-13BN congenic strains. PMID:21257920
Activation-induced cytidine deaminase induces reproducible DNA breaks at many non-Ig Loci in activated B cells. PMID:21255732
DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. PMID:21251332
Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi. PMID:21247460
Identifying viral integration sites using SeqMap 2.0. PMID:21245052
RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts. PMID:21245033
Comparison of Current BLAST Software on Nucleotide Sequences. PMID:21243090
Bioinformatic identification of novel protein phosphatases in the dog genome. PMID:21240543
Expression, splicing, and evolution of the myosin gene family in plants. PMID:21233331
AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision. PMID:21233167
A systematic evaluation of expression of HERV-W elements; influence of genomic context, viral structure and orientation. PMID:21226900
Adaptive seeds tame genomic sequence comparison. PMID:21209072
Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea. PMID:21194483
Aromatase is a direct target of FOXL2: C134W in granulosa cell tumors via a single highly conserved binding site in the ovarian specific promoter. PMID:21188138
The evolutionary analysis of emerging low frequency HIV-1 CXCR4 using variants through time--an ultra-deep approach. PMID:21187908
The solute carrier families have a remarkably long evolutionary history with the majority of the human families present before divergence of Bilaterian species. PMID:21186191
Extraordinary sequence divergence at Tsga8, an X-linked gene involved in mouse spermiogenesis. PMID:21186189
Polycomb preferentially targets stalled promoters of coding and noncoding transcripts. PMID:21177970
Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome. PMID:21177965
The Drosophila melanogaster transcriptome by paired-end RNA sequencing. PMID:21177959
Genomic and transcriptomic analysis of the AP2/ERF superfamily in Vitis vinifera. PMID:21171999
Disease-associated XMRV sequences are consistent with laboratory contamination. PMID:21171979
Gene duplication and divergence of long wavelength-sensitive opsin genes in the guppy, Poecilia reticulata. PMID:21170644
Genome-wide interrogation of Mammalian stem cell fate determinants by nested chromosome deletions. PMID:21170304
A case-by-case evolutionary analysis of four imprinted retrogenes. PMID:21166792
Initial steps towards a production platform for DNA sequence analysis on the grid. PMID:21156038
Genomic mRNA profiling reveals compensatory mechanisms for the requirement of the essential splicing factor U2AF. PMID:21149581
Sequence analysis of the genome of an oil-bearing tree, Jatropha curcas L. PMID:21149391
Identifying novel genes in C. elegans using SAGE tags. PMID:21143975
Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. PMID:21131573
Mining Affymetrix microarray data for long non-coding RNAs: altered expression in the nucleus accumbens of heroin abusers. PMID:21128942
Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists. PMID:21126361
The parental non-equivalence of imprinting control regions during mammalian development and evolution. PMID:21124941
Analyses of copy number variation of GK rat reveal new putative type 2 diabetes susceptibility loci. PMID:21124896
Structure-function analyses point to a polynucleotide-accommodating groove essential for APOBEC3A restriction activities. PMID:21123384
Pseudogene: lessons from PCR bias, identification and resurrection. PMID:21116863
Molecular description and industrial potential of Tn6098 conjugative transfer conferring alpha-galactoside metabolism in Lactococcus lactis. PMID:21115709
Cross-validated methods for promoter/transcription start site mapping in SL trans-spliced genes, established using the Ciona intestinalis troponin I gene. PMID:21109525
Recurrent interstitial 1p36 deletions: Evidence for germline mosaicism and complex rearrangement breakpoints. PMID:21108392
Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads. PMID:21106091
Genetic diversity in India and the inference of Eurasian population expansion. PMID:21106085
The rapid generation of chimerical genes expanding protein diversity in zebrafish. PMID:21106061
Fine genetic mapping localizes cucumber scab resistance gene Ccu into an R gene cluster. PMID:21104067
Multiplexed DNA sequence capture of mitochondrial genomes using PCR products. PMID:21103372
dbDNV: a resource of duplicated gene nucleotide variants in human genome. PMID:21097891
Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing. PMID:21092284
Nme gene family evolutionary history reveals pre-metazoan origins and high conservation between humans and the sea anemone, Nematostella vectensis. PMID:21085602
HMMSplicer: a tool for efficient and sensitive discovery of known and novel splice junctions in RNA-Seq data. PMID:21079731
Expression of type II chorionic gonadotropin genes supports a role in the male reproductive system. PMID:21078876
Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. PMID:21076406
Identification of alternatively spliced transcripts using a proteomic informatics approach. PMID:21063957
Genomic tools development for Aquilegia: construction of a BAC-based physical map. PMID:21059242
Dating primate divergences through an integrated analysis of palaeontological and molecular data. PMID:21051775
Assessment of genetic variation for the LINE-1 retrotransposon from next generation sequence data. PMID:21044359
Enrichment of mRNA-like noncoding RNAs in the divergence of Drosophila males. PMID:21041796
Epigenetic control of retrotransposon expression in human embryonic stem cells. PMID:21041477
Scaffolding a Caenorhabditis nematode genome with RNA-seq. PMID:20980554
Computational Epigenetics: the new scientific paradigm. PMID:20978607
An integrated physical, genetic and cytogenetic map of Brachypodium distachyon, a model system for grass research. PMID:20976139
Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon. PMID:20973991
FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data. PMID:20964841
The UCSC Genome Browser database: update 2011. PMID:20959295
Identification and characterisation of the BPI/LBP/PLUNC-like gene repertoire in chickens reveals the absence of a LBP gene. PMID:20959152
Genome of Helicobacter pylori strain 908. PMID:20952566
Ab initio identification of transcription start sites in the Rhesus macaque genome by histone modification and RNA-Seq. PMID:20952408
Comparing de novo assemblers for 454 transcriptome data. PMID:20950480
Expression proteomics of UPF1 knockdown in HeLa cells reveals autoregulation of hnRNP A2/B1 mediated by alternative splicing resulting in nonsense-mediated mRNA decay. PMID:20946641
Quail Genomics: a knowledgebase for Northern bobwhite. PMID:20946596
Discovery and characterization of mammalian endogenous parvoviruses. PMID:20943964
GenHtr: a tool for comparative assessment of genetic heterogeneity in microbial genomes generated by massive short-read sequencing. PMID:20939910
Geoseq: a tool for dissecting deep-sequencing datasets. PMID:20939882
T1DBase: update 2011, organization and presentation of large-scale data sets for type 1 diabetes research. PMID:20937630
De novo assembly and analysis of RNA-seq data. PMID:20935650
Whole-genome positive selection and habitat-driven evolution in a shallow and a deep-sea urchin. PMID:20935062
The evolution and expression of the snaR family of small non-coding RNAs. PMID:20935053
Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia. PMID:20932287
Cloning and characterization of a novel alternatively spliced transcript of the human CHD7 putative helicase. PMID:20925924
Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control. PMID:20924354
Gene discovery for the bark beetle-vectored fungal tree pathogen Grosmannia clavigera. PMID:20920358
Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control. PMID:20924354
Gene discovery for the bark beetle-vectored fungal tree pathogen Grosmannia clavigera. PMID:20920358
Identification of disease-causing mutations in autosomal dominant retinitis pigmentosa (adRP) using next-generation DNA sequencing. PMID:20861475
Expression profiling in canine osteosarcoma: identification of biomarkers and pathways associated with outcome. PMID:20860831
The FLIGHT Drosophila RNAi database: 2010 update. PMID:20855970
Long- and short-term selective forces on malaria parasite genomes. PMID:20838588
Exploring zebrafish genomic, functional and phenotypic data using ZFIN. PMID:20836073
Genome rearrangements detected by SNP microarrays in individuals with intellectual disability referred with possible Williams syndrome. PMID:20824207
FragGeneScan: predicting genes in short and error-prone reads. PMID:20805240
SAW: a method to identify splicing events from RNA-Seq data based on splicing fingerprints. PMID:20706591
A network of conserved co-occurring motifs for the regulation of alternative splicing. PMID:20702423
Exon-level transcriptome profiling in murine breast cancer reveals splicing changes specific to tumors with different metastatic abilities. PMID:20700505
Genome-wide high-throughput integrome analyses by nrLAM-PCR and next-generation sequencing. PMID:20671722
Isolation of SPINK6 in human skin: selective inhibitor of kallikrein-related peptidases. PMID:20667819
Polyploidy did not predate the evolution of nodulation in all legumes. PMID:20661290
Gene duplication and environmental adaptation within yeast populations. PMID:20660110
Characterization of the first beta-class carbonic anhydrase from an arthropod (Drosophila melanogaster) and phylogenetic analysis of beta-class carbonic anhydrases in invertebrates. PMID:20659325
Heritability in the efficiency of nonsense-mediated mRNA decay in humans. PMID:20657766
Inherited neuroaxonal dystrophy in dogs causing lethal, fetal-onset motor system dysfunction and cerebellar hypoplasia. PMID:20653033
A novel single cDNA amplicon pyrosequencing method for high-throughput, cost-effective sequence-based HLA class I genotyping. PMID:20650293
Tissue-specific regulatory regions of the PTH gene localized by novel chromosome 11 rearrangement breakpoints in a parathyroid adenoma. PMID:20641034
Quantitative gene expression profiles in real time from expressed sequence tag databases. PMID:20635574
Integration preferences of wildtype AAV-2 for consensus rep-binding sites at numerous loci in the human genome. PMID:20628575
The role of nucleosome positioning in the evolution of gene regulation. PMID:20625544
Semi-automated library preparation for high-throughput DNA sequencing platforms. PMID:20625503
Evolution of a bitter taste receptor gene cluster in a New World sparrow. PMID:20624740
Serious limitations of the QTL/microarray approach for QTL gene discovery. PMID:20624276
Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition. PMID:20622855
Transcriptomic analyses of xylan degradation by Prevotella bryantii and insights into energy acquisition by xylanolytic bacteroidetes. PMID:20622018
Characterization of C1q in teleosts: insight into the molecular and functional evolution of C1q family and classical pathway. PMID:20615881
LINE-1 retrotransposition activity in human genomes. PMID:20602998
RNA-seq analysis of sulfur-deprived Chlamydomonas cells reveals aspects of acclimation critical for cell survival. PMID:20587772
Targeted next-generation sequencing of DNA regions proximal to a conserved GXGXXG signaling motif enables systematic discovery of tyrosine kinase fusions in cancer. PMID:20587502
Local alignment of generalized k-base encoded DNA sequence. PMID:20576157
Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types. PMID:20565788
Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays. PMID:20565764
Design and evaluation of genome-wide libraries for RNA interference screens. PMID:20550664
Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity. PMID:20547834
An mRNA blueprint for C4 photosynthesis derived from comparative transcriptomics of closely related C3 and C4 species. PMID:20543093
Genomic SELEX: a discovery tool for genomic aptamers. PMID:20541015
Prevalence of alternative splicing choices in Arabidopsis thaliana. PMID:20525311
Challenges of sequencing human genomes. PMID:20519329
Most "dark matter" transcripts are associated with known genes. PMID:20502517
SFmap: a web server for motif analysis and prediction of splicing factor binding sites. PMID:20501600
Some novel intron positions in conserved Drosophila genes are caused by intron sliding or tandem duplication. PMID:20500887
Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline. PMID:20487544
A genome-wide association study on androstenone levels in pigs reveals a cluster of candidate genes on chromosome 6. PMID:20487517
Towards a comprehensive structural variation map of an individual human genome. PMID:20482838
Cost-effective sequencing of full-length cDNA clones powered by a de novo-reference hybrid assembly. PMID:20479877
Rapid identification of heterozygous mutations in Drosophila melanogaster using genomic capture sequencing. PMID:20472684
Classification of DNA sequences using Bloom filters. PMID:20472541
BAGEL2: mining for bacteriocins in genomic data. PMID:20462861
A survey of sequence alignment algorithms for next-generation sequencing. PMID:20460430
eHive: an artificial intelligence workflow system for genomic analysis. PMID:20459813
Computational analysis of unassigned high-quality MS/MS spectra in proteomic data sets. PMID:20455209
Genome analysis of Moraxella catarrhalis strain BBH18, [corrected] a human respiratory tract pathogen. PMID:20453089
Natural selection on cis and trans regulation in yeasts. PMID:20445163
E-RNAi: a web application for the multi-species design of RNAi reagents--2010 update. PMID:20444868
Organization of the variable region of the immunoglobulin heavy-chain gene locus of the rat. PMID:20442993
Molecular genetic analysis of Chd3 and polytene chromosome region 76B-D in Drosophila melanogaster. PMID:20439780
The molecular evolution of PL10 homologs. PMID:20438638
An EST resource for tilapia based on 17 normalized libraries and assembly of 116,899 sequence tags. PMID:20433739
Cgaln: fast and space-efficient whole-genome alignment. PMID:20433723
The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance. PMID:20430781
A novel role for minimal introns: routing mRNAs to the cytosol. PMID:20419085
Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome. PMID:20418490
BS Seeker: precise mapping for bisulfite sequencing. PMID:20416082
MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana. PMID:20407027
Transcriptional profiles underlying parent-of-origin effects in seeds of Arabidopsis thaliana. PMID:20406451
EuGène-maize: a web site for maize gene prediction. PMID:20400755
Replacement of Rbpj with Rbpjl in the PTF1 complex controls the final maturation of pancreatic acinar cells. PMID:20398665
Unconstrained mining of transcript data reveals increased alternative splicing complexity in the human transcriptome. PMID:20385588
Genome-wide analysis of mRNA abundance in two life-cycle stages of Trypanosoma brucei and identification of splicing and polyadenylation sites. PMID:20385579
mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus. PMID:20360389
Mutation@A Glance: an integrative web application for analysing mutations from human genetic diseases. PMID:20360267
Genomic organization of duplicated short wave-sensitive and long wave-sensitive opsin genes in the green swordtail, Xiphophorus helleri. PMID:20353595
Histone H3 trimethylated at lysine 4 is enriched at probable transcription start sites in Trypanosoma brucei. PMID:20347883
Validation of rearrangement break points identified by paired-end sequencing in natural populations of Drosophila melanogaster. PMID:20333226
Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species. PMID:20331785
Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. PMID:20308636
Analysis of the genome content of Lactococcus garvieae by genomic interspecies microarray hybridization. PMID:20233401
Agrobacterium-meditated gene disruption using split-marker in Grosmannia clavigera, a mountain pine beetle associated pathogen. PMID:20229292
Heads or tails: L1 insertion-associated 5' homopolymeric sequences. PMID:20226075
Gallin; an antimicrobial peptide member of a new avian defensin family, the ovodefensins, has been subject to recent gene duplication. PMID:20226050
Positional variations among heterogeneous nucleosome maps give dynamical information on chromatin. PMID:20224866
Testing the coding potential of conserved short genomic sequences. PMID:20224812
KRAB-zinc finger proteins and KAP1 can mediate long-range transcriptional repression through heterochromatin spreading. PMID:20221260
Analysis of human small nucleolar RNAs (snoRNA) and the development of snoRNA modulator of gene expression vectors. PMID:20219969
PanCGHweb: a web tool for genotype calling in pangenome CGH data. PMID:20219865
Validation and application of normalization factors for gene expression studies in rubella virus-infected cell lines with quantitative real-time PCR. PMID:20217898
High-throughput sequence analysis of Ciona intestinalis SL trans-spliced mRNAs: alternative expression modes and gene function correlates. PMID:20212022
Alterations in the steroid hormone receptor co-chaperone FKBPL are associated with male infertility: a case-control study. PMID:20210997
Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates. PMID:20210993
Genome-wide synteny through highly sensitive sequence alignment: Satsuma. PMID:20208069
Efficient discovery of ASCL1 regulatory sequences through transgene pooling. PMID:20206680
A human gut microbial gene catalogue established by metagenomic sequencing. PMID:20203603
Gene family size conservation is a good indicator of evolutionary rates. PMID:20194423
Chaperonin genes on the rise: new divergent classes and intense duplication in human and other vertebrate genomes. PMID:20193073
Chromosomal position effects on AAV-mediated gene targeting. PMID:20185563
Rapid pair-wise synteny analysis of large bacterial genomes using web-based GeneOrder4.0. PMID:20178631
Evolution of spliceosomal introns following endosymbiotic gene transfer. PMID:20178587
Endothelial cell processing and alternatively spliced transcripts of factor VIII: potential implications for coagulation cascades and pulmonary hypertension. PMID:20174619
Six RNA viruses and forty-one hosts: viral small RNAs and modulation of small RNA repertoires in vertebrate and invertebrate systems. PMID:20169186
Comparative analysis of nuclear tRNA genes of Nasonia vitripennis and other arthropods, and relationships to codon usage bias. PMID:20167017
Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii. PMID:20163725
Acceleration of Ungapped Extension in Mercury BLAST. PMID:20160873
Gramene QTL database: development, content and applications. PMID:20157478
Proviruses selected for high and stable expression of transduced genes accumulate in broadly transcribed genome areas. PMID:20147411
Fast and SNP-tolerant detection of complex variants and splicing in short reads. PMID:20147302
Parameters for accurate genome alignment. PMID:20144198
Human and non-human primate genomes share hotspots of positive selection. PMID:20140238
Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation. PMID:20137068
Defining transcribed regions using RNA-seq. PMID:20134426
MicroRNA regulation of IFN-beta protein expression: rapid and sensitive modulation of the innate immune response. PMID:20130213
Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses. PMID:20128909
hAT transposable elements and their derivatives: an analysis in the 12 Drosophila genomes. PMID:20127503
Distinct phases of siRNA synthesis in an endogenous RNAi pathway in C. elegans soma. PMID:20116306
Periostin shows increased evolutionary plasticity in its alternatively spliced region. PMID:20109226
Fast and accurate long-read alignment with Burrows-Wheeler transform. PMID:20080505
Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction. PMID:20078885
A manual collection of Syt, Esyt, Rph3a, Rph3al, Doc2, and Dblc2 genes from 46 metazoan genomes--an open access resource for neuroscience and evolutionary biology. PMID:20078875
A method of predicting changes in human gene splicing induced by genetic variants in context of cis-acting elements. PMID:20067640
A systems approach reveals that the myogenesis genome network is regulated by the transcriptional repressor RP58. PMID:20059953
Characterization of the zebrafish T cell receptor beta locus. PMID:20054533
Phylogenetic comparative assembly. PMID:20047659
A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins. PMID:20047656
Evidence for bacterial origin of heat shock RNA-1. PMID:20040589
Microarray probes and probe sets. PMID:20036881
Genes targeted by the estrogen and progesterone receptors in the human endometrial cell lines HEC1A and RL95-2. PMID:20034404
Large intron 14 rearrangement in APC results in splice defect and attenuated FAP. PMID:20033212
Targets of the Tal1 transcription factor in erythrocytes: E2 ubiquitin conjugase regulation by Tal1. PMID:20028976
Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells. PMID:20026622
A SNP discovery method to assess variant allele probability from next-generation resequencing data. PMID:20019143
ECRG4 is a candidate tumor suppressor gene frequently hypermethylated in colorectal carcinoma and glioma. PMID:20017917
r2cat: synteny plots and comparative assembly. PMID:20015948
Fine-scale variation and genetic determinants of alternative splicing across individuals. PMID:20011102
Sex-specific and lineage-specific alternative splicing in primates. PMID:20009012
BLAST+: architecture and applications. PMID:20003500
A hybrid, de novo based, genome-wide database search approach applied to the sea urchin neuropeptidome. PMID:20000637
Building the sequence map of the human pan-genome. PMID:19997067
PhosSNP for systematic analysis of genetic polymorphisms that influence protein phosphorylation. PMID:19995808
Comprehensive genomic access to vector integration in clinical gene therapy. PMID:19966782
RExPrimer: an integrated primer designing tool increases PCR effectiveness by avoiding 3' SNP-in-primer and mis-priming from structural variation. PMID:19958502
COMUS: Clinician-Oriented locus-specific MUtation detection and deposition System. PMID:19958500
PDbase: a database of Parkinson's disease-related genes and genetic variation using substantia nigra ESTs. PMID:19958497
An empirical study of choosing efficient discriminative seeds for oligonucleotide design. PMID:19958494
BOAT: Basic Oligonucleotide Alignment Tool. PMID:19958483
MapNext: a software tool for spliced and unspliced alignments and SNP detection of short sequence reads. PMID:19958476
The UCSC Genome Browser. PMID:19957273
Tandem repeats modify the structure of human genes hosted in segmental duplications. PMID:19954527
Runx2 regulates survivin expression in prostate cancer cells. PMID:19949374
Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila. PMID:19948818
Microarray-based cytogenetic profiling reveals recurrent and subtype-associated genomic copy number aberrations in feline sarcomas. PMID:19941159
Discovery of Plasmodium modulators by genome-wide analysis of circulating hemocytes in Anopheles gambiae. PMID:19940242
Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs. PMID:19936069
Fine-scale phylogenetic discordance across the house mouse genome. PMID:19936022
MouseIndelDB: a database integrating genomic indel polymorphisms that distinguish mouse strains. PMID:19933259
Combining next-generation pyrosequencing with microarray for large scale expression analysis in non-model species. PMID:19930683
Expression profiling of rainbow trout testis development identifies evolutionary conserved genes involved in spermatogenesis. PMID:19925684
A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data. PMID:19923232
Complexity of genome evolution by segmental rearrangement in Brassica rapa revealed by sequence-level analysis. PMID:19922648
Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer. PMID:19922616
The Pfam protein families database. PMID:19920124
Detection of pathogenic copy number variants in children with idiopathic intellectual disability using 500 K SNP array genomic hybridization. PMID:19917086
Development of a DNA microarray to detect antimicrobial resistance genes identified in the National Center for Biotechnology Information database. PMID:19916789
GenomeRNAi: a database for cell-based RNAi phenotypes. 2009 update. PMID:19910367
Correlation of microsynteny conservation and disease gene distribution in mammalian genomes. PMID:19909546
The effect of sequencing errors on metagenomic gene prediction. PMID:19909532
BFAST: an alignment tool for large scale genome resequencing. PMID:19907642
The UCSC Genome Browser database: update 2010. PMID:19906737
ChimerDB 2.0--a knowledgebase for fusion genes updated. PMID:19906715
PLANdbAffy: probe-level annotation database for Affymetrix expression microarrays. PMID:19906711
MetaBioME: a database to explore commercially useful enzymes in metagenomic datasets. PMID:19906710
Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes. PMID:19906700
An expression database for roots of the model legume Medicago truncatula under salt stress. PMID:19906315
High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians. PMID:19900272
Computational prediction of splicing regulatory elements shared by Tetrapoda organisms. PMID:19889216
Detection, validation, and downstream analysis of allelic variation in gene expression. PMID:19884314
An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer. PMID:19881495
inGAP: an integrated next-generation genome analysis pipeline. PMID:19880367
iTriplet, a rule-based nucleic acid sequence motif finder. PMID:19874606
Genetical genomic determinants of alcohol consumption in rats and humans. PMID:19874574
Hematopoietic immortalizing function of the NKL-subclass homeobox gene TLX1. PMID:19862821
A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat. PMID:19860896
Nme protein family evolutionary history, a vertebrate perspective. PMID:19852809
G-compass: a web-based comparative genome browser between human and other vertebrate genomes. PMID:19846439
A syndrome of short stature, microcephaly and speech delay is associated with duplications reciprocal to the common Sotos syndrome deletion. PMID:19844260
Positive selection for the male functionality of a co-retroposed gene in the hominoids. PMID:19832993
Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell. PMID:19832986
The subtelomere of Oryza sativa chromosome 3 short arm as a hot bed of new gene origination in rice. PMID:19825586
Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication. PMID:19821981
miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression. PMID:19821977
BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum. PMID:19820115
Dynamic Proteomics: a database for dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells. PMID:19820112
A modified sleeping beauty transposon system that can be used to model a wide variety of human cancers in mice. PMID:19808965
A Caenorhabditis elegans RNA-directed RNA polymerase in sperm development and endogenous RNA interference. PMID:19805814
Functional identification of tumor-suppressor genes through an in vivo RNA interference screen in a mouse lymphoma model. PMID:19800577
A scalable method for analysis and display of DNA sequences. PMID:19798412
Extensive structural renovation of retrogenes in the evolution of the Populus genome. PMID:19789289
Collection of Macaca fascicularis cDNAs derived from bone marrow, kidney, liver, pancreas, spleen, and thymus. PMID:19785770
An N- and C-terminal truncated isoform of zinc finger X-linked duplicated C protein represses MHC class II transcription. PMID:19777325
Direct RNA sequencing. PMID:19776739
Many LINE1 elements contribute to the transcriptome of human somatic cells. PMID:19772661
The completion of the Mammalian Gene Collection (MGC). PMID:19767417
A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos. PMID:19758566
Distribution and neuronal expression of phosphatidylinositol phosphate kinase IIgamma in the mouse brain. PMID:19757494
Characterization of a novel human HMBOX1 splicing variant lacking the homeodomain and with attenuated transcription repressor activity. PMID:19757162
Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth. PMID:19747392
Blimp-1/Prdm1 alternative promoter usage during mouse development and plasma cell differentiation. PMID:19737919
GASZ is essential for male meiosis and suppression of retrotransposon expression in the male germline. PMID:19730684
Recent de novo origin of human protein-coding genes. PMID:19726446
Response of gastric epithelial progenitors to Helicobacter pylori Isolates obtained from Swedish patients with chronic atrophic gastritis. PMID:19723631
Systematic identification and characterization of chicken (Gallus gallus) ncRNAs. PMID:19720738
Somatic cell nuclear transfer in zebrafish. PMID:19718031
Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. PMID:19717792
BatchGenAna: a batch platform for large-scale genomic analysis of mammalian small RNAs. PMID:19707298
Loss of epigenetic silencing in tumors preferentially affects primate-specific retroelements. PMID:19699787
Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PMID:19693277
Cell contact-dependent acquisition of cellular and viral nonautonomously encoded small RNAs. PMID:19684116
The transcriptionally active regions in the genome of Bacillus subtilis. PMID:19682248
Mapping the human membrane proteome: a majority of the human membrane proteins can be classified according to function and evolutionary origin. PMID:19678920
PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. PMID:19675096
Natural antisense transcript of natriuretic peptide precursor A (NPPA): structural organization and modulation of NPPA expression. PMID:19671135
Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence. PMID:19662163
Retroviral vector integration in post-transplant hematopoiesis in mice conditioned with either submyeloablative or ablative irradiation. PMID:19657370
Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. PMID:19654876
The sea lamprey Petromyzon marinus genome reveals the early origin of several chemosensory receptor families in the vertebrate lineage. PMID:19646260
Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing. PMID:19646242
MLGA: a cost-effective approach to the diagnosis of gene deletions in eye development anomalies. PMID:19641633
Meiotic behavior of aneuploid chromatin in mouse models of Down syndrome. PMID:19639331
Mapping accuracy of short reads from massively parallel sequencing and the implications for quantitative expression profiling. PMID:19636379
Exon-trapping mediated by the human retrotransposon SVA. PMID:19635844
Repertoire of bovine miRNA and miRNA-like small regulatory RNAs expressed upon viral infection. PMID:19633723
Using microarrays to identify positional candidate genes for QTL: the case study of ACTH response in pigs. PMID:19615114
Comparison of three microarray probe annotation pipelines: differences in strategies and their effect on downstream analysis. PMID:19615109
In silico identification of a core regulatory network of OCT4 in human embryonic stem cells using an integrated approach. PMID:19604364
Conservation of domain structure in a fast-evolving heterochromatic SUUR protein in drosophilids. PMID:19596903
Integration of genetic and genomic methods for identification of genes and gene variants encoding QTLs in the nonhuman primate. PMID:19596448
A Multiparent Advanced Generation Inter-Cross to fine-map quantitative traits in Arabidopsis thaliana. PMID:19593375
RazerS--fast read mapping with sensitivity control. PMID:19592482
HaMStR: profile hidden markov model based search for orthologs in ESTs. PMID:19586527
Age-associated inflammation and toll-like receptor dysfunction prime the lungs for pneumococcal pneumonia. PMID:19586419
Evolution of Tom, 297, 17.6 and rover retrotransposons in Drosophilidae species. PMID:19585148
Identifying concerted evolution and gene conversion in mammalian gene pairs lasting over 100 million years. PMID:19583854
Global discovery of primate-specific genes in the human genome. PMID:19581580
SNP-o-matic. PMID:19574284
k-link EST clustering: evaluating error introduced by chimeric sequences under different degrees of linkage. PMID:19570806
mGene: accurate SVM-based gene finding with an application to nematode genomes. PMID:19564452
HAPLOWSER: a whole-genome haplotype browser for personal genome and metagenome. PMID:19561337
Rodent-specific alternative exons are more frequent in rapidly evolving genes and in paralogs. PMID:19558667
Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution. PMID:19557196
The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes. PMID:19545381
Copy number variation at 1q21.1 associated with neuroblastoma. PMID:19536264
Statistical assessment of discriminative features for protein-coding and non coding cross-species conserved sequence elements. PMID:19534745
EasyCluster: a fast and efficient gene-oriented clustering tool for large-scale transcriptome data. PMID:19534735
In vivo selection of hematopoietic progenitor cells and temozolomide dose intensification in rhesus macaques through lentiviral transduction with a drug resistance gene. PMID:19509470
Local alignment of two-base encoded DNA sequence. PMID:19508732
Internal priming: an opportunistic pathway for L1 and Alu retrotransposition in hominins. PMID:19501635
A comparative approach shows differences in patterns of numt insertion during hominoid evolution. PMID:19471988
The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. PMID:19470904
Primate phylogenomics: developing numerous nuclear non-coding, non-repetitive markers for ecological and phylogenetic applications and analysis of evolutionary rate variation. PMID:19470178
WebGMAP: a web service for mapping and aligning cDNA sequences to genomes. PMID:19465381
A comprehensive in silico expression analysis of RNA binding proteins in normal and tumor tissue: Identification of potential players in tumor formation. PMID:19458496
Conserved introns reveal novel transcripts in Drosophila melanogaster. PMID:19458021
Detection of intergenic non-coding RNAs expressed in the main developmental stages in Drosophila melanogaster. PMID:19451167
A novel L1 retrotransposon marker for HeLa cell line identification. PMID:19450234
DNA Sudoku--harnessing high-throughput sequencing for multiplexed specimen analysis. PMID:19447965
Source gene composition and gene conversion of the AluYh and AluYi lineages of retrotransposons. PMID:19442302
MapToGenome: a comparative genomic tool that aligns transcript maps to sequenced genomes. PMID:19430601
Sim4cc: a cross-species spliced alignment program. PMID:19429899
TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences. PMID:19429695
Orphelia: predicting genes in metagenomic sequencing reads. PMID:19429689
A newly-developed community microarray resource for transcriptome profiling in Brassica species enables the confirmation of Brassica-specific expressed sequences. PMID:19426481
Drosophila P transposons of the urochordata Ciona intestinalis. PMID:19424726
