The UCSC Archaeal Genome Browser
Names
More detailed information about this field from each metasource.
The UCSC Archaeal Genome Browser
metasource: Fairsharing.org
version: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
UCSC Archaeal Genome Browser
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Names
More detailed information about this field from each metasource.
The UCSC Archaeal Genome Browser
metasource: Fairsharing.orgversion: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
UCSC Archaeal Genome Browser
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Other names: UCSC Archaeal Genome Browser
Names
More detailed information about this field from each metasource.
The UCSC Archaeal Genome Browser
metasource: Fairsharing.orgversion: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
UCSC Archaeal Genome Browser
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
The UCSC Archaeal Genome Browser is a window on the biology of more than 100 microbial species from the domain Archaea. Basic gene annotation is derived from NCBI Genbank/RefSeq entries, with overlays of sequence conservation across multiple species, nucleotide and protein motifs, non-coding RNA predictions, operon predictions, and other types of bioinformatic analyses. In addition, we display available gene expression data (microarray or high-throughput RNA sequencing). Direct contributions or notices of publication of functional genomic data or bioinformatic analyses from archaeal research labs are very welcome.
Description
More detailed information about this field from each metasource.
The UCSC Archaeal Genome Browser is a window on the biology of more than 100 microbial species from the domain Archaea. Basic gene annotation is derived from NCBI Genbank/RefSeq entries, with overlays of sequence conservation across multiple species, nucleotide and protein motifs, non-coding RNA predictions, operon predictions, and other types of bioinformatic analyses. In addition, we display available gene expression data (microarray or high-throughput RNA sequencing). Direct contributions or notices of publication of functional genomic data or bioinformatic analyses from archaeal research labs are very welcome.
metasource: Fairsharing.orgversion: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
Now that a significant number of archaeal species have been sequenced, effective research and analysis tools are needed to collect and compare the diverse information available for any given locus. We have created a group of integrated genome browsers for all sequenced archaeal species using the feature-rich UCSC Genome Browser system. The browser flexibly displays any combination of features such as G/C content, gene and operon annotation from multiple sources, sequence motifs (i.e., promoters, Shine-Dalgarno, terminators), protein domains, non-coding RNA analyses, GO/COG/KEGG classification information, microarray expression data, multi-genome alignments, and protein conservation across phylogenetic and habitat categories. We continue to add new analyses, both generated within our group as well as those published by other groups. We strongly encourage submission of experimental and bioinformatic analyses from new contributors. The primary aims of this tool are to aid biological discovery and facilitate greater collaboration among the archaeal research community.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Webpage:
http://archaea.ucsc.eduWebpage
More detailed information about this field from each metasource.
http://archaea.ucsc.edu
metasource: Fairsharing.orgversion: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
http://archaea.ucsc.edu/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Publications:
Publications
More detailed information about this field from each metasource.
BLAT--the BLAST-like alignment tool
PMID: 11932250
metasource: Fairsharing.org
version: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
The UCSC Table Browser data retrieval tool
PMID: 14681465
metasource: Fairsharing.org
version: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
The UCSC Archaeal Genome Browser
PMID: 16381898
metasource: Fairsharing.org
version: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
http://dx.doi.org/10.1093/nar/GKR990
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.
BLAT--the BLAST-like alignment tool
PMID: 11932250
metasource: Fairsharing.org
version: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
The UCSC Table Browser data retrieval tool
PMID: 14681465
metasource: Fairsharing.org
version: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
The UCSC Archaeal Genome Browser
PMID: 16381898
metasource: Fairsharing.org
version: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
http://dx.doi.org/10.1093/nar/GKR990
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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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 Archaeal Genome Browser
PubMed citations: 69.
