Ensembl Zebrafish Genome Browser
Other names: ensembl_zebrafish_genome_browser
This ensembl website features the zebrafish whole genome shotgun assembly sequence.
Description
More detailed information about this field from each metasource.
This ensembl website features the zebrafish whole genome shotgun assembly sequence.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:42.880153
Webpage:
http://www.ensembl.org/Danio_rerio/Webpage
More detailed information about this field from each metasource.
http://www.ensembl.org/Danio_rerio/
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:42.880153
Publications:
Publications
More detailed information about this field from each metasource.
The Ensembl genome database project
PMID: 11752248
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:42.880153
Publications
More detailed information about this field from each metasource.
The Ensembl genome database project
PMID: 11752248
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:42.880153
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The Ensembl genome database project
PubMed citations: 653.
653 articles citing: The Ensembl genome database project
Transcriptomic and proteomic retinal pigment epithelium signatures of age-related macular degeneration. PMID:35882847
Ecosystem-specific microbiota and microbiome databases in the era of big data. PMID:35842686
PR-1-Like Protein as a Potential Target for the Identification of Fusarium oxysporum: An In Silico Approach. PMID:35822818
Molecular Analysis and Conformational Dynamics of Human MC4R Disease-Causing Mutations. PMID:35807283
SperoPredictor: An Integrated Machine Learning and Molecular Docking-Based Drug Repurposing Framework With Use Case of COVID-19. PMID:35784208
Meta-Analysis Suggests That Intron Retention Can Affect Quantification of Transposable Elements from RNA-Seq Data. PMID:35741347
A Comparison of Methods for Gene-Based Testing That Account for Linkage Disequilibrium. PMID:35601489
Identifying common transcriptome signatures of cancer by interpreting deep learning models. PMID:35581644
Mapping and Validation of scRNA-Seq-Derived Cell-Cell Communication Networks in the Tumor Microenvironment. PMID:35572582
In Silico Analysis Revealed Five Novel High-Risk Single-Nucleotide Polymorphisms (rs200384291, rs201163886, rs193141883, rs201139487, and rs201723157) in ELANE Gene Causing Autosomal Dominant Severe Congenital Neutropenia 1 and Cyclic Hematopoiesis. PMID:35571273
Dietary antigens suppress the proliferation of type 2 innate lymphoid cells by restraining homeostatic IL-25 production. PMID:35523930
Comparative analysis of web-based programs for single amino acid substitutions in proteins. PMID:35507592
Distinct and additive effects of calorie restriction and rapamycin in aging skeletal muscle. PMID:35440545
Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content. PMID:35388368
Splice Junction Identification using Long Short-Term Memory Neural Networks. PMID:35283668
A nonredundant role for T cell-derived interleukin 22 in antibacterial defense of colonic crypts. PMID:35263568
Impact of deleterious missense PRKCI variants on structural and functional dynamics of protein. PMID:35260606
Small open reading frames in plant research: from prediction to functional characterization. PMID:35251879
Microautophagy Mediates Vacuolar Delivery of Storage Proteins in Maize Aleurone Cells. PMID:35251104
Insights into glucosinolate accumulation and metabolic pathways in Isatis indigotica Fort. PMID:35193497
WAFNRLTG: A Novel Model for Predicting LncRNA Target Genes Based on Weighted Average Fusion Network Representation Learning Method. PMID:35127729
Transcription factor motif activity as a biomarker of muscle aging. PMID:35083472
DANSR: A Tool for the Detection of Annotated and Novel Small RNAs. PMID:35076605
Genomic studies controvert the existence of the CUX1 p75 isoform. PMID:34997000
DNA methylation mediates the association between breastfeeding and early-life growth trajectories. PMID:34937578
Navigating Multi-Scale Cancer Systems Biology Towards Model-Driven Clinical Oncology and Its Applications in Personalized Therapeutics. PMID:34900668
Investigation of Antidepressant Properties of Yohimbine by Employing Structure-Based Computational Assessments. PMID:34889886
Probing Isoform Switching Events in Various Cancer Types: Lessons From Pan-Cancer Studies. PMID:34888349
Compound heterozygous c.598_612del and c.1746-20C > G CAPN3 genotype cause autosomal recessive limb-girdle muscular dystrophy-1: a case report. PMID:34863162
Unifying heterogeneous expression data to predict targets for CAR-T cell therapy. PMID:34858726
msRepDB: a comprehensive repetitive sequence database of over 80 000 species. PMID:34850956
Origins and Function of VL30 lncRNA Packaging in Small Extracellular Vesicles: Implications for Cellular Physiology and Pathology. PMID:34829970
Impact of Deleterious Mutations on Structure, Function and Stability of Serum/Glucocorticoid Regulated Kinase 1: A Gene to Diseases Correlation. PMID:34805284
The length scale of multivalent interactions is evolutionarily conserved in fungal and vertebrate phase-separating proteins. PMID:34791214
Evolution Analyses of CAMTA Transcription Factor in Plants and Its Enhancing Effect on Cold-tolerance. PMID:34790215
Contamination in Reference Sequence Databases: Time for Divide-and-Rule Tactics. PMID:34745061
Refining models of archaic admixture in Eurasia with ArchaicSeeker 2.0. PMID:34716342
Prioritizing natural-selection signals from the deep-sequencing genomic data suggests multi-variant adaptation in Tibetan highlanders. PMID:34691999
Investigating single amino acid substitutions in PIM1 kinase: A structural genomics approach. PMID:34679086
ERp29 forms a feedback regulation loop with microRNA-135a-5p and promotes progression of colorectal cancer. PMID:34667160
caAtlas: An immunopeptidome atlas of human cancer. PMID:34622160
Gosling: A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization. PMID:34596551
Genetic predisposition to tinnitus in the UK Biobank population. PMID:34518561
Multivariate analysis of 1.5 million people identifies genetic associations with traits related to self-regulation and addiction. PMID:34446935
Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing. PMID:34418978
Spared Nerve Injury Causes Sexually Dimorphic Mechanical Allodynia and Differential Gene Expression in Spinal Cords and Dorsal Root Ganglia in Rats. PMID:34331199
Targeting cancer stem cells in medulloblastoma by inhibiting AMBRA1 dual function in autophagy and STAT3 signalling. PMID:34302498
Comparison of Transcriptional Response of C3 and C4 Plants to Drought Stress Using Meta-Analysis and Systems Biology Approach. PMID:34276729