Genomic analysis of Campylobacter fetus subspecies: identification of candidate virulence determinants and diagnostic assay targets. PMID:19422718
Improving gene-finding in Chlamydomonas reinhardtii:GreenGenie2. PMID:19422688
Proteomics and comparative genomic investigations reveal heterogeneity in evolutionary rate of male reproductive proteins in mice (Mus domesticus). PMID:19420050
Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner. PMID:19414532
Translation of an STR-based biomarker into a clinically compatible SNP-based platform for loss of heterozygosity. PMID:19407369
SNP discovery and haplotype analysis in the segmentally duplicated DRD5 coding region. PMID:19397556
An examination of positive selection and changing effective population size in Angus and Holstein cattle populations (Bos taurus) using a high density SNP genotyping platform and the contribution of ancient polymorphism to genomic diversity in Domestic cattle. PMID:19393053
The bovine lactation genome: insights into the evolution of mammalian milk. PMID:19393040
Molecular identification and expression analysis of filaggrin-2, a member of the S100 fused-type protein family. PMID:19384417
Genetic structures of copy number variants revealed by genotyping single sperm. PMID:19384415
ESTPiper--a web-based analysis pipeline for expressed sequence tags. PMID:19383159
A transcriptional sketch of a primary human breast cancer by 454 deep sequencing. PMID:19379481
High resolution mapping of expression QTLs in heterogeneous stock mice in multiple tissues. PMID:19376938
Conservation of core gene expression in vertebrate tissues. PMID:19371447
Single feature polymorphisms between two rice cultivars detected using a median polish method. PMID:19370320
Four histone variants mark the boundaries of polycistronic transcription units in Trypanosoma brucei. PMID:19369410
Analysis of transcribed human endogenous retrovirus W env loci clarifies the origin of multiple sclerosis-associated retrovirus env sequences. PMID:19368703
Geometric aspects of biological sequence comparison. PMID:19361329
Gene structures, biochemical characterization and distribution of rat melatonin receptors. PMID:19340560
Influence of genetic background on tumor karyotypes: evidence for breed-associated cytogenetic aberrations in canine appendicular osteosarcoma. PMID:19337847
Prediction of novel microRNA genes in cancer-associated genomic regions--a combined computational and experimental approach. PMID:19324892
Transcription and splicing regulation in human umbilical vein endothelial cells under hypoxic stress conditions by exon array. PMID:19320972
Computational and analytical framework for small RNA profiling by high-throughput sequencing. PMID:19307293
A genome-wide association study of pulmonary function measures in the Framingham Heart Study. PMID:19300500
The apolipoprotein L family of programmed cell death and immunity genes rapidly evolved in primates at discrete sites of host-pathogen interactions. PMID:19299565
Lowly expressed human microRNA genes evolve rapidly. PMID:19299536
Tandem stop codons in ciliates that reassign stop codons. PMID:19294453
Transcriptional enhancers induce insertional gene deregulation independently from the vector type and design. PMID:19293778
TopHat: discovering splice junctions with RNA-Seq. PMID:19289445
RBF-TSS: identification of transcription start site in human using radial basis functions network and oligonucleotide positional frequencies. PMID:19287502
Application of 'next-generation' sequencing technologies to microbial genetics. PMID:19287448
The human vaginal bacterial biota and bacterial vaginosis. PMID:19282975
A novel endo-hydrogenase activity recycles hydrogen produced by nitrogen fixation. PMID:19277114
CNV-seq, a new method to detect copy number variation using high-throughput sequencing. PMID:19267900
Gene targeting in mouse embryonic stem cells. PMID:19266325
Finding genes in Schistosoma japonicum: annotating novel genomes with help of extrinsic evidence. PMID:19264800
Big genomes facilitate the comparative identification of regulatory elements. PMID:19259274
FragIdent--automatic identification and characterisation of cDNA-fragments. PMID:19254371
QSRA: a quality-value guided de novo short read assembler. PMID:19239711
Transcription factor binding sites are genetic determinants of retroviral integration in the human genome. PMID:19238208
PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. PMID:19236709
Widespread evidence for horizontal transfer of transposable elements across Drosophila genomes. PMID:19226459
ChIP-seq accurately predicts tissue-specific activity of enhancers. PMID:19212405
Short read DNA fragment anchoring algorithm. PMID:19208116
Strategies for reliable exploitation of evolutionary concepts in high throughput biology. PMID:19204813
The serum response factor and a putative novel transcription factor regulate expression of the immediate-early gene Arc/Arg3.1 in neurons. PMID:19193899
Identification of lympho-epithelial Kazal-type inhibitor 2 in human skin as a kallikrein-related peptidase 5-specific protease inhibitor. PMID:19190773
A domestic cat X chromosome linkage map and the sex-linked orange locus: mapping of orange, multiple origins and epistasis over nonagouti. PMID:19189955
Multiple whole-genome alignments without a reference organism. PMID:19176791
Primary microRNA transcripts are processed co-transcriptionally. PMID:19172742
Genome and gene alterations by insertions and deletions in the evolution of human and chimpanzee chromosome 22. PMID:19171065
Orientation, distance, regulation and function of neighbouring genes. PMID:19164091
Identification of an ancient Bmp4 mesoderm enhancer located 46 kb from the promoter. PMID:19159624
Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. PMID:19148287
An expanded clade of rodent Trim5 genes. PMID:19147168
The G protein-coupled receptor subset of the dog genome is more similar to that in humans than rodents. PMID:19146662
Genic regions of a large salamander genome contain long introns and novel genes. PMID:19144141
Modulation of gene expression in U251 glioblastoma cells by binding of mutant p53 R273H to intronic and intergenic sequences. PMID:19139068
Transcriptome sequencing to detect gene fusions in cancer. PMID:19136943
Mining for single nucleotide polymorphisms in pig genome sequence data. PMID:19126189
Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer. PMID:19118015
Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts. PMID:19116412
Expressed sequence tag analysis of guinea pig (Cavia porcellus) eye tissues for NEIBank. PMID:19104676
Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains. PMID:19099592
Dynamic evolution of oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set. PMID:19098269
Gene expression levels are a target of recent natural selection in the human genome. PMID:19091723
Functional analysis of novel SNPs and mutations in human and mouse genomes. PMID:19091009
Short homologous sequences are strongly associated with the generation of chimeric RNAs in eukaryotes. PMID:19089307
A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate. PMID:19088305
Optimal neighborhood indexing for protein similarity search. PMID:19087280
Annotating genomes with massive-scale RNA sequencing. PMID:19087247
Epigenomic consequences of immortalized plant cell suspension culture. PMID:19071958
Human chromosomal translocations at CpG sites and a theoretical basis for their lineage and stage specificity. PMID:19070581
Chromatin structure analyses identify miRNA promoters. PMID:19056895
Regulation of neural macroRNAs by the transcriptional repressor REST. PMID:19050060
ProSeeK: a web server for MLPA probe design. PMID:19040730
LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice. PMID:19038031
The mouse hairy ears mutation exhibits an extended growth (anagen) phase in hair follicles and altered Hoxc gene expression in the ears. PMID:19037915
Design and analysis of ChIP-seq experiments for DNA-binding proteins. PMID:19029915
VectorBase: a data resource for invertebrate vector genomics. PMID:19028744
Gene regulation in primates evolves under tissue-specific selection pressures. PMID:19023414
A high-density single nucleotide polymorphism map for Neurospora crassa. PMID:19015548
De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. PMID:19015323
Analysis of the Pythium ultimum transcriptome using Sanger and Pyrosequencing approaches. PMID:19014603
CoCoNUT: an efficient system for the comparison and analysis of genomes. PMID:19014477
Non-coding RNAs revealed during identification of genes involved in chicken immune responses. PMID:19009289
Genotype-phenotype correlations in Down syndrome identified by array CGH in 30 cases of partial trisomy and partial monosomy chromosome 21. PMID:19002211
The UCSC Genome Browser Database: update 2009. PMID:18996895
High-resolution copy-number variation map reflects human olfactory receptor diversity and evolution. PMID:18989455
Using retroviruses as a mutagenesis tool to explore the zebrafish genome. PMID:18977782
Width of gene expression profile drives alternative splicing. PMID:18974852
Whole population, genome-wide mapping of hidden relatedness. PMID:18971310
An epigenetic aberration increased in intergenic regions of cloned mice. PMID:18958525
Identification and classification of genes regulated by phosphatidylinositol 3-kinase- and TRKB-mediated signalling pathways during neuronal differentiation in two subtypes of the human neuroblastoma cell line SH-SY5Y. PMID:18957096
UTR dinucleotide simple sequence repeat evolution exhibits recurring patterns including regulatory sequence motif replacements. PMID:18955121
The role of CLCA proteins in inflammatory airway disease. PMID:18954282
Rfam: updates to the RNA families database. PMID:18953034
Evolution of Arabidopsis thaliana microRNAs from random sequences. PMID:18952822
An alternative pathway for Alu retrotransposition suggests a role in DNA double-strand break repair. PMID:18951971
A high-resolution cat radiation hybrid and integrated FISH mapping resource for phylogenomic studies across Felidae. PMID:18951970
Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. PMID:18923076
Agglomerative epigenetic aberrations are a common event in human breast cancer. PMID:18922938
Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations. PMID:18854010
Nested Patch PCR enables highly multiplexed mutation discovery in candidate genes. PMID:18849522
Biosequence Similarity Search on the Mercury System. PMID:18846267
High-resolution mapping of expression-QTLs yields insight into human gene regulation. PMID:18846210
MachiBase: a Drosophila melanogaster 5'-end mRNA transcription database. PMID:18842623
Retrocopy contributions to the evolution of the human genome. PMID:18842134
SNPinProbe_1.0: a database for filtering out probes in the Affymetrix GeneChip human exon 1.0 ST array potentially affected by SNPs. PMID:18841244
Identification of nuclear and cytoplasmic mRNA targets for the shuttling protein SF2/ASF. PMID:18841201
GenBlastA: enabling BLAST to identify homologous gene sequences. PMID:18838612
Haplotype sorting using human fosmid clone end-sequence pairs. PMID:18836033
Dispensability of mammalian DNA. PMID:18832441
Epigenetic silencing of human immunodeficiency virus (HIV) transcription by formation of restrictive chromatin structures at the viral long terminal repeat drives the progressive entry of HIV into latency. PMID:18829756
Lentiviral integration preferences in transgenic mice. PMID:18821598
RiceGeneThresher: a web-based application for mining genes underlying QTL in rice genome. PMID:18820292
The effect of temperature on Natural Antisense Transcript (NAT) expression in Aspergillus flavus. PMID:18813928
WebScipio: an online tool for the determination of gene structures using protein sequences. PMID:18801164
SQUAT: A web tool to mine human, murine and avian SAGE data. PMID:18801154
Large-scale gene trapping in C57BL/6N mouse embryonic stem cells. PMID:18799693
Search for informative polymorphisms in candidate genes: clock genes and circadian behaviour in blue tits. PMID:18792794
Human MLPA Probe Design (H-MAPD): a probe design tool for both electrophoresis-based and bead-coupled human multiplex ligation-dependent probe amplification assays. PMID:18783624
Conserved chromosomal clustering of genes governed by chromatin regulators in Drosophila. PMID:18783608
Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana. PMID:18776934
Unexpected complexity at breakpoint junctions in phenotypically normal individuals and mechanisms involved in generating balanced translocations t(1;22)(p36;q13). PMID:18765821
Aryl hydrocarbon receptor-dependent induction of flavin-containing monooxygenase mRNAs in mouse liver. PMID:18765683
Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3'-end of genes. PMID:18757892
Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. PMID:18757608
Identification and correction of abnormal, incomplete and mispredicted proteins in public databases. PMID:18752676
Horizontal gene transfers link a human MRSA pathogen to contagious bovine mastitis bacteria. PMID:18728754
SynBlast: assisting the analysis of conserved synteny information. PMID:18721485
Novel SLC7A7 large rearrangements in lysinuric protein intolerance patients involving the same AluY repeat. PMID:18716612
Multilocus patterns of nucleotide polymorphism and the demographic history of Populus tremula. PMID:18716330
Mapping short DNA sequencing reads and calling variants using mapping quality scores. PMID:18714091
Fast comparison of DNA sequences by oligonucleotide profiling. PMID:18710530
Genomic analysis of the relationship between gene expression variation and DNA polymorphism in Drosophila simulans. PMID:18700012
SeqMap: mapping massive amount of oligonucleotides to the genome. PMID:18697769
ZOOM! Zillions of oligos mapped. PMID:18684737
The impact of microRNAs on protein output. PMID:18668037
Expression patterns of transcribed human endogenous retrovirus HERV-K(HML-2) loci in human tissues and the need for a HERV Transcriptome Project. PMID:18664271
Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array. PMID:18655706
The status of dosage compensation in the multiple X chromosomes of the platypus. PMID:18654631
Tissue-specific splicing factor gene expression signatures. PMID:18653532
NEIBank: genomics and bioinformatics resources for vision research. PMID:18648525
MAGIC database and interfaces: an integrated package for gene discovery and expression. PMID:18629159
11th Intelligent Systems for Molecular Biology 2003 (ISMB 2003). PMID:18629025
The protist, Monosiga brevicollis, has a tyrosine kinase signaling network more elaborate and diverse than found in any known metazoan. PMID:18621719
A discontinuous hammerhead ribozyme embedded in a mammalian messenger RNA. PMID:18615019
Transcriptional autoregulation controls pancreatic Ptf1a expression during development and adulthood. PMID:18606784
Unfolded protein response genes regulated by CED-1 are required for Caenorhabditis elegans innate immunity. PMID:18606143
Gene duplication in early vertebrates results in tissue-specific subfunctionalized adaptor proteins: CASP and GRASP. PMID:18600293
On the extent and origins of genic novelty in the phylum Nematoda. PMID:18596977
Species-specific Differences among KCNMB3 BK beta3 auxiliary subunits: some beta3 N-terminal variants may be primate-specific subunits. PMID:18591419
A robust framework for detecting structural variations in a genome. PMID:18586745
Conservation of inter-protein binding sites in RUSH and RFBP, an ATP11B isoform. PMID:18584949
Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation. PMID:18584029
Automated analysis of viral integration sites in gene therapy research using the SeqMap web resource. PMID:18580967
Database indexing for production MegaBLAST searches. PMID:18567917
The amphioxus genome illuminates vertebrate origins and cephalochordate biology. PMID:18562680
Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. PMID:18562676
Predicting functional regulatory polymorphisms. PMID:18562267
Polymorphic microsatellite loci for the common marmoset (Callithrix jacchus) designed using a cost- and time-efficient method. PMID:18561252
Scipio: using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species. PMID:18554390
On the origin of new genes in Drosophila. PMID:18550802
Genome-wide identification of coding and non-coding conserved sequence tags in human and mouse genomes. PMID:18547402
Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites. PMID:18533028
The RHNumtS compilation: features and bioinformatics approaches to locate and quantify Human NumtS. PMID:18522722
A member of the p38 mitogen-activated protein kinase family is responsible for transcriptional induction of Dopa decarboxylase in the epidermis of Drosophila melanogaster during the innate immune response. PMID:18519585
Splign: algorithms for computing spliced alignments with identification of paralogs. PMID:18495041
Expressed sequence tags with cDNA termini: previously overlooked resources for gene annotation and transcriptome exploration in Chlamydomonas reinhardtii. PMID:18493042
Characterization of genome-wide p53-binding sites upon stress response. PMID:18474530
Different evolutionary strategies for the origin of caspase-1 inhibitors. PMID:18473111
A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. PMID:18469162
Identification of the sensory neuron specific regulatory region for the mouse gene encoding the voltage-gated sodium channel NaV1.8. PMID:18466327
Genotypic features of lentivirus transgenic mice. PMID:18463153
OREST: the online resource for EST analysis. PMID:18463135
Genome-wide assessments reveal extremely high levels of polymorphism of two active families of mouse endogenous retroviral elements. PMID:18454193
Clinical uses of microarrays in cancer research. PMID:18453086
Comparative analysis of sequence features involved in the recognition of tandem splice sites. PMID:18447903
Designating eukaryotic orthology via processed transcription units. PMID:18445630
Organization and transcriptional output of a novel mRNA-like piRNA gene (mpiR) located on mouse chromosome 10. PMID:18441047
HIV-1 latency in actively dividing human T cell lines. PMID:18439275
Identification of ancient remains through genomic sequencing. PMID:18426903
Non-random retention of protein-coding overlapping genes in Metazoa. PMID:18416813
How many human genes can be defined as housekeeping with current expression data? PMID:18416810
Genome level analysis of rice mRNA 3'-end processing signals and alternative polyadenylation. PMID:18411206
Cassandra retrotransposons carry independently transcribed 5S RNA. PMID:18408163
Hidden layers of human small RNAs. PMID:18402656
Detailed characterization of the mouse embryonic stem cell transcriptome reveals novel genes and intergenic splicing associated with pluripotency. PMID:18400104
Genome-wide analysis of abnormal H3K9 acetylation in cloned mice. PMID:18398451
WAMIDEX: a web atlas of murine genomic imprinting and differential expression. PMID:18398312
A novel method of differential gene expression analysis using multiple cDNA libraries applied to the identification of tumour endothelial genes. PMID:18394197
Characterization of mouse Dactylaplasia mutations: a model for human ectrodactyly SHFM3. PMID:18392654
Chromosomal gene movements reflect the recent origin and biology of therian sex chromosomes. PMID:18384235
GPCR genes are preferentially retained after whole genome duplication. PMID:18382678
Evolution, expression and effectiveness in a cluster of novel bovine beta-defensins. PMID:18369613
HTLV-1 integration into transcriptionally active genomic regions is associated with proviral expression and with HAM/TSP. PMID:18369476
Retrotransposition as a source of new promoters. PMID:18367464
Fast evolution of core promoters in primate genomes. PMID:18367463
xMAN: extreme MApping of OligoNucleotides. PMID:18366610
A sequence-based survey of the complex structural organization of tumor genomes. PMID:18364049
Alternative splicing of the G protein-coupled receptor superfamily in human airway smooth muscle diversifies the complement of receptors. PMID:18362331
Identification of a novel human lactate dehydrogenase gene LDHAL6A, which activates transcriptional activities of AP1(PMA). PMID:18351441
Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays. PMID:18348734
A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence. PMID:18344523
Characterization of new hAT transposable elements in 12 Drosophila genomes. PMID:18340538
Acetylcholinesterase expression in muscle is specifically controlled by a promoter-selective enhancesome in the first intron. PMID:18322091
Cross-kingdom patterns of alternative splicing and splice recognition. PMID:18321378
Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis. PMID:18307801
Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza. PMID:18304353
An imputed genotype resource for the laboratory mouse. PMID:18301946
Gene conversion in the rice genome. PMID:18298833
Linking the genomes of nonmodel teleosts through comparative genomics. PMID:18297360
Opossum carboxylesterases: sequences, phylogeny and evidence for CES gene duplication events predating the marsupial-eutherian common ancestor. PMID:18289373
Proportionally more deleterious genetic variation in European than in African populations. PMID:18288194
Complementary RNA amplification methods enhance microarray identification of transcripts expressed in the C. elegans nervous system. PMID:18284693
Clustering exact matches of pairwise sequence alignments by weighted linear regression. PMID:18282291
Accurate splice site prediction using support vector machines. PMID:18269701
Genome-wide pattern of TCF7L2/TCF4 chromatin occupancy in colorectal cancer cells. PMID:18268006
Supervised Lowess normalization of comparative genome hybridization data--application to lactococcal strain comparisons. PMID:18267014
Bioinformatics challenges of new sequencing technology. PMID:18262676
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. PMID:18258921
A genomic view of the NOD-like receptor family in teleost fish: identification of a novel NLR subfamily in zebrafish. PMID:18254971
Comparative genomic analysis of the arthropod muscle myosin heavy chain genes allows ancestral gene reconstruction and reveals a new type of 'partially' processed pseudogene. PMID:18254963
The Groucho/TLE/Grg family of transcriptional co-repressors. PMID:18254933
High-resolution mapping and characterization of open chromatin across the genome. PMID:18243105
Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding. PMID:18230180
hsp70 genes in the human genome: Conservation and differentiation patterns predict a wide array of overlapping and specialized functions. PMID:18215318
Whole-genome expression profiling of the marine diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses. PMID:18212125
Repeats and EST analysis for new organisms. PMID:18205940
LINE-1 family member GCRG123 gene is up-regulated in human gastric signet-ring cell carcinoma. PMID:18205268
The amphioxus (Branchiostoma floridae) genome contains a highly diversified set of G protein-coupled receptors. PMID:18199322
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. PMID:18190707
Multiple organism algorithm for finding ultraconserved elements. PMID:18186941
Identification of novel homologous microRNA genes in the rhesus macaque genome. PMID:18186931
Specific expression of long noncoding RNAs in the mouse brain. PMID:18184812
Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome. PMID:18173853
Conserved and species-specific alternative splicing in mammalian genomes. PMID:18154685
CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction. PMID:18096039
Canine population structure: assessment and impact of intra-breed stratification on SNP-based association studies. PMID:18091995
The UCSC Genome Browser Database: 2008 update. PMID:18086701
Comparative genomics search for losses of long-established genes on the human lineage. PMID:18085818
A role for microRNAs in maintenance of mouse mammary epithelial progenitor cells. PMID:18079172
Contribution of telomerase RNA retrotranscription to DNA double-strand break repair during mammalian genome evolution. PMID:18067655
The genome browser at UCSC for locating genes, and much more! PMID:18058261
Bacterial flora-typing with targeted, chip-based Pyrosequencing. PMID:18047683
Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray. PMID:18043742
Phylogenetic footprinting analysis in the upstream regulatory regions of the Drosophila enhancer of split genes. PMID:18039873
G9a histone methyltransferase contributes to imprinting in the mouse placenta. PMID:18039842
Extragenic accumulation of RNA polymerase II enhances transcription by RNA polymerase III. PMID:18039033
A recurrent inversion on the eutherian X chromosome. PMID:18003915
Constraint and turnover in sex-biased gene expression in the genus Drosophila. PMID:17994089
Targeted discovery of novel human exons by comparative genomics. PMID:17989246
Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PMID:17988176
UTRome.org: a platform for 3'UTR biology in C. elegans. PMID:17986455
Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees. PMID:17982176
CTCFBSDB: a CTCF-binding site database for characterization of vertebrate genomic insulators. PMID:17981843
How accurately is ncRNA aligned within whole-genome multiple alignments? PMID:17963514
Exonization of active mouse L1s: a driver of transcriptome evolution? PMID:17963496
Large-scale analysis by SAGE reveals new mechanisms of v-erbA oncogene action. PMID:17961265
Alu recombination-mediated structural deletions in the chimpanzee genome. PMID:17953488
Short sequence motifs, overrepresented in mammalian conserved non-coding sequences. PMID:17945028
Genome-wide expression profiling of the Arabidopsis female gametophyte identifies families of small, secreted proteins. PMID:17937500
Gallus GBrowse: a unified genomic database for the chicken. PMID:17933775
CG dinucleotide clustering is a species-specific property of the genome. PMID:17932072
The ribosomal protein genes and Minute loci of Drosophila melanogaster. PMID:17927810
Demographic histories of ERV-K in humans, chimpanzees and rhesus monkeys. PMID:17925874
PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. PMID:17921354
The G protein-coupled receptor subset of the rat genome. PMID:17892602
SmedGD: the Schmidtea mediterranea genome database. PMID:17881371
A cross-species alignment tool (CAT). PMID:17880681
Differential gene expression in an elite hybrid rice cultivar (Oryza sativa, L) and its parental lines based on SAGE data. PMID:17877838
Novel rapidly evolving hominid RNAs bind nuclear factor 90 and display tissue-restricted distribution. PMID:17855395
Dual-specificity splice sites function alternatively as 5' and 3' splice sites. PMID:17848517
Adaptive evolution of conserved noncoding elements in mammals. PMID:17845075
Rod-derived Cone Viability Factor-2 is a novel bifunctional-thioredoxin-like protein with therapeutic potential. PMID:17764561
antiCODE: a natural sense-antisense transcripts database. PMID:17760969
Genome analysis of Minibacterium massiliensis highlights the convergent evolution of water-living bacteria. PMID:17722982
Adaptive evolution of recently duplicated accessory gland protein genes in desert Drosophila. PMID:17720912
PyCogent: a toolkit for making sense from sequence. PMID:17708774
Hairpin structure within the 3'UTR of DNA polymerase beta mRNA acts as a post-transcriptional regulatory element and interacts with Hax-1. PMID:17704138
A physical map of the bovine genome. PMID:17697342
WASP: a Web-based Allele-Specific PCR assay designing tool for detecting SNPs and mutations. PMID:17697334
Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification. PMID:17686789
Translational regulation of human methionine synthase by upstream open reading frames. PMID:17683808
Divergent evolution of human p53 binding sites: cell cycle versus apoptosis. PMID:17677004
Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution. PMID:17675364
Gene copy number variation spanning 60 million years of human and primate evolution. PMID:17666543
Bird and mammal sex-chromosome orthologs map to the same autosomal region in a salamander (ambystoma). PMID:17660573
Optimized design and assessment of whole genome tiling arrays. PMID:17646297
C. elegans sequences that control trans-splicing and operon pre-mRNA processing. PMID:17630324
A correlation with exon expression approach to identify cis-regulatory elements for tissue-specific alternative splicing. PMID:17626050
Widely variable endogenous retroviral methylation levels in human placenta. PMID:17617638
Analysis of the features and source gene composition of the AluYg6 subfamily of human retrotransposons. PMID:17603915
Common functions for diverse small RNAs of land plants. PMID:17601824
Morphine effects on striatal transcriptome in mice. PMID:17598886
Development of the first marmoset-specific DNA microarray (EUMAMA): a new genetic tool for large-scale expression profiling in a non-human primate. PMID:17592630
Functional analysis of the human N-acetyltransferase 1 major promoter: quantitation of tissue expression and identification of critical sequence elements. PMID:17591675
Genome position and gene amplification. PMID:17584934
Comparative analysis of structured RNAs in S. cerevisiae indicates a multitude of different functions. PMID:17577407
Restauro-G: a rapid genome re-annotation system for comparative genomics. PMID:17572364
Simultaneous identification of long similar substrings in large sets of sequences. PMID:17570866
LongSAGE profiling of nine human embryonic stem cell lines. PMID:17570852
Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs). PMID:17568001
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. PMID:17567995
Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome. PMID:17567992
Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi. PMID:17567986
Tissue expression and genomic sequences of rat N-acetyltransferases rNat1, rNat2, rNat3, and Functional characterization of a novel rNat3*2 genetic variant. PMID:17567587
Large-scale identification of human genes implicated in epidermal barrier function. PMID:17562024
Comparative genomics reveals functional transcriptional control sequences in the Prop1 gene. PMID:17557180
Differing patterns of selection in alternative and constitutive splice sites. PMID:17556528
Identification of the circadian transcriptome in adult mouse skeletal muscle. PMID:17550994
GeneHub-GEPIS: digital expression profiling for normal and cancer tissues based on an integrated gene database. PMID:17545196
Ion channel gene expression in the inner ear. PMID:17541769
Comparative analysis of eubacterial DNA polymerase III alpha subunits. PMID:17531796
Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey. PMID:17524145
Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome. PMID:17506886
Patterns of gene duplication and intron loss in the ENCODE regions suggest a confounding factor. PMID:17499477
Comparative cross-species alternative splicing in plants. PMID:17496110
The zinc finger proteins ZXDA and ZXDC form a complex that binds CIITA and regulates MHC II gene transcription. PMID:17493635
cis-Decoder discovers constellations of conserved DNA sequences shared among tissue-specific enhancers. PMID:17490485
Multiple whole genome alignments and novel biomedical applications at the VISTA portal. PMID:17488840
MicroRNA genes are frequently located near mouse cancer susceptibility loci. PMID:17470785
A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii. PMID:17470535
Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays. PMID:17470268
Functional characterization of spliceosomal introns and identification of U2, U4, and U5 snRNAs in the deep-branching eukaryote Entamoeba histolytica. PMID:17468393
The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. PMID:17460045
A cricket Gene Index: a genomic resource for studying neurobiology, speciation, and molecular evolution. PMID:17459168
Discovery of tissue-specific exons using comprehensive human exon microarrays. PMID:17456239
Origin and evolution of human microRNAs from transposable elements. PMID:17435244
A primary assembly of a bovine haplotype block map based on a 15,036-single-nucleotide polymorphism panel genotyped in holstein-friesian cattle. PMID:17435229
Gene models from ESTs (GeneModelEST): an application on the Solanum lycopersicum genome. PMID:17430576
Distinct mechanisms for trans-mediated mobilization of cellular RNAs by the LINE-1 reverse transcriptase. PMID:17416749
Transcriptional interferences in cis natural antisense transcripts of humans and mice. PMID:17409075
DNA microarray data integration by ortholog gene analysis reveals potential molecular mechanisms of estrogen-dependent growth of human uterine fibroids. PMID:17407572
Extensive polycistronism and antisense transcription in the mammalian Hox clusters. PMID:17406680
Identification of five mouse mu-opioid receptor (MOR) gene (Oprm1) splice variants containing a newly identified alternatively spliced exon. PMID:17398041
Evolutionary pathways of the tirant LTR retrotransposon in the Drosophila melanogaster subgroup of species. PMID:17390093
Non-random genomic divergence in repetitive sequences of human and chimpanzee in genes of different functional categories. PMID:17375324
A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome. PMID:17374142
Sense-antisense pairs in mammals: functional and evolutionary considerations. PMID:17371592
Review of the literature examining the correlation among DNA microarray technologies. PMID:17370338
The strength of selection on ultraconserved elements in the human genome. PMID:17357075
EST assembly supported by a draft genome sequence: an analysis of the Chlamydomonas reinhardtii transcriptome. PMID:17355987
Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing. PMID:17351049
Comparative physical mapping between Oryza sativa (AA genome type) and O. punctata (BB genome type). PMID:17339227
SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis. PMID:17338820
Tentative mapping of transcription-induced interchromosomal interaction using chimeric EST and mRNA data. PMID:17330142
Improving the Caenorhabditis elegans genome annotation using machine learning. PMID:17319737
A family of human microRNA genes from miniature inverted-repeat transposable elements. PMID:17301878
A screen for retrotransposed imprinted genes reveals an association between X chromosome homology and maternal germ-line methylation. PMID:17291163
Identification of N-acetyltransferase 2 (NAT2) transcription start sites and quantitation of NAT2-specific mRNA in human tissues. PMID:17287389
A gene-based radiation hybrid map of the gilthead sea bream Sparus aurata refines and exploits conserved synteny with Tetraodon nigroviridis. PMID:17286862
Mapping of transcription start sites of human retina expressed genes. PMID:17286855
A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. PMID:17270048
Complex genomic rearrangement in CCS-LacZ transgenic mice. PMID:17269130
A mobile element-based evolutionary history of guenons (tribe Cercopithecini). PMID:17266768