69 articles citing: The UCSC Archaeal Genome Browser
Binding of the RNA Chaperone Hfq on Target mRNAs Promotes the Small RNA RyhB-Induced Degradation in Escherichia coli. PMID:34698252
The Role of Archaeal Chromatin in Transcription. PMID:31082442
Molecular Factors of Hypochlorite Tolerance in the Hypersaline Archaeon Haloferax volcanii. PMID:30463375
Heterologous Complementation Studies With the YscX and YscY Protein Families Reveals a Specificity for Yersinia pseudotuberculosis Type III Secretion. PMID:29616194
An Archaeal Fluoride-Responsive Riboswitch Provides an Inducible Expression System for Hyperthermophiles. PMID:29352088
Contrasting silencing mechanisms of the same target mRNA by two regulatory RNAs in Escherichia coli. PMID:29294085
An archaeal RNA binding protein, FAU-1, is a novel ribonuclease related to rRNA stability in Pyrococcus and Thermococcus. PMID:28978920
A genome-wide association scan of biological processes involved in oral lichen planus and oral squamous cell carcinoma. PMID:28640079
Rapid Sampling of Escherichia coli After Changing Oxygen Conditions Reveals Transcriptional Dynamics. PMID:28264512
Comparative analysis of codon usage bias in Crenarchaea and Euryarchaea genome reveals differential preference of synonymous codons to encode highly expressed ribosomal and RNA polymerase proteins. PMID:27659324
Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families. PMID:27322404
Identification of sRNA interacting with a transcript of interest using MS2-affinity purification coupled with RNA sequencing (MAPS) technology. PMID:26484242
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
Revisiting the structure/function relationships of H/ACA(-like) RNAs: a unified model for Euryarchaea and Crenarchaea. PMID:26240384
Novel pili-like surface structures of Halobacterium salinarum strain R1 are crucial for surface adhesion. PMID:25628607
Potassium stress growth characteristics and energetics in the haloarchaeon Haloarcula marismortui. PMID:25503059
Generation of comprehensive transposon insertion mutant library for the model archaeon, Haloferax volcanii, and its use for gene discovery. PMID:25488358
The conserved GTPase LepA contributes mainly to translation initiation in Escherichia coli. PMID:25378333
Using first passage statistics to extract environmentally dependent amino acid correlations. PMID:25000191
Biodiversity and multifunctionality in a microbial community: a novel theoretical approach to quantify functional redundancy. PMID:24352945
Wolbachia variants induce differential protection to viruses in Drosophila melanogaster: a phenotypic and phylogenomic analysis. PMID:24348259
Conservative sex and the benefits of transformation in Streptococcus pneumoniae. PMID:24244172
A combination of improved differential and global RNA-seq reveals pervasive transcription initiation and events in all stages of the life-cycle of functional RNAs in Propionibacterium acnes, a major contributor to wide-spread human disease. PMID:24034785
An alternative beads-on-a-string chromatin architecture in Thermococcus kodakarensis. PMID:23835508
Interfacing cellular networks of S. cerevisiae and E. coli: connecting dynamic and genetic information. PMID:23663484
Chromosome painting in silico in a bacterial species reveals fine population structure. PMID:23505045
High depth, whole-genome sequencing of cholera isolates from Haiti and the Dominican Republic. PMID:22963323
Abstracts of the 11th Annual UT-ORNL-KBRIN Bioinformatics Summit 2012. Louisville, Kentucky, USA. March 30-April 1, 2012. PMID:22873757
Using Galaxy to perform large-scale interactive data analyses. PMID:22700312
Programmable sequence-specific click-labeling of RNA using archaeal box C/D RNP methyltransferases. PMID:22564896
Discovery of Pyrobaculum small RNA families with atypical pseudouridine guide RNA features. PMID:22282340
Primordial soup or vinaigrette: did the RNA world evolve at acidic pH? PMID:22264281
Functional genomic and advanced genetic studies reveal novel insights into the metabolism, regulation, and biology of Haloferax volcanii. PMID:22190865
Purine biosynthesis in archaea: variations on a theme. PMID:22168471
CAGO: a software tool for dynamic visual comparison and correlation measurement of genome organization. PMID:22114666
The UCSC Archaeal Genome Browser: 2012 update. PMID:22080555
Functional promiscuity of the COG0720 family. PMID:21999246
Metabolic network modularity in archaea depends on growth conditions. PMID:21998711
Identification of CRISPR and riboswitch related RNAs among novel noncoding RNAs of the euryarchaeon Pyrococcus abyssi. PMID:21668986
Identification of prokaryotic small proteins using a comparative genomic approach. PMID:21551138
Discovery of permuted and recently split transfer RNAs in Archaea. PMID:21489296
RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data. PMID:21357752
Neuronal genes for subcutaneous fat thickness in human and pig are identified by local genomic sequencing and combined SNP association study. PMID:21311593
Accessibility and evolutionary conservation mark bacterial small-rna target-binding regions. PMID:21278294
Histone and TK0471/TrmBL2 form a novel heterogeneous genome architecture in the hyperthermophilic archaeon Thermococcus kodakarensis. PMID:21148291
Discovery of a minimal form of RNase P in Pyrobaculum. PMID:21135215
GlpR represses fructose and glucose metabolic enzymes at the level of transcription in the haloarchaeon Haloferax volcanii. PMID:20935102
Integration and visualization of systems biology data in context of the genome. PMID:20642854
Comparative genomics of the family Vibrionaceae reveals the wide distribution of genes encoding virulence-associated proteins. PMID:20537180
Haloferax volcanii flagella are required for motility but are not involved in PibD-dependent surface adhesion. PMID:20363933
Discovery and characterization of an amidinotransferase involved in the modification of archaeal tRNA. PMID:20129918
Template-dependent 3'-5' nucleotide addition is a shared feature of tRNAHis guanylyltransferase enzymes from multiple domains of life. PMID:20080734
Deep sequencing analysis of the Methanosarcina mazei Gö1 transcriptome in response to nitrogen availability. PMID:19996181
A comparative genomics, network-based approach to understanding virulence in Vibrio cholerae. PMID:19666715
Identification of a crenarchaeal orthologue of Elf1: implications for chromatin and transcription in Archaea. PMID:19640276