A Methodology to Study Pseudogenized lincRNAs. PMID:34165708
A PGE2-MEF2A axis enables context-dependent control of inflammatory gene expression. PMID:34129840
PRoBE the cloud toolkit: finding the best biomarkers of drug response within a breast cancer clinical trial. PMID:34095775
Enhancement of myogenic differentiation and inhibition of rhabdomyosarcoma progression by miR-28-3p and miR-193a-5p regulated by SNAIL. PMID:34094709
The history and evolution of the Denisovan-EPAS1 haplotype in Tibetans. PMID:34050022
Comparative proteomic analysis to annotate the structural and functional association of the hypothetical proteins of S. maltophilia k279a and predict potential T and B cell targets for vaccination. PMID:34043709
Differential gene expression profile by RNA sequencing study of elderly osteoporotic hip fracture patients with sarcopenia. PMID:34036042
Comprehensive transcriptome analysis of colorectal cancer risk of hyperglycemia in humans. PMID:34012653
Structural genomics approach to investigate deleterious impact of nsSNPs in conserved telomere maintenance component 1. PMID:33986331
Polyadenylation-related isoform switching in human evolution revealed by full-length transcript structure. PMID:33973996
Molecular evolutionary analysis of human primary microcephaly genes. PMID:33941077
The transcriptional landscape of a hepatoma cell line grown on scaffolds of extracellular matrix proteins. PMID:33823809
Discovery of novel antagonists targeting the DNA binding domain of androgen receptor by integrated docking-based virtual screening and bioassays. PMID:33767381
Conserved dual-mode gene regulation programs in higher eukaryotes. PMID:33621342
Molecular and phenotypic analysis of rodent models reveals conserved and species-specific modulators of human sarcopenia. PMID:33580198
MicroExonator enables systematic discovery and quantification of microexons across mouse embryonic development. PMID:33482885
DeepLPI: a multimodal deep learning method for predicting the interactions between lncRNAs and protein isoforms. PMID:33461501
Machine learning based CRISPR gRNA design for therapeutic exon skipping. PMID:33417623
Myogenic regulatory factors are key players in determining muscle mass and meat quality in Jeju native and Berkshire pigs. PMID:33372732
Multipath: An R Package to Generate Integrated Reproducible Pathway Models. PMID:33371258
Bioinformatic analysis and functional predictions of selected regeneration-associated transcripts expressed by zebrafish microglia. PMID:33287696
Early lung cancer diagnostic biomarker discovery by machine learning methods. PMID:33217646
Plant miRNAs Reduce Cancer Cell Proliferation by Targeting MALAT1 and NEAT1: A Beneficial Cross-Kingdom Interaction. PMID:33193626
Epigenetic Studies Revealed a Ghost Proteome in PC1/3 KD Macrophages under Antitumoral Resistance Induced by IL-10. PMID:33163760
Transcriptomic profiling of feline teeth highlights the role of matrix metalloproteinase 9 (MMP9) in tooth resorption. PMID:33144645
Effects of early life stage exposure of largemouth bass to atrazine or a model estrogen (17α-ethinylestradiol). PMID:33072434
Bayesian Analysis of the Association between Casein Complex Haplotype Variants and Milk Yield, Composition, and Curve Shape Parameters in Murciano-Granadina Goats. PMID:33050522
Natural Selection on the Phase-Separation Properties of FUS during 160 My of Mammalian Evolution. PMID:33022038
lncRNAKB, a knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA. PMID:33020484
Liquid lncRNA Biopsy for the Evaluation of Locally Advanced and Metastatic Squamous Cell Carcinomas of the Head and Neck. PMID:32947877
Identification of a Core Module for Bone Mineral Density through the Integration of a Co-expression Network and GWAS Data. PMID:32937138
The neuromuscular junction is a focal point of mTORC1 signaling in sarcopenia. PMID:32908143
Pathogenic impact of transcript isoform switching in 1,209 cancer samples covering 27 cancer types using an isoform-specific interaction network. PMID:32879328
MUTYH: Not just polyposis. PMID:32821650
The longevity-associated variant of BPIFB4 improves a CXCR4-mediated striatum-microglia crosstalk preventing disease progression in a mouse model of Huntington's disease. PMID:32683420
TH17 cells require ongoing classic IL-6 receptor signaling to retain transcriptional and functional identity. PMID:32680955
The transcriptional signature associated with human motile cilia. PMID:32616903
Genome-Wide Identification of RNA Silencing-Related Genes and Their Expressional Analysis in Response to Heat Stress in Barley (Hordeum vulgare L.). PMID:32570964
An improved clear cell renal cell carcinoma stage prediction model based on gene sets. PMID:32513106
Novel Comprehensive Bioinformatics Approaches to Determine the Molecular Genetic Susceptibility Profile of Moderate and Severe Asthma. PMID:32512817
ASAP 2020 update: an open, scalable and interactive web-based portal for (single-cell) omics analyses. PMID:32449934
Effect of aging on the transcriptomic changes associated with the expression of the HERV-K (HML-2) provirus at 1q22. PMID:32435269
RiboToolkit: an integrated platform for analysis and annotation of ribosome profiling data to decode mRNA translation at codon resolution. PMID:32427338
The crystal structure of the TonB-dependent transporter YncD reveals a positively charged substrate-binding site. PMID:32355044
HMGA1-pseudogene7 transgenic mice develop B cell lymphomas. PMID:32341372
Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex. PMID:32327568
A benchmark study of ab initio gene prediction methods in diverse eukaryotic organisms. PMID:32272892
ADH7, miR-3065 and LINC01133 are associated with cervical cancer progression in different age groups. PMID:32194732
Integrating Casein Complex SNPs Additive, Dominance and Epistatic Effects on Genetic Parameters and Breeding Values Estimation for Murciano-Granadina Goat Milk Yield and Components. PMID:32183253
Role of non-coding RNA networks in leukemia progression, metastasis and drug resistance. PMID:32164715
Angiotensin-(1-9) prevents cardiomyocyte hypertrophy by controlling mitochondrial dynamics via miR-129-3p/PKIA pathway. PMID:32152556
Dynamic Alternative Splicing During Mouse Preimplantation Embryo Development. PMID:32117919
Exploring Integrative Analysis Using the BioMedical Evidence Graph. PMID:32097025
Mitochondrial transfer from MSCs to T cells induces Treg differentiation and restricts inflammatory response. PMID:31984629
ISOGO: Functional annotation of protein-coding splice variants. PMID:31974522
The landscape of chimeric RNAs in non-diseased tissues and cells. PMID:31965184
MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets. PMID:31956905
Long walk to genomics: History and current approaches to genome sequencing and assembly. PMID:31890139
Small noncoding RNA discovery and profiling with sRNAtools based on high-throughput sequencing. PMID:31885040
SpliceFinder: ab initio prediction of splice sites using convolutional neural network. PMID:31881982
Targeted sequencing of the LRRTM gene family in suicide attempters with bipolar disorder. PMID:31854516
Tasks, Techniques, and Tools for Genomic Data Visualization. PMID:31768085
Oncogenes, tumor suppressor and differentiation genes represent the oldest human gene classes and evolve concurrently. PMID:31712655
Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling. PMID:31701028
Protease-associated import systems are widespread in Gram-negative bacteria. PMID:31613892
VariED: the first integrated database of gene annotation and expression profiles for variants related to human diseases. PMID:31317185
A novel CHD7 variant disrupting acceptor splice site in a patient with mild features of CHARGE syndrome: a case report. PMID:31315586
Toxins from scratch? Diverse, multimodal gene origins in the predatory robber fly Dasypogon diadema indicate a dynamic venom evolution in dipteran insects. PMID:31289835
Structural Analysis and Conformational Dynamics of STN1 Gene Mutations Involved in Coat Plus Syndrome. PMID:31245382
Evolutionary history of the human multigene families reveals widespread gene duplications throughout the history of animals. PMID:31221090
Cyberbiosecurity Challenges of Pathogen Genome Databases. PMID:31157218
Rapid identification and interpretation of gene-environment associations using the new R.SamBada landscape genomics pipeline. PMID:31136078
PathMe: merging and exploring mechanistic pathway knowledge. PMID:31092193
Weighting sequence variants based on their annotation increases the power of genome-wide association studies in dairy cattle. PMID:31077144
An atypical pulmonary fibrosis is associated with co-inheritance of mutations in the calcium binding protein genes S100A3 and S100A13. PMID:31073086
De novo emergence and potential function of human-specific tandem repeats in brain-related loci. PMID:31069507
Identification of a long noncoding RNA signature to predict outcomes of glioblastoma. PMID:31059035
Structural and functional impact of non-synonymous SNPs in the CST complex subunit TEN1: structural genomics approach. PMID:31028137
Impact of Genetic Variation on CRISPR-Cas Targeting. PMID:31021199
Predicting synthetic lethal interactions using conserved patterns in protein interaction networks. PMID:30995217
Evolution of Deeper Rooting 1-like homoeologs in wheat entails the C-terminus mutations as well as gain and loss of auxin response elements. PMID:30947257
Prioritizing candidate genes for fertility in dairy cows using gene-based analysis, functional annotation and differential gene expression. PMID:30935378
PKD1 Duplicated regions limit clinical Utility of Whole Exome Sequencing for Genetic Diagnosis of Autosomal Dominant Polycystic Kidney Disease. PMID:30858458
The sequence and de novo assembly of Oxygymnocypris stewartii genome. PMID:30720802
Risk gene-set and pathways in 22q11.2 deletion-related schizophrenia: a genealogical molecular approach. PMID:30710087
Identification of exon skipping events associated with Alzheimer's disease in the human hippocampus. PMID:30704480
Regulation of RNA editing by RNA-binding proteins in human cells. PMID:30652130
Defensin-like peptides in wheat analyzed by whole-transcriptome sequencing: a focus on structural diversity and role in induced resistance. PMID:30643692
Single cell functional genomics reveals the importance of mitochondria in cell-to-cell phenotypic variation. PMID:30638445
Genome-wide mapping of nucleotide excision repair with XR-seq. PMID:30552409
Functional genomics of the digestive tract in broilers. PMID:30545300
Aging-associated patterns in the expression of human endogenous retroviruses. PMID:30513106
RNA-sequencing analysis of umbilical cord plasma microRNAs from healthy newborns. PMID:30507953
Variant information systems for precision oncology. PMID:30463544
Optimised isolation method for RNA extraction suitable for RNA sequencing from feline teeth collected in a clinical setting and at post mortem. PMID:30402716
Arena-Idb: a platform to build human non-coding RNA interaction networks. PMID:30367585
Sc-ncDNAPred: A Sequence-Based Predictor for Identifying Non-coding DNA in Saccharomyces cerevisiae. PMID:30258427
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. PMID:30239679
Targeted Genomic Screen Reveals Focal Long Non-Coding RNA Copy Number Alterations in Cancer Cell Lines. PMID:30217017
HeteroMeth: A Database of Cell-to-cell Heterogeneity in DNA Methylation. PMID:30196115
Prioritizing candidate genes post-GWAS using multiple sources of data for mastitis resistance in dairy cattle. PMID:30189836
Detecting long non-coding RNA biomarkers in prostate cancer liquid biopsies: Hype or hope? PMID:30159441
ESCC ATLAS: A population wide compendium of biomarkers for Esophageal Squamous Cell Carcinoma. PMID:30143675
Conserved temporal ordering of promoter activation implicates common mechanisms governing the immediate early response across cell types and stimuli. PMID:30089658
Integrative omics analyses broaden treatment targets in human cancer. PMID:30053901
Making genome browsers portable and personal. PMID:30016986
RabGTD: a comprehensive database of rabbit genome and transcriptome. PMID:30010730
Loose ends: almost one in five human genes still have unresolved coding status. PMID:29982784
Transcriptome Analysis Provides Insight into the Molecular Mechanisms Underlying gametophyte factor 2-Mediated Cross-Incompatibility in Maize. PMID:29899298
Genetic variation affecting exon skipping contributes to brain structural atrophy in Alzheimer's disease. PMID:29888056
Kinact: a computational approach for predicting activating missense mutations in protein kinases. PMID:29788456
Reconstruction of a replication-competent ancestral murine endogenous retrovirus-L. PMID:29716624
Genomic insights into natural selection in the common loon (Gavia immer): evidence for aquatic adaptation. PMID:29703132
New perspectives: systems medicine in cardiovascular disease. PMID:29699591
Curated compendium of human transcriptional biomarker data. PMID:29664470
Pangenomic Definition of Prokaryotic Species and the Phylogenetic Structure of Prochlorococcus spp. PMID:29593678
SpliceDetector: a software for detection of alternative splicing events in human and model organisms directly from transcript IDs. PMID:29567976