Considerations in the identification of functional RNA structural elements in genomic alignments. PMID:17263882
Global DNA methylation profiling reveals silencing of a secreted form of Epha7 in mouse and human germinal center B-cell lymphomas. PMID:17260020
A complex rearrangement in GBE1 causes both perinatal hypoglycemic collapse and late-juvenile-onset neuromuscular degeneration in glycogen storage disease type IV of Norwegian forest cats. PMID:17257876
Automated querying of genome databases. PMID:17257048
Processing of intronic microRNAs. PMID:17255951
Asymptotic behaviour and optimal word size for exact and approximate word matches between random sequences. PMID:17254306
Isolation, sequencing, and functional analysis of the TATA-less murine ATPase II promoter and structural analysis of the ATPase II gene. PMID:17239457
Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips. PMID:17224057
Ashbya Genome Database 3.0: a cross-species genome and transcriptome browser for yeast biologists. PMID:17212814
Widespread mRNA polyadenylation events in introns indicate dynamic interplay between polyadenylation and splicing. PMID:17210931
A tale of two templates: automatically resolving double traces has many applications, including efficient PCR-based elucidation of alternative splices. PMID:17210930
A high-resolution map of segmental DNA copy number variation in the mouse genome. PMID:17206864
PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes. PMID:17202160
A high-resolution map of synteny disruptions in gibbon and human genomes. PMID:17196042
Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. PMID:17194304
Dynamic use of multiple parameter sets in sequence alignment. PMID:17182633
Lengsin is a survivor of an ancient family of class I glutamine synthetases re-engineered by evolution for a role in the vertebrate lens. PMID:17161372
Evolution of the metazoan protein phosphatase 2C superfamily. PMID:17160364
Systematic variation in mRNA 3'-processing signals during mouse spermatogenesis. PMID:17158511
Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST. PMID:17156431
Mammalian small nucleolar RNAs are mobile genetic elements. PMID:17154719
VectorBase: a home for invertebrate vectors of human pathogens. PMID:17145709
The UCSC genome browser database: update 2007. PMID:17142222
Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome. PMID:17134480
Simultaneous host and parasite expression profiling identifies tissue-specific transcriptional programs associated with susceptibility or resistance to experimental cerebral malaria. PMID:17118208
Genome assembly comparison identifies structural variants in the human genome. PMID:17115057
Characterization of a cancer/testis (CT) antigen gene family capable of eliciting humoral response in cancer patients. PMID:17114284
Towards pathogenomics: a web-based resource for pathogenicity islands. PMID:17090594
SAGE detects microRNA precursors. PMID:17090314
The TIGR Plant Transcript Assemblies database. PMID:17088284
Evolution and comparative analysis of the MHC Class III inflammatory region. PMID:17081307
Exon-based mapping of microarray probes: recovering differential gene expression signal in underpowered hypoxia experiment. PMID:17071053
Recent assembly of an imprinted domain from non-imprinted components. PMID:17069464
CAFTAN: a tool for fast mapping, and quality assessment of cDNAs. PMID:17064411
CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes. PMID:17062155
Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation. PMID:17059607
Prediction of trans-antisense transcripts in Arabidopsis thaliana. PMID:17040561
Functionality of intergenic transcription: an evolutionary comparison. PMID:17040132
Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin. PMID:17038564
Nonrandom representation of sex-biased genes on chicken Z chromosome. PMID:17031459
Design factors that influence PCR amplification success of cross-species primers among 1147 mammalian primer pairs. PMID:17029642
Heterogeneous genomic molecular clocks in primates. PMID:17029560
A high throughput method for genome-wide analysis of retroviral integration. PMID:17028098
Analysis of cytoskeletal and motility proteins in the sea urchin genome assembly. PMID:17027957
Identification, genome mapping, and CTCF binding of potential insulators within the FXYD5-COX7A1 locus of human chromosome 19q13.12. PMID:17019650
MICA: desktop software for comprehensive searching of DNA databases. PMID:17018144
Ancient genomic architecture for mammalian olfactory receptor clusters. PMID:17010214
Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. PMID:17010196
Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. PMID:17003129
Comparison of methods for genomic localization of gene trap sequences. PMID:16982004
Ultra-high resolution array painting facilitates breakpoint sequencing. PMID:16971479
SyMAP: A system for discovering and viewing syntenic regions of FPC maps. PMID:16951135
The echinoderm adhesome. PMID:16950242
A founder mutation for ichthyosis prematurity syndrome restricted to 76 kb by haplotype association. PMID:16946994
In vivo requirement of the small subunit of U2AF for recognition of a weak 3' splice site. PMID:16940179
Gene expression profiling of chicken primordial germ cell ESTs. PMID:16939661
Gene order data from a model amphibian (Ambystoma): new perspectives on vertebrate genome structure and evolution. PMID:16939647
Sex-specific expression of alternative transcripts in Drosophila. PMID:16934145
An integrative method for accurate comparative genome mapping. PMID:16933978
Genome-wide analysis of mRNAs bound to the histone stem-loop binding protein. PMID:16931877
JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions. PMID:16925843
Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA. PMID:16925841
Pairagon+N-SCAN_EST: a model-based gene annotation pipeline. PMID:16925839
AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome. PMID:16925833
Oligonucleotide microarray analysis of genomic imbalance in children with mental retardation. PMID:16909388
Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments. PMID:16904011
Phylogenetic analysis of the tenascin gene family: evidence of origin early in the chordate lineage. PMID:16893461
G-InforBIO: integrated system for microbial genomics. PMID:16887044
Polymorphisms in the glucocerebrosidase gene and pseudogene urge caution in clinical analysis of Gaucher disease allele c.1448T>C (L444P). PMID:16887033
NF-Y, AP2, Nrf1 and Sp1 regulate the fragile X-related gene 2 (FXR2). PMID:16886907
The cnidarian-bilaterian ancestor possessed at least 56 homeoboxes: evidence from the starlet sea anemone, Nematostella vectensis. PMID:16867185
Chromosome-wide identification of novel imprinted genes using microarrays and uniparental disomies. PMID:16855283
An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes. PMID:16855282
Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species. PMID:16849434
Identification and analysis of genes and pseudogenes within duplicated regions in the human and mouse genomes. PMID:16846249
MutScreener: primer design tool for PCR-direct sequencing. PMID:16845093
U1-like snRNAs lacking complementarity to canonical 5' splice sites. PMID:16829670
Identification and characterization of functional rat arylamine N-acetyltransferase 3: comparisons with rat arylamine N-acetyltransferases 1 and 2. PMID:16829624
High rate of chimeric gene origination by retroposition in plant genomes. PMID:16829590
Genomic overview of mRNA 5'-leader trans-splicing in the ascidian Ciona intestinalis. PMID:16822859
A unifying framework for seed sensitivity and its application to subset seeds. PMID:16819802
Using ESTs to improve the accuracy of de novo gene prediction. PMID:16817966
A first-generation metric linkage disequilibrium map of bovine chromosome 6. PMID:16816421
Genomic characterization of five deletions in the LDL receptor gene in Danish Familial Hypercholesterolemic subjects. PMID:16796766
Characterization of phagosome trafficking and identification of PhoP-regulated genes important for survival of Yersinia pestis in macrophages. PMID:16790745
Parametric alignment of Drosophila genomes. PMID:16789815
Gene expression profiling in the striatum of inbred mouse strains with distinct opioid-related phenotypes. PMID:16772024
Evidence for variation in abundance of antisense transcripts between multicellular animals but no relationship between antisense transcriptionand organismic complexity. PMID:16769979
Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure. PMID:16751343
Positive selection on the nonhomologous end-joining factor Cernunnos-XLF in the human lineage. PMID:16749933
The G protein-coupled receptor subset of the chicken genome. PMID:16741557
Learning interpretable SVMs for biological sequence classification. PMID:16723012
Widespread ectopic expression of olfactory receptor genes. PMID:16716209
Automatic generation of gene finders for eukaryotic species. PMID:16712739
Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. PMID:16683036
SPA: a probabilistic algorithm for spliced alignment. PMID:16683023
Autosomal dominant optic atrophy associated with hearing impairment and impaired glucose regulation caused by a missense mutation in the WFS1 gene. PMID:16648378
Evaluation of an extended set of 15 candidate STR loci for paternity and kinship analysis in an Austrian population sample. PMID:16642351
Differential expression of a new isoform of DLG2 in renal oncocytoma. PMID:16640776
Characterization of a complex rearrangement with interstitial deletions and inversion on human chromosome 1. PMID:16628498
Identification and classification of conserved RNA secondary structures in the human genome. PMID:16628248
Analysis of 10,000 ESTs from lymphocytes of the cynomolgus monkey to improve our understanding of its immune system. PMID:16618371
ZXDC, a novel zinc finger protein that binds CIITA and activates MHC gene transcription. PMID:16600381
The PLAC1-homology region of the ZP domain is sufficient for protein polymerisation. PMID:16600035
Reference based annotation with GeneMapper. PMID:16600017
Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server. PMID:16584563
Periodicity of SNP distribution around transcription start sites. PMID:16579865
Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms. PMID:16569258
GENOMEMASKER package for designing unique genomic PCR primers. PMID:16566824
Regions of extreme synonymous codon selection in mammalian genes. PMID:16556911
LINE-1 RNA splicing and influences on mammalian gene expression. PMID:16554555
Histone H3 acetylated at lysine 9 in promoter is associated with low nucleosome density in the vicinity of transcription start site in human cell. PMID:16544193
Choosing the best heuristic for seeded alignment of DNA sequences. PMID:16533404
Duplication and relocation of the functional DPY19L2 gene within low copy repeats. PMID:16526957
AGRIS and AtRegNet. a platform to link cis-regulatory elements and transcription factors into regulatory networks. PMID:16524982
TOPAAS, a tomato and potato assembly assistance system for selection and finishing of bacterial artificial chromosomes. PMID:16524981
Identification of alternatively spliced dab1 isoforms in zebrafish. PMID:16520940
Grey, a novel mutation in the murine Lyst gene, causes the beige phenotype by skipping of exon 25. PMID:16518687
dbRIP: a highly integrated database of retrotransposon insertion polymorphisms in humans. PMID:16511833
Comparison of dot chromosome sequences from D. melanogaster and D. virilis reveals an enrichment of DNA transposon sequences in heterochromatic domains. PMID:16507169
Identifying repeat domains in large genomes. PMID:16507140
Quantitative comparison of EST libraries requires compensation for systematic biases in cDNA generation. PMID:16503995
A map of recent positive selection in the human genome. PMID:16494531
Neighboring-nucleotide effects on the mutation patterns of the rice genome. PMID:16487081
Sex-dependent gene expression in early brain development of chicken embryos. PMID:16480516
Expression profiling identifies novel candidate genes for ethanol sensitivity QTLs. PMID:16465594
Gene losses during human origins. PMID:16464126
Decoding the fine-scale structure of a breast cancer genome and transcriptome. PMID:16461635
Comparison of human (and other) genome browsers. PMID:16460652
Comparative analysis of cancer genes in the human and chimpanzee genomes. PMID:16438707
Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex. PMID:16435885
Foamy virus vector integration sites in normal human cells. PMID:16428288
Unusual intron conservation near tissue-regulated exons found by splicing microarrays. PMID:16424921
A novel approach to identifying regulatory motifs in distantly related genomes. PMID:16420672
Mammalian alpha I-spectrin is a neofunctionalized polypeptide adapted to small highly deformable erythrocytes. PMID:16407147
Application of a superword array in genome assembly. PMID:16397298
Fast-Find: a novel computational approach to analyzing combinatorial motifs. PMID:16393334
MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data. PMID:16381984
The TIGR Maize Database. PMID:16381977
The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information. PMID:16381971
The UCSC Genome Browser Database: update 2006. PMID:16381938
The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context. PMID:16381934
Tetrahymena Genome Database (TGD): a new genomic resource for Tetrahymena thermophila research. PMID:16381920
The UCSC Archaeal Genome Browser. PMID:16381898
VMD: a community annotation database for oomycetes and microbial genomes. PMID:16381891
ChimerDB--a knowledgebase for fusion sequences. PMID:16381848
snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. PMID:16381836
A computational screen for mammalian pseudouridylation guide H/ACA RNAs. PMID:16373490
Large-scale structure of genomic methylation patterns. PMID:16365381
Integrating probe-level expression changes across generations of Affymetrix arrays. PMID:16356924
Distortion of quantitative genomic and expression hybridization by Cot-1 DNA: mitigation of this effect. PMID:16356923
Identification of transposable elements using multiple alignments of related genomes. PMID:16354754
A method for accurate detection of genomic microdeletions using real-time quantitative PCR. PMID:16351727
Validation of mRNA/EST-based gene predictions in human Xp11.4 revealed differences to the organization of the orthologous mouse locus. PMID:16341673
Primate-specific endogenous cis-antisense transcription in the human 5q31 protocadherin gene cluster. PMID:16341467
Efficient single nucleotide polymorphism discovery in laboratory rat strains using wild rat-derived SNP candidates. PMID:16316463
A retrocopy of a gene can functionally displace the source gene in evolution. PMID:16314324
Gene identification in novel eukaryotic genomes by self-training algorithm. PMID:16314312
Characterization of 954 bovine full-CDS cDNA sequences. PMID:16305752
Construction and characterization of a genomic BAC library for the Mus m. musculus mouse subspecies (PWD/Ph inbred strain). PMID:16288658
Cataloging transcription factor and major signaling molecule genes for functional genomic studies in Ciona intestinalis. PMID:16252120
Survey of allelic expression using EST mining. PMID:16251468
Traffic of genetic information between segmental duplications flanking the typical 22q11.2 deletion in velo-cardio-facial syndrome/DiGeorge syndrome. PMID:16251458
Dynamic structure of the SPANX gene cluster mapped to the prostate cancer susceptibility locus HPCX at Xq27. PMID:16251457
MAASE: an alternative splicing database designed for supporting splicing microarray applications. PMID:16251387
A method of precise mRNA/DNA homology-based gene structure prediction. PMID:16242044
Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms. PMID:16237126
A genome-wide survey demonstrates widespread non-linear mRNA in expressed sequences from multiple species. PMID:16237125
ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences. PMID:16207377
EVOPRINTER, a multigenomic comparative tool for rapid identification of functionally important DNA. PMID:16203978
Random sheared fosmid library as a new genomic tool to accelerate complete finishing of rice (Oryza sativa spp. Nipponbare) genome sequence: sequencing of gap-specific fosmid clones uncovers new euchromatic portions of the genome. PMID:16200416
Chromosomal copy number changes in patients with non-syndromic X linked mental retardation detected by array CGH. PMID:16169931
A method for finding single-nucleotide polymorphisms with allele frequencies in sequences of deep coverage. PMID:16146575
The evolutionary fate of MULE-mediated duplications of host gene fragments in rice. PMID:16140995
Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates. PMID:16140992
Integration targeting by avian sarcoma-leukosis virus and human immunodeficiency virus in the chicken genome. PMID:16140779
Multiple fates of L1 retrotransposition intermediates in cultured human cells. PMID:16107723
Tools and strategies for physiological genomics: the Rat Genome Database. PMID:16106031
Large-scale analysis of adeno-associated virus vector integration sites in normal human cells. PMID:16103194
Using multiple alignments to improve seeded local alignment algorithms. PMID:16100379
Genome-wide promoter extraction and analysis in human, mouse, and rat. PMID:16086854
A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription. PMID:16083503
Characterization of CA XV, a new GPI-anchored form of carbonic anhydrase. PMID:16083424
Transcription of mammalian messenger RNAs by a nuclear RNA polymerase of mitochondrial origin. PMID:16079853
Assembly of polymorphic genomes: algorithms and application to Ciona savignyi. PMID:16077012
miBLAST: scalable evaluation of a batch of nucleotide sequence queries with BLAST. PMID:16061938
Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages. PMID:16034026
A computational approach for identifying pathogenicity islands in prokaryotic genomes. PMID:16033657
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. PMID:16024819
Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray. PMID:15998450
ASePCR: alternative splicing electronic RT-PCR in multiple tissues and organs. PMID:15980562
Dcode.org anthology of comparative genomic tools. PMID:15980535
MuPlex: multi-objective multiplex PCR assay design. PMID:15980531
A genetic linkage map for the tiger pufferfish, Takifugu rubripes. PMID:15972462
Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture. PMID:15960804
Exploring hepatic hormone actions using a compilation of gene expression profiles. PMID:15953391
Satellog: a database for the identification and prioritization of satellite repeats in disease association studies. PMID:15949044
Linkage mapping bovine EST-based SNP. PMID:15943875
Identification of coexpressed gene clusters in a comparative analysis of transcriptome and proteome in mouse tissues. PMID:15939889
Chromosomal aberrations induced by double strand DNA breaks. PMID:15935739
Composite genome map and recombination parameters derived from three archetypal lineages of Toxoplasma gondii. PMID:15911631
CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome. PMID:15911630
A multistep bioinformatic approach detects putative regulatory elements in gene promoters. PMID:15904489
AnoEST: toward A. gambiae functional genomics. PMID:15899967
Nine unknown rearrangements in 16p13.3 and 11p15.4 causing alpha- and beta-thalassaemia characterised by high resolution multiplex ligation-dependent probe amplification. PMID:15894596
The institute for genomic research Osa1 rice genome annotation database. PMID:15888674
Characterisation and application of a bovine U6 promoter for expression of short hairpin RNAs. PMID:15885150
Refined repetitive sequence searches utilizing a fast hash function and cross species information retrievals. PMID:15869708
Genome-wide assembly and analysis of alternative transcripts in mouse. PMID:15867436
Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. PMID:15867429
Under the genomic radar: the stealth model of Alu amplification. PMID:15867427
A tiling microarray expression analysis of rice chromosome 4 suggests a chromosome-level regulation of transcription. PMID:15863518
A newly discovered human alpha-globin gene. PMID:15855277
Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana. PMID:15833117
Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser. PMID:15826305
Retropseudogenes derived from the human Ro/SS-A autoantigen-associated hY RNAs. PMID:15817567
ECgene: genome-based EST clustering and gene modeling for alternative splicing. PMID:15805497
Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana. PMID:15805491
Symmetrical base preferences surrounding HIV-1, avian sarcoma/leukosis virus, and murine leukemia virus integration sites. PMID:15802467
Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release. PMID:15784138
Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example. PMID:15752422
The synthetic form of a novel chicken beta-defensin identified in silico is predominantly active against intestinal pathogens. PMID:15744537
Genome-wide transcriptional analysis of flagellar regeneration in Chlamydomonas reinhardtii identifies orthologs of ciliary disease genes. PMID:15738400
Identification of functional SNPs in the 5-prime flanking sequences of human genes. PMID:15717931
Complex genomic rearrangements lead to novel primate gene function. PMID:15710750
Identification of ciliated sensory neuron-expressed genes in Caenorhabditis elegans using targeted pull-down of poly(A) tails. PMID:15693946
Pooled genomic indexing of rhesus macaque. PMID:15687293
The Genomes of Oryza sativa: a history of duplications. PMID:15685292
Genome-scale analysis of positional clustering of mouse testis-specific genes. PMID:15656914
A large-scale analysis of mRNA polyadenylation of human and mouse genes. PMID:15647503
Computational prediction of miRNAs in Arabidopsis thaliana. PMID:15632092
Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes. PMID:15613238
Identifying estrogen receptor alpha target genes using integrated computational genomics and chromatin immunoprecipitation microarray. PMID:15608294
DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants. PMID:15608291
GeneTide--Terra Incognita Discovery Endeavor: a new transcriptome focused member of the GeneCards/GeneNote suite of databases. PMID:15608261
T1DBase, a community web-based resource for type 1 diabetes research. PMID:15608258
The UCSC Proteome Browser. PMID:15608236
ChickVD: a sequence variation database for the chicken genome. PMID:15608233
WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. PMID:15608221
SPD--a web-based secreted protein database. PMID:15608170
UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. PMID:15608165
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. PMID:15592405
Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence. PMID:15588320
The mouse genome: experimental examination of gene predictions and transcriptional start sites. PMID:15574821
Distinct genomic integration of MLV and SIV vectors in primate hematopoietic stem and progenitor cells. PMID:15550989
Discovery of functional noncoding elements by digital analysis of chromatin structure. PMID:15550541
An interactive bovine in silico SNP database (IBISS). PMID:15520884
Open reading frame sequencing and structure-based alignment of polypeptides encoded by RT1-Bb, RT1-Ba, RT1-Db, and RT1-Da alleles. PMID:15517241
Natural genetic variation caused by transposable elements in humans. PMID:15514065
Combining gene expression data from different generations of oligonucleotide arrays. PMID:15504239
WormBase as an integrated platform for the C. elegans ORFeome. PMID:15489338
Systematic recovery and analysis of full-ORF human cDNA clones. PMID:15489330
1274 full-open reading frames of transcripts expressed in the developing mouse nervous system. PMID:15489326
Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing. PMID:15489323
Improved hit criteria for DNA local alignment. PMID:15485572
Genome-wide mutagenesis of Zea mays L. using RescueMu transposons. PMID:15461800
Alternative splicing of mouse transcription factors affects their DNA-binding domain architecture and is tissue specific. PMID:15461794
Comprehensive association analysis of APOE regulatory region polymorphisms in Alzheimer disease. PMID:15455263
Over 20% of human transcripts might form sense-antisense pairs. PMID:15356298
A genome-wide screen identifies a single beta-defensin gene cluster in the chicken: implications for the origin and evolution of mammalian defensins. PMID:15310403
The Alternative Splicing Gallery (ASG): bridging the gap between genome and transcriptome. PMID:15292448
Genetic divergence of the rhesus macaque major histocompatibility complex. PMID:15289473
Regional patterns of gene expression in human and chimpanzee brains. PMID:15289471
Gene trap as a tool for genome annotation and analysis of X chromosome inactivation in human embryonic stem cells. PMID:15284332
Comparative genomics: methods and applications. PMID:15278216
Molecular structure of double-minute chromosomes bearing amplified copies of the epidermal growth factor receptor gene in gliomas. PMID:15269346
Comparative evolutionary genomics of androgen-binding protein genes. PMID:15256509
Evolutionary conservation and selection of human disease gene orthologs in the rat and mouse genomes. PMID:15239832
ProbeLynx: a tool for updating the association of microarray probes to genes. PMID:15215432
e2g: an interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequences. PMID:15215398
ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes. PMID:15215395
VISTA: computational tools for comparative genomics. PMID:15215394
PromoSer: improvements to the algorithm, visualization and accessibility. PMID:15215378
ASmodeler: gene modeling of alternative splicing from genomic alignment of mRNA, EST and protein sequences. PMID:15215376
siRNA Selection Server: an automated siRNA oligonucleotide prediction server. PMID:15215365
Selective pressures on the olfactory receptor repertoire since the human-chimpanzee divergence. PMID:15178761
Building genomic profiles for uncovering segmental homology in the twilight zone. PMID:15173115
Differential alu mobilization and polymorphism among the human and chimpanzee lineages. PMID:15173113
A neutral model of transcriptome evolution. PMID:15138501
ELXR: a resource for rapid exon-directed sequence analysis. PMID:15128450
The Ensembl automatic gene annotation system. PMID:15123590
A gene atlas of the mouse and human protein-encoding transcriptomes. PMID:15075390
Integration of the rat recombination and EST maps in the rat genomic sequence and comparative mapping analysis with the mouse genome. PMID:15060020
High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence. PMID:15060019
MAVID: constrained ancestral alignment of multiple sequences. PMID:15060012
Automated whole-genome multiple alignment of rat, mouse, and human. PMID:15060011
Pash: efficient genome-scale sequence anchoring by Positional Hashing. PMID:15060009
Evolution and comparative genomics of odorant- and pheromone-associated genes in rodents. PMID:15060000
Genomic analysis of the nuclear receptor family: new insights into structure, regulation, and evolution from the rat genome. PMID:15059999
Comparative recombination rates in the rat, mouse, and human genomes. PMID:15059993
Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes. PMID:15059991
Assessment of clusters of transcription factor binding sites in relationship to human promoter, CpG islands and gene expression. PMID:15053842
Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion. PMID:15045028
Fine mapping a gene for pediatric gastroesophageal reflux on human chromosome 13q14. PMID:15014979
Evolutionary implication of human endogenous retrovirus HERV-H family. PMID:15007706
Eukaryotic regulatory element conservation analysis and identification using comparative genomics. PMID:14993210
Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array. PMID:14993208
Novel antigen identification method for discovery of protective malaria antigens by rapid testing of DNA vaccines encoding exons from the parasite genome. PMID:14977966
Noncoding sequences conserved in a limited number of mammals in the SIM2 interval are frequently functional. PMID:14962988
Genome annotation by high-throughput 5' RNA end determination. PMID:14757812
Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites. PMID:14732688
Packaging and reverse transcription of snRNAs by retroviruses may generate pseudogenes. PMID:14730028
Elevated rates of protein secretion, evolution, and disease among tissue-specific genes. PMID:14707169
The mouse salivary androgen-binding protein (ABP) gene cluster on chromosomes 7: characterization and evolutionary relationships. PMID:14694904
Transcriptome analysis of mouse stem cells and early embryos. PMID:14691545
Hembase: browser and genome portal for hematology and erythroid biology. PMID:14681483
RTCGD: retroviral tagged cancer gene database. PMID:14681473
HGVbase: a curated resource describing human DNA variation and phenotype relationships. PMID:14681471
FREP: a database of functional repeats in mouse cDNAs. PMID:14681460
Full-malaria 2004: an enlarged database for comparative studies of full-length cDNAs of malaria parasites, Plasmodium species. PMID:14681428
HemoPDB: Hematopoiesis Promoter Database, an information resource of transcriptional regulation in blood cell development. PMID:14681365
Xpro: database of eukaryotic protein-encoding genes. PMID:14681359
HERVd: the Human Endogenous RetroViruses Database: update. PMID:14681356
1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. PMID:14672980
Multiple variable first exons: a mechanism for cell- and tissue-specific gene regulation. PMID:14672974
Expressed sequence tag profiling identifies developmental and anatomic partitioning of gene expression in the mouse prostate. PMID:14659016
Shuffling of genes within low-copy repeats on 22q11 (LCR22) by Alu-mediated recombination events during evolution. PMID:14656960
Mastering seeds for genomic size nucleotide BLAST searches. PMID:14627826
Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates. PMID:14611660
Identification of a novel liver-specific expressed gene, TCP10L, encoding a human leucine zipper protein with transcription inhibition activity. PMID:14586771
Matrix attachment region (MAR) properties and abnormal expansion of AT island minisatellites in FRA16B fragile sites in leukemic CEM cells. PMID:14576323
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. PMID:14500829
Annotating large genomes with exact word matches. PMID:12975312
SPAM1 (PH-20) protein and mRNA expression in the epididymides of humans and macaques: utilizing laser microdissection/RT-PCR. PMID:12932297
A general approach for identifying distant regulatory elements applied to the Gdf6 gene. PMID:12915490
Locating sequence on FPC maps and selecting a minimal tiling path. PMID:12915486
Assessing the Drosophila melanogaster and Anopheles gambiae genome annotations using genome-wide sequence comparisons. PMID:12840038
DNannotator: Annotation software tool kit for regional genomic sequences. PMID:12824405
PromoSer: A large-scale mammalian promoter and transcription start site identification service. PMID:12824364
AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. PMID:12820902
GeneLynx mouse: integrated portal to the mouse genome. PMID:12819149
G protein-coupled receptor genes in the FANTOM2 database. PMID:12819145
Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage. PMID:12819134
Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome. PMID:12819126
Identification of promoter regions in the human genome by using a retroviral plasmid library-based functional reporter gene assay. PMID:12805274
Computational discovery of internal micro-exons. PMID:12799353
Mutations in the fumarate hydratase gene cause hereditary leiomyomatosis and renal cell cancer in families in North America. PMID:12772087
Identification of conserved regulatory elements by comparative genome analysis. PMID:12760745
Assessment of SAGE in transcript identification. PMID:12743019
Multiple, dispersed human U6 small nuclear RNA genes with varied transcriptional efficiencies. PMID:12711679
ProSplicer: a database of putative alternative splicing information derived from protein, mRNA and expressed sequence tag sequence data. PMID:12702210
A 1-Mb resolution radiation hybrid map of the canine genome. PMID:12700351
Comparative genomic tools and databases: providing insights into the human genome. PMID:12697725
LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. PMID:12654723
ATLAS: a system to selectively identify human-specific L1 insertions. PMID:12632328
Genome-wide single-nucleotide polymorphism analysis defines haplotype patterns in mouse. PMID:12612341
Molecular classification of familial non-BRCA1/BRCA2 breast cancer. PMID:12610208
Large differences between LINE-1 amplification rates in the human and chimpanzee lineages. PMID:12574987
Identification of a novel Bardet-Biedl syndrome protein, BBS7, that shares structural features with BBS1 and BBS2. PMID:12567324
A complexity reduction algorithm for analysis and annotation of large genomic sequences. PMID:12566410
Discovery of the breast cancer gene BASE using a molecular approach to enrich for genes encoding membrane and secreted proteins. PMID:12538848
Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome. PMID:12537575
Apollo: a sequence annotation editor. PMID:12537571
Computational comparison of two mouse draft genomes and the human golden path. PMID:12537546
Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics. PMID:12529507
Human-mouse alignments with BLASTZ. PMID:12529312
Strategies and tools for whole-genome alignments. PMID:12529308
Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. PMID:12529304
Reevaluating human gene annotation: a second-generation analysis of chromosome 22. PMID:12529303
Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. PMID:12529302
Cross-species sequence comparisons: a review of methods and available resources. PMID:12529301
Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE. PMID:12519968
WormBase: a cross-species database for comparative genomics. PMID:12519966
The UCSC Genome Browser Database. PMID:12519945
POTE, a highly homologous gene family located on numerous chromosomes and expressed in prostate, ovary, testis, placenta, and prostate cancer. PMID:12475935
Development and production of an oligonucleotide MuscleChip: use for validation of ambiguous ESTs. PMID:12456269
Comparison of whole genome assemblies of the human genome. PMID:12434005
Identification of candidate genes regulating HDL cholesterol using a chromosomal region expression array. PMID:12421756
A computational/functional genomics approach for the enrichment of the retinal transcriptome and the identification of positional candidate retinopathy genes. PMID:12391299
The human genome browser at UCSC. PMID:12045153 -
The UCSC Table Browser data retrieval tool
PubMed citations: 1176.