A Gateway platform for functional genomics in Haloferax volcanii: deletion of three tRNA modification genes. PMID:19478918
Evolution of complex RNA polymerases: the complete archaeal RNA polymerase structure. PMID:19419240
Manual annotation, transcriptional analysis, and protein expression studies reveal novel genes in the agl cluster responsible for N glycosylation in the halophilic archaeon Haloferax volcanii. PMID:19251857
Tri-split tRNA is a transfer RNA made from 3 transcripts that provides insight into the evolution of fragmented tRNAs in archaea. PMID:19190180
Transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. PMID:19047344
sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes. PMID:19015153
GtRNAdb: a database of transfer RNA genes detected in genomic sequence. PMID:18984615
Biosynthesis of 7-deazaguanosine-modified tRNA nucleosides: a new role for GTP cyclohydrolase I. PMID:18931107
RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes. PMID:18844986
Genome information management and integrated data analysis with HaloLex. PMID:18592220
The 5e motif of eukaryotic signal recognition particle RNA contains a conserved adenosine for the binding of SRP72. PMID:18441046
Using galaxy to perform large-scale interactive data analyses. PMID:18428782
On the evolution of the tRNA-dependent amidotransferases, GatCAB and GatDE. PMID:18279892
Divergence of selenocysteine tRNA recognition by archaeal and eukaryotic O-phosphoseryl-tRNASec kinase. PMID:18267971 - http://dx.doi.org/10.1093/nar/GKR990
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More detailed information about this field from each metasource.
crispr
metasource: Fairsharing.org
version: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
computational predictions
metasource: Fairsharing.org
version: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
dna sequence data
metasource: Fairsharing.org
version: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
gc content
metasource: Fairsharing.org
version: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
gene expression data
metasource: Fairsharing.org
version: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
gene functional annotation
metasource: Fairsharing.org
version: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
genome map
metasource: Fairsharing.org
version: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
insertion sequence
metasource: Fairsharing.org
version: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
multiple sequence alignment
metasource: Fairsharing.org
version: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
non-coding rna
metasource: Fairsharing.org
version: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
nucleic acid sequence alignment
metasource: Fairsharing.org
version: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
operon prediction
metasource: Fairsharing.org
version: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
orthologous
metasource: Fairsharing.org
version: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
paralogous
metasource: Fairsharing.org
version: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
promoter
metasource: Fairsharing.org
version: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
rna sequence
metasource: Fairsharing.org
version: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
sequence annotation
metasource: Fairsharing.org
version: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
transcription factor binding site prediction
metasource: Fairsharing.org
version: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
genomics databases (non-vertebrate)
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
prokaryotic genome databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Tags
More detailed information about this field from each metasource.
crispr
metasource: Fairsharing.orgversion: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
computational predictions
metasource: Fairsharing.orgversion: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
dna sequence data
metasource: Fairsharing.orgversion: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
gc content
metasource: Fairsharing.orgversion: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
gene expression data
metasource: Fairsharing.orgversion: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
gene functional annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
genome map
metasource: Fairsharing.orgversion: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
insertion sequence
metasource: Fairsharing.orgversion: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
multiple sequence alignment
metasource: Fairsharing.orgversion: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
non-coding rna
metasource: Fairsharing.orgversion: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
nucleic acid sequence alignment
metasource: Fairsharing.orgversion: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
operon prediction
metasource: Fairsharing.orgversion: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
orthologous
metasource: Fairsharing.orgversion: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
paralogous
metasource: Fairsharing.orgversion: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
promoter
metasource: Fairsharing.orgversion: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
rna sequence
metasource: Fairsharing.orgversion: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
sequence annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
transcription factor binding site prediction
metasource: Fairsharing.orgversion: FAIRsharing.org: The UCSC Archaeal Genome Browser; The UCSC Archaeal Genome Browser; DOI: https://doi.org/10.25504/FAIRsharing.12yd2z; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:05 p.m.
genomics databases (non-vertebrate)
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
prokaryotic genome databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
crispr computational predictions dna sequences gc content gene expression gene functional annotation genome map insertion sequence multiple sequence alignment non-coding rna nucleic acid sequence alignment operon prediction orthology paralogous promoter rna sequence sequence annotation transcription factor binding site prediction genomics prokaryotic genome
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