Novel candidate genes important for asthma and hypertension comorbidity revealed from associative gene networks. PMID:29504915
Δ9-Tetrahydrocannabinol changes the brain lipidome and transcriptome differentially in the adolescent and the adult. PMID:29408467
Transcriptome-wide identification of the RNA-binding landscape of the chromatin-associated protein PARP1 reveals functions in RNA biogenesis. PMID:29387452
Finding Nemo: hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the clownfish (Amphiprion ocellaris) genome assembly. PMID:29342277
Integrated sequencing of exome and mRNA of large-sized single cells. PMID:29321653
Cancer transcriptome profiling at the juncture of clinical translation. PMID:29279605
Non-coding RNAs profiling in head and neck cancers. PMID:29263803
In-Cardiome: integrated knowledgebase for coronary artery disease enabling translational research. PMID:29220465
Construction of PRDM9 allele-specific recombination maps in cattle using large-scale pedigree analysis and genome-wide single sperm genomics. PMID:29186399
Genome-wide DNase hypersensitivity, and occupancy of RUNX2 and CTCF reveal a highly dynamic gene regulome during MC3T3 pre-osteoblast differentiation. PMID:29176792
Ensembl 2018. PMID:29155950
Dynamic Visualization and Comparative Analysis of Multiple Collinear Genomic Data. PMID:29119144
Tracing the spatio-temporal dynamics of endangered fin whales (Balaenoptera physalus) within baleen whale (Mysticeti) lineages: a mitogenomic perspective. PMID:29103106
Structure-mediated modulation of mRNA abundance by A-to-I editing. PMID:29093448
Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system. PMID:29087374
Lnc2Meth: a manually curated database of regulatory relationships between long non-coding RNAs and DNA methylation associated with human disease. PMID:29069510
DNA sequencing at 40: past, present and future. PMID:29019985
HUMA: A platform for the analysis of genetic variation in humans. PMID:28967693
De novo assembly and characterization of breast cancer transcriptomes identifies large numbers of novel fusion-gene transcripts of potential functional significance. PMID:28851357
The Adaptive Evolution Database (TAED): A New Release of a Database of Phylogenetically Indexed Gene Families from Chordates. PMID:28795237
Structural variants in genes associated with human Williams-Beuren syndrome underlie stereotypical hypersociability in domestic dogs. PMID:28776031
Comprehensive discovery of noncoding RNAs in acute myeloid leukemia cell transcriptomes. PMID:28760689
Prognostic cancer gene signatures share common regulatory motifs. PMID:28684851
Bridging Plant and Human Radiation Response and DNA Repair through an In Silico Approach. PMID:28587301
Properties of genes essential for mouse development. PMID:28562614
UPR transducer BBF2H7 allows export of type II collagen in a cargo- and developmental stage-specific manner. PMID:28500182
Microbial Biogeography and Core Microbiota of the Rat Digestive Tract. PMID:28374781
Identification of long non-coding transcripts with feature selection: a comparative study. PMID:28335739
Pan-cancer analysis distinguishes transcriptional changes of aneuploidy from proliferation. PMID:28320919
Identification and Expression of Equine MER-Derived miRNAs. PMID:28320202
Facial cutaneo-mucosal venous malformations can develop independently of mutation of TEK gene but may be associated with excessive expression of Src and p-Src. PMID:28316284
NEUROD2 Regulates Stim1 Expression and Store-Operated Calcium Entry in Cortical Neurons. PMID:28303257
Development of Bioinformatics Infrastructure for Genomics Research. PMID:28302555
Role of Structural Bioinformatics in Drug Discovery by Computational SNP Analysis: Analyzing Variation at the Protein Level. PMID:28302551
Genomic characterisation of Eμ-Myc mouse lymphomas identifies Bcor as a Myc co-operative tumour-suppressor gene. PMID:28262675
Integrative multi-omics analysis revealed SNP-lncRNA-mRNA (SLM) networks in human peripheral blood mononuclear cells. PMID:28243742
Individualized analysis reveals CpG sites with methylation aberrations in almost all lung adenocarcinoma tissues. PMID:28178989
Detecting Positive Selection of Korean Native Goat Populations Using Next-Generation Sequencing. PMID:27989103
DIVAN: accurate identification of non-coding disease-specific risk variants using multi-omics profiles. PMID:27923386
Genome-scale characterization of RNA tertiary structures and their functional impact by RNA solvent accessibility prediction. PMID:27807179
Emerging Putative Associations between Non-Coding RNAs and Protein-Coding Genes in Neuropathic Pain: Added Value from Reusing Microarray Data. PMID:27803687
Transcriptome Sequencing Identified Genes and Gene Ontologies Associated with Early Freezing Tolerance in Maize. PMID:27774095
Differential morphology and transcriptome profile between the incompletely fused carpels ovary and its wild-type in maize. PMID:27587343
Structure and regulation of human troponin genes. PMID:27520667
How to talk about protein-level false discovery rates in shotgun proteomics. PMID:27503675
Gene-Disease Interaction Retrieval from Multiple Sources: A Network Based Method. PMID:27478829
Systems analysis of cis-regulatory motifs in C4 photosynthesis genes using maize and rice leaf transcriptomic data during a process of de-etiolation. PMID:27436282
CAT7 and cat7l Long Non-coding RNAs Tune Polycomb Repressive Complex 1 Function during Human and Zebrafish Development. PMID:27405765
The Ensembl gene annotation system. PMID:27337980
ELAVL2-regulated transcriptional and splicing networks in human neurons link neurodevelopment and autism. PMID:27260404
Cloning the Horse RNA Polymerase I Promoter and Its Application to Studying Influenza Virus Polymerase Activity. PMID:27258298
Research Resources for Nuclear Receptor Signaling Pathways. PMID:27216565
Multi-omic data integration and analysis using systems genomics approaches: methods and applications in animal production, health and welfare. PMID:27130220
Evolutionary constraints over microsatellite abundance in larger mammals as a potential mechanism against carcinogenic burden. PMID:27125812
Molecular evolution of WDR62, a gene that regulates neocorticogenesis. PMID:27114917
Molecular Basis of the Ligand Binding Specificity of αvβ8 Integrin. PMID:27033701
The life cycle of a genome project: perspectives and guidelines inspired by insect genome projects. PMID:27006757
Analysis of computational footprinting methods for DNase sequencing experiments. PMID:26901649
Comparative analysis of housekeeping and tissue-selective genes in human based on network topologies and biological properties. PMID:26897376