1176 articles citing: The UCSC Table Browser data retrieval tool
SNP-to-gene linking strategies reveal contributions of enhancer-related and candidate master-regulator genes to autoimmune disease. PMID:35873673
TCF7L2 promotes anoikis resistance and metastasis of gastric cancer by transcriptionally activating PLAUR. PMID:35864968
Homologous recombination deficiency (HRD) score in aggressive prostatic adenocarcinoma with or without intraductal carcinoma of the prostate (IDC-P). PMID:35864546
Enrichment of centromeric DNA from human cells. PMID:35853083
Somatic Mutations Detected in Parkinson Disease Could Affect Genes With a Role in Synaptic and Neuronal Processes. PMID:35821807
Chromosome-level assembly and annotation of the blue catfish Ictalurus furcatus, an aquaculture species for hybrid catfish reproduction, epigenetics, and heterosis studies. PMID:35809049
Acetaldehyde makes a distinct mutation signature in single-stranded DNA. PMID:35776120
A new deep learning technique reveals the exclusive functional contributions of individual cancer mutations. PMID:35753349
Blood-derived lncRNAs as biomarkers for cancer diagnosis: the Good, the Bad and the Beauty. PMID:35729321
DNA Methylation Analysis of Turner Syndrome BAV. PMID:35711915
An NF-κB- and Therapy-Related Regulatory Network in Glioma: A Potential Mechanism of Action for Natural Antiglioma Agents. PMID:35625673
Dnmt3a knockout in excitatory neurons impairs postnatal synapse maturation and increases the repressive histone modification H3K27me3. PMID:35604009
Cell-Free RNA as a Novel Biomarker for Response to Therapy in Head & Neck Cancer. PMID:35600369
Whole-genome Methylation Analysis of APOBEC Enzyme-converted DNA (~5 kb) by Nanopore Sequencing. PMID:35592605
Differential Regulation of Mouse Hippocampal Gene Expression Sex Differences by Chromosomal Content and Gonadal Sex. PMID:35589920
Different hotspot p53 mutants exert distinct phenotypes and predict outcome of colorectal cancer patients. PMID:35589715
Glioblastoma Embryonic-like Stem Cells Exhibit Immune-Evasive Phenotype. PMID:35565200
DNA methylation may affect beef tenderness through signal transduction in Bos indicus. PMID:35562812
Sox2 levels regulate the chromatin occupancy of WNT mediators in epiblast progenitors responsible for vertebrate body formation. PMID:35550614
Massively parallel identification of functionally consequential noncoding genetic variants in undiagnosed rare disease patients. PMID:35534523
Selective clonal persistence of human retroviruses in vivo: Radial chromatin organization, integration site, and host transcription. PMID:35486737
Large-scale discovery of novel neurodevelopmental disorder-related genes through a unified analysis of single-nucleotide and copy number variants. PMID:35468861
Profiling Genome-Wide DNA Methylation Patterns in Human Aortic and Mitral Valves. PMID:35463757
A protocol for CRISPR-mediated activation and repression of human endogenous retroviruses in human pluripotent stem cells. PMID:35463468
Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes. PMID:35410384
Machine-learning of complex evolutionary signals improves classification of SNVs. PMID:35402908
Deciphering Genetic Susceptibility to Tuberculous Meningitis. PMID:35401413
Eukaryotic tRNA sequences present conserved and amino acid-specific structural signatures. PMID:35380696
Coordinated changes in gene expression, H1 variant distribution and genome 3D conformation in response to H1 depletion. PMID:35380694
Nuclear Tkt promotes ischemic heart failure via the cleaved Parp1/Aif axis. PMID:35380314
Multilayered control of splicing regulatory networks by DAP3 leads to widespread alternative splicing changes in cancer. PMID:35379802
Phenome-Wide Association Study of Polygenic Risk Score for Alzheimer's Disease in Electronic Health Records. PMID:35370621
Immunopeptidomic analyses of colorectal cancers with and without microsatellite instability. PMID:35367648
ENNGene: an Easy Neural Network model building tool for Genomics. PMID:35361122
Identifying genes with conserved splicing structure and orthologous isoforms in human, mouse and dog. PMID:35303798
A network of transcription factors governs the dynamics of NODAL/Activin transcriptional responses. PMID:35302162
Changes of Small Non-coding RNAs by Severe Acute Respiratory Syndrome Coronavirus 2 Infection. PMID:35281271
Longitudinal Circulating Tumor DNA Profiling in Metastatic Colorectal Cancer During Anti-EGFR Therapy. PMID:35280779
RNA transcription and degradation of Alu retrotransposons depends on sequence features and evolutionary history. PMID:35253846
Selective chemical tracking of Dnmt1 catalytic activity in live cells. PMID:35245449
Bioinformatics pipeline to guide late-onset Alzheimer's disease (LOAD) post-GWAS studies: Prioritizing transcription regulatory variants within LOAD-associated regions. PMID:35229021
HyperChIP: identification of hypervariable signals across ChIP-seq or ATAC-seq samples. PMID:35227282
Whole Genome DNA Methylation Profiling of D2 Medium Spiny Neurons in Mouse Nucleus Accumbens Using Two Independent Library Preparation Methods. PMID:35205351
New Genomic Signals Underlying the Emergence of Human Proto-Genes. PMID:35205330
Spatial and Genomic Correlates of HIV-1 Integration Site Targeting. PMID:35203306
Gag-like proteins: Novel mediators of prenatal alcohol exposure in neural development. PMID:35187673
Analysis of Ribosome Profiling Data. PMID:35171478
Neurodevelopmental Syndrome with Intellectual Disability, Speech Impairment, and Quadrupedia Is Associated with Glutamate Receptor Delta 2 Gene Defect. PMID:35159210
Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population. PMID:35135873
Mouse genomic and cellular annotations. PMID:35124726
Genomic patterns of transcription-replication interactions in mouse primary B cells. PMID:35100392
Making sense of the linear genome, gene function and TADs. PMID:35090532
Variant interpretation: UCSC Genome Browser Recommended Track Sets. PMID:35088925
Differential roles for DNAJ isoforms in HTT-polyQ and FUS aggregation modulation revealed by chaperone screens. PMID:35082301
The MuvB complex binds and stabilizes nucleosomes downstream of the transcription start site of cell-cycle dependent genes. PMID:35082292
TPL-2 Inhibits IFN-β Expression via an ERK1/2-TCF-FOS Axis in TLR4-Stimulated Macrophages. PMID:35082159
Variant pathogenic prediction by locus variability: the importance of the current picture of evolution. PMID:35079159
Assessment of the Molecular Heterogeneity of E-Cadherin Expression in Invasive Lobular Breast Cancer. PMID:35053458
Capturing SNP Association across the NK Receptor and HLA Gene Regions in Multiple Sclerosis by Targeted Penalised Regression Models. PMID:35052430
DAJIN enables multiplex genotyping to simultaneously validate intended and unintended target genome editing outcomes. PMID:35041655
Germline sequence variants contributing to cancer susceptibility in South African breast cancer patients of African ancestry. PMID:35039564
Core promoter mutation contributes to abnormal gene expression in bladder cancer. PMID:35033028
Functional coding haplotypes and machine-learning feature elimination identifies predictors of Methotrexate Response in Rheumatoid Arthritis patients. PMID:35022146
Secondary loss of miR-3607 reduced cortical progenitor amplification during rodent evolution. PMID:35020425
Myotonic dystrophy type 1 embryonic stem cells show decreased myogenic potential, increased CpG methylation at the DMPK locus and RNA mis-splicing. PMID:35019138
A BAFF ligand-based CAR-T cell targeting three receptors and multiple B cell cancers. PMID:35017485
Catulin Based Reporter System to Track and Characterize the Population of Invasive Cancer Cells in the Head and Neck Squamous Cell Carcinoma. PMID:35008571
Establishment of developmental gene silencing by ordered polycomb complex recruitment in early zebrafish embryos. PMID:34982026
piRNAQuest V.2: an updated resource for searching through the piRNAome of multiple species. PMID:34965192
Changes in chromatin accessibility landscape and histone H3 core acetylation during valproic acid-induced differentiation of embryonic stem cells. PMID:34955095
Comprehensive epigenomic profiling of human alveolar epithelial differentiation identifies key epigenetic states and transcription factor co-regulatory networks for maintenance of distal lung identity. PMID:34922464
PharmVIP: A Web-Based Tool for Pharmacogenomic Variant Analysis and Interpretation. PMID:34834582
Origins and Function of VL30 lncRNA Packaging in Small Extracellular Vesicles: Implications for Cellular Physiology and Pathology. PMID:34829970
Enhanced epigenetic profiling of classical human monocytes reveals a specific signature of healthy aging in the DNA methylome. PMID:34796338
Structural variants in the Chinese population and their impact on phenotypes, diseases and population adaptation. PMID:34764282
Comparative methylation and RNA-seq expression analysis in CpG context to identify genes involved in Backfat vs. Liver diversification in Nanchukmacdon Pig. PMID:34743693
Disease-associated human genetic variation through the lens of precursor and mature RNA structure. PMID:34741198
Replication timing analysis in polyploid cells reveals Rif1 uses multiple mechanisms to promote underreplication in Drosophila. PMID:34740250
Transposable elements that have recently been mobile in the human genome. PMID:34732136
Amygdala DCX and blood Cdk14 are implicated as cross-species indicators of individual differences in fear, extinction, and resilience to trauma exposure. PMID:34728797
Self-inactivating, all-in-one AAV vectors for precision Cas9 genome editing via homology-directed repair in vivo. PMID:34725353
The UCSC Genome Browser database: 2022 update. PMID:34718705
Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci. PMID:34699533
Embryonic LTR retrotransposons supply promoter modules to somatic tissues. PMID:34675070
KDM5B promotes immune evasion by recruiting SETDB1 to silence retroelements. PMID:34671158
The translatome of neuronal cell bodies, dendrites, and axons. PMID:34670838
Characterization of chromatin accessibility in psoriasis. PMID:34669155
Sequence features of retrotransposons allow for epigenetic variability. PMID:34668484
Rare Variants in RPPH1 Real-Time Quantitative PCR Control Assay Binding Sites Result in Incorrect Copy Number Calls. PMID:34656763
Short single-stranded DNAs with putative non-canonical structures comprise a new class of plasma cell-free DNA. PMID:34649537
Chromosome X-wide Analysis of Positive Selection in Human Populations: Common and Private Signals of Selection and its Impact on Inactivated Genes and Enhancers. PMID:34646300
Seed sequence polymorphism rs2168518 and allele-specific target gene regulation of hsa-miR-4513. PMID:34605899
Admixture with indigenous people helps local adaptation: admixture-enabled selection in Polynesians. PMID:34551727
Integrative Transcriptome-Wide Analyses Uncover Novel Risk-Associated MicroRNAs in Hormone-Dependent Cancers. PMID:34512726
ACE2 Netlas: In silico Functional Characterization and Drug-Gene Interactions of ACE2 Gene Network to Understand Its Potential Involvement in COVID-19 Susceptibility. PMID:34512723
YAP regulates alveolar epithelial cell differentiation and AGER via NFIB/KLF5/NKX2-1. PMID:34466790
Developmental and evolutionary dynamics of cis-regulatory elements in mouse cerebellar cells. PMID:34446581
3'aQTL-atlas: an atlas of 3'UTR alternative polyadenylation quantitative trait loci across human normal tissues. PMID:34432052
Histone H4 lysine 20 mono-methylation directly facilitates chromatin openness and promotes transcription of housekeeping genes. PMID:34417450
Translational control by DHX36 binding to 5'UTR G-quadruplex is essential for muscle stem-cell regenerative functions. PMID:34413292
Placental DNA methylation marks are associated with maternal depressive symptoms during early pregnancy. PMID:34401410
The native cistrome and sequence motif families of the maize ear. PMID:34383745
Loss of the MAF Transcription Factor in Laryngeal Squamous Cell Carcinoma. PMID:34356658
Deficient H2A.Z deposition is associated with genesis of uterine leiomyoma. PMID:34349258
Using de novo assembly to identify structural variation of eight complex immune system gene regions. PMID:34343164
De novo DNA methylation controls neuronal maturation during adult hippocampal neurogenesis. PMID:34337766
Adipose Tissue Inflammation Is Directly Linked to Obesity-Induced Insulin Resistance, while Gut Dysbiosis and Mitochondrial Dysfunction Are Not Required. PMID:34278304
Folate Deficiency Triggers the Abnormal Segregation of a Region With Large Cluster of CG-Rich Trinucleotide Repeats on Human Chromosome 2. PMID:34276797
HnRNP K mislocalisation is a novel protein pathology of frontotemporal lobar degeneration and ageing and leads to cryptic splicing. PMID:34274995
Resolving diverse protein-DNA footprints from exonuclease-based ChIP experiments. PMID:34252930
A direct capture method for purification and detection of viral nucleic acid enables epidemiological surveillance of SARS-CoV-2. PMID:34252764
Joint disease-specificity at the regulatory base-pair level. PMID:34230488
TAD cliques predict key features of chromatin organization. PMID:34217222
In Silico Prediction of Transcription Factor Collaborations Underlying Phenotypic Sexual Dimorphism in Zebrafish (Danio rerio). PMID:34200177
A Bayesian inference transcription factor activity model for the analysis of single-cell transcriptomes. PMID:34193535
Orphan CpG islands amplify poised enhancer regulatory activity and determine target gene responsiveness. PMID:34183853
Pure Distal 7q Duplication: Describing a Macrocephalic Neurodevelopmental Syndrome, Case Report and Review of the Literature. PMID:34177432
An Analysis of Methylome Evolution in Primates. PMID:34175932
rigrag: high-resolution mapping of genic targeting preferences during HIV-1 integration in vitro and in vivo. PMID:34165568
Environmental enrichment preserves a young DNA methylation landscape in the aged mouse hippocampus. PMID:34162876
CD8+ T cell immunity blocks the metastasis of carcinogen-exposed breast cancer. PMID:34144976
The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence. PMID:34140314
Shifting epigenetic contexts influence regulatory variation and disease risk. PMID:34138751
Hearing Sensitivity of Primates: Recurrent and Episodic Positive Selection in Hair Cells and Stereocilia Protein-Coding Genes. PMID:34137817
DNA methylation profile of liver of mice conceived by in vitro fertilization. PMID:34121654
Runx1 shapes the chromatin landscape via a cascade of direct and indirect targets. PMID:34111109
The derepression of transposable elements in lung cells is associated with the inflammatory response and gene activation in idiopathic pulmonary fibrosis. PMID:34108012
Widespread Exaptation of L1 Transposons for Transcription Factor Binding in Breast Cancer. PMID:34070697
The RNA-Binding Protein HuD Regulates Alternative Splicing and Alternative Polyadenylation in the Mouse Neocortex. PMID:34064652
pegIT - a web-based design tool for prime editing. PMID:34060619
Genetic effects on liver chromatin accessibility identify disease regulatory variants. PMID:34038741
Comprehensive machine-learning-based analysis of microRNA-target interactions reveals variable transferability of interaction rules across species. PMID:34030625
Population genomics of invasive rodents on islands: Genetic consequences of colonization and prospects for localized synthetic gene drive. PMID:34025776
Long-read whole-genome methylation patterning using enzymatic base conversion and nanopore sequencing. PMID:34019650
Wavelet Screening identifies regions highly enriched for differentially methylated loci for orofacial clefts. PMID:33987535
piRNA-mediated gene regulation and adaptation to sex-specific transposon expression in D. melanogaster male germline. PMID:33985970
3D facial phenotyping by biometric sibling matching used in contemporary genomic methodologies. PMID:33983923
Selective Requirement of MYB for Oncogenic Hyperactivation of a Translocated Enhancer in Leukemia. PMID:33980539
Integrated OMICs unveil the bone-marrow microenvironment in human leukemia. PMID:33979628
An age-downregulated ribosomal RpS28 protein variant regulates the muscle proteome. PMID:33974070
ATRX Alteration Contributes to Tumor Growth and Immune Escape in Pleomorphic Sarcomas. PMID:33946962
An intron variant of the GLI family zinc finger 3 (GLI3) gene differentiates resistance training-induced muscle fiber hypertrophy in younger men. PMID:33891350
Conservation of Aging and Cancer Epigenetic Signatures across Human and Mouse. PMID:33871658
Glioblastomas acquire myeloid-affiliated transcriptional programs via epigenetic immunoediting to elicit immune evasion. PMID:33857425
The dystonia gene THAP1 controls DNA double-strand break repair choice. PMID:33857404
Cellular mRNA triggers structural transformation of Ebola virus matrix protein VP40 to its essential regulatory form. PMID:33852858
Integrated transcription factor profiling with transcriptome analysis identifies L1PA2 transposons as global regulatory modulators in a breast cancer model. PMID:33850167
Genome-wide characterization of human minisatellite VNTRs: population-specific alleles and gene expression differences. PMID:33849068
Disruption of the MSL complex inhibits tumour maintenance by exacerbating chromosomal instability. PMID:33837287
Whole genome variation in 27 Mexican indigenous populations, demographic and biomedical insights. PMID:33831079
Antisense RNAs during early vertebrate development are divided in groups with distinct features. PMID:33795334
Epigenomic tensor predicts disease subtypes and reveals constrained tumor evolution. PMID:33789109
Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex. PMID:33789096
Ultraconserved enhancer function does not require perfect sequence conservation. PMID:33782603
Genomic association with pathogen carriage in bighorn sheep (Ovis canadensis). PMID:33767816
Genetic basis and identification of candidate genes for wooden breast and white striping in commercial broiler chickens. PMID:33762630
Remus: A Web Application for Prioritization of Regulatory Regions and Variants in Monogenic Diseases. PMID:33747049
Whole genome mapping and identification of single nucleotide polymorphisms of four Bangladeshi individuals and their functional significance. PMID:33743798
A unified framework for inferring the multi-scale organization of chromatin domains from Hi-C. PMID:33724986
Epigenetic effects of Bisphenol A on granulosa cells of mouse follicles during in vitro culture: An experimental study. PMID:33718757
Transcriptome Analysis of Dnmt3l Knock-Out Mice Derived Multipotent Mesenchymal Stem/Stromal Cells During Osteogenic Differentiation. PMID:33718357
Aptardi predicts polyadenylation sites in sample-specific transcriptomes using high-throughput RNA sequencing and DNA sequence. PMID:33712618
Global discovery of lupus genetic risk variant allelic enhancer activity. PMID:33712590
aniFOUND: analysing the associated proteome and genomic landscape of the repaired nascent non-replicative chromatin. PMID:33693861
Gene Size Matters: An Analysis of Gene Length in the Human Genome. PMID:33643374
Haplotype-resolved diverse human genomes and integrated analysis of structural variation. PMID:33632895
Benchmarking workflows to assess performance and suitability of germline variant calling pipelines in clinical diagnostic assays. PMID:33627090
Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT. PMID:33597613
Accurate SNV detection in single cells by transposon-based whole-genome amplification of complementary strands. PMID:33593904
Identification and analysis of RNA structural disruptions induced by single nucleotide variants using Riprap and RiboSNitchDB. PMID:33575608
Genetic control of the human brain proteome. PMID:33571421
Dynamic effects of genetic variation on gene expression revealed following hypoxic stress in cardiomyocytes. PMID:33554857
Topologically associating domain boundaries that are stable across diverse cell types are evolutionarily constrained and enriched for heritability. PMID:33545030
Induction of muscle-regenerative multipotent stem cells from human adipocytes by PDGF-AB and 5-azacytidine. PMID:33523875
Postnatal Arx transcriptional activity regulates functional properties of PV interneurons. PMID:33490907
Transposable element subfamily annotation has a reproducibility problem. PMID:33485368
TNF-α Regulates Human Plasmacytoid Dendritic Cells by Suppressing IFN-α Production and Enhancing T Cell Activation. PMID:33441439
Spatiotemporal analysis of human intestinal development at single-cell resolution. PMID:33406409
Discovery of Genomic Characteristics and Selection Signatures in Southern Chinese Local Cattle. PMID:33391332
RTEL1 Regulates G4/R-Loops to Avert Replication-Transcription Collisions. PMID:33357438
RNA-Mediated Feedback Control of Transcriptional Condensates. PMID:33333019
Intron retention is a robust marker of intertumoral heterogeneity in pancreatic ductal adenocarcinoma. PMID:33311498
Genome-wide association study of asthma exacerbations despite inhaled corticosteroid use. PMID:33303529
Autozygosity mapping and time-to-spontaneous delivery in Norwegian parent-offspring trios. PMID:33291140
Insights into the genetic architecture of the human face. PMID:33288918
Functionally impaired plasmacytoid dendritic cells and non-haematopoietic sources of type I interferon characterize human autoimmunity. PMID:33262343
ncVarDB: a manually curated database for pathogenic non-coding variants and benign controls. PMID:33258967
The Intergenerational Impacts of Paternal Diet on DNA Methylation and Offspring Phenotypes in Sheep. PMID:33250925
Evaluating the Genomic Parameters Governing rAAV-Mediated Homologous Recombination. PMID:33248247
Origins and Long-Term Patterns of Copy-Number Variation in Rhesus Macaques. PMID:33226085
Pathogenic variants causing ABL1 malformation syndrome cluster in a myristoyl-binding pocket and increase tyrosine kinase activity. PMID:33223528
The UCSC Genome Browser database: 2021 update. PMID:33221922
Are spliced ncRNA host genes distinct classes of lncRNAs? PMID:33219910
MAnorm2 for quantitatively comparing groups of ChIP-seq samples. PMID:33208455
Computer vision for pattern detection in chromosome contact maps. PMID:33199682
ID1 As a Prognostic Biomarker and Promising Drug Target Plays a Pivotal Role in Deterioration of Clear Cell Renal Cell Carcinoma. PMID:33178820
ACE2 Netlas: In-silico functional characterization and drug-gene interactions of ACE2 gene network to understand its potential involvement in COVID-19 susceptibility. PMID:33140059
Effects of NT5C2 Germline Variants on 6-Mecaptopurine Metabolism in Children With Acute Lymphoblastic Leukemia. PMID:33124053
LncRBase V.2: an updated resource for multispecies lncRNAs and ClinicLSNP hosting genetic variants in lncRNAs for cancer patients. PMID:33112702
Intrinsic DNA topology as a prioritization metric in genomic fine-mapping studies. PMID:33084892
Ancient genomes reveal tropical bovid species in the Tibetan Plateau contributed to the prevalence of hunting game until the late Neolithic. PMID:33077602
Sensitive alignment using paralogous sequence variants improves long-read mapping and variant calling in segmental duplications. PMID:33035301
Automated Classification of Osteosarcoma and Benign Tumors using RNA-seq and Plain X-ray. PMID:33018194
Sex-specific epigenetic profile of inner cell mass of mice conceived in vivo or by IVF. PMID:33010164
Characterization of universal features of partially methylated domains across tissues and species. PMID:33008446
Host Gene Regulation by Transposable Elements: The New, the Old and the Ugly. PMID:32993145
Urine as a high-quality source of host genomic DNA from wild populations. PMID:32985084
Burden of rare deleterious variants in WNT signaling genes among 511 myelomeningocele patients. PMID:32970752
Genome-wide alterations of uracil distribution patterns in human DNA upon chemotherapeutic treatments. PMID:32956035
A genetic memory initiates the epigenetic loop necessary to preserve centromere position. PMID:32945564
Evaluating the informativeness of deep learning annotations for human complex diseases. PMID:32943643
FGF18-FGFR2 signaling triggers the activation of c-Jun-YAP1 axis to promote carcinogenesis in a subgroup of gastric cancer patients and indicates translational potential. PMID:32934314
Molecular basis of a new ovine model for human 3M syndrome-2. PMID:32933480
Super-enhancer switching drives a burst in gene expression at the mitosis-to-meiosis transition. PMID:32895557
Genome-wide identification of genes regulating DNA methylation using genetic anchors for causal inference. PMID:32859263
Background Selection Does Not Mimic the Patterns of Genetic Diversity Produced by Selective Sweeps. PMID:32847814
PINCER: improved CRISPR/Cas9 screening by efficient cleavage at conserved residues. PMID:32821942
MARTX Toxin-Stimulated Interplay between Human Cells and Vibrio vulnificus. PMID:32817457
Genetic Variability in the Italian Heavy Draught Horse from Pedigree Data and Genomic Information. PMID:32751586
Genome-wide R-loop analysis defines unique roles for DDX5, XRN2, and PRMT5 in DNA/RNA hybrid resolution. PMID:32747416
Index and biological spectrum of human DNase I hypersensitive sites. PMID:32728217
Breed Differences in Dog Cognition Associated with Brain-Expressed Genes and Neurological Functions. PMID:32726413
Human L1 Transposition Dynamics Unraveled with Functional Data Analysis. PMID:32722770
Accounting for diverse evolutionary forces reveals mosaic patterns of selection on human preterm birth loci. PMID:32709900
ASNEO: Identification of personalized alternative splicing based neoantigens with RNA-seq. PMID:32697765
Ketogenesis activates metabolically protective γδ T cells in visceral adipose tissue. PMID:32694683
SPOCD1 is an essential executor of piRNA-directed de novo DNA methylation. PMID:32674113
The circular RNA landscape in specific peripheral blood mononuclear cells of critically ill patients with sepsis. PMID:32660590
Detection of copy-number variations from NGS data using read depth information: a diagnostic performance evaluation. PMID:32591635
The Transcription Co-Repressors MTG8 and MTG16 Regulate Exit of Intestinal Stem Cells From Their Niche and Differentiation Into Enterocyte vs Secretory Lineages. PMID:32553763
Phenotype-specific differences in polygenicity and effect size distribution across functional annotation categories revealed by AI-MiXeR. PMID:32539089
Giant Island Mice Exhibit Widespread Gene Expression Changes in Key Metabolic Organs. PMID:32531054
Multi-branch Convolutional Neural Network for Identification of Small Non-coding RNA genomic loci. PMID:32528107
Genetic Diversity and Signatures of Selection in a Native Italian Horse Breed Based on SNP Data. PMID:32521830
Efficient Nuclease-Directed Integration of Lentivirus Vectors into the Human Ribosomal DNA Locus. PMID:32504545
Mutational bias and the protein code shape the evolution of splicing enhancers. PMID:32504065
GC-AG Introns Features in Long Non-coding and Protein-Coding Genes Suggest Their Role in Gene Expression Regulation. PMID:32499820
Expression of RUNX1-ETO Rapidly Alters the Chromatin Landscape and Growth of Early Human Myeloid Precursor Cells. PMID:32460028
Identifying Cattle Breed-Specific Partner Choice of Transcription Factors during the African Trypanosomiasis Disease Progression Using Bioinformatics Analysis. PMID:32456126
The Evolution of Human Cancer Gene Duplications across Mammals. PMID:32421773
Characterizing the Causal Pathway for Genetic Variants Associated with Neurological Phenotypes Using Human Brain-Derived Proteome Data. PMID:32413284
Copy number variants and fixed duplications among 198 rhesus macaques (Macaca mulatta). PMID:32392208
Unblending of Transcriptional Condensates in Human Repeat Expansion Disease. PMID:32386547
The cell line A-to-I RNA editing catalogue. PMID:32383740
ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data. PMID:32345345
The H2B ubiquitin-protein ligase RNF40 is required for somatic cell reprogramming. PMID:32341358
HSF1: Primary Factor in Molecular Chaperone Expression and a Major Contributor to Cancer Morbidity. PMID:32331382
Lung Function in African American Children with Asthma Is Associated with Novel Regulatory Variants of the KIT Ligand KITLG/SCF and Gene-By-Air-Pollution Interaction. PMID:32327564
Partial loss of CFIm25 causes learning deficits and aberrant neuronal alternative polyadenylation. PMID:32319885
Characterization of RNP Networks of PUM1 and PUM2 Post-Transcriptional Regulators in TCam-2 Cells, a Human Male Germ Cell Model. PMID:32316190
Characterization of the chromatin accessibility in an Alzheimer's disease (AD) mouse model. PMID:32293531
Selective inhibition of cancer cell self-renewal through a Quisinostat-histone H1.0 axis. PMID:32286289
Gallop Racing Shifts Mature mRNA towards Introns: Does Exercise-Induced Stress Enhance Genome Plasticity? PMID:32283859
Division of Labor between PCNA Loaders in DNA Replication and Sister Chromatid Cohesion Establishment. PMID:32277910
Genetic Variability in the Iron Homeostasis Pathway and Patient Outcomes After Aneurysmal Subarachnoid Hemorrhage. PMID:32246437
Genotype-phenotype association and variant characterization in Diamond-Blackfan anemia caused by pathogenic variants in RPL35A. PMID:32241839
Evolutionary Selection and Constraint on Human Knee Chondrocyte Regulation Impacts Osteoarthritis Risk. PMID:32220312
Genetic Differentiation of the Two Types of Polish Cold-blooded Horses Included in the National Conservation Program. PMID:32214005
A Fine-Scale Genetic Map for Vervet Monkeys. PMID:32211856
Multi-omics Analysis of Primary Cell Culture Models Reveals Genetic and Epigenetic Basis of Intratumoral Phenotypic Diversity. PMID:32205176
CIViCpy: A Python Software Development and Analysis Toolkit for the CIViC Knowledgebase. PMID:32191543
Genomic loci susceptible to systematic sequencing bias in clinical whole genomes. PMID:32156711
Toward an Evolutionarily Appropriate Null Model: Jointly Inferring Demography and Purifying Selection. PMID:32152045
Rif1 Functions in a Tissue-Specific Manner To Control Replication Timing Through Its PP1-Binding Motif. PMID:32144132
Ancient evolutionary signals of protein-coding sequences allow the discovery of new genes in the Drosophila melanogaster genome. PMID:32138644
Locally acting transcription factors regulate p53-dependent cis-regulatory element activity. PMID:32133495
Differential Allele-Specific Expression Uncovers Breast Cancer Genes Dysregulated by Cis Noncoding Mutations. PMID:32078798
Familial analysis reveals rare risk variants for migraine in regulatory regions. PMID:32076896
Age-, tumor-, and metastatic tissue-associated DNA hypermethylation of a T-box brain 1 locus in human kidney tissue. PMID:32070431
Suppressing proteasome mediated processing of topoisomerase II DNA-protein complexes preserves genome integrity. PMID:32057297
Unmasking Retinitis Pigmentosa complex cases by a whole genome sequencing algorithm based on open-access tools: hidden recessive inheritance and potential oligogenic variants. PMID:32050993
A post-transcriptional program of chemoresistance by AU-rich elements and TTP in quiescent leukemic cells. PMID:32039742
Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. PMID:32024996
Dynamic Lamin B1-Gene Association During Oligodendrocyte Progenitor Differentiation. PMID:32020491
Loss of Kat2a enhances transcriptional noise and depletes acute myeloid leukemia stem-like cells. PMID:31985402
MicroRNA and transcription factor co-regulatory networks and subtype classification of seminoma and non-seminoma in testicular germ cell tumors. PMID:31965022
The Expression of Decidual Protein Induced by Progesterone (DEPP) is Controlled by Three Distal Consensus Hypoxia Responsive Element (HRE) in Hypoxic Retinal Epithelial Cells. PMID:31963726
Influenza-induced monocyte-derived alveolar macrophages confer prolonged antibacterial protection. PMID:31932810
TP63 isoform expression is linked with distinct clinical outcomes in cancer. PMID:31927310
The SUMO Ligase Su(var)2-10 Controls Hetero- and Euchromatic Gene Expression via Establishing H3K9 Trimethylation and Negative Feedback Regulation. PMID:31901448
Su(var)2-10 and the SUMO Pathway Link piRNA-Guided Target Recognition to Chromatin Silencing. PMID:31901446
Functional annotation of de novo variants from healthy individuals. PMID:31896246
High degree of polyclonality hinders somatic mutation calling in lung brush samples of COPD cases and controls. PMID:31882973
Intra-Vκ Cluster Recombination Shapes the Ig Kappa Locus Repertoire. PMID:31875554
Autism risk in offspring can be assessed through quantification of male sperm mosaicism. PMID:31873310
Identification of pathogenic variant enriched regions across genes and gene families. PMID:31871067
MethylToSNP: identifying SNPs in Illumina DNA methylation array data. PMID:31861999
Investigating skewness to understand gene expression heterogeneity in large patient cohorts. PMID:31861976
Depolarization-Associated CircRNA Regulate Neural Gene Expression and in Some Cases May Function as Templates for Translation. PMID:31861825
Topologically Associated Domains Delineate Susceptibility to Somatic Hypermutation. PMID:31851922
A tRNA-Derived Small RNA Regulates Ribosomal Protein S28 Protein Levels after Translation Initiation in Humans and Mice. PMID:31851915
Genetic susceptibility to severe childhood asthma and rhinovirus-C maintained by balancing selection in humans for 150 000 years. PMID:31841129
Targeted deep-intronic sequencing in a cohort of unexplained cases of suspected Lynch syndrome. PMID:31822864
Human gene expression variability and its dependence on methylation and aging. PMID:31810449
GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering. PMID:31808801
Programmed DNA elimination of germline development genes in songbirds. PMID:31784533
Characterization of genetic subclonal evolution in pancreatic cancer mouse models. PMID:31780749
Ketogenic diet activates protective γδ T cell responses against influenza virus infection. PMID:31732517
Virtual methylome dissection facilitated by single-cell analyses. PMID:31711526
UCSC Genome Browser enters 20th year. PMID:31691824
Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells: An integrative approach using high-throughput datasets. PMID:31682597
Expression of Protein-Coding Gene Orthologs in Zebrafish and Mouse Inner Ear Non-sensory Supporting Cells. PMID:31680844
Distinct H3K9me3 and DNA methylation modifications during mouse spermatogenesis. PMID:31662436
53BP1 Enforces Distinct Pre- and Post-resection Blocks on Homologous Recombination. PMID:31653568
Whole genome analysis of Black Bengal goat from Savar Goat Farm, Bangladesh. PMID:31651366
Comprehensive Analysis of Human microRNA-mRNA Interactome. PMID:31649721
The Tudor SND1 protein is an m6A RNA reader essential for replication of Kaposi's sarcoma-associated herpesvirus. PMID:31647415
Introducing the first whole genomes of nationals from the United Arab Emirates. PMID:31604968