An integrated in silico approach for functional and structural impact of non- synonymous SNPs in the MYH1 gene in Jeju Native Pigs. PMID:26847462
Insulin-like growth factor axis in pregnancies affected by fetal growth disorders. PMID:26823688
Cascade: an RNA-seq visualization tool for cancer genomics. PMID:26810393
Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins. PMID:26787667
The drug target genes show higher evolutionary conservation than non-target genes. PMID:26716901
Light-RCV: a lightweight read coverage viewer for next generation sequencing data. PMID:26680734
Prioritizing and selecting likely novel miRNAs from NGS data. PMID:26635395
Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. PMID:26615025
TCGASpliceSeq a compendium of alternative mRNA splicing in cancer. PMID:26602693
The UCSC Genome Browser database: 2016 update. PMID:26590259
Expression of microRNAs and isomiRs in the porcine endometrium: implications for gene regulation at the maternal-conceptus interface. PMID:26546342
DNA Editing of LTR Retrotransposons Reveals the Impact of APOBECs on Vertebrate Genomes. PMID:26541172
Coexpression Network Analysis of miRNA-142 Overexpression in Neuronal Cells. PMID:26539539
Genes with stable DNA methylation levels show higher evolutionary conservation than genes with fluctuant DNA methylation levels. PMID:26515589
PDID: database of molecular-level putative protein-drug interactions in the structural human proteome. PMID:26504143
Whole exome sequencing of microdissected splenic marginal zone lymphoma: a study to discover novel tumor-specific mutations. PMID:26498442
Exploration of Novel Inhibitors for Class I Histone Deacetylase Isoforms by QSAR Modeling and Molecular Dynamics Simulation Assays. PMID:26431201
New genes drive the evolution of gene interaction networks in the human and mouse genomes. PMID:26424194
Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR. PMID:26379229
The Structural Characterization of Tumor Fusion Genes and Proteins. PMID:26347798
Data integration in biological research: an overview. PMID:26336651
Selection of recombinant anti-SH3 domain antibodies by high-throughput phage display. PMID:26332758
The Intolerance of Regulatory Sequence to Genetic Variation Predicts Gene Dosage Sensitivity. PMID:26332131
Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future. PMID:26309733
Comprehensive assembly of novel transcripts from unmapped human RNA-Seq data and their association with cancer. PMID:26253570
Integrated sequence and expression analysis of ovarian cancer structural variants underscores the importance of gene fusion regulation. PMID:26177635
Differential and coherent processing patterns from small RNAs. PMID:26166713
QuickNGS elevates Next-Generation Sequencing data analysis to a new level of automation. PMID:26126663
The Role of Transposable Elements in the Origin and Evolution of MicroRNAs in Human. PMID:26115450
Discovery and characterization of long intergenic non-coding RNAs (lincRNA) module biomarkers in prostate cancer: an integrative analysis of RNA-Seq data. PMID:26100580
Possible Human Papillomavirus 38 Contamination of Endometrial Cancer RNA Sequencing Samples in The Cancer Genome Atlas Database. PMID:26085148
Towards New Drug Targets? Function Prediction of Putative Proteins of Neisseria meningitidis MC58 and Their Virulence Characterization. PMID:26076386
A low-latency, big database system and browser for storage, querying and visualization of 3D genomic data. PMID:25990738
GermlncRNA: a unique catalogue of long non-coding RNAs and associated regulations in male germ cell development. PMID:25982314
Variation in DNAH1 may contribute to primary ciliary dyskinesia. PMID:25927852
Integrative Analysis of CRISPR/Cas9 Target Sites in the Human HBB Gene. PMID:25918715
NOTCH1 regulates matrix gla protein and calcification gene networks in human valve endothelium. PMID:25871831
MAFCO: a compression tool for MAF files. PMID:25816229
RNA sequencing of laser-capture microdissected compartments of the maize kernel identifies regulatory modules associated with endosperm cell differentiation. PMID:25783031
GASS: genome structural annotation for Eukaryotes based on species similarity. PMID:25764973
The fate of recent duplicated genes following a fourth-round whole genome duplication in a tetraploid fish, common carp (Cyprinus carpio). PMID:25645996
Prioritizing causal disease genes using unbiased genomic features. PMID:25633252
Cetaceans evolution: insights from the genome sequences of common minke whales. PMID:25609461
plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants. PMID:25566282
microRNA profiling in three main stages during porcine spermatogenesis. PMID:25563581
RNA-binding proteins in pluripotency, differentiation, and reprogramming. PMID:25554730
Comparative genomics reveals molecular features unique to the songbird lineage. PMID:25494627
The UCSC Genome Browser database: 2015 update. PMID:25428374
Role of recurrent hypoxia-ischemia in preterm white matter injury severity. PMID:25390897
Identification of candidate long noncoding RNAs associated with left ventricular hypertrophy. PMID:25382655
APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals. PMID:25378337
An update on LNCipedia: a database for annotated human lncRNA sequences. PMID:25378313
A novel virus-inducible enhancer of the interferon-β gene with tightly linked promoter and enhancer activities. PMID:25348400
Comparative analyses of C₄ and C₃ photosynthesis in developing leaves of maize and rice. PMID:25306245
Balancing selection on CDH2 may be related to the behavioral features of the Belgian Malinois. PMID:25303325
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
Genome-wide analysis of noncoding regulatory mutations in cancer. PMID:25261935
Renal Gene Expression Database (RGED): a relational database of gene expression profiles in kidney disease. PMID:25252782
Neighbor preferences of amino acids and context-dependent effects of amino acid substitutions in human, mouse, and dog. PMID:25210846
We are all individuals... bioinformatics in the personalized medicine era. PMID:25204962
MiR-7 promotes epithelial cell transformation by targeting the tumor suppressor KLF4. PMID:25181544
Thoroughbred Horse Single Nucleotide Polymorphism and Expression Database: HSDB. PMID:25178365
Parallel selection on gene copy number variations through evolution of three-spined stickleback genomes. PMID:25168270
Computational Methods for MicroRNA Target Prediction. PMID:25153283
Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations. PMID:25149441
Annotated features of domestic cat - Felis catus genome. PMID:25143822
Differential Evolution between Monotocous and Polytocous Species. PMID:25049975
Notch signaling functions in retinal pericyte survival. PMID:25015359
RNA-binding protein RBM20 represses splicing to orchestrate cardiac pre-mRNA processing. PMID:24960161
BLAT-based comparative analysis for transposable elements: BLATCAT. PMID:24959585
IIS--Integrated Interactome System: a web-based platform for the annotation, analysis and visualization of protein-metabolite-gene-drug interactions by integrating a variety of data sources and tools. PMID:24949626
Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes. PMID:24939910
Identification of potential therapeutic targets in a model of neuropathic pain. PMID:24904634
Infinium monkeys: Infinium 450K array for the Cynomolgus macaque (Macaca fascicularis). PMID:24815017
Interactive visualization and analysis of large-scale sequencing datasets using ZENBU. PMID:24727769
Molecular evolution of the vertebrate FK506 binding protein 25. PMID:24724077
Bovine exome sequence analysis and targeted SNP genotyping of recessive fertility defects BH1, HH2, and HH3 reveal a putative causative mutation in SMC2 for HH3. PMID:24667746
Long non-coding RNA and alternative splicing modulations in Parkinson's leukocytes identified by RNA sequencing. PMID:24651478
Whole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution. PMID:24602261
Cell cycle, oncogenic and tumor suppressor pathways regulate numerous long and macro non-protein-coding RNAs. PMID:24594072
A novel two-layer SVM model in miRNA Drosha processing site detection. PMID:24565218
Cell-type and transcription factor specific enrichment of transcriptional cofactor motifs in ENCODE ChIP-seq data. PMID:24564528
Prioritizing disease-linked variants, genes, and pathways with an interactive whole-genome analysis pipeline. PMID:24478219
The gene family of dehydration responsive element-binding transcription factors in grape (Vitis vinifera): genome-wide identification and analysis, expression profiles, and involvement in abiotic stress resistance. PMID:24402876
Functional annotation of conserved hypothetical proteins from Haemophilus influenzae Rd KW20. PMID:24391926
Lack of TEK Gene Mutation in Patients with Cutaneomucosal Venous Malformations from the North-Western Region of Algeria. PMID:24386570
Genomics of alternative splicing: evolution, development and pathophysiology. PMID:24378600
Time for the zebrafish ENCODE. PMID:24371190
The roles of FMRP-regulated genes in autism spectrum disorder: single- and multiple-hit genetic etiologies. PMID:24207117
Large-scale mass spectrometric detection of variant peptides resulting from nonsynonymous nucleotide differences. PMID:24175627
Exploring evolution of brain genes involved in microcephaly through phylogeny and synteny analysis. PMID:24148351
NSD1 mitigates caspase-1 activation by listeriolysin O in macrophages. PMID:24058709
PharmGKB summary: very important pharmacogene information for the epidermal growth factor receptor. PMID:23962910
GnpIS: an information system to integrate genetic and genomic data from plants and fungi. PMID:23959375
Identification of differentially evolved genes: an alternative approach to detection of accelerated molecular evolution from genome-wide comparative data. PMID:23926417
Unraveling genomic variation from next generation sequencing data. PMID:23885890
GEMINI: integrative exploration of genetic variation and genome annotations. PMID:23874191
Browsing (Epi)genomes: a guide to data resources and epigenome browsers for stem cell researchers. PMID:23827707
bioNerDS: exploring bioinformatics' database and software use through literature mining. PMID:23768135
Unravelling the hidden DNA structural/physical code provides novel insights on promoter location. PMID:23761436
Alternative splicing tends to avoid partial removals of protein-protein interaction sites. PMID:23758645
Computational framework to support integration of biomolecular and clinical data within a translational approach. PMID:23742129
Identification of novel arthropod vector G protein-coupled receptors. PMID:23705687
Equivalent indels--ambiguous functional classes and redundancy in databases. PMID:23658777
Hypertension and genetic variation in endothelial-specific genes. PMID:23637959
Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq. PMID:23629695
Peeling back the evolutionary layers of molecular mechanisms responsive to exercise-stress in the skeletal muscle of the racing horse. PMID:23580538
The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in GC. PMID:23558341
HCFC1 is a common component of active human CpG-island promoters and coincides with ZNF143, THAP11, YY1, and GABP transcription factor occupancy. PMID:23539139
Transcriptome sequencing of tumor subpopulations reveals a spectrum of therapeutic options for squamous cell lung cancer. PMID:23527012
Prediction of structure of human WNT-CRD (FZD) complex for computational drug repurposing. PMID:23372744
Finding protein-coding genes through human polymorphisms. PMID:23349826
Large-scale reverse docking profiles and their applications. PMID:23282219
Transcriptome-wide identification of A > I RNA editing sites by inosine specific cleavage. PMID:23264566
Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study. PMID:23237380
iPiG: integrating peptide spectrum matches into genome browser visualizations. PMID:23226516
Evaluating high-throughput ab initio gene finders to discover proteins encoded in eukaryotic pathogen genomes missed by laboratory techniques. PMID:23226328
Wiki-pi: a web-server of annotated human protein-protein interactions to aid in discovery of protein function. PMID:23209562
Variants affecting exon skipping contribute to complex traits. PMID:23133393
NOD2 Polymorphisms and Their Impact on Haematopoietic Stem Cell Transplant Outcome. PMID:23119165
29 mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome. PMID:22952639
Genome-wide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci. PMID:22923516
Human developmental enhancers conserved between deuterostomes and protostomes. PMID:22876195
Newly evolved introns in human retrogenes provide novel insights into their evolutionary roles. PMID:22839428
Purifying selection modulates the estimates of population differentiation and confounds genome-wide comparisons across single-nucleotide polymorphisms. PMID:22826460
Colon cancer associated genes exhibit signatures of positive selection at functionally significant positions. PMID:22788692
Expression sequence tag library derived from peripheral blood mononuclear cells of the chlorocebus sabaeus. PMID:22726727
IMGT-ONTOLOGY 2012. PMID:22654892
Comparative analysis and visualization of multiple collinear genomes. PMID:22536897
High levels of RNA-editing site conservation amongst 15 laboratory mouse strains. PMID:22524474