Spatial heterogeneity of the T cell receptor repertoire reflects the mutational landscape in lung cancer. PMID:31591606
Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression. PMID:31568525
Pathway Analysis Integrating Genome-Wide and Functional Data Identifies PLCG2 as a Candidate Gene for Age-Related Macular Degeneration. PMID:31560769
Discovery of Novel Sequences in 1,000 Swedish Genomes. PMID:31560401
Bioinformatics Discovery of Putative Enhancers within Mouse Odorant Receptor Gene Clusters. PMID:31529021
Coding regions affect mRNA stability in human cells. PMID:31527111
A purely bioinformatic pipeline for the prediction of mammalian odorant receptor gene enhancers. PMID:31521109
The Impact of Natural Selection on the Evolution and Function of Placentally Expressed Galectins. PMID:31504490
Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data. PMID:31501864
Codon bias confers stability to human mRNAs. PMID:31482640
The 22q11 low copy repeats are characterized by unprecedented size and structural variability. PMID:31481461
NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements. PMID:31477927
Redistribution of EZH2 promotes malignant phenotypes by rewiring developmental programmes. PMID:31468686
Comparative analysis demonstrates cell type-specific conservation of SOX9 targets between mouse and chicken. PMID:31467356
Copper associates with differential methylation in placentae from two US birth cohorts. PMID:31462129
Regulation of Co-transcriptional Pre-mRNA Splicing by m6A through the Low-Complexity Protein hnRNPG. PMID:31445886
Hamiltonian energy as an efficient approach to identify the significant key regulators in biological networks. PMID:31442253
AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design. PMID:31416467
SIRT6 transcriptionally regulates global protein synthesis through transcription factor Sp1 independent of its deacetylase activity. PMID:31372634
Mechanistic interpretation of non-coding variants for discovering transcriptional regulators of drug response. PMID:31362726
Challenges in funding and developing genomic software: roots and remedies. PMID:31358028
Ribosome profiling of selenoproteins in vivo reveals consequences of pathogenic Secisbp2 missense mutations. PMID:31350336
Hidden Markov models lead to higher resolution maps of mutation signature activity in cancer. PMID:31349863
Human Artificial Chromosomes that Bypass Centromeric DNA. PMID:31348889
Coordinated transcriptional regulation by thyroid hormone and glucocorticoid interaction in adult mouse hippocampus-derived neuronal cells. PMID:31348800
JMJD6 is a tumorigenic factor and therapeutic target in neuroblastoma. PMID:31346162
Activation of neuronal genes via LINE-1 elements upon global DNA demethylation in human neural progenitors. PMID:31320637
Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing. PMID:31316107
Mutant CEBPA directly drives the expression of the targetable tumor-promoting factor CD73 in AML. PMID:31309149
Association of imputed prostate cancer transcriptome with disease risk reveals novel mechanisms. PMID:31308362
Relation between DNA ionization potentials, single base substitutions and pathogenic variants. PMID:31307386
Geno2proteo, a Tool for Batch Retrieval of DNA and Protein Sequences from Any Genomic or Protein Regions. PMID:31301672
NFAT5/TonEBP controls early acquisition of notochord phenotypic markers, collagen composition, and sonic hedgehog signaling during mouse intervertebral disc embryogenesis. PMID:31301300
Identifying, understanding, and correcting technical artifacts on the sex chromosomes in next-generation sequencing data. PMID:31289836
Bioinformatics strategy to advance the interpretation of Alzheimer's disease GWAS discoveries: The roads from association to causation. PMID:31262699
The Impact of Population Variation in the Analysis of microRNA Target Sites. PMID:31234531
Atlas of Subcellular RNA Localization Revealed by APEX-Seq. PMID:31230715
Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods. PMID:31226924
Non-canonical translation initiation in yeast generates a cryptic pool of mitochondrial proteins. PMID:31216041
MRLR: unraveling high-resolution meiotic recombination by linked reads. PMID:31214684
Topoisomerase II-Induced Chromosome Breakage and Translocation Is Determined by Chromosome Architecture and Transcriptional Activity. PMID:31202577
A pan-cancer analysis of synonymous mutations. PMID:31189880
Open Chromatin Profiling in Adipose Tissue Marks Genomic Regions with Functional Roles in Cardiometabolic Traits. PMID:31186305
Phosphorylation of TET2 by AMPK is indispensable in myogenic differentiation. PMID:31164154
Analysis of a Protein Network Related to Copy Number Variations in Autism Spectrum Disorder. PMID:31161481
Haplotype-aware diplotyping from noisy long reads. PMID:31159868
The perils of intralocus recombination for inferences of molecular convergence. PMID:31154973
Genome-Wide Scan Identifies Selection Signatures in Chinese Wagyu Cattle Using a High-Density SNP Array. PMID:31151238
Evolution of Mechanisms that Control Mating in Drosophila Males. PMID:31141679
Lens differentiation is characterized by stage-specific changes in chromatin accessibility correlating with differentiation state-specific gene expression. PMID:31136738
Computational identification of tissue-specific transcription factor cooperation in ten cattle tissues. PMID:31095599
Centromeric Satellite DNAs: Hidden Sequence Variation in the Human Population. PMID:31072070
SeqTailor: a user-friendly webserver for the extraction of DNA or protein sequences from next-generation sequencing data. PMID:31045209
YeasTSS: an integrative web database of yeast transcription start sites. PMID:31032841
Targeted re-sequencing of F8, F9 and VWF: Characterization of Ion Torrent data and clinical implications for mutation screening. PMID:31026269
Autism risk genes are evolutionarily ancient and maintain a unique feature landscape that echoes their function. PMID:31025836
Galectin-3, a novel endogenous TREM2 ligand, detrimentally regulates inflammatory response in Alzheimer's disease. PMID:31006066
Gene expression differences between matched pairs of ovarian cancer patient tumors and patient-derived xenografts. PMID:31004097
Broad domains of histone 3 lysine 4 trimethylation are associated with transcriptional activation in CA1 neurons of the hippocampus during memory formation. PMID:31002880
NF-κB Signaling and IL-4 Signaling Regulate SATB1 Expression via Alternative Promoter Usage During Th2 Differentiation. PMID:31001272
Overlapping Activities of Two Neuronal Splicing Factors Switch the GABA Effect from Excitatory to Inhibitory by Regulating REST. PMID:30995482
Coordinated host-pathogen transcriptional dynamics revealed using sorted subpopulations and single macrophages infected with Candida albicans. PMID:30962448
A generally conserved response to hypoxia in iPSC-derived cardiomyocytes from humans and chimpanzees. PMID:30958265
Mendelian Inconsistent Signatures from 1314 Ancestrally Diverse Family Trios Distinguish Biological Variation from Sequencing Error. PMID:30942611
CHD1 Loss Alters AR Binding at Lineage-Specific Enhancers and Modulates Distinct Transcriptional Programs to Drive Prostate Tumorigenesis. PMID:30930119
Transposable elements drive widespread expression of oncogenes in human cancers. PMID:30926969
DNA methylation and functional characterization of the XIST gene during in vitro early embryo development in cattle. PMID:30925851
SMARCAD1 ATPase activity is required to silence endogenous retroviruses in embryonic stem cells. PMID:30902974
Hoxa13 regulates expression of common Hox target genes involved in cartilage development to coordinate the expansion of the autopodal anlage. PMID:30895612
Meta-Analysis of Genomewide Association Studies Reveals Genetic Variants for Hip Bone Geometry. PMID:30888730
Fine-Scale Characterization of Genomic Structural Variation in the Human Genome Reveals Adaptive and Biomedically Relevant Hotspots. PMID:30887040
Cellular response to small molecules that selectively stall protein synthesis by the ribosome. PMID:30875366
Genome-wide profiling of Epstein-Barr virus integration by targeted sequencing in Epstein-Barr virus associated malignancies. PMID:30867819
Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2. PMID:30864654
Deciphering the complex role of thrombospondin-1 in glioblastoma development. PMID:30850588
Cohesin-Mediated Genome Architecture Does Not Define DNA Replication Timing Domains. PMID:30836708
Colonic epithelial cell diversity in health and inflammatory bowel disease. PMID:30814735
Amplification of a broad transcriptional program by a common factor triggers the meiotic cell cycle in mice. PMID:30810530
Combined analysis of dissimilar promoter accessibility and gene expression profiles identifies tissue-specific genes and actively repressed networks. PMID:30795793
The bovine alveolar macrophage DNA methylome is resilient to infection with Mycobacterium bovis. PMID:30728374
Interrogation of Eukaryotic Stop Codon Readthrough Signals by in Vitro RNA Selection. PMID:30698415
Genomic clustering of fitness-affecting mutations favors the evolution of chromosomal instability. PMID:30697341
Discovery of gene regulatory elements through a new bioinformatics analysis of haploid genetic screens. PMID:30695034
Diversifying selection signatures among divergently selected subpopulations of Polish Red cattle. PMID:30685825
PLZF targets developmental enhancers for activation during osteogenic differentiation of human mesenchymal stem cells. PMID:30672466
Redundancy of human ATG4 protease isoforms in autophagy and LC3/GABARAP processing revealed in cells. PMID:30661429
Differential regulation of CpG island methylation within divergent and unidirectional promoters in colorectal cancer. PMID:30637877
MicroRNA-messenger RNA interactions involving JAK-STAT signaling genes in colorectal cancer. PMID:30603058
Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy. PMID:30598455
Pathogenicity and selective constraint on variation near splice sites. PMID:30587507
Gene code CD274/PD-L1: from molecular basis toward cancer immunotherapy. PMID:30574211
HLA-DO Modulates the Diversity of the MHC-II Self-peptidome. PMID:30573663
Properties of LINE-1 proteins and repeat element expression in the context of amyotrophic lateral sclerosis. PMID:30564290
DeltaNp63-dependent super enhancers define molecular identity in pancreatic cancer by an interconnected transcription factor network. PMID:30541891
Identification of deleterious and regulatory genomic variations in known asthma loci. PMID:30541564
RELACS nuclei barcoding enables high-throughput ChIP-seq. PMID:30534606
Borders of Cis-Regulatory DNA Sequences Preferentially Harbor the Divergent Transcription Factor Binding Motifs in the Human Genome. PMID:30524473
Identification of potential genetic risk factors for bipolar disorder by whole-exome sequencing. PMID:30518751
Parkinson-Associated SNCA Enhancer Variants Revealed by Open Chromatin in Mouse Dopamine Neurons. PMID:30503521
Trophoblast organoids as a model for maternal-fetal interactions during human placentation. PMID:30487605
Transcriptome Profiling of Layer 5 Intratelencephalic Projection Neurons From the Mature Mouse Motor Cortex. PMID:30483051
Identification, Characterization, and Heritability of Murine Metastable Epialleles: Implications for Non-genetic Inheritance. PMID:30454646
Insights into mammalian transcription control by systematic analysis of ChIP sequencing data. PMID:30453943
Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection. PMID:30446528
Replicative and non-replicative mechanisms in the formation of clustered CNVs are indicated by whole genome characterization. PMID:30419018
Single cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development. PMID:30413530
Impact of somatic and germline mutations on the outcome of systemic mastocytosis. PMID:30373888
Defining Essentiality Score of Protein-Coding Genes and Long Noncoding RNAs. PMID:30356729
A reference haplotype panel for genome-wide imputation of short tandem repeats. PMID:30353011
Expression of renal cell markers and detection of 3p loss links endolymphatic sac tumor to renal cell carcinoma and warrants careful evaluation to avoid diagnostic pitfalls. PMID:30340515
RNA Polymerase II Phosphorylated on CTD Serine 5 Interacts with the Spliceosome during Co-transcriptional Splicing. PMID:30340024
The developmental transcriptome of the human heart. PMID:30337648
Ethanol-Induced Behavioral Sensitization Alters the Synaptic Transcriptome and Exon Utilization in DBA/2J Mice. PMID:30319688
Phenotype-Specific Enrichment of Mendelian Disorder Genes near GWAS Regions across 62 Complex Traits. PMID:30290150
Chromatin conformation and transcriptional activity are permissive regulators of DNA replication initiation in Drosophila. PMID:30279224
psichomics: graphical application for alternative splicing quantification and analysis. PMID:30277515
A survey of inter-individual variation in DNA methylation identifies environmentally responsive co-regulated networks of epigenetic variation in the human genome. PMID:30273333
Transcriptional addiction in cancer cells is mediated by YAP/TAZ through BRD4. PMID:30224758
Alternative splicing links histone modifications to stem cell fate decision. PMID:30217220
Whole genome sequencing identifies high-impact variants in well-known pharmacogenomic genes. PMID:30214008
Proteomics, Post-translational Modifications, and Integrative Analyses Reveal Molecular Heterogeneity within Medulloblastoma Subgroups. PMID:30205044
Umap and Bismap: quantifying genome and methylome mappability. PMID:30169659
Study of mitotic chromatin supports a model of bookmarking by histone modifications and reveals nucleosome deposition patterns. PMID:30166406
Dot2dot: accurate whole-genome tandem repeats discovery. PMID:30165507
To ERV Is Human: A Phenotype-Wide Scan Linking Polymorphic Human Endogenous Retrovirus-K Insertions to Complex Phenotypes. PMID:30154825
RNA Sequencing (RNA-Seq) Reveals Extremely Low Levels of Reticulocyte-Derived Globin Gene Transcripts in Peripheral Blood From Horses (Equus caballus) and Cattle (Bos taurus). PMID:30154823
Sexual difference of small RNA expression in Tetralogy of Fallot. PMID:30150777
STRetch: detecting and discovering pathogenic short tandem repeat expansions. PMID:30129428
Transfer RNA genes experience exceptionally elevated mutation rates. PMID:30127029
Promoter expression of HERV-K (HML-2) provirus-derived sequences is related to LTR sequence variation and polymorphic transcription factor binding sites. PMID:30126415
Intron retention is a source of neoepitopes in cancer. PMID:30114007
Dual Roles of Poly(dA:dT) Tracts in Replication Initiation and Fork Collapse. PMID:30078706
Whole-genome sequencing analysis of CNV using low-coverage and paired-end strategies is efficient and outperforms array-based CNV analysis. PMID:30061371
Assembly and Analysis of Unmapped Genome Sequence Reads Reveal Novel Sequence and Variation in Dogs. PMID:30022108
Proteogenomic Analysis of Surgically Resected Lung Adenocarcinoma. PMID:30017829
Genome-wide association and HLA fine-mapping studies identify risk loci and genetic pathways underlying allergic rhinitis. PMID:30013184
Conflicts of CpG density and DNA methylation are proximally and distally involved in gene regulation in human and mouse tissues. PMID:30009687
The TGFβ-signaling pathway and colorectal cancer: associations between dysregulated genes and miRNAs. PMID:29986714
Identification of transcribed protein coding sequence remnants within lincRNAs. PMID:29986053
A characterization of postzygotic mutations identified in monozygotic twins. PMID:29980163
BROCKMAN: deciphering variance in epigenomic regulators by k-mer factorization. PMID:29970004
Defects in the Alternative Splicing-Dependent Regulation of REST Cause Deafness. PMID:29961578
CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness. PMID:29945659
Multivariate genome-wide association analysis identifies novel and relevant variants associated with anterior cruciate ligament rupture risk in the dog model. PMID:29940858
c-Myc is a novel Leishmania virulence factor by proxy that targets the host miRNA system and is essential for survival in human macrophages. PMID:29934305
T Cell Receptor-Major Histocompatibility Complex Interaction Strength Defines Trafficking and CD103+ Memory Status of CD8 T Cells in the Brain. PMID:29922298
An integrated -omics analysis of the epigenetic landscape of gene expression in human blood cells. PMID:29914364
Genome-Wide Analysis of Interchromosomal Interaction Probabilities Reveals Chained Translocations and Overrepresentation of Translocation Breakpoints in Genes in a Cutaneous T-Cell Lymphoma Cell Line. PMID:29900125
Association mapping from sequencing reads using k-mers. PMID:29897334
A survey of microRNA single nucleotide polymorphisms identifies novel breast cancer susceptibility loci in a case-control, population-based study of African-American women. PMID:29871690
The p53-signaling pathway and colorectal cancer: Interactions between downstream p53 target genes and miRNAs. PMID:29860032
Stage-dependent piRNAs in chicken implicated roles in modulating male germ cell development. PMID:29859049
Characterization of Transcription Termination-Associated RNAs: New Insights into their Biogenesis, Tailing, and Expression in Primary Tumors. PMID:29854718
Landscape of Microsatellite Instability Across 39 Cancer Types. PMID:29850653
Breast cancer associated germline structural variants harboring small noncoding RNAs impact post-transcriptional gene regulation. PMID:29760470
Identification of polymorphisms in the bovine collagenous lectins and their association with infectious diseases in cattle. PMID:29744529
miRNA involvement in cell cycle regulation in colorectal cancer cases. PMID:29725503
Palladin Is a Neuron-Specific Translational Target of mTOR Signaling That Regulates Axon Morphogenesis. PMID:29712777
Exercise training alters the genomic response to acute exercise in human adipose tissue. PMID:29671347
SeedVicious: Analysis of microRNA target and near-target sites. PMID:29664927
Similarity in replication timing between polytene and diploid cells is associated with the organization of the Drosophila genome. PMID:29659604
Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs. PMID:29648536
The MAPK-Signaling Pathway in Colorectal Cancer: Dysregulated Genes and Their Association With MicroRNAs. PMID:29636593
Up-Regulation of PI 3-Kinases and the Activation of PI3K-Akt Signaling Pathway in Cancer Stem-Like Cells Through DNA Hypomethylation Mediated by the Cancer Microenvironment. PMID:29621663
Comparative Serum Challenges Show Divergent Patterns of Gene Expression and Open Chromatin in Human and Chimpanzee. PMID:29608722
Genome-Wide Profiling of DNA Methyltransferases in Mammalian Cells. PMID:29605852
Cardiac circRNAs arise mainly from constitutive exons rather than alternatively spliced exons. PMID:29567830
Integrative single-cell omics analyses reveal epigenetic heterogeneity in mouse embryonic stem cells. PMID:29561833
Expression of Carbonic Anhydrase III, a Nucleus Pulposus Phenotypic Marker, is Hypoxia-responsive and Confers Protection from Oxidative Stress-induced Cell Death. PMID:29559661
Demethylator phenotypes in acute myeloid leukemia. PMID:29556023
Adult height is associated with increased risk of ovarian cancer: a Mendelian randomisation study. PMID:29555990
Linear assembly of a human centromere on the Y chromosome. PMID:29553574
Peripubertal serum dioxin concentrations and subsequent sperm methylome profiles of young Russian adults. PMID:29550351
Identification of putative promoters in 48 eukaryotic genomes on the basis of DNA free energy. PMID:29540741
Effects of Cadmium Exposure on DNA Methylation at Imprinting Control Regions and Genome-Wide in Mothers and Newborn Children. PMID:29529597
Dysregulated genes and miRNAs in the apoptosis pathway in colorectal cancer patients. PMID:29516317
Dissecting super-enhancer hierarchy based on chromatin interactions. PMID:29507293
Circulating miRNAs, isomiRs and small RNA clusters in human plasma and breast milk. PMID:29505615
The Transcriptionally Permissive Chromatin State of Embryonic Stem Cells Is Acutely Tuned to Translational Output. PMID:29499153
Association of Genetic Variants of Small Non-Coding RNAs with Survival in Colorectal Cancer. PMID:29483812
Expression of Wnt-signaling pathway genes and their associations with miRNAs in colorectal cancer. PMID:29464056
DRUID: a pipeline for transcriptome-wide measurements of mRNA stability. PMID:29438994
The DNA double-strand "breakome" of mouse spermatids. PMID:29417179
Endurance training remodels sperm-borne small RNA expression and methylation at neurological gene hotspots. PMID:29416570
A high throughput screen for active human transposable elements. PMID:29390960
Genome-wide oxidative bisulfite sequencing identifies sex-specific methylation differences in the human placenta. PMID:29376485
Targeted deletion of a 170-kb cluster of LINE-1 repeats and implications for regional control. PMID:29367313
A survey on cellular RNA editing activity in response to Candida albicans infections. PMID:29363428
Conserved and species-specific transcription factor co-binding patterns drive divergent gene regulation in human and mouse. PMID:29361190
High-resolution TADs reveal DNA sequences underlying genome organization in flies. PMID:29335486
Base-Resolution Analysis of DNA Methylation Patterns Downstream of Dnmt3a in Mouse Naïve B Cells. PMID:29326230
Allele-specific SHAPE-MaP assessment of the effects of somatic variation and protein binding on mRNA structure. PMID:29317542
Enrichment of megabase-sized DNA molecules for single-molecule optical mapping and next-generation sequencing. PMID:29263336
Analysis of chromatin accessibility in decidualizing human endometrial stromal cells. PMID:29259032
MicroRNA-transcription factor interactions and their combined effect on target gene expression in colon cancer cases. PMID:29226599
RetrogeneDB-a database of plant and animal retrocopies. PMID:29220443
Genome-wide admixture and association study of subclinical atherosclerosis in the Women's Interagency HIV Study (WIHS). PMID:29206233
Using variant databases for variant prioritization and to detect erroneous genotype-phenotype associations. PMID:29191167
The NF-κB signalling pathway in colorectal cancer: associations between dysregulated gene and miRNA expression. PMID:29188362
Software for rapid time dependent ChIP-sequencing analysis (TDCA). PMID:29178831
Comparison of ChIP-Seq Data and a Reference Motif Set for Human KRAB C2H2 Zinc Finger Proteins. PMID:29146583
Intron retention enhances gene regulatory complexity in vertebrates. PMID:29141666
Dynamic reorganization of open chromatin underlies diverse transcriptomes during spermatogenesis. PMID:29126117
A causal mediation model of ischemia reperfusion injury in the retina. PMID:29121052
Identification of Splicing Quantitative Trait Loci (sQTL) in Drosophila melanogaster with Developmental Lead (Pb2+) Exposure. PMID:29114259
Polygenic risk score in postmortem diagnosed sporadic early-onset Alzheimer's disease. PMID:29103623
Translation efficiency is a determinant of the magnitude of miRNA-mediated repression. PMID:29097662
Vitamin D receptor-binding site variants affect prostate cancer progression. PMID:29088772
mirTrans: a resource of transcriptional regulation on microRNAs for human cell lines. PMID:29077896
OverGeneDB: a database of 5' end protein coding overlapping genes in human and mouse genomes. PMID:29069459
The PI3K/AKT signaling pathway: Associations of miRNAs with dysregulated gene expression in colorectal cancer. PMID:29068474
Cross-tissue integration of genetic and epigenetic data offers insight into autism spectrum disorder. PMID:29066808
Genome-wide profiling of transcribed enhancers during macrophage activation. PMID:29061167
Association analysis identifies 65 new breast cancer risk loci. PMID:29059683
KIT performed as a driver gene candidate affecting the survival status of patients with stomach adenocarcinoma. PMID:29050270
Mechanisms of HERV-K (HML-2) Transcription during Human Mammary Epithelial Cell Transformation. PMID:29046454
Integrating networks and comparative genomics reveals retroelement proliferation dynamics in hominid genomes. PMID:29043294
Loci associated with skin pigmentation identified in African populations. PMID:29025994
Genome-wide mapping of large deletions and their population-genetic properties in dairy cattle. PMID:28985340
Evolution of Alu Subfamily Structure in the Saimiri Lineage of New World Monkeys. PMID:28957461
Analysis of chromatin accessibility in human epidermis identifies putative barrier dysfunction-sensing enhancers. PMID:28953906
Regulation of cancer epigenomes with a histone-binding synthetic transcription factor. PMID:28919981
Incidence of pancreatic cancer is dramatically increased by a high fat, high calorie diet in KrasG12D mice. PMID:28886117
High performance of targeted next generation sequencing on variance detection in clinical tumor specimens in comparison with current conventional methods. PMID:28882180
Characterization of the microDNA through the response to chemotherapeutics in lymphoblastoid cell lines. PMID:28877255
Increased Vascular Permeability in the Bone Marrow Microenvironment Contributes to Disease Progression and Drug Response in Acute Myeloid Leukemia. PMID:28870739
Genome-wide identification of histone H2A and histone variant H2A.Z-interacting proteins by bPPI-seq. PMID:28862252
X Chromosome Evolution in Cetartiodactyla. PMID:28858207
Testing Two Evolutionary Theories of Human Aging with DNA Methylation Data. PMID:28855307
The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology. PMID:28855259
DNA Methylation of Synaptic Genes in the Prefrontal Cortex Is Associated with Aging and Age-Related Cognitive Impairment. PMID:28824413
Cancerouspdomains: comprehensive analysis of cancer type-specific recurrent somatic mutations in proteins and domains. PMID:28814324
Annotating long intergenic non-coding RNAs under artificial selection during chicken domestication. PMID:28810830
Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex. PMID:28798132
Orion: Detecting regions of the human non-coding genome that are intolerant to variation using population genetics. PMID:28797091
Genome-wide screen for differentially methylated long noncoding RNAs identifies Esrp2 and lncRNA Esrp2-as regulated by enhancer DNA methylation with prognostic relevance for human breast cancer. PMID:28759043
Co-option of the cardiac transcription factor Nkx2.5 during development of the emu wing. PMID:28743862
Genome Organization Drives Chromosome Fragility. PMID:28735753
Digoxin reveals a functional connection between HIV-1 integration preference and T-cell activation. PMID:28727807
m6aViewer: software for the detection, analysis, and visualization of N6-methyladenosine peaks from m6A-seq/ME-RIP sequencing data. PMID:28724534
Screening of potentially crucial genes and regulatory factors involved in epithelial ovarian cancer using microarray analysis. PMID:28693226
An Assessment of Database-Validated microRNA Target Genes in Normal Colonic Mucosa: Implications for Pathway Analysis. PMID:28690395
Transcription factor-microRNA associations and their impact on colorectal cancer survival. PMID:28667784
Gene expression allelic imbalance in ovine brown adipose tissue impacts energy homeostasis. PMID:28665992
Investigation of the STR loci noise distributions of PowerSeq™ Auto System. PMID:28613038
Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls. PMID:28606096
Generating testable hypotheses for schizophrenia and rheumatoid arthritis pathogenesis by integrating epidemiological, genomic, and protein interaction data. PMID:28560257
Inflammation-associated DNA methylation patterns in epithelium of ulcerative colitis. PMID:28557546
ATAD3 gene cluster deletions cause cerebellar dysfunction associated with altered mitochondrial DNA and cholesterol metabolism. PMID:28549128
Coordinates and intervals in graph-based reference genomes. PMID:28521770
Novel genes involved in severe early-onset obesity revealed by rare copy number and sequence variants. PMID:28489853
Soft Sweeps Are the Dominant Mode of Adaptation in the Human Genome. PMID:28482049
Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. PMID:28481359
CHD1 regulates cell fate determination by activation of differentiation-induced genes. PMID:28475736
RegulatorTrail: a web service for the identification of key transcriptional regulators. PMID:28472408
EnHERV: Enrichment analysis of specific human endogenous retrovirus patterns and their neighboring genes. PMID:28472109
Genetic polymorphisms associated with pancreatic cancer survival: a genome-wide association study. PMID:28470677
Zipper plot: visualizing transcriptional activity of genomic regions. PMID:28464823
ChIP-seq analysis of genomic binding regions of five major transcription factors highlights a central role for ZIC2 in the mouse epiblast stem cell gene regulatory network. PMID:28455373
Links between DNA methylation and nucleosome occupancy in the human genome. PMID:28413449
Physical Confirmation and Comparative Genomics of the Rat Mammary carcinoma susceptibility 3 Quantitative Trait Locus. PMID:28391240
Cancer-associated noncoding mutations affect RNA G-quadruplex-mediated regulation of gene expression. PMID:28386116
DNA Methylation Divergence and Tissue Specialization in the Developing Mouse Placenta. PMID:28379409
Comparative analysis of MBD-seq and MeDIP-seq and estimation of gene expression changes in a rodent model of schizophrenia. PMID:28365388
Dietary restriction protects from age-associated DNA methylation and induces epigenetic reprogramming of lipid metabolism. PMID:28351387
Stepwise analysis of MIR9 loci identifies miR-9-5p to be involved in Oestrogen regulated pathways in breast cancer patients. PMID:28345661
Translation of CircRNAs. PMID:28344080
Variants in the host genome may inhibit tumour growth in devil facial tumours: evidence from genome-wide association. PMID:28341828
PosiGene: automated and easy-to-use pipeline for genome-wide detection of positively selected genes. PMID:28334822
Estimating error models for whole genome sequencing using mixtures of Dirichlet-multinomial distributions. PMID:28334373
GENE-IS: Time-Efficient and Accurate Analysis of Viral Integration Events in Large-Scale Gene Therapy Data. PMID:28325279
Allele-specific non-CG DNA methylation marks domains of active chromatin in female mouse brain. PMID:28320934
Hyper- and hypo- nutrition studies of the hepatic transcriptome and epigenome suggest that PPARα regulates anaerobic glycolysis. PMID:28282965
Identifying Novel Transcriptional and Epigenetic Features of Nuclear Lamina-associated Genes. PMID:28273906
Human centromeric CENP-A chromatin is a homotypic, octameric nucleosome at all cell cycle points. PMID:28235947
RNF40 regulates gene expression in an epigenetic context-dependent manner. PMID:28209164
Variant discovery in the sheep milk transcriptome using RNA sequencing. PMID:28202015
Co-chaperone Hsp70/Hsp90-organizing protein (Hop) is required for transposon silencing and Piwi-interacting RNA (piRNA) biogenesis. PMID:28193840
Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer. PMID:28188128
Individualized analysis reveals CpG sites with methylation aberrations in almost all lung adenocarcinoma tissues. PMID:28178989
Insulin-like signalling to the maternal germline controls progeny response to osmotic stress. PMID:28166192
Polymorphisms in MicroRNA Binding Sites Predict Colorectal Cancer Survival. PMID:28138309
Both Maintenance and Avoidance of RNA-Binding Protein Interactions Constrain Coding Sequence Evolution. PMID:28138077
A Homozygous Mutation in GPT2 Associated with Nonsyndromic Intellectual Disability in a Consanguineous Family from Costa Rica. PMID:28130718
Targeted Sequencing of Lung Function Loci in Chronic Obstructive Pulmonary Disease Cases and Controls. PMID:28114305
RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets. PMID:28108657
Identification of coding and non-coding mutational hotspots in cancer genomes. PMID:28056774
Cell-Free DNA Provides a Good Representation of the Tumor Genome Despite Its Biased Fragmentation Patterns. PMID:28046008
Molecular mechanisms underlying noncoding risk variations in psychiatric genetic studies. PMID:28044063
Heterogeneity in sarcoma cell lines reveals enhanced motility of tetraploid versus diploid cells. PMID:28035071
A bedr way of genomic interval processing. PMID:27999613
Identification of a novel 15.5 kb SHOX deletion associated with marked intrafamilial phenotypic variability and analysis of its molecular origin. PMID:27994182
Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists. PMID:27993330
Knockout of miR-221 and miR-222 reveals common and specific targets for paralogous miRNAs. PMID:27981894
The intron-enriched HERV-K(HML-10) family suppresses apoptosis, an indicator of malignant transformation. PMID:27980690
"Gap hunting" to characterize clustered probe signals in Illumina methylation array data. PMID:27980682
Epigenetic stress responses induce muscle stem-cell ageing by Hoxa9 developmental signals. PMID:27919074
p53 Specifically Binds Triplex DNA In Vitro and in Cells. PMID:27907175
The UCSC Genome Browser database: 2017 update. PMID:27899642
Single Amino Acid Repeats in the Proteome World: Structural, Functional, and Evolutionary Insights. PMID:27893794
Peripheral self-reactivity regulates antigen-specific CD8 T-cell responses and cell division under physiological conditions. PMID:27881740
Computational Identification of Tissue-Specific Splicing Regulatory Elements in Human Genes from RNA-Seq Data. PMID:27861625
Single nucleotide polymorphisms within MicroRNAs, MicroRNA targets, and MicroRNA biogenesis genes and their impact on colorectal cancer survival. PMID:27859935
Global analysis of somatic structural genomic alterations and their impact on gene expression in diverse human cancers. PMID:27856756
AnnoLnc: a web server for systematically annotating novel human lncRNAs. PMID:27852242
Pleiotropic Mechanisms Indicated for Sex Differences in Autism. PMID:27846226
Stringent comparative sequence analysis reveals SOX10 as a putative inhibitor of glial cell differentiation. PMID:27821050
Evolutionary switches between two serine codon sets are driven by selection. PMID:27799560
Identification of Binding Targets of a Pyrrole-Imidazole Polyamide KR12 in the LS180 Colorectal Cancer Genome. PMID:27798693
Hi-C-constrained physical models of human chromosomes recover functionally-related properties of genome organization. PMID:27786255
Computational Analysis of G-Quadruplex Forming Sequences across Chromosomes Reveals High Density Patterns Near the Terminal Ends. PMID:27776185
ZSCAN5B and primate-specific paralogs bind RNA polymerase III genes and extra-TFIIIC (ETC) sites to modulate mitotic progression. PMID:27732952
Identification of selective sweeps reveals divergent selection between Chinese Holstein and Simmental cattle populations. PMID:27716022
iDamIDseq and iDEAR: an improved method and computational pipeline to profile chromatin-binding proteins. PMID:27707796