Fast homozygosity mapping and identification of a zebrafish ENU-induced mutation by whole-genome sequencing. PMID:22496837
Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function. PMID:22446687
Transcriptome analysis reveals the time of the fourth round of genome duplication in common carp (Cyprinus carpio). PMID:22424280
Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA. PMID:22344696
When one and one gives more than two: challenges and opportunities of integrative omics. PMID:22303399
Fishing the molecular bases of Treacher Collins syndrome. PMID:22295061
R-SAP: a multi-threading computational pipeline for the characterization of high-throughput RNA-sequencing data. PMID:22287631
ABrowse--a customizable next-generation genome browser framework. PMID:22222089
Organization, complexity and allelic diversity of the porcine (Sus scrofa domestica) immunoglobulin lambda locus. PMID:22186825
Overview of biological database mapping services for interoperation between different 'omics' datasets. PMID:22155608
Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88. PMID:22115825
Evolution of the porcine (Sus scrofa domestica) immunoglobulin kappa locus through germline gene conversion. PMID:22109540
The UCSC Genome Browser database: extensions and updates 2011. PMID:22086951
Segtor: rapid annotation of genomic coordinates and single nucleotide variations using segment trees. PMID:22069465
Deep proteome and transcriptome mapping of a human cancer cell line. PMID:22068331
gViz, a novel tool for the visualization of co-expression networks. PMID:22032859
No excess gene movement is detected off the avian or lepidopteran Z chromosome. PMID:22024813
Novel germline PALB2 truncating mutations in African American breast cancer patients. PMID:21932393
Retinal disease course in Usher syndrome 1B due to MYO7A mutations. PMID:21873662
A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data. PMID:21873452
Three periods of regulatory innovation during vertebrate evolution. PMID:21852499
Positive Darwinian selection drives the evolution of the morphology-related gene, EPCAM, in particularly species-rich lineages of African cichlid fishes. PMID:21811860
Exome sequencing identifies NBEAL2 as the causative gene for gray platelet syndrome. PMID:21765411
S3QL: a distributed domain specific language for controlled semantic integration of life sciences data. PMID:21756325
Extensive relationship between antisense transcription and alternative splicing in the human genome. PMID:21719572
Protein 4.1R regulates cell adhesion, spreading, migration and motility of mouse keratinocytes by modulating surface expression of beta1 integrin. PMID:21693581
Evolutionarily conserved bias of amino-acid usage refines the definition of PDZ-binding motif. PMID:21649932
ParkDB: a Parkinson's disease gene expression database. PMID:21593080
PSAR: measuring multiple sequence alignment reliability by probabilistic sampling. PMID:21576232
Integrating human genome database into electronic health record with sequence alignment and compression mechanism. PMID:21559844
DomainRBF: a Bayesian regression approach to the prioritization of candidate domains for complex diseases. PMID:21504591
MAISTAS: a tool for automatic structural evaluation of alternative splicing products. PMID:21498402
Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome. PMID:21460061
Rice-Map: a new-generation rice genome browser. PMID:21450055
Fast local fragment chaining using sum-of-pair gap costs. PMID:21418573
Knowledge management for systems biology a general and visually driven framework applied to translational medicine. PMID:21375767
FINDSITE-metal: integrating evolutionary information and machine learning for structure-based metal-binding site prediction at the proteome level. PMID:21287609
The gene regulatory cascade linking proneural specification with differentiation in Drosophila sensory neurons. PMID:21283833
RNA-seq analyses of blood-induced changes in gene expression in the mosquito vector species, Aedes aegypti. PMID:21276245
The Genomic HyperBrowser: inferential genomics at the sequence level. PMID:21182759
The PluriNetWork: an electronic representation of the network underlying pluripotency in mouse, and its applications. PMID:21179244
Expanding the landscape of chromatin modification (CM)-related functional domains and genes in human. PMID:21124763
LocDB: experimental annotations of localization for Homo sapiens and Arabidopsis thaliana. PMID:21071420
dbCRID: a database of chromosomal rearrangements in human diseases. PMID:21051346
Evaluation of SPARC as a candidate gene of juvenile-onset primary open-angle glaucoma by mutation and copy number analyses. PMID:21042566
The GMOD Drupal bioinformatic server framework. PMID:20971988
PathEx: a novel multi factors based datasets selector web tool. PMID:20969778
FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data. PMID:20964841
Ab initio identification of transcription start sites in the Rhesus macaque genome by histone modification and RNA-Seq. PMID:20952408
PEPPI: a peptidomic database of human protein isoforms for proteomics experiments. PMID:20946618
Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes. PMID:20929876
Murasaki: a fast, parallelizable algorithm to find anchors from multiple genomes. PMID:20885980
Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq. PMID:20617162
Using semantic web rules to reason on an ontology of pseudogenes. PMID:20529940
SOBA: sequence ontology bioinformatics analysis. PMID:20494974
Flanking region sequence information to refine microRNA target predictions. PMID:20413915
Detection of novel 3' untranslated region extensions with 3' expression microarrays. PMID:20346121
Testing the coding potential of conserved short genomic sequences. PMID:20224812
Mutations in Grxcr1 are the basis for inner ear dysfunction in the pirouette mouse. PMID:20137774
An integrated mass-spectrometry pipeline identifies novel protein coding-regions in the human genome. PMID:20126623
A unified method for purification of basic proteins. PMID:20109435
Integrating the multiple dimensions of genomic and epigenomic landscapes of cancer. PMID:20108112
SoyDB: a knowledge database of soybean transcription factors. PMID:20082720
Expression profiling of rainbow trout testis development identifies evolutionary conserved genes involved in spermatogenesis. PMID:19925684
Next-generation gap. PMID:19844227
KAIKObase: an integrated silkworm genome database and data mining tool. PMID:19843344
The completion of the Mammalian Gene Collection (MGC). PMID:19767417
Accurate discrimination of conserved coding and non-coding regions through multiple indicators of evolutionary dynamics. PMID:19737408