Variable Autosomal and X Divergence Near and Far from Genes Affects Estimates of Male Mutation Bias in Great Apes. PMID:27702816
Male-Specific Transcription Factor Occupancy Alone Does Not Account for Differential Methylation at Imprinted Genes in the mouse Germ Cell Lineage. PMID:27694116
Are sites with multiple single nucleotide variants in cancer genomes a consequence of drivers, hypermutable sites or sequencing errors? PMID:27688957
The Impact of Linked Selection in Chimpanzees: A Comparative Study. PMID:27678122
Atopic Dermatitis Susceptibility Variants in Filaggrin Hitchhike Hornerin Selective Sweep. PMID:27678121
BRD4 localization to lineage-specific enhancers is associated with a distinct transcription factor repertoire. PMID:27651452
SpermBase: A Database for Sperm-Borne RNA Contents. PMID:27628216
Integrative analysis of mutational and transcriptional profiles reveals driver mutations of metastatic breast cancers. PMID:27625789
FBW7 suppression leads to SOX9 stabilization and increased malignancy in medulloblastoma. PMID:27625374
PGD: a pangolin genome hub for the research community. PMID:27616775
Clustered somatic mutations are frequent in transcription factor binding motifs within proximal promoter regions in melanoma and other cutaneous malignancies. PMID:27611953
Epigenetic regulation of OAS2 shows disease-specific DNA methylation profiles at individual CpG sites. PMID:27572959
A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease. PMID:27569544
Explorations to improve the completeness of exome sequencing. PMID:27568008
Clonal haematopoiesis harbouring AML-associated mutations is ubiquitous in healthy adults. PMID:27546487
NF-Y Binding Site Architecture Defines a C-Fos Targeted Promoter Class. PMID:27517874
The CD4(+) T cell methylome contributes to a distinct CD4(+) T cell transcriptional signature in Mycobacterium bovis-infected cattle. PMID:27507428
Design and application of a target capture sequencing of exons and conserved non-coding sequences for the rat. PMID:27506932
Evolutionary dynamics of selfish DNA explains the abundance distribution of genomic subsequences. PMID:27488939
Ubiquitously expressed genes participate in cell-specific functions via alternative promoter usage. PMID:27466324
Secondary structure impacts patterns of selection in human lncRNAs. PMID:27457204
Conservation of the Exon-Intron Structure of Long Intergenic Non-Coding RNA Genes in Eutherian Mammals. PMID:27429005
Uncovering the liver's role in immunity through RNA co-expression networks. PMID:27401171
Heat*seq: an interactive web tool for high-throughput sequencing experiment comparison with public data. PMID:27378302
Transcriptome Analysis on Monocytes from Patients with Neovascular Age-Related Macular Degeneration. PMID:27374485
CTCF contributes in a critical way to spermatogenesis and male fertility. PMID:27345455
Identification of Gene Loci That Overlap Between Schizophrenia and Educational Attainment. PMID:27338279
Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia. PMID:27322744
Rare coding TTN variants are associated with electrocardiographic QT interval in the general population. PMID:27321809
Zerone: a ChIP-seq discretizer for multiple replicates with built-in quality control. PMID:27288492
A catalog of hemizygous variation in 127 22q11 deletion patients. PMID:27274857
Detection of differential DNA methylation in repetitive DNA of mice and humans perinatally exposed to bisphenol A. PMID:27267941
Whole-gene sequencing investigation of SAT1 in attempted suicide. PMID:27229768
Prediction and Quantification of Splice Events from RNA-Seq Data. PMID:27218464
miRNA-dependent target regulation: functional characterization of single-nucleotide polymorphisms identified in genome-wide association studies of Alzheimer's disease. PMID:27215977
Improved definition of the mouse transcriptome via targeted RNA sequencing. PMID:27197243
Distinct transcription factor complexes act on a permissive chromatin landscape to establish regionalized gene expression in CNS stem cells. PMID:27197220
Genomic analysis of mouse VL30 retrotransposons. PMID:27158269
Etiology matters - Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy. PMID:27157830
RISC-mediated control of selected chromatin regulators stabilizes ground state pluripotency of mouse embryonic stem cells. PMID:27154007
Genome-wide non-CpG methylation of the host genome during M. tuberculosis infection. PMID:27112593
Characterization of piRNAs across postnatal development in mouse brain. PMID:27112104
Impact of polymorphisms in microRNA biogenesis genes on colon cancer risk and microRNA expression levels: a population-based, case-control study. PMID:27107574
DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets. PMID:27084938
Clustered mutations in hominid genome evolution are consistent with APOBEC3G enzymatic activity. PMID:27056836
Computational Detection of Stage-Specific Transcription Factor Clusters during Heart Development. PMID:27047536
The Chromatin Remodelling Enzymes SNF2H and SNF2L Position Nucleosomes adjacent to CTCF and Other Transcription Factors. PMID:27019336
Long noncoding RNAs expressed in human hepatic stellate cells form networks with extracellular matrix proteins. PMID:27007663
Improving diagnosis and broadening the phenotypes in early-onset seizure and severe developmental delay disorders through gene panel analysis. PMID:26993267
High-fat diet reprograms the epigenome of rat spermatozoa and transgenerationally affects metabolism of the offspring. PMID:26977389
Crambled: A Shiny application to enable intuitive resolution of conflicting cellularity estimates. PMID:26962434
dbPEC: a comprehensive literature-based database for preeclampsia related genes and phenotypes. PMID:26946289
High-throughput discovery of post-transcriptional cis-regulatory elements. PMID:26941072
Autism Linked to Increased Oncogene Mutations but Decreased Cancer Rate. PMID:26934580
The effect of non-coding DNA variations on P53 and cMYC competitive inhibition at cis-overlapping motifs. PMID:26908612
Comprehensive Phylogenetic Analysis Sheds Light on the Diversity and Origin of the MLO Family of Integral Membrane Proteins. PMID:26893454
Genome-wide methylation analysis of retrocopy-associated CpG islands and their genomic environment. PMID:26890210
Feature co-localization landscape of the human genome. PMID:26854351
RDDpred: a condition-specific RNA-editing prediction model from RNA-seq data. PMID:26817607
Human Lineage-Specific Transcriptional Regulation through GA-Binding Protein Transcription Factor Alpha (GABPa). PMID:26814189
Differential DNA methylation patterns of homeobox genes in proximal and distal colon epithelial cells. PMID:26812987
Purifying Selection on Exonic Splice Enhancers in Intronless Genes. PMID:26802218
New observations on maternal age effect on germline de novo mutations. PMID:26781218
Relationship between microRNA genes incidence and cancer-associated genomic regions in canine tumors: a comprehensive bioinformatics study. PMID:26780769
Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. PMID:26780094
Rsite2: an efficient computational method to predict the functional sites of noncoding RNAs. PMID:26751501
UCSC Data Integrator and Variant Annotation Integrator. PMID:26740527
Derivation of consensus inactivation status for X-linked genes from genome-wide studies. PMID:26719789
Epigenomic Landscape of Human Fetal Brain, Heart, and Liver. PMID:26719341
BigQ: a NoSQL based framework to handle genomic variants in i2b2. PMID:26714792
Identifying rhesus macaque gene orthologs using heterospecific human CNV probes. PMID:26697375
RNA polymerase errors cause splicing defects and can be regulated by differential expression of RNA polymerase subunits. PMID:26652005
Identification of Low-Confidence Regions in the Pig Reference Genome (Sscrofa10.2). PMID:26640477
Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell type-specific hypomethylation in the regulation of cell identity genes. PMID:26635396
TET-catalyzed 5-hydroxymethylcytosine regulates gene expression in differentiating colonocytes and colon cancer. PMID:26631571
PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information. PMID:26627005
Genome-wide Association Analysis of Psoriatic Arthritis and Cutaneous Psoriasis Reveals Differences in Their Genetic Architecture. PMID:26626624
An Evolutionarily Young Polar Bear (Ursus maritimus) Endogenous Retrovirus Identified from Next Generation Sequence Data. PMID:26610552
The UCSC Genome Browser database: 2016 update. PMID:26590259
Inferring Selective Constraint from Population Genomic Data Suggests Recent Regulatory Turnover in the Human Brain. PMID:26590212
SomamiR 2.0: a database of cancer somatic mutations altering microRNA-ceRNA interactions. PMID:26578591
Knowledge-based analysis of functional impacts of mutations in microRNA seed regions. PMID:26564979
Determinants of the Usage of Splice-Associated cis-Motifs Predict the Distribution of Human Pathogenic SNPs. PMID:26545919
A potential endophenotype for Alzheimer's disease: cerebrospinal fluid clusterin. PMID:26545630
DNA Editing of LTR Retrotransposons Reveals the Impact of APOBECs on Vertebrate Genomes. PMID:26541172
The evolutionary landscape of intergenic trans-splicing events in insects. PMID:26521696
TARDIS, a targeted RNA directional sequencing method for rare RNA discovery. PMID:26513670
DNA methylation patterns of protein-coding genes and long non-coding RNAs in males with schizophrenia. PMID:26503909
Genome-wide evolutionary and functional analysis of the Equine Repetitive Element 1: an insertion in the myostatin promoter affects gene expression. PMID:26503543
Increased Transcript Complexity in Genes Associated with Chronic Obstructive Pulmonary Disease. PMID:26480348
Evaluation of whole-genome sequencing of four Chinese crested dogs for variant detection using the ion proton system. PMID:26457193
Copy number variation associates with mortality in long-lived individuals: a genome-wide assessment. PMID:26446717
A novel locus of resistance to severe malaria in a region of ancient balancing selection. PMID:26416757
BIDCHIPS: bias decomposition and removal from ChIP-seq data clarifies true binding signal and its functional correlates. PMID:26388941
BET inhibitor resistance emerges from leukaemia stem cells. PMID:26367796
Short interspersed DNA elements and miRNAs: a novel hidden gene regulation layer in zebrafish? PMID:26363800
Genome-wide target analysis of NEUROD2 provides new insights into regulation of cortical projection neuron migration and differentiation. PMID:26341353
Pervasive pleiotropy between psychiatric disorders and immune disorders revealed by integrative analysis of multiple GWAS. PMID:26340901
Cell type-selective disease-association of genes under high regulatory load. PMID:26338775
CoSREM: a graph mining algorithm for the discovery of combinatorial splicing regulatory elements. PMID:26337677
Prenatal Exposure to Cadmium and Cotinine and CpG island DNA methylation in Mother-Infant Pairs. PMID:26295018
Evolution of the unspliced transcriptome. PMID:26289325
A convex formulation for joint RNA isoform detection and quantification from multiple RNA-seq samples. PMID:26286719
Predicting chromatin organization using histone marks. PMID:26272203
Molecular and phenotypic distinction of the very recently evolved insular subspecies Mus musculus helgolandicus ZIMMERMANN, 1953. PMID:26268354
'Cut from the same cloth': Shared microsatellite variants among cancers link to ectodermal tissues-neural tube and crest cells. PMID:26246470
Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes. PMID:26235384
Common polygenic variation contributes to risk of migraine in the Norfolk Island population. PMID:26220684
DNA methylation in ductal carcinoma in situ related with future development of invasive breast cancer. PMID:26213588
VaccineDA: Prediction, design and genome-wide screening of oligodeoxynucleotide-based vaccine adjuvants. PMID:26212482
Improved Methods to Generate Spheroid Cultures from Tumor Cells, Tumor Cells & Fibroblasts or Tumor-Fragments: Microenvironment, Microvesicles and MiRNA. PMID:26208323
Integrated sequence and expression analysis of ovarian cancer structural variants underscores the importance of gene fusion regulation. PMID:26177635
Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach. PMID:26167643
Differential and coherent processing patterns from small RNAs. PMID:26166713
Genomic copy number variation in Mus musculus. PMID:26141061
Human bone marrow- and adipose-mesenchymal stem cells secrete exosomes enriched in distinctive miRNA and tRNA species. PMID:26129847
Sequencing of the TBX6 Gene in Families with Familial Idiopathic Scoliosis. PMID:26120555
Conditional entropy in variation-adjusted windows detects selection signatures associated with expression quantitative trait loci (eQTLs). PMID:26111110
Annotation of the Protein Coding Regions of the Equine Genome. PMID:26107351
Transposable Element Insertions in Long Intergenic Non-Coding RNA Genes. PMID:26106594
Np9, a cellular protein of retroviral ancestry restricted to human, chimpanzee and gorilla, binds and regulates ubiquitin ligase MDM2. PMID:26103464
Interlocus gene conversion explains at least 2.7% of single nucleotide variants in human segmental duplications. PMID:26077037
Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation. PMID:26056000
Coherence analysis discriminates between retroviral integration patterns in CD34(+) cells transduced under differing clinical trial conditions. PMID:26029726
Controlling for conservation in genome-wide DNA methylation studies. PMID:26024968
Exome sequencing identifies rare variants in multiple genes in atrioventricular septal defect. PMID:25996639
Comparison of Exome and Genome Sequencing Technologies for the Complete Capture of Protein-Coding Regions. PMID:25973577
NGS-based approach to determine the presence of HPV and their sites of integration in human cancer genome. PMID:25973533
Discovering associations among diagnosis groups using topic modeling. PMID:25954576
PACCMIT/PACCMIT-CDS: identifying microRNA targets in 3' UTRs and coding sequences. PMID:25948580
i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly. PMID:25925574
Comparative methylome analysis in solid tumors reveals aberrant methylation at chromosome 6p in nasopharyngeal carcinoma. PMID:25924914
Coordinated tissue-specific regulation of adjacent alternative 3' splice sites in C. elegans. PMID:25922281
Argonaute 2 Binds Directly to tRNA Genes and Promotes Gene Repression in cis. PMID:25918241
Regulatory networks in retinal ischemia-reperfusion injury. PMID:25902940
No significant viral transcription detected in whole breast cancer transcriptomes. PMID:25884932
GeneTIER: prioritization of candidate disease genes using tissue-specific gene expression profiles. PMID:25861967
Using epigenomics data to predict gene expression in lung cancer. PMID:25861082
Functional loss of semaphorin 3C and/or semaphorin 3D and their epistatic interaction with ret are critical to Hirschsprung disease liability. PMID:25839327
T-cell receptor α enhancer is inactivated in αβ T lymphocytes. PMID:25831496
H4K12ac is regulated by estrogen receptor-alpha and is associated with BRD4 function and inducible transcription. PMID:25788266
Canine urothelial carcinoma: genomically aberrant and comparatively relevant. PMID:25783786
Differential expression of HERV-K (HML-2) proviruses in cells and virions of the teratocarcinoma cell line Tera-1. PMID:25746218
Computational methodology for ChIP-seq analysis. PMID:25741452
Circulating nucleic acids damage DNA of healthy cells by integrating into their genomes. PMID:25740145
Targeting IL-17B-IL-17RB signaling with an anti-IL-17RB antibody blocks pancreatic cancer metastasis by silencing multiple chemokines. PMID:25732306
Nuclear p120-catenin regulates the anoikis resistance of mouse lobular breast cancer cells through Kaiso-dependent Wnt11 expression. PMID:25713299
Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins. PMID:25695952
Integrative analysis of 111 reference human epigenomes. PMID:25693563
C2H2 zinc finger proteins greatly expand the human regulatory lexicon. PMID:25690854
Tissue-specific effects of genetic and epigenetic variation on gene regulation and splicing. PMID:25634236
Genome wide chromatin occupancy of mrhl RNA and its role in gene regulation in mouse spermatogonial cells. PMID:25584904
MIWI and piRNA-mediated cleavage of messenger RNAs in mouse testes. PMID:25582079
PD_NGSAtlas: a reference database combining next-generation sequencing epigenomic and transcriptomic data for psychiatric disorders. PMID:25551368
Uncapped 5' ends of mRNAs targeted by cytoplasmic capping map to the vicinity of downstream CAGE tags. PMID:25541487
Are special read alignment strategies necessary and cost-effective when handling sequencing reads from patient-derived tumor xenografts? PMID:25539684
De novo mutations discovered in 8 Mexican American families through whole genome sequencing. PMID:25519376
Human cells contain natural double-stranded RNAs with potential regulatory functions. PMID:25504323
Potassium stress growth characteristics and energetics in the haloarchaeon Haloarcula marismortui. PMID:25503059
HGV&TB: a comprehensive online resource on human genes and genetic variants associated with tuberculosis. PMID:25502817
High throughput exome coverage of clinically relevant cardiac genes. PMID:25496018
Guanine quadruplexes are formed by specific regions of human transposable elements. PMID:25431265
microPIR2: a comprehensive database for human-mouse comparative study of microRNA-promoter interactions. PMID:25425035
Distance-based assessment of the localization of functional annotations in 3D genome reconstructions. PMID:25407917
Essential nutrient supplementation prevents heritable metabolic disease in multigenerational intrauterine growth-restricted rats. PMID:25395450
Splicing mutation analysis reveals previously unrecognized pathways in lymph node-invasive breast cancer. PMID:25394353
Identifying splicing regulatory elements with de Bruijn graphs. PMID:25393830
An update on LNCipedia: a database for annotated human lncRNA sequences. PMID:25378313
Novel genes in Human Asthma Based on a Mouse Model of Allergic Airway Inflammation and Human Investigations. PMID:25374748
Characterization of human chromosomal material exchange with regard to the chromosome translocations using next-generation sequencing data. PMID:25349267
VISPA: a computational pipeline for the identification and analysis of genomic vector integration sites. PMID:25342980
Distinct roles for histone chaperones in the deposition of Htz1 in chromatin. PMID:25338502
Comparative FAIRE-seq analysis reveals distinguishing features of the chromatin structure of ground state- and primed-pluripotent cells. PMID:25335464
R-loops induce repressive chromatin marks over mammalian gene terminators. PMID:25296254
Functional annotation of putative regulatory elements at cancer susceptibility Loci. PMID:25288875
A genome-wide map of adeno-associated virus-mediated human gene targeting. PMID:25282150
Molecular signatures of mouse TRPV1-lineage neurons revealed by RNA-Seq transcriptome analysis. PMID:25281809
HTLV-1 proviral integration sites differ between asymptomatic carriers and patients with HAM/TSP. PMID:25270762
Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences. PMID:25254093
LncRBase: an enriched resource for lncRNA information. PMID:25233092
Genetic variation in taste receptor pseudogenes provides evidence for a dynamic role in human evolution. PMID:25216916
Somatic intronic microsatellite loci differentiate glioblastoma from lower-grade gliomas. PMID:25153720
Detecting translational regulation by change point analysis of ribosome profiling data sets. PMID:25147239
Comparative assembly hubs: web-accessible browsers for comparative genomics. PMID:25138168
Systematic identification of 3'-UTR regulatory elements in activity-dependent mRNA stability in hippocampal neurons. PMID:25135970
Evaluation of exome sequencing to estimate tumor burden in plasma. PMID:25133800
Alternative polyadenylation regulates CELF1/CUGBP1 target transcripts following T cell activation. PMID:25123787
Circadian regulation of myocardial sarcomeric Titin-cap (Tcap, telethonin): identification of cardiac clock-controlled genes using open access bioinformatics data. PMID:25121604
Glucocorticoid receptor binds half sites as a monomer and regulates specific target genes. PMID:25085117
The dynamic exome: acquired variants as individuals age. PMID:25063753
Underreplicated regions in Drosophila melanogaster are enriched with fast-evolving genes and highly conserved noncoding sequences. PMID:25062918
An efficient and sensitive method for preparing cDNA libraries from scarce biological samples. PMID:25056322
Insulin-like peptide 5 is an orexigenic gastrointestinal hormone. PMID:25028498
Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression. PMID:25018785
Bromodomain protein BRD4 is required for estrogen receptor-dependent enhancer activation and gene transcription. PMID:25017071
A novel reannotation strategy for dissecting DNA methylation patterns of human long intergenic non-coding RNAs in cancers. PMID:25013169
Development and performance of a targeted whole exome sequencing enrichment kit for the dog (Canis Familiaris Build 3.1). PMID:24998260
Whole genome and exome sequencing of monozygotic twins discordant for Crohn's disease. PMID:24996980
Chimpanzee-specific endogenous retrovirus generates genomic variations in the chimpanzee genome. PMID:24987855
Exploring the miRNA-mRNA regulatory network in clear cell renal cell carcinomas by next-generation sequencing expression profiles. PMID:24977165
Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7. PMID:24973960
Genetic Determinants for Enzymatic Digestion of Lignocellulosic Biomass Are Independent of Those for Lignin Abundance in a Maize Recombinant Inbred Population. PMID:24972714
Fine-scale population epigenetic structure in relation to gastrointestinal parasite load in red grouse (Lagopus lagopus scotica). PMID:24943398
Dicer-microRNA-Myc circuit promotes transcription of hundreds of long noncoding RNAs. PMID:24929436
Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment. PMID:24927817
Sorting signal targeting mRNA into hepatic extracellular vesicles. PMID:24921245
Copy number variants and selective sweeps in natural populations of the house mouse (Mus musculus domesticus). PMID:24917877
A bioinformatic and computational study of myosin phosphatase subunit diversity. PMID:24898838
Genome-wide haplotypic testing in a Finnish cohort identifies a novel association with low-density lipoprotein cholesterol. PMID:24896150
Dynamics of mRNA and polysomal abundance in early 3T3-L1 adipogenesis. PMID:24886538
Integration of mRNA expression profile, copy number alterations, and microRNA expression levels in breast cancer to improve grade definition. PMID:24866763
CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. PMID:24861617
An enhancer polymorphism at the cardiomyocyte intercalated disc protein NOS1AP locus is a major regulator of the QT interval. PMID:24857694
A Bayesian method to incorporate hundreds of functional characteristics with association evidence to improve variant prioritization. PMID:24844982
Microfluidic single-cell whole-transcriptome sequencing. PMID:24782542
Using VAAST to Identify Disease-Associated Variants in Next-Generation Sequencing Data. PMID:24763993
Overrepresentation of glutamate signaling in Alzheimer's disease: network-based pathway enrichment using meta-analysis of genome-wide association studies. PMID:24755620
Site-specific association with host and viral chromatin by Kaposi's sarcoma-associated herpesvirus LANA and its reversal during lytic reactivation. PMID:24696474
Identifying mRNA sequence elements for target recognition by human Argonaute proteins. PMID:24663241
Quantitative theory of entropic forces acting on constrained nucleotide sequences applied to viruses. PMID:24639520
A nucleosomal approach to inferring causal relationships of histone modifications. PMID:24564627
AnnotateGenomicRegions: a web application. PMID:24564446
Molecular evolution of multiple-level control of heme biosynthesis pathway in animal kingdom. PMID:24489775
Coding sequence density estimation via topological pressure. PMID:24448658
Axonal guidance signaling pathway interacting with smoking in modifying the risk of pancreatic cancer: a gene- and pathway-based interaction analysis of GWAS data. PMID:24419231
Transcriptome-wide analysis of UTRs in non-small cell lung cancer reveals cancer-related genes with SNV-induced changes on RNA secondary structure and miRNA target sites. PMID:24416147
DevMouse, the mouse developmental methylome database and analysis tools. PMID:24408217
A computational framework to infer human disease-associated long noncoding RNAs. PMID:24392133
Differential inhibition of LINE1 and LINE2 retrotransposition by vertebrate AID/APOBEC proteins. PMID:24344916
A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics. PMID:24324667
SVD identifies transcript length distribution functions from DNA microarray data and reveals evolutionary forces globally affecting GBM metabolism. PMID:24282503
Rates of evolution of hominoid seminal proteins are correlated with function and expression, rather than mating system. PMID:24281413
1000 Genomes Selection Browser 1.0: a genome browser dedicated to signatures of natural selection in modern humans. PMID:24275494
Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. PMID:24227676
Many human accelerated regions are developmental enhancers. PMID:24218637
Cadmium exposure and the epigenome: Exposure-associated patterns of DNA methylation in leukocytes from mother-baby pairs. PMID:24169490
PolymiRTS Database 3.0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways. PMID:24163105
Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing. PMID:24142049
Genes-environment interactions in obesity- and diabetes-associated pancreatic cancer: a GWAS data analysis. PMID:24136929
Comprehensive analysis of human endogenous retrovirus group HERV-W locus transcription in multiple sclerosis brain lesions by high-throughput amplicon sequencing. PMID:24109235
Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder. PMID:24094742
Condensin I associates with structural and gene regulatory regions in vertebrate chromosomes. PMID:24088984
Master regulators of FGFR2 signalling and breast cancer risk. PMID:24043118
Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. PMID:24037425
targetHub: a programmable interface for miRNA-gene interactions. PMID:24013925
Quantitative epigenetic co-variation in CpG islands and co-regulation of developmental genes. PMID:23999385
Spatial compartmentalization at the nuclear periphery characterized by genome-wide mapping. PMID:23987233
A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes. PMID:23966869
MYRF is a membrane-associated transcription factor that autoproteolytically cleaves to directly activate myelin genes. PMID:23966833
Gene-smoking interactions in multiple Rho-GTPase pathway genes in an early-onset coronary artery disease cohort. PMID:23907653
THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data. PMID:23895164
MicroRNA discovery by similarity search to a database of RNA-seq profiles. PMID:23874353
Detection of Human Endogenous Retrovirus K (HERV-K) Transcripts in Human Prostate Cancer Cell Lines. PMID:23847768
Loss of corepressor PER2 under hypoxia up-regulates OCT1-mediated EMT gene expression and enhances tumor malignancy. PMID:23836662
VAAST 2.0: improved variant classification and disease-gene identification using a conservation-controlled amino acid substitution matrix. PMID:23836555
DNA methylation patterns facilitate the identification of microRNA transcription start sites: a brain-specific study. PMID:23826117
Natural selection in a bangladeshi population from the cholera-endemic ganges river delta. PMID:23825302
Pipit: visualizing functional impacts of structural variations. PMID:23803468
Unravelling the hidden DNA structural/physical code provides novel insights on promoter location. PMID:23761436
Passive and active DNA methylation and the interplay with genetic variation in gene regulation. PMID:23755361
A novel endogenous betaretrovirus group characterized from polar bears (Ursus maritimus) and giant pandas (Ailuropoda melanoleuca). PMID:23725819
Evolution of the human gastrokine locus and confounding factors regarding the pseudogenicity of GKN3. PMID:23715263
Genetic architecture of Wistar-Kyoto rat and spontaneously hypertensive rat substrains from different sources. PMID:23673728
Cytoplasmic organelle DNA preferentially inserts into open chromatin. PMID:23661564
miRNA biogenesis enzyme Drosha is required for vascular smooth muscle cell survival. PMID:23637774
Potential Impact of miR-137 and Its Targets in Schizophrenia. PMID:23637704
Molecular hierarchy of mammary differentiation yields refined markers of mammary stem cells. PMID:23580620
OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds. PMID:23571760
Genome-wide determinants of proviral targeting, clonal abundance and expression in natural HTLV-1 infection. PMID:23555266
Positively charged residues are the major determinants of ribosomal velocity. PMID:23554576
Multiple transcription factor binding sites predict AID targeting in non-Ig genes. PMID:23514741
Kdm2b maintains murine embryonic stem cell status by recruiting PRC1 complex to CpG islands of developmental genes. PMID:23502314
Promzea: a pipeline for discovery of co-regulatory motifs in maize and other plant species and its application to the anthocyanin and phlobaphene biosynthetic pathways and the Maize Development Atlas. PMID:23497159
Global regulation of alternative splicing by adenosine deaminase acting on RNA (ADAR). PMID:23474544
Identity-by-descent mapping to detect rare variants conferring susceptibility to multiple sclerosis. PMID:23472070
The vast, conserved mammalian lincRNome. PMID:23468607
Additional annotation enhances potential for biologically-relevant analysis of the Illumina Infinium HumanMethylation450 BeadChip array. PMID:23452981
A composite method based on formal grammar and DNA structural features in detecting human polymerase II promoter region. PMID:23437045
Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution. PMID:23433480
Searching the coding region for microRNA targets. PMID:23404894
Genome-wide copy number variant analysis in inbred chickens lines with different susceptibility to Marek's disease. PMID:23390598
Predicting cell types and genetic variations contributing to disease by combining GWAS and epigenetic data. PMID:23382893
Genome-wide analysis of human hotspot intersected genes highlights the roles of meiotic recombination in evolution and disease. PMID:23368819
Effects of DNA methylation on nucleosome stability. PMID:23355616
A Hyperactive Transposase Promotes Persistent Gene Transfer of a piggyBac DNA Transposon. PMID:23344650
MicroRNA-181a* Targets Nanog in a Subpopulation of CD34(+) Cells Isolated From Peripheral Blood. PMID:23344176
Transcriptional profiling of human endogenous retrovirus group HERV-K(HML-2) loci in melanoma. PMID:23338945
Transcriptome-wide expansion of non-coding regulatory switches: evidence from co-occurrence of Alu exonization, antisense and editing. PMID:23303787
MaSC: mappability-sensitive cross-correlation for estimating mean fragment length of single-end short-read sequencing data. PMID:23300135
RNA-guided human genome engineering via Cas9. PMID:23287722
Reverse genetics screen in zebrafish identifies a role of miR-142a-3p in vascular development and integrity. PMID:23285103
A novel Bayesian change-point algorithm for genome-wide analysis of diverse ChIPseq data types. PMID:23271069
Transcriptome-wide identification of A > I RNA editing sites by inosine specific cleavage. PMID:23264566
Bioinformatics of Cancer ncRNA in High Throughput Sequencing: Present State and Challenges. PMID:23251139
An arrayed genome-scale lentiviral-enabled short hairpin RNA screen identifies lethal and rescuer gene candidates. PMID:23198867
Genetic analysis of DNA methylation and gene expression levels in whole blood of healthy human subjects. PMID:23157493
A histone arginine methylation localizes to nucleosomes in satellite II and III DNA sequences in the human genome. PMID:23153121
An arrayed RNA interference genome-wide screen identifies candidate genes involved in the MicroRNA 21 biogenesis pathway. PMID:23153064
Genome-wide chromatin remodeling identified at GC-rich long nucleosome-free regions. PMID:23144837
A streamlined method for detecting structural variants in cancer genomes by short read paired-end sequencing. PMID:23144753
Novel Foxo1-dependent transcriptional programs control T(reg) cell function. PMID:23135404
Integrative analysis of somatic mutations altering microRNA targeting in cancer genomes. PMID:23091610
dsPIG: a tool to predict imprinted genes from the deep sequencing of whole transcriptomes. PMID:23083219
A hybrid distance measure for clustering expressed sequence tags originating from the same gene family. PMID:23071763
In vivo tumorigenesis was observed after injection of in vitro expanded neural crest stem cells isolated from adult bone marrow. PMID:23071568
"Orphan" retrogenes in the human genome. PMID:23066043
Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia. PMID:23064414
Insights into pancreatic cancer etiology from pathway analysis of genome-wide association study data. PMID:23056513
Systematic analysis of microRNA targeting impacted by small insertions and deletions in human genome. PMID:23049969
EpiExplorer: live exploration and global analysis of large epigenomic datasets. PMID:23034089
Tethering of the conserved piggyBac transposase fusion protein CSB-PGBD3 to chromosomal AP-1 proteins regulates expression of nearby genes in humans. PMID:23028371
Genome-wide methylation profiling identifies hypermethylated biomarkers in high-grade cervical intraepithelial neoplasia. PMID:23018867
Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse (Mus musculus). PMID:22956910
Evidence of abundant purifying selection in humans for recently acquired regulatory functions. PMID:22956687
Some phenotype association tools in Galaxy: looking for disease SNPs in a full genome. PMID:22948727
siSPOTR: a tool for designing highly specific and potent siRNAs for human and mouse. PMID:22941647
Transcriptome sequencing in Sezary syndrome identifies Sezary cell and mycosis fungoides-associated lncRNAs and novel transcripts. PMID:22936659
A simple method for analyzing actives in random RNAi screens: introducing the "H Score" for hit nomination & gene prioritization. PMID:22934950
Sequencing and characterization of the FVB/NJ mouse genome. PMID:22916792
Personal receptor repertoires: olfaction as a model. PMID:22908908
Genome-wide localization of protein-DNA binding and histone modification by a Bayesian change-point method with ChIP-seq data. PMID:22844240
Newly evolved introns in human retrogenes provide novel insights into their evolutionary roles. PMID:22839428
Proximity of H2A.Z containing nucleosome to the transcription start site influences gene expression levels in the mammalian liver and brain. PMID:22821566
MolBioLib: a C++11 framework for rapid development and deployment of bioinformatics tasks. PMID:22815363
Different genes interact with particulate matter and tobacco smoke exposure in affecting lung function decline in the general population. PMID:22792237
DNA hypermethylation of alternatively spliced and repeat sequences in humans. PMID:22740315
Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. PMID:22737091
Regulation of alternative splicing by the circadian clock and food related cues. PMID:22721557
Using Galaxy to perform large-scale interactive data analyses. PMID:22700312
Fine mapping and conditional analysis identify a new mutation in the autoimmunity susceptibility gene BLK that leads to reduced half-life of the BLK protein. PMID:22696686
siRNA off-target effects in genome-wide screens identify signaling pathway members. PMID:22645644
Cis-acting polymorphisms affect complex traits through modifications of microRNA regulation pathways. PMID:22606281
On the presence and role of human gene-body DNA methylation. PMID:22577155
Bioinformatic clonality analysis of next-generation sequencing-derived viral vector integration sites. PMID:22559057
BEAT: Bioinformatics Exon Array Tool to store, analyze and visualize Affymetrix GeneChip Human Exon Array data from disease experiments. PMID:22536968
The distribution of a germline methylation marker suggests a regional mechanism of LINE-1 silencing by the piRNA-PIWI system. PMID:22530917
microPIR: an integrated database of microRNA target sites within human promoter sequences. PMID:22439011
Optimal use of conservation and accessibility filters in microRNA target prediction. PMID:22384176
Discovering dysfunction of multiple microRNAs cooperation in disease by a conserved microRNA co-expression network. PMID:22384175
Spliceman--a computational web server that predicts sequence variations in pre-mRNA splicing. PMID:22328782
Thousands of Novel Transcripts Identified in Mouse Cerebrum, Testis, and ES Cells Based on ribo-minus RNA Sequencing. PMID:22303387
R-SAP: a multi-threading computational pipeline for the characterization of high-throughput RNA-sequencing data. PMID:22287631
The combination of a genome-wide association study of lymphocyte count and analysis of gene expression data reveals novel asthma candidate genes. PMID:22286170
Genetic variation in GPX1 is associated with GPX1 activity in a comprehensive analysis of genetic variations in selenoenzyme genes and their activity and oxidative stress in humans. PMID:22259188
Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis. PMID:22203992
Phenotype-specific effect of chromosome 1q21.1 rearrangements and GJA5 duplications in 2436 congenital heart disease patients and 6760 controls. PMID:22199024
Polymorphic NumtS trace human population relationships. PMID:22160368
GenomeRunner: automating genome exploration. PMID:22155868
A systematic analysis on DNA methylation and the expression of both mRNA and microRNA in bladder cancer. PMID:22140553
Transcription factor binding sites are highly enriched within microRNA precursor sequences. PMID:22136256
Dr.VIS: a database of human disease-related viral integration sites. PMID:22135288
Distribution of a marker of germline methylation differs between major families of transposon-derived repeats in the human genome. PMID:22093876
Prediction of transposable element derived enhancers using chromatin modification profiles. PMID:22087331
Rigorous and thorough bioinformatic analyses of olfactory receptor promoters confirm enrichment of O/E and homeodomain binding sites but reveal no new common motifs. PMID:22085861
The UCSC Archaeal Genome Browser: 2012 update. PMID:22080555
Negative correlation between expression level and evolutionary rate of long intergenic noncoding RNAs. PMID:22071789
HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. PMID:22064851
Selection and optimization of asymmetric siRNA targeting the human c-MET gene. PMID:22058018
deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns. PMID:22053076
Identification of gene fusion transcripts by transcriptome sequencing in BRCA1-mutated breast cancers and cell lines. PMID:22032724
Exploratory analysis of genomic segmentations with Segtools. PMID:22029426
Characterization and potential functional significance of human-chimpanzee large INDEL variation. PMID:22024410
Very few RNA and DNA sequence differences in the human transcriptome. PMID:22022455
Establishing the baseline level of repetitive element expression in the human cortex. PMID:21985647
The UCSC Genome Browser. PMID:21975940
A comparative analysis of exome capture. PMID:21958622
Late replicating domains are highly recombining in females but have low male recombination rates: implications for isochore evolution. PMID:21949720
Alu pair exclusions in the human genome. PMID:21943335
Genome-wide prediction and analysis of human chromatin boundary elements. PMID:21930510
Protein-binding microarray analysis of tumor suppressor AP2α target gene specificity. PMID:21876733
Context-dependent individualization of nucleotides and virtual genomic hybridization allow the precise location of human SNPs. PMID:21876154
Learning Hidden Markov Models for Regression using Path Aggregation. PMID:21785575
Large-scale methylation domains mark a functional subset of neuronally expressed genes. PMID:21784875
Making whole genome multiple alignments usable for biologists. PMID:21775304
Evidence for post-transcriptional regulation of clustered microRNAs in Drosophila. PMID:21771325
High-throughput mapping of the promoters of the mouse olfactory receptor genes reveals a new type of mammalian promoter and provides insight into olfactory receptor gene regulation. PMID:21705439
Substitution rate variation at human CpG sites correlates with non-CpG divergence, methylation level and GC content. PMID:21696599
Small molecule amiloride modulates oncogenic RNA alternative splicing to devitalize human cancer cells. PMID:21694768
The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA. PMID:21690198
Predicting housekeeping genes based on Fourier analysis. PMID:21687628
Substitution patterns are GC-biased in divergent sequences across the metazoans. PMID:21670083
Genome-wide analysis reveals PADI4 cooperates with Elk-1 to activate c-Fos expression in breast cancer cells. PMID:21655091
Inferring transcription factor complexes from ChIP-seq data. PMID:21602262
Genome-wide RNA-seq analysis of human and mouse platelet transcriptomes. PMID:21596849
The first sequenced carnivore genome shows complex host-endogenous retrovirus relationships. PMID:21589882
Integrating diverse databases into an unified analysis framework: a Galaxy approach. PMID:21531983
A multiplex RNA-seq strategy to profile poly(A+) RNA: application to analysis of transcription response and 3' end formation. PMID:21515359
The sufficient minimal set of miRNA seed types. PMID:21441577
MicroRNA genes derived from repetitive elements and expanded by segmental duplication events in mammalian genomes. PMID:21436881
NAViGaTing the micronome--using multiple microRNA prediction databases to identify signalling pathway-associated microRNAs. PMID:21364759
Effect of the transposable element environment of human genes on gene length and expression. PMID:21362639
Annotating genes and genomes with DNA sequences extracted from biomedical articles. PMID:21325301
QDMR: a quantitative method for identification of differentially methylated regions by entropy. PMID:21306990
Signatures of murine B-cell development implicate Yy1 as a regulator of the germinal center-specific program. PMID:21282644
Genome-wide association analysis and fine mapping of NT-proBNP level provide novel insight into the role of the MTHFR-CLCN6-NPPA-NPPB gene cluster. PMID:21273288
Quantification of gene transcripts with deep sequencing analysis of gene expression (DSAGE) using 1 to 2 µg total RNA. PMID:21225638
SeqWare Query Engine: storing and searching sequence data in the cloud. PMID:21210981
Cohesin organizes chromatin loops at DNA replication factories. PMID:21159821
Sequence-dependent histone variant positioning signatures. PMID:21143812
Coordinated genome-wide modifications within proximal promoter cis-regulatory elements during vertebrate evolution. PMID:21118975
Origin and evolution of a placental-specific microRNA family in the human genome. PMID:21067568
Extensive recombination rate variation in the house mouse species complex inferred from genetic linkage maps. PMID:20978138
Detecting sequence polymorphisms associated with meiotic recombination hotspots in the human genome. PMID:20961408
The UCSC Genome Browser database: update 2011. PMID:20959295
Human microRNA oncogenes and tumor suppressors show significantly different biological patterns: from functions to targets. PMID:20927335
A Gibbs sampling strategy applied to the mapping of ambiguous short-sequence tags. PMID:20871106
MetMap enables genome-scale Methyltyping for determining methylation states in populations. PMID:20856582
mRNA degradation plays a significant role in the program of gene expression regulated by phosphatidylinositol 3-kinase signaling. PMID:20855526
Context dependent substitution biases vary within the human genome. PMID:20843365
Detection of functional overlapping genes: simulation and case studies. PMID:20820768
Efficient use of accessibility in microRNA target prediction. PMID:20805242
Genome architecture marked by retrotransposons modulates predisposition to DNA methylation in cancer. PMID:20716667
Chondro/osteoblastic and cardiovascular gene modulation in human artery smooth muscle cells that calcify in the presence of phosphate and calcitriol or paricalcitol. PMID:20665672
Integration and visualization of systems biology data in context of the genome. PMID:20642854
Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq. PMID:20617162
Identification of baboon microRNAs expressed in liver and lymphocytes. PMID:20594335
microRNA evolution in a human transcription factor and microRNA regulatory network. PMID:20584335
Alternative splicing is frequent during early embryonic development in mouse. PMID:20573213
Characteristics of transposable element exonization within human and mouse. PMID:20532223
Discovery of microRNAs and other small RNAs in solid tumors. PMID:20483914
A database and API for variation, dense genotyping and resequencing data. PMID:20459810
Adaptive Evolution Hotspots at the GC-Extremes of the Human Genome: Evidence for Two Functionally Distinct Pathways of Positive Selection. PMID:20454629
Dual-targeting siRNAs. PMID:20410240
PuTmiR: a database for extracting neighboring transcription factors of human microRNAs. PMID:20398296
Unconstrained mining of transcript data reveals increased alternative splicing complexity in the human transcriptome. PMID:20385588
Diversity in the glucose transporter-4 gene (SLC2A4) in humans reflects the action of natural selection along the old-world primates evolution. PMID:20352120
Conservation of neutral substitution rate and substitutional asymmetries in mammalian genes. PMID:20333222
Evidence that replication-associated mutation alone does not explain between-chromosome differences in substitution rates. PMID:20333173
Chromosomal position effects on AAV-mediated gene targeting. PMID:20185563
Endothelial cell processing and alternatively spliced transcripts of factor VIII: potential implications for coagulation cascades and pulmonary hypertension. PMID:20174619
Analysis of a normalised expressed sequence tag (EST) library from a key pollinator, the bumblebee Bombus terrestris. PMID:20156341
hAT transposable elements and their derivatives: an analysis in the 12 Drosophila genomes. PMID:20127503
Overlapping splicing regulatory motifs--combinatorial effects on splicing. PMID:20110253
Highly punctuated patterns of population structure on the X chromosome and implications for African evolutionary history. PMID:20085712
Galaxy: a web-based genome analysis tool for experimentalists. PMID:20069535
Genome-wide identification of hypoxia-inducible factor binding sites and target genes by a probabilistic model integrating transcription-profiling data and in silico binding site prediction. PMID:20061373
Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements. PMID:20008508
The UCSC Genome Browser. PMID:19957273
The UCSC Genome Browser database: update 2010. PMID:19906737
Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes. PMID:19906700
Screening for microsatellite instability identifies frequent 3'-untranslated region mutation of the RB1-inducible coiled-coil 1 gene in colon tumors. PMID:19888451
Hematopoietic immortalizing function of the NKL-subclass homeobox gene TLX1. PMID:19862821
CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes. PMID:19854943
A c-Myc regulatory subnetwork from human transposable element sequences. PMID:19763338
Human miRNA precursors with box H/ACA snoRNA features. PMID:19763159
Identifiability of isoform deconvolution from junction arrays and RNA-Seq. PMID:19762346
High resolution genome-wide analysis of chromosomal alterations in Burkitt's lymphoma. PMID:19759907
Relationship between estrogen receptor alpha location and gene induction reveals the importance of downstream sites and cofactors. PMID:19689805
H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions. PMID:19633671
Integration of genetic and genomic methods for identification of genes and gene variants encoding QTLs in the nonhuman primate. PMID:19596448
OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif. PMID:19583839
Patterns of oligonucleotide sequences in viral and host cell RNA identify mediators of the host innate immune system. PMID:19536338
Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships. PMID:19483094
Analyzing miRNA co-expression networks to explore TF-miRNA regulation. PMID:19476620
Noisy splicing, more than expression regulation, explains why some exons are subject to nonsense-mediated mRNA decay. PMID:19442261
Adaptive evolution of young gene duplicates in mammals. PMID:19411603
Repetitive DNA elements, nucleosome binding and human gene expression. PMID:19393174
The bovine lactation genome: insights into the evolution of mammalian milk. PMID:19393040
Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data. PMID:19390574
Profile analysis and prediction of tissue-specific CpG island methylation classes. PMID:19383127
Transcriptional features of genomic regulatory blocks. PMID:19374772
A robust linkage map of the porcine autosomes based on gene-associated SNPs. PMID:19327136
Localization of multiple pleiotropic genes for lipoprotein metabolism in baboons. PMID:19270339
Connections between ETV6-modulated genes: identification of shared features. PMID:19259410
A groupwise association test for rare mutations using a weighted sum statistic. PMID:19214210
Cepred: predicting the co-expression patterns of the human intronic microRNAs with their host genes. PMID:19204784
Understanding genome browsing. PMID:19204697
HapMap methylation-associated SNPs, markers of germline DNA methylation, positively correlate with regional levels of human meiotic recombination. PMID:19158364
Transcriptome sequencing to detect gene fusions in cancer. PMID:19136943
Upstream sequence elements direct post-transcriptional regulation of gene expression under stress conditions in yeast. PMID:19128476
Prediction of alternatively skipped exons and splicing enhancers from exon junction arrays. PMID:19021909
The UCSC Genome Browser Database: update 2009. PMID:18996895
PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. PMID:18981473
Numt-mediated double-strand break repair mitigates deletions during primate genome evolution. PMID:18949041
Advanced genomic data mining. PMID:18818719
A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence. PMID:18812516
Short tandem repeats in human exons: a target for disease mutations. PMID:18789129
Small deletion variants have stable breakpoints commonly associated with alu elements. PMID:18769679
Genome-wide occupancy of SREBP1 and its partners NFY and SP1 reveals novel functional roles and combinatorial regulation of distinct classes of genes. PMID:18654640
Structural conservation versus functional divergence of maternally expressed microRNAs in the Dlk1/Gtl2 imprinting region. PMID:18651963
Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster. PMID:18583644
In silico regulatory analysis for exploring human disease progression. PMID:18564415
Patterns of evolution and host gene mimicry in influenza and other RNA viruses. PMID:18535658
Standard and generalized McDonald-Kreitman test: a website to detect selection by comparing different classes of DNA sites. PMID:18515345
Classifying transcription factor targets and discovering relevant biological features. PMID:18513408
Evolutionary origin of regulatory regions of retrogenes in Drosophila. PMID:18498650
Predicting failure rate of PCR in large genomes. PMID:18492719
Highly conserved regimes of neighbor-base-dependent mutation generated the background primary-structural heterogeneities along vertebrate chromosomes. PMID:18478116
Confirming the phylogeny of mammals by use of large comparative sequence data sets. PMID:18453548
Two strategies for gene regulation by promoter nucleosomes. PMID:18448704
Using galaxy to perform large-scale interactive data analyses. PMID:18428782
eIF4GI links nutrient sensing by mTOR to cell proliferation and inhibition of autophagy. PMID:18426977
The human ABC transporter pseudogene family: Evidence for transcription and gene-pseudogene interference. PMID:18405356
HTLV-1 integration into transcriptionally active genomic regions is associated with proviral expression and with HAM/TSP. PMID:18369476
Characterization of new hAT transposable elements in 12 Drosophila genomes. PMID:18340538
A genome-wide screen for noncoding elements important in primate evolution. PMID:18215302
Alternative approach to a heavy weight problem. PMID:18096750
Genome-wide analysis reveals regulatory role of G4 DNA in gene transcription. PMID:18096746
The UCSC Genome Browser Database: 2008 update. PMID:18086701
Monoallelic expression of multiple genes in the CNS. PMID:18074017
Evaluating the protein coding potential of exonized transposable element sequences. PMID:18036258
RNA sequence analysis defines Dicer's role in mouse embryonic stem cells. PMID:17989215
TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates. PMID:17986453
28-way vertebrate alignment and conservation track in the UCSC Genome Browser. PMID:17984227
The full-ORF clone resource of the German cDNA Consortium. PMID:17974005
Fine-tuning enhancer models to predict transcriptional targets across multiple genomes. PMID:17973026
Evolution of Nova-dependent splicing regulation in the brain. PMID:17937501
Waves of genomic hitchhikers shed light on the evolution of gamebirds (Aves: Galliformes). PMID:17925025
Molecular targets of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) within the zebrafish ovary: insights into TCDD-induced endocrine disruption and reproductive toxicity. PMID:17884332
Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification. PMID:17686789
A periodic pattern of SNPs in the human genome. PMID:17673700
Use of tiling array data and RNA secondary structure predictions to identify noncoding RNA genes. PMID:17645787
Germ-line DNA copy number variation frequencies in a large North American population. PMID:17638019
Localizing recent adaptive evolution in the human genome. PMID:17542651
Origin and evolution of human microRNAs from transposable elements. PMID:17435244
Splicy: a web-based tool for the prediction of possible alternative splicing events from Affymetrix probeset data. PMID:17430561
A family of human microRNA genes from miniature inverted-repeat transposable elements. PMID:17301878
Evolution of motif variants and positional bias of the cyclic-AMP response element. PMID:17288573
Identifying synergistic regulation involving c-Myc and sp1 in human tissues. PMID:17264126
Automated querying of genome databases. PMID:17257048
MicroRNAs regulate the expression of the alternative splicing factor nPTB during muscle development. PMID:17210790
The ENCODE Project at UC Santa Cruz. PMID:17166863
Variation resources at UC Santa Cruz. PMID:17151077
A specialized learner for inferring structured cis-regulatory modules. PMID:17147812
The UCSC genome browser database: update 2007. PMID:17142222
Ancient genomic architecture for mammalian olfactory receptor clusters. PMID:17010214
Ultra-high resolution array painting facilitates breakpoint sequencing. PMID:16971479
In vivo requirement of the small subunit of U2AF for recognition of a weak 3' splice site. PMID:16940179
Transposable element derived DNaseI-hypersensitive sites in the human genome. PMID:16857058
CEAS: cis-regulatory element annotation system. PMID:16845068
Intronic alternative splicing regulators identified by comparative genomics in nematodes. PMID:16839192
Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses. PMID:16805923
MicroRNA enrichment among short 'ultraconserved' sequences in insects. PMID:16698958
Further understanding human disease genes by comparing with housekeeping genes and other genes. PMID:16504025
Comparison of human (and other) genome browsers. PMID:16460652
Foamy virus vector integration sites in normal human cells. PMID:16428288
The UCSC Genome Browser Database: update 2006. PMID:16381938
The UCSC Archaeal Genome Browser. PMID:16381898
L1 integration in a transgenic mouse model. PMID:16365384
Selective constraint on noncoding regions of hominid genomes. PMID:16362073
Modeling haplotype block variation using Markov chains. PMID:16361244
Analysis of concordance of different haplotype block partitioning algorithms. PMID:16356172
Hotspots of mutation and breakage in dog and human chromosomes. PMID:16339377
Sequence features in regions of weak and strong linkage disequilibrium. PMID:16251462
Galaxy: a platform for interactive large-scale genome analysis. PMID:16169926
Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences. PMID:16024817
Identification of coexpressed gene clusters in a comparative analysis of transcriptome and proteome in mouse tissues. PMID:15939889
Exploring relationships and mining data with the UCSC Gene Sorter. PMID:15867434
Promoter features related to tissue specificity as measured by Shannon entropy. PMID:15833120
HAGR: the Human Ageing Genomic Resources. PMID:15608256
RatMap--rat genome tools and data. PMID:15608244
The UCSC Proteome Browser. PMID:15608236
SPD--a web-based secreted protein database. PMID:15608170
An overview of Ensembl. PMID:15078858 -
The UCSC Genome Browser Database
PubMed citations: 736.
736 articles citing: The UCSC Genome Browser Database
The impact of rare germline variants on human somatic mutation processes. PMID:35764656
Pan-cancer pervasive upregulation of 3' UTR splicing drives tumourigenesis. PMID:35618746
i5hmCVec: Identifying 5-Hydroxymethylcytosine Sites of Drosophila RNA Using Sequence Feature Embeddings. PMID:35591855
A Reference Genome Assembly of Hybrid-Derived California Wild Radish (Raphanus sativus × raphanistrum). PMID:35575080
Alternative splicing modulation by G-quadruplexes. PMID:35504902
Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies in a consanguineous Iranian family is associated with a homozygous start loss variant in the PRUNE1 gene. PMID:35379233
Selective Cleavage at CCA Ends and Anticodon Loops of tRNAs by Stress-Induced RNases. PMID:35300117
Genetic variants associated mRNA stability in lung. PMID:35272635
Fusion Gene Detection Using Whole-Exome Sequencing Data in Cancer Patients. PMID:35251131
Bioinformatics pipeline to guide late-onset Alzheimer's disease (LOAD) post-GWAS studies: Prioritizing transcription regulatory variants within LOAD-associated regions. PMID:35229021
A Transfer-Learning-Based Deep Convolutional Neural Network for Predicting Leukemia-Related Phosphorylation Sites from Protein Primary Sequences. PMID:35163663
Identification and Characterization of TF-lncRNA Regulatory Networks Involved in the Tumorigenesis and Development of Adamantinomatous Craniopharyngioma. PMID:35155179
Protein disulfide isomerase A1‑associated pathways in the development of stratified breast cancer therapies. PMID:35014681
Origins and Function of VL30 lncRNA Packaging in Small Extracellular Vesicles: Implications for Cellular Physiology and Pathology. PMID:34829970
NF-κB modifies the mammalian circadian clock through interaction with the core clock protein BMAL1. PMID:34807912
Potential protective role of a NOD2 polymorphism in the susceptibility to multiple sclerosis is not associated with interferon therapy. PMID:34667597
Gosling: A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization. PMID:34596551
Association of grandmaternal smoking during pregnancy with DNA methylation of grandchildren: the Isle of Wight study. PMID:34596434
Multi-phenotype genome-wide association studies of the Norfolk Island isolate implicate pleiotropic loci involved in chronic kidney disease. PMID:34593906
Identification of Key Genes Mutations Associated With the Radiosensitivity by Whole Exome Sequencing in Pancreatic Cancer. PMID:34434896
Development of mammary cancer in γ-irradiated F1 hybrids of susceptible Sprague-Dawley and resistant Copenhagen rats, with copy-number losses that pinpoint potential tumor suppressors. PMID:34388197
Differential Regulation of Lacto-/Neolacto- Glycosphingolipid Biosynthesis Pathway Reveals Transcription Factors as Potential Candidates in Triple-Negative Breast Cancer. PMID:34283051
History of the methodology of disease gene identification. PMID:34159713
Bridging chromatin structure and function over a range of experimental spatial and temporal scales by molecular modeling. PMID:34046090
m6A RNA methylation of major satellite repeat transcripts facilitates chromatin association and RNA:DNA hybrid formation in mouse heterochromatin. PMID:33999208
Identification of a novel MICU1 nonsense variant causes myopathy with extrapyramidal signs in an Iranian consanguineous family. PMID:33969448
Novel manifestations of Warburg micro syndrome type 1 caused by a new splicing variant of RAB3GAP1: a case report. PMID:33910511
Prediction of single-cell mechanisms for disease progression in hypertrophic remodelling by a trans-omics approach. PMID:33854108
miR-132/212 Impairs Cardiomyocytes Contractility in the Failing Heart by Suppressing SERCA2a. PMID:33816571
Association of structural variation with cardiometabolic traits in Finns. PMID:33798444
G-quadruplexes originating from evolutionary conserved L1 elements interfere with neuronal gene expression in Alzheimer's disease. PMID:33758195
Preneoplastic Alterations Define CLL DNA Methylome and Persist through Disease Progression and Therapy. PMID:33604581
RIP-seq reveals LINE-1 ORF1p association with p-body enriched mRNAs. PMID:33563338
MicroExonator enables systematic discovery and quantification of microexons across mouse embryonic development. PMID:33482885
RNA-Seq Whole Transcriptome Analysis of Bovine Mammary Epithelial Cells in Response to Intracellular Staphylococcus aureus. PMID:33426011
Epigenomic Reprogramming toward Mesenchymal-Epithelial Transition in Ovarian-Cancer-Associated Mesenchymal Stem Cells Drives Metastasis. PMID:33296650
Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED. PMID:33257863
Novel homozygous variants in the TMC1 and CDH23 genes cause autosomal recessive nonsyndromic hearing loss. PMID:33205915
A High Quality Asian Genome Assembly Identifies Features of Common Missing Regions. PMID:33202901
LHX6 Affects Erlotinib Resistance and Migration of EGFR-Mutant Non-Small-Cell Lung Cancer HCC827 Cells Through Suppressing Wnt/β-Catenin Signaling. PMID:33149613
IndiGenomes: a comprehensive resource of genetic variants from over 1000 Indian genomes. PMID:33095885
Globally learning gene regulatory networks based on hidden atomic regulators from transcriptomic big data. PMID:33054712
Regulation of neuronal commitment in mouse embryonic stem cells by the Reno1/Bahcc1 locus. PMID:32969152
Bimodal function of chromatin remodeler Hmga1 in neural crest induction and Wnt-dependent emigration. PMID:32965216
Paternal DNA Methylation May Be Associated With Gestational Age at Birth. PMID:32964196
Multi-omics profiling reveals microRNA-mediated insulin signaling networks. PMID:32938376
Identifying Circular RNA and Predicting Its Regulatory Interactions by Machine Learning. PMID:32849764
Novel imaging and clinical phenotypes of CONDSIAS disorder caused by a homozygous frameshift variant of ADPRHL2: a case report. PMID:32746785
A non-pharmacological therapeutic approach in the gut triggers distal metabolic rewiring capable of ameliorating diet-induced dysfunctions encompassed by metabolic syndrome. PMID:32737396
Hypomethylation Causes MIR21 Overexpression in Tumors. PMID:32637580
The transcriptional signature associated with human motile cilia. PMID:32616903
Seq-ing answers: Current data integration approaches to uncover mechanisms of transcriptional regulation. PMID:32612756
Small Cell Carcinoma of the Ovary, Hypercalcemic Type (SCCOHT) beyond SMARCA4 Mutations: A Comprehensive Genomic Analysis. PMID:32575483
Dynamic TF-lncRNA Regulatory Networks Revealed Prognostic Signatures in the Development of Ovarian Cancer. PMID:32478062
Personalized and graph genomes reveal missing signal in epigenomic data. PMID:32450900
Reprogramming Axial Level Identity to Rescue Neural-Crest-Related Congenital Heart Defects. PMID:32369742
Transposable elements contribute to cell and species-specific chromatin looping and gene regulation in mammalian genomes. PMID:32286261
ADH7, miR-3065 and LINC01133 are associated with cervical cancer progression in different age groups. PMID:32194732
Genome-wide Association Analysis in Humans Links Nucleotide Metabolism to Leukocyte Telomere Length. PMID:32109421
Assembly of Mitochondrial Complex I Requires the Low-Complexity Protein AMC1 in Chlamydomonas reinhardtii. PMID:32075865
Screening of Prognostic Factors in Early-Onset Breast Cancer. PMID:32028860
Whole-exome sequencing identified a novel variant in an Iranian patient affected by pycnodysostosis. PMID:31944631
Evolution of the new head by gradual acquisition of neural crest regulatory circuits. PMID:31645763
Regional Gene Repression by DNA Double-Strand Breaks in G1 Phase Cells. PMID:31591143
Gene Regulatory Networks in Peripheral Mononuclear Cells Reveals Critical Regulatory Modules and Regulators of Multiple Sclerosis. PMID:31484947
An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi). PMID:31367745
Challenges in funding and developing genomic software: roots and remedies. PMID:31358028
Bioinformatics strategy to advance the interpretation of Alzheimer's disease GWAS discoveries: The roads from association to causation. PMID:31262699
Genome-wide RNA pol II initiation and pausing in neural progenitors of the rat. PMID:31185909
Epigenome-wide effects of vitamin D on asthma bronchial epithelial cells. PMID:31122150
A combination of transcription factors mediates inducible interchromosomal contacts. PMID:31081754
Transcriptome-wide identification and functional investigation of the RDR2- and DCL3-dependent small RNAs encoded by long non-coding RNAs in Arabidopsis thaliana. PMID:31081714
HPV73 a nonvaccine type causes cervical cancer. PMID:30963559
Mechanical stretch induces hair regeneration through the alternative activation of macrophages. PMID:30944305
EnDisease: a manually curated database for enhancer-disease associations. PMID:30788500
The radish genome database (RadishGD): an integrated information resource for radish genomics. PMID:30722041
Mesoscale modeling reveals formation of an epigenetically driven HOXC gene hub. PMID:30718394
Epigenetically modulated FOXM1 suppresses dendritic cell maturation in pancreatic cancer and colon cancer. PMID:30628173
RAEdb: a database of enhancers identified by high-throughput reporter assays. PMID:30624654
Genomes reveal marked differences in the adaptive evolution between orangutan species. PMID:30428903
RAiSD detects positive selection based on multiple signatures of a selective sweep and SNP vectors. PMID:30271960
ASXL1 impairs osteoclast formation by epigenetic regulation of NFATc1. PMID:30266822
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. PMID:30239679
CircRNAFisher: a systematic computational approach for de novo circular RNA identification. PMID:30013032
Stable and reproducible transgene expression independent of proliferative or differentiated state using BAC TG-EMBED. PMID:29930343
MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis. PMID:29927748
Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation. PMID:29884752
Set-Based Tests for the Gene-Environment Interaction in Longitudinal Studies. PMID:29780190
Ouroboros resembling competitive endogenous loop (ORCEL) in circular RNAs revealed through transcriptome sequencing dataset analysis. PMID:29764361
Genome-wide association study for bone strength in laying hens. PMID:29701819
PlantRNA_Sniffer: A SVM-Based Workflow to Predict Long Intergenic Non-Coding RNAs in Plants. PMID:29657283
Homo sapiens-Specific Binding Site Variants within Brain Exclusive Enhancers Are Subject to Accelerated Divergence across Human Population. PMID:29608725
Depletion of DNMT1 in differentiated human cells highlights key classes of sensitive genes and an interplay with polycomb repression. PMID:29598829
Decreased A-to-I RNA editing as a source of keratinocytes' dsRNA in psoriasis. PMID:29592874
iDREM: Interactive visualization of dynamic regulatory networks. PMID:29538379
OVAS: an open-source variant analysis suite with inheritance modelling. PMID:29422027
Mapping the Chromatin State Dynamics in Myoblasts. PMID:29376142
Enrichment analysis with EpiAnnotator. PMID:29329372
Systematic target function annotation of human transcription factors. PMID:29325558
Eukaryotic translational termination efficiency is influenced by the 3' nucleotides within the ribosomal mRNA channel. PMID:29325104
THiCweed: fast, sensitive detection of sequence features by clustering big datasets. PMID:29267972
MiRIAD update: using alternative polyadenylation, protein interaction network analysis and additional species to enhance exploration of the role of intragenic miRNAs and their host genes. PMID:29220447
Optimization of CRISPR/Cas9 genome editing for loss-of-function in the early chick embryo. PMID:29150011
Identification of islet-enriched long non-coding RNAs contributing to β-cell failure in type 2 diabetes. PMID:29107288
Lumbosacral stenosis in Labrador retriever military working dogs - an exomic exploratory study. PMID:29085643
Framework and resource for more than 11,000 gene-transcript-protein-reaction associations in human metabolism. PMID:29078384
Biological function integrated prediction of severe radiographic progression in rheumatoid arthritis: a nested case control study. PMID:29065906
Integrating networks and comparative genomics reveals retroelement proliferation dynamics in hominid genomes. PMID:29043294
CSCD: a database for cancer-specific circular RNAs. PMID:29036403
A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action. PMID:29036168
Prognostic cancer gene signatures share common regulatory motifs. PMID:28684851
Genetic variability of the activity of bidirectional promoters: a pilot study in bovine muscle. PMID:28338730
Identifying key genes associated with Hirschsprung's disease based on bioinformatics analysis of RNA-sequencing data. PMID:28120235
TCGA2BED: extracting, extending, integrating, and querying The Cancer Genome Atlas. PMID:28049410
Tools for Sequence-Based miRNA Target Prediction: What to Choose? PMID:27941681
Identification of key genes induced by platelet-rich plasma in human dermal papilla cells using bioinformatics methods. PMID:27922680
Extensive RNA editing and splicing increase immune self-representation diversity in medullary thymic epithelial cells. PMID:27776542
Evolutionary Analyses of Hanwoo (Korean Cattle)-Specific Single-Nucleotide Polymorphisms and Genes Using Whole-Genome Resequencing Data of a Hanwoo Population. PMID:27640093
Determining the Effect of Natural Selection on Linked Neutral Divergence across Species. PMID:27508305
Comparative Transcriptome Analysis Reveals Substantial Tissue Specificity in Human Aortic Valve. PMID:27493474
Wiz binds active promoters and CTCF-binding sites and is required for normal behaviour in the mouse. PMID:27410475
Y-Chromosome Structural Diversity in the Bonobo and Chimpanzee Lineages. PMID:27358426
Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis. PMID:27309962
Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research. PMID:27297499
Design of pathway preferential estrogens that provide beneficial metabolic and vascular effects without stimulating reproductive tissues. PMID:27221711
tRF2Cancer: A web server to detect tRNA-derived small RNA fragments (tRFs) and their expression in multiple cancers. PMID:27179031
Brucella melitensis and Mycobacterium tuberculosis depict overlapping gene expression patterns induced in infected THP-1 macrophages. PMID:27175205
Xenopus genomic data and browser resources. PMID:27039265
Comparative assessment of methods for the fusion transcripts detection from RNA-Seq data. PMID:26862001
UCSC Data Integrator and Variant Annotation Integrator. PMID:26740527
Loss of serum response factor induces microRNA-mediated apoptosis in intestinal smooth muscle cells. PMID:26633717
Pooled Sequencing of Candidate Genes Implicates Rare Variants in the Development of Asthma Following Severe RSV Bronchiolitis in Infancy. PMID:26587832
DNA Editing of LTR Retrotransposons Reveals the Impact of APOBECs on Vertebrate Genomes. PMID:26541172
Role of microRNAs in the age-associated decline of pancreatic beta cell function in rat islets. PMID:26474776
Mouse superkiller-2-like helicase DDX60 is dispensable for type I IFN induction and immunity to multiple viruses. PMID:26457795
Evaluation of whole-genome sequencing of four Chinese crested dogs for variant detection using the ion proton system. PMID:26457193
MeSiC: A Model-Based Method for Estimating 5 mC Levels at Single-CpG Resolution from MeDIP-seq. PMID:26424089
Epiviz: a view inside the design of an integrated visual analysis software for genomics. PMID:26328750
Male and female mice show significant differences in hepatic transcriptomic response to 2,3,7,8-tetrachlorodibenzo-p-dioxin. PMID:26290441
Reporter Gene Silencing in Targeted Mouse Mutants Is Associated with Promoter CpG Island Methylation. PMID:26275310
TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets. PMID:26206304
Differential and coherent processing patterns from small RNAs. PMID:26166713
Chemorepulsion from the Quorum Signal Autoinducer-2 Promotes Helicobacter pylori Biofilm Dispersal. PMID:26152582
An integrated approach to reveal miRNAs' impacts on the functional consequence of copy number alterations in cancer. PMID:26099552
Collembolan Transcriptomes Highlight Molecular Evolution of Hexapods and Provide Clues on the Adaptation to Terrestrial Life. PMID:26075903
Identification of Owl Monkey CD4 Receptors Broadly Compatible with Early-Stage HIV-1 Isolates. PMID:26063421
From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data. PMID:25902288
Low levels of IGFBP7 expression in high-grade serous ovarian carcinoma is associated with patient outcome. PMID:25886299
GASS: genome structural annotation for Eukaryotes based on species similarity. PMID:25764973
Integrative analysis of 111 reference human epigenomes. PMID:25693563
Identifying mutation specific cancer pathways using a structurally resolved protein interaction network. PMID:25592571
Setting up a wide panel of patient-derived tumor xenografts of non-small cell lung cancer by improving the preanalytical steps. PMID:25470237
Cross-species transcriptomic analysis elucidates constitutive aryl hydrocarbon receptor activity. PMID:25467400
Prediction of MicroRNA Precursors Using Parsimonious Feature Sets. PMID:25392687
Master regulators, regulatory networks, and pathways of glioblastoma subtypes. PMID:25368508
Transcriptomic analysis identifies gene networks regulated by estrogen receptor α (ERα) and ERβ that control distinct effects of different botanical estrogens. PMID:25363786
Genetic influences on translation in yeast. PMID:25340754
CREB modulates calcium signaling in cAMP-induced bone marrow stromal cells (BMSCs). PMID:25154887
IRBIS: a systematic search for conserved complementarity. PMID:25142064
Genome-wide association study combined with biological context can reveal more disease-related SNPs altering microRNA target seed sites. PMID:25106527
Identifying microRNA targets in different gene regions. PMID:25077573
SNP@lincTFBS: an integrated database of polymorphisms in human LincRNA transcription factor binding sites. PMID:25075616
piRNAQuest: searching the piRNAome for silencers. PMID:24997126
Genomic landscape of human, bat, and ex vivo DNA transposon integrations. PMID:24809961
Expression data analysis to identify biomarkers associated with asthma in children. PMID:24790987
RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE). PMID:24779366
Semantic Modeling for SNPs Associated with Ethnic Disparities in HapMap Samples. PMID:24748859
Transcriptional regulation of YWHAZ, the gene encoding 14-3-3ζ. PMID:24690670
Insight into insulin secretion from transcriptome and genetic analysis of insulin-producing cells of Drosophila. PMID:24558258
Construction of pancreatic cancer double-factor regulatory network based on chip data on the transcriptional level. PMID:24469724
A systems' biology approach to study microRNA-mediated gene regulatory networks. PMID:24350286
Wolbachia variants induce differential protection to viruses in Drosophila melanogaster: a phenotypic and phylogenomic analysis. PMID:24348259
Differential inhibition of LINE1 and LINE2 retrotransposition by vertebrate AID/APOBEC proteins. PMID:24344916
Evolutionary rate patterns of genes involved in the Drosophila Toll and Imd signaling pathway. PMID:24209511
Tissue-specific differences in the regulation of KIBRA gene expression involve transcription factor TCF7L2 and a complex alternative promoter system. PMID:24072042
Systematic pharmacogenomics analysis of a Malay whole genome: proof of concept for personalized medicine. PMID:24009664
Dynamic expression of 3' UTRs revealed by Poisson hidden Markov modeling of RNA-Seq: implications in gene expression profiling. PMID:23845781
Rate-limiting steps in yeast protein translation. PMID:23791185
Estrogen regulation of microRNAs, target genes, and microRNA expression associated with vitellogenesis in the zebrafish. PMID:23767875
Next-generation sequencing of paired tyrosine kinase inhibitor-sensitive and -resistant EGFR mutant lung cancer cell lines identifies spectrum of DNA changes associated with drug resistance. PMID:23733853
The role of retrotransposons in gene family expansions: insights from the mouse Abp gene family. PMID:23718880
CD34(+) expansion with Delta-1 and HOXB4 promotes rapid engraftment and transfusion independence in a Macaca nemestrina cord blood transplant model. PMID:23587923
Overexpressing the CCL2 chemokine in an epithelial ovarian cancer cell line results in latency of in vivo tumourigenicity. PMID:23552840
A global map for dissecting phenotypic variants in human lincRNAs. PMID:23463026
Signaling between transforming growth factor β (TGF-β) and transcription factor SNAI2 represses expression of microRNA miR-203 to promote epithelial-mesenchymal transition and tumor metastasis. PMID:23447531
VGLL3 expression is associated with a tumor suppressor phenotype in epithelial ovarian cancer. PMID:23415753
CpGIMethPred: computational model for predicting methylation status of CpG islands in human genome. PMID:23369266
JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison. PMID:23324080
Inhibition of the Pim1 oncogene results in diminished visual function. PMID:23300608
The limits of de novo DNA motif discovery. PMID:23144830
Stem cell selection in vivo using foamy vectors cures canine pyruvate kinase deficiency. PMID:23028826
SP transcription factor paralogs and DNA-binding sites coevolve and adaptively converge in mammals and birds. PMID:23019068
Linking the DNA strand asymmetry to the spatio-temporal replication program. I. About the role of the replication fork polarity in genome evolution. PMID:23001787
ggbio: an R package for extending the grammar of graphics for genomic data. PMID:22937822
Cell-type specificity of ChIP-predicted transcription factor binding sites. PMID:22863112
An integrated regulatory network reveals pervasive cross-regulation among transcription and splicing factors. PMID:22844237
Computational analysis of target hub gene repression regulated by multiple and cooperative miRNAs. PMID:22798498
TAPDANCE: an automated tool to identify and annotate transposon insertion CISs and associations between CISs from next generation sequence data. PMID:22748055
Using Galaxy to perform large-scale interactive data analyses. PMID:22700312
Genomic variation in natural populations of Drosophila melanogaster. PMID:22673804
Savant Genome Browser 2: visualization and analysis for population-scale genomics. PMID:22638571
Evolution of a tissue-specific silencer underlies divergence in the expression of pax2 and pax8 paralogues. PMID:22617288
Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters. PMID:22609971
Novel association approach for variable number tandem repeats (VNTRs) identifies DOCK5 as a susceptibility gene for severe obesity. PMID:22595969
Extended survival of glioblastoma patients after chemoprotective HSC gene therapy. PMID:22572881
Detection of gene expression changes at chromosomal rearrangement breakpoints in evolution. PMID:22536904
Severe combined immunodeficiency (SCID): from the detection of a new mutation to preimplantation genetic diagnosis. PMID:22527898
Identification of Wnt/β-catenin modulated genes in the developing retina. PMID:22509096
Case-control admixture mapping in Latino populations enriches for known asthma-associated genes. PMID:22502797
Spatial proximity and similarity of the epigenetic state of genome domains. PMID:22496774
Replication fork polarity gradients revealed by megabase-sized U-shaped replication timing domains in human cell lines. PMID:22496629
Bidirectional regulation between WDR83 and its natural antisense transcript DHPS in gastric cancer. PMID:22491477
Meta-analyses of genome-wide linkage scans of anxiety-related phenotypes. PMID:22473089
A genome-wide analysis of common fragile sites: what features determine chromosomal instability in the human genome? PMID:22456607
Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans. PMID:22439699
Integrated sequence-structure motifs suffice to identify microRNA precursors. PMID:22438883
Microcephaly, intellectual impairment, bilateral vesicoureteral reflux, distichiasis, and glomuvenous malformations associated with a 16q24.3 contiguous gene deletion and a Glomulin mutation. PMID:22407726
U12-type spliceosomal introns of Insecta. PMID:22393306
Combined chromatin and expression analysis reveals specific regulatory mechanisms within cytokine genes in the macrophage early immune response. PMID:22384210
Expression profiling of uterine leiomyomata cytogenetic subgroups reveals distinct signatures in matched myometrium: transcriptional profilingof the t(12;14) and evidence in support of predisposing genetic heterogeneity. PMID:22343407
Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data. PMID:22329341
Resequencing candidate genes implicates rare variants in asthma susceptibility. PMID:22325360
Knowledge-based reconstruction of mRNA transcripts with short sequencing reads for transcriptome research. PMID:22312447
HIV-1 capsid-targeting domain of cleavage and polyadenylation specificity factor 6. PMID:22301135
VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. PMID:22300766
Evolution and function of CAG/polyglutamine repeats in protein-protein interaction networks. PMID:22287626
Estimation of correlations between copy-number variants in non-coding DNA. PMID:22255599
Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs. PMID:22227116
ABrowse--a customizable next-generation genome browser framework. PMID:22222089
Comprehensive gene-based association study of a chromosome 20 linked region implicates novel risk loci for depressive symptoms in psychotic illness. PMID:22220189
Evidence for sequential and increasing activation of replication origins along replication timing gradients in the human genome. PMID:22219720
Methods, challenges, and promise of next-generation sequencing in cancer biology. PMID:22180681
Hematopoietic stem cell expansion facilitates multilineage engraftment in a nonhuman primate cord blood transplantation model. PMID:22155723
Evidence for widespread association of mammalian splicing and conserved long-range RNA structures. PMID:22128342
Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements. PMID:22115494
De novo origin of human protein-coding genes. PMID:22102831
Prediction of transposable element derived enhancers using chromatin modification profiles. PMID:22087331
Human tRNA genes function as chromatin insulators. PMID:22085927
Characterization and potential functional significance of human-chimpanzee large INDEL variation. PMID:22024410
The UCSC Genome Browser. PMID:21975940
Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons. PMID:21974994
Chronic virus infection enforces demethylation of the locus that encodes PD-1 in antigen-specific CD8(+) T cells. PMID:21943489
Visualization and exploration of conserved regulatory modules using ReXSpecies 2. PMID:21942985
Genome-wide prediction and analysis of human chromatin boundary elements. PMID:21930510
Podbat: a novel genomic tool reveals Swr1-independent H2A.Z incorporation at gene coding sequences through epigenetic meta-analysis. PMID:21901086
The NFI-Regulome Database: A tool for annotation and analysis of control regions of genes regulated by Nuclear Factor I transcription factors. PMID:21884625
The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details. PMID:21856757
Tight associations between transcription promoter type and epigenetic variation in histone positioning and modification. PMID:21846408
A boundary element between Tsix and Xist binds the chromatin insulator Ctcf and contributes to initiation of X-chromosome inactivation. PMID:21840866
mRNA levels in control rat liver display strain-specific, hereditary, and AHR-dependent components. PMID:21760882
S3QL: a distributed domain specific language for controlled semantic integration of life sciences data. PMID:21756325
MicroRNA genes preferentially expressed in dendritic cells contain sites for conserved transcription factor binding motifs in their promoters. PMID:21708028
Long conserved fragments upstream of Mammalian polyadenylation sites. PMID:21705472
Three tiers of genome evolution in reptiles. PMID:21669810
Identification of novel targets of CSL-dependent Notch signaling in hematopoiesis. PMID:21637838
ComB: SNP calling and mapping analysis for color and nucleotide space platforms. PMID:21563978
A ChIP-Seq benchmark shows that sequence conservation mainly improves detection of strong transcription factor binding sites. PMID:21533218
c-Myc regulates RNA splicing of the A-Raf kinase and its activation of the ERK pathway. PMID:21512137
OryzaPG-DB: rice proteome database based on shotgun proteogenomics. PMID:21486466
H3 lysine 4 is acetylated at active gene promoters and is regulated by H3 lysine 4 methylation. PMID:21483810
Rice-Map: a new-generation rice genome browser. PMID:21450055
Motif-guided sparse decomposition of gene expression data for regulatory module identification. PMID:21426557
Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. PMID:21412275
Correlated evolution of nearby residues in Drosophilid proteins. PMID:21383965
C/EBPβ regulates dexamethasone-induced muscle cell atrophy and expression of atrogin-1 and MuRF1. PMID:21381078
RNA-seq analysis of gene expression and alternative splicing by double-random priming strategy. PMID:21365495
Bioinformatic detection of E47, E2F1 and SREBP1 transcription factors as potential regulators of genes associated to acquisition of endometrial receptivity. PMID:21272326
Genetic variations within the ERE motif modulate plasticity and energetics of binding of DNA to the ERα nuclear receptor. PMID:21216218
A novel HMM-based method for detecting enriched transcription factor binding sites reveals RUNX3 as a potential target in pancreatic cancer biology. PMID:21203558
The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment. PMID:21172049
RepTar: a database of predicted cellular targets of host and viral miRNAs. PMID:21149264
Preimplantation genetic diagnosis (PGD) for SHOX-related haploinsufficiency in conjunction with trisomy 21 detection by molecular analysis. PMID:21120598
Enrichment of ultraconserved elements among genomic imbalances causing mental delay and congenital anomalies. PMID:21092253
Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs. PMID:21085120
Expanded CTG repeat demarcates a boundary for abnormal CpG methylation in myotonic dystrophy patient tissues. PMID:21044947
The UCSC Genome Browser database: update 2011. PMID:20959295
Expression proteomics of UPF1 knockdown in HeLa cells reveals autoregulation of hnRNP A2/B1 mediated by alternative splicing resulting in nonsense-mediated mRNA decay. PMID:20946641
Expression profiling in canine osteosarcoma: identification of biomarkers and pathways associated with outcome. PMID:20860831
Genome rearrangements detected by SNP microarrays in individuals with intellectual disability referred with possible Williams syndrome. PMID:20824207
An approach based on a genome-wide association study reveals candidate loci for narcolepsy. PMID:20677014
Large-scale analysis of structural, sequence and thermodynamic characteristics of A-to-I RNA editing sites in human Alu repeats. PMID:20667096
Tissue-specific regulatory regions of the PTH gene localized by novel chromosome 11 rearrangement breakpoints in a parathyroid adenoma. PMID:20641034
Quantitative gene expression profiles in real time from expressed sequence tag databases. PMID:20635574
Annotating non-coding regions of the genome. PMID:20628352
Characterization of the apoptotic response of human leukemia cells to organosulfur compounds. PMID:20598143
Identification of baboon microRNAs expressed in liver and lymphocytes. PMID:20594335
Downregulation of homologous recombination DNA repair genes by HDAC inhibition in prostate cancer is mediated through the E2F1 transcription factor. PMID:20585447
Deep sequencing of human nuclear and cytoplasmic small RNAs reveals an unexpectedly complex subcellular distribution of miRNAs and tRNA 3' trailers. PMID:20498841
TassDB2 - A comprehensive database of subtle alternative splicing events. PMID:20429909
Contrasts between adaptive coding and noncoding changes during human evolution. PMID:20385805
The comparison of different pre- and post-analysis filters for determination of exon-level alternative splicing events using Affymetrix arrays. PMID:20357982
Detection of novel 3' untranslated region extensions with 3' expression microarrays. PMID:20346121
Conservation of human microsatellites across 450 million years of evolution. PMID:20333231
Both noncoding and protein-coding RNAs contribute to gene expression evolution in the primate brain. PMID:20333225
The mechanism of expansion and the volatility it created in three pheromone gene clusters in the mouse (Mus musculus) genome. PMID:20333217
Locus-specific decoupling of base composition evolution at synonymous sites and introns along the Drosophila melanogaster and Drosophila sechellia lineages. PMID:20333178
Coregulation mapping based on individual phenotypic variation in response to virus infection. PMID:20298589
Bioinformatic tools for identifying disease gene and SNP candidates. PMID:20238089
Epigenetic histone modifications of human transposable elements: genome defense versus exaptation. PMID:20226072
Trinucleotide repeats in human genome and exome. PMID:20215431
Integrative meta-analysis of differential gene expression in acute myeloid leukemia. PMID:20209125
Notch and delta mRNAs in early-stage and mid-stage drosophila embryos exhibit complementary patterns of protein-producing potentials. PMID:20201103
Analysis of deep sequencing microRNA expression profile from human embryonic stem cells derived mesenchymal stem cells reveals possible role of let-7 microRNA family in downstream targeting of hepatic nuclear factor 4 alpha. PMID:20158877
S-phase progression in mammalian cells: modelling the influence of nuclear organization. PMID:20155315
hAT transposable elements and their derivatives: an analysis in the 12 Drosophila genomes. PMID:20127503
SOX2 is an oncogene activated by recurrent 3q26.3 amplifications in human lung squamous cell carcinomas. PMID:20126410
Predicting microRNA precursors with a generalized Gaussian components based density estimation algorithm. PMID:20122227
Human variation in short regions predisposed to deep evolutionary conservation. PMID:20093432
Association between genes on chromosome 4p16 and non-syndromic oral clefts in four populations. PMID:20087401
Conservation and regulatory associations of a wide affinity range of mouse transcription factor binding sites. PMID:20079828
Identification of condition-specific regulatory modules through multi-level motif and mRNA expression analysis. PMID:20054984
A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins. PMID:20047656
Regulatory divergence of the duplicated chromosomal loci sox11a/b by subpartitioning and sequence evolution of enhancers in zebrafish. PMID:20039180
Predicting functional alternative splicing by measuring RNA selection pressure from multigenome alignments. PMID:20019791
The histone variant macroH2A1 marks repressed autosomal chromatin, but protects a subset of its target genes from silencing. PMID:20008927
The UCSC Genome Browser. PMID:19957273
Fine-scale phylogenetic discordance across the house mouse genome. PMID:19936022
The UCSC Genome Browser database: update 2010. PMID:19906737
Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site. PMID:19906316
iTriplet, a rule-based nucleic acid sequence motif finder. PMID:19874606
Comprehensive gene and microRNA expression profiling reveals a role for microRNAs in human liver development. PMID:19841744
A modified sleeping beauty transposon system that can be used to model a wide variety of human cancers in mice. PMID:19808965
Dioxin-dependent and dioxin-independent gene batteries: comparison of liver and kidney in AHR-null mice. PMID:19759094
Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. PMID:19741643
Exhaustive search for over-represented DNA sequence motifs with CisFinder. PMID:19740934
Preimplantation genetic diagnosis (PGD) for nonsyndromic deafness by polar body and blastomere biopsy. PMID:19728075
Gastric Cancer (Biomarkers) Knowledgebase (GCBKB): A Curated and Fully Integrated Knowledgebase of Putative Biomarkers Related to Gastric Cancer. PMID:19690644
Open chromatin encoded in DNA sequence is the signature of 'master' replication origins in human cells. PMID:19671527
Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence. PMID:19662163
IGF-I activates the mouse type IIb myosin heavy chain gene. PMID:19657059
Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation. PMID:19630943
The disruptive positions in human G-quadruplex motifs are less polymorphic and more conserved than their neutral counterparts. PMID:19617376
Identifying the molecular signature of the interstitial deletion 7q subgroup of uterine leiomyomata using a paired analysis. PMID:19603527
Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation. PMID:19578405
Genome desertification in eutherians: can gene deserts explain the uneven distribution of genes in placental mammalian genomes? PMID:19568804
Genetic association study of endothelin-1 and its receptors EDNRA and EDNRB in migraine with aura. PMID:19558538
Increased microRNA activity in human cancers. PMID:19557174
Patterns of oligonucleotide sequences in viral and host cell RNA identify mediators of the host innate immune system. PMID:19536338
Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencing. PMID:19508715
A deletion of the HBII-85 class of small nucleolar RNAs (snoRNAs) is associated with hyperphagia, obesity and hypogonadism. PMID:19498035
Development of an integrative database with 499 novel microsatellite markers for Macaca fascicularis. PMID:19497132
Modulation of alternative splicing by long-range RNA structures in Drosophila. PMID:19465384
SEPT9 gene sequencing analysis reveals recurrent mutations in hereditary neuralgic amyotrophy. PMID:19451530
Apollo: a community resource for genome annotation editing. PMID:19439563
Weak preservation of local neutral substitution rates across mammalian genomes. PMID:19416516
Patterns of insertion and deletion in Mammalian genomes. PMID:19412437
A general integrative genomic feature transcription factor binding site prediction method applied to analysis of USF1 binding in cardiovascular disease. PMID:19403457
Evidence of maternal QTL affecting growth and obesity in adult mice. PMID:19399551
Repetitive DNA elements, nucleosome binding and human gene expression. PMID:19393174
Analysis of the complement and molecular evolution of tRNA genes in cow. PMID:19393063
Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans. PMID:19372376
Evolution of alternative and constitutive regions of mammalian 5'UTRs. PMID:19371439
Inherent signals in sequencing-based Chromatin-ImmunoPrecipitation control libraries. PMID:19367334
Regulation of p110delta PI 3-kinase gene expression. PMID:19357769
A robust linkage map of the porcine autosomes based on gene-associated SNPs. PMID:19327136
Molecular evolution and functional diversification of fatty acid desaturases after recurrent gene duplication in Drosophila. PMID:19307313
Using ChIP-chip and ChIP-seq to study the regulation of gene expression: genome-wide localization studies reveal widespread regulation of transcription elongation. PMID:19275938
Gene targeting in mouse embryonic stem cells. PMID:19266325
Prediction and verification of mouse tRNA gene families. PMID:19246989
Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes. PMID:19246569
Atypical X-chromosome inactivation in an X;1 translocation patient demonstrating Xq28 functional disomy. PMID:19215059
Yin yang 1 modulates taxane response in epithelial ovarian cancer. PMID:19208743
ACC2 is expressed at high levels in human white adipose and has an isoform with a novel N-terminus [corrected]. PMID:19190759
Genetics of Sex-linked yellow in the Syrian hamster. PMID:19189957
Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements. PMID:19168912
Evolution of regulatory sequences in 12 Drosophila species. PMID:19132088
Complex organizational structure of the genome revealed by genome-wide analysis of single and alternative promoters in Drosophila melanogaster. PMID:19128496
Mismatch oligonucleotides in human and yeast: guidelines for probe design on tiling microarrays. PMID:19117516
Global expression profiling in atopic eczema reveals reciprocal expression of inflammatory and lipid genes. PMID:19107207
Using a kernel density estimation based classifier to predict species-specific microRNA precursors. PMID:19091019
Determination of tag density required for digital transcriptome analysis: application to an androgen-sensitive prostate cancer model. PMID:19088194
Ultraconserved elements in the Olig2 promoter. PMID:19079603
Hypermutable non-synonymous sites are under stronger negative selection. PMID:19043566
The HuRef Browser: a web resource for individual human genomics. PMID:19036787
Butyrate and vitamin D3 induce transcriptional attenuation at the cyclin D1 locus in colonic carcinoma cells. PMID:19034928
Does selection against transcriptional interference shape retroelement-free regions in mammalian genomes? PMID:19018283
MotifMap: a human genome-wide map of candidate regulatory motif sites. PMID:19017655
Induction of PPM1D following DNA-damaging treatments through a conserved p53 response element coincides with a shift in the use of transcription initiation sites. PMID:19015127
Non-coding RNAs revealed during identification of genes involved in chicken immune responses. PMID:19009289
Marine organism cell biology and regulatory sequence discoveryin comparative functional genomics. PMID:19003267
The UCSC Genome Browser Database: update 2009. PMID:18996895
CompMoby: comparative MobyDick for detection of cis-regulatory motifs. PMID:18950538
Domain-specific regulation of foxP2 CNS expression by lef1. PMID:18950487
Optimization of experimental design parameters for high-throughput chromatin immunoprecipitation studies. PMID:18940864
An analysis of human microRNA and disease associations. PMID:18923704
Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. PMID:18923076
Knowledge-guided multi-scale independent component analysis for biomarker identification. PMID:18837990
Transcription factor and microRNA regulation in androgen-dependent and -independent prostate cancer cells. PMID:18831788
Lentiviral integration preferences in transgenic mice. PMID:18821598
A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence. PMID:18812516
Transcriptomic responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in liver: comparison of rat and mouse. PMID:18796159
Increased cyclin D1 expression can mediate BRAF inhibitor resistance in BRAF V600E-mutated melanomas. PMID:18790768
Copy number variation and evolution in humans and chimpanzees. PMID:18775914
Small deletion variants have stable breakpoints commonly associated with alu elements. PMID:18769679
Self containment, a property of modular RNA structures, distinguishes microRNAs. PMID:18725951
A human genome-wide library of local phylogeny predictions for whole-genome inference problems. PMID:18710563
Selective constraints in experimentally defined primate regulatory regions. PMID:18704158
A conserved E2F6-binding element in murine meiosis-specific gene promoters. PMID:18667754
A core paired-type and POU homeodomain-containing transcription factor program drives retinal bipolar cell gene expression. PMID:18667607
Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation. PMID:18653530
Phylogenetic analyses suggest multiple changes of substrate specificity within the glycosyl hydrolase 20 family. PMID:18647384
Ribosomal mutations cause p53-mediated dark skin and pleiotropic effects. PMID:18641651
Myc oncogene-induced genomic instability: DNA palindromes in bursal lymphomagenesis. PMID:18636108
MicroRNA regulation and the variability of human cortical gene expression. PMID:18617573
Asymmetric histone modifications between the original and derived loci of human segmental duplications. PMID:18598352
Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster. PMID:18583644
In silico regulatory analysis for exploring human disease progression. PMID:18564415
On the origin of new genes in Drosophila. PMID:18550802
Patterns of evolution and host gene mimicry in influenza and other RNA viruses. PMID:18535658
The evolution of the DLK1-DIO3 imprinted domain in mammals. PMID:18532878
Complex management of a patient with a contiguous Xp11.4 gene deletion involving ornithine transcarbamylase: a role for detailed molecular analysis in complex presentations of classical diseases. PMID:18524659
Genome-wide survey of allele-specific splicing in humans. PMID:18518984
Uprobe 2008: an online resource for universal overgo hybridization-based probe retrieval and design. PMID:18515352
Classifying transcription factor targets and discovering relevant biological features. PMID:18513408
Highly conserved regimes of neighbor-base-dependent mutation generated the background primary-structural heterogeneities along vertebrate chromosomes. PMID:18478116
A transcriptional enhancer from the coding region of ADAMTS5. PMID:18478108
A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. PMID:18469162
The multiplicity problem in linkage analysis of gene expression data - the power of differentiating cis- and trans-acting regulators. PMID:18466486
A novel Bayesian DNA motif comparison method for clustering and retrieval. PMID:18463706
Human-macaque comparisons illuminate variation in neutral substitution rates. PMID:18447906
Genomewide recruitment analysis of Rpb4, a subunit of polymerase II in Saccharomyces cerevisiae, reveals its involvement in transcription elongation. PMID:18441121
Using galaxy to perform large-scale interactive data analyses. PMID:18428782
ReXSpecies--a tool for the analysis of the evolution of gene regulation across species. PMID:18410675
Local conservation scores without a priori assumptions on neutral substitution rates. PMID:18405366
Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer. PMID:18404202
Molecular and cytogenetic characterization of plexiform leiomyomata provide further evidence for genetic heterogeneity underlying uterine fibroids. PMID:18403592
Fast evolution of core promoters in primate genomes. PMID:18367463
Identification of transcription factor and microRNA binding sites in responsible to fetal alcohol syndrome. PMID:18366608
Integrative genome-wide expression analysis bears evidence of estrogen receptor-independent transcription in heregulin-stimulated MCF-7 cells. PMID:18350142
Characterization of new hAT transposable elements in 12 Drosophila genomes. PMID:18340538
Acetylcholinesterase expression in muscle is specifically controlled by a promoter-selective enhancesome in the first intron. PMID:18322091
Negative-feedback regulation of FGF signalling by DUSP6/MKP-3 is driven by ERK1/2 and mediated by Ets factor binding to a conserved site within the DUSP6/MKP-3 gene promoter. PMID:18321244
Complex microsatellite dynamics in the myostatin gene within ruminants. PMID:18320259
Proportionally more deleterious genetic variation in European than in African populations. PMID:18288194
Predicted functional RNAs within coding regions constrain evolutionary rates of yeast proteins. PMID:18270559
Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees. PMID:18269696
Commonality of functional annotation: a method for prioritization of candidate genes from genome-wide linkage studies. PMID:18263617
Systematic functional characterization of cis-regulatory motifs in human core promoters.