Forging links between human mental retardation-associated CNVs and mouse gene knockout models. PMID:19557186
Validation of a primer optimisation matrix to improve the performance of reverse transcription - quantitative real-time PCR assays. PMID:19549292
OmicBrowse: a Flash-based high-performance graphics interface for genomic resources. PMID:19528066
Development of an integrative database with 499 novel microsatellite markers for Macaca fascicularis. PMID:19497132
Evidence of maternal QTL affecting growth and obesity in adult mice. PMID:19399551
Gene expression during the oocyte-to-embryo transition in mammals. PMID:19363788
Molecular evolution of the junctophilin gene family. PMID:19318539
Angiotensin-converting enzyme is a modifier of hypertensive end organ damage. PMID:19307186
Next generation tools for the annotation of human SNPs. PMID:19181721
Studying alternative splicing regulatory networks through partial correlation analysis. PMID:19133160
Inferring selection on amino acid preference in protein domains. PMID:19095755
Genotype-phenotype databases: challenges and solutions for the post-genomic era. PMID:19065136
The HuRef Browser: a web resource for individual human genomics. PMID:19036787
Ensembl 2009. PMID:19033362
Fast gene ontology based clustering for microarray experiments. PMID:19025591
Accurate whole human genome sequencing using reversible terminator chemistry. PMID:18987734
HGVbaseG2P: a central genetic association database. PMID:18948288
Quality of regulatory elements in Drosophila retrogenes. PMID:18848618
Prioritization of candidate cancer genes--an aid to oncogenomic studies. PMID:18710882
The Synergizer service for translating gene, protein and other biological identifiers. PMID:18697767
Reduced purifying selection prevails over positive selection in human copy number variant evolution. PMID:18687881
Transcriptional regulatory network analysis during epithelial-mesenchymal transformation of retinal pigment epithelium. PMID:18682805
Identify alternative splicing events based on position-specific evolutionary conservation. PMID:18665247
Towards Interoperability in Genome Databases: The MAtDB (MIPS Arabidopsis Thaliana Database) Experience. PMID:18629123
The Gene Ontology Annotation (GOA) Project--Application of GO in SWISS-PROT, TrEMBL and InterPro. PMID:18629103
The Xenopus FcR family demonstrates continually high diversification of paired receptors in vertebrate evolution. PMID:18485190
Conserved co-expression for candidate disease gene prioritization. PMID:18433471
Chromosomal gene movements reflect the recent origin and biology of therian sex chromosomes. PMID:18384235
Neocentromeres: new insights into centromere structure, disease development, and karyotype evolution. PMID:18252209
In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators. PMID:18052534
Genome-wide changes in expression profile of murine endogenous retroviruses (MuERVs) in distant organs after burn injury. PMID:18045489
Immunoglobulin light chain (IgL) genes in zebrafish: Genomic configurations and inversional rearrangements between (V(L)-J(L)-C(L)) gene clusters. PMID:18022691
The vertebrate genome annotation (Vega) database. PMID:18003653
Lactation transcriptomics in the Australian marsupial, Macropus eugenii: transcript sequencing and quantification. PMID:17997866
Regulatory evolution in proteins by turnover and lineage-specific changes of cyclin-dependent kinase consensus sites. PMID:17978194
Characterization of oligopeptide patterns in large protein sets. PMID:17908308
Linking microarray reporters with protein functions. PMID:17897448
Deep analysis of cellular transcriptomes - LongSAGE versus classic MPSS. PMID:17892551
An immune response gene expression module identifies a good prognosis subtype in estrogen receptor negative breast cancer. PMID:17683518
oPOSSUM: integrated tools for analysis of regulatory motif over-representation. PMID:17576675
Genome-wide association study identifies novel breast cancer susceptibility loci. PMID:17529967
ProtSweep, 2Dsweep and DomainSweep: protein analysis suite at DKFZ. PMID:17526514
Discovery of tissue-specific exons using comprehensive human exon microarrays. PMID:17456239
A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection. PMID:17395691
Species-specific evolution of the FcR family in endothermic vertebrates. PMID:17356879
Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase. PMID:17316440
TICdb: a collection of gene-mapped translocation breakpoints in cancer. PMID:17257420
DiscoverySpace: an interactive data analysis application. PMID:17210078
CYCLONET--an integrated database on cell cycle regulation and carcinogenesis. PMID:17202170
A consensus prognostic gene expression classifier for ER positive breast cancer. PMID:17076897
Local mutagenic impact of insertions of LTR retrotransposons on the mouse genome. PMID:17075698
CAFTAN: a tool for fast mapping, and quality assessment of cDNAs. PMID:17064411
MMASS: an optimized array-based method for assessing CpG island methylation. PMID:17041235
Relating tissue specialization to the differentiation of expression of singleton and duplicate mouse proteins. PMID:17029626
yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes. PMID:16859520
AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system. PMID:16855290
Chromosome-wide identification of novel imprinted genes using microarrays and uniparental disomies. PMID:16855283
Differences in the evolutionary history of disease genes affected by dominant or recessive mutations. PMID:16817963
BioMediator data integration: beyond genomics to neuroscience data. PMID:16779146
The abundance of short proteins in the mammalian proteome. PMID:16683031
Pseudo-messenger RNA: phantoms of the transcriptome. PMID:16683022
Predicting deleterious nsSNPs: an analysis of sequence and structural attributes. PMID:16630345
Predicting disease genes using protein-protein interactions. PMID:16611749
Crystal structure of Homo sapiens PTD012 reveals a zinc-containing hydrolase fold. PMID:16522806
Tracking the evolution of alternatively spliced exons within the Dscam family. PMID:16483367
Bias of selection on human copy-number variants. PMID:16482228
Role of positive selection in the retention of duplicate genes in mammalian genomes. PMID:16461903
MitoRes: a resource of nuclear-encoded mitochondrial genes and their products in Metazoa. PMID:16433928
Molecular processes during fat cell development revealed by gene expression profiling and functional annotation. PMID:16420668
Micro-array analyses decipher exceptional complex familial chromosomal rearrangement. PMID:16395598
Heterogeneous duplications in patients with Pelizaeus-Merzbacher disease suggest a mechanism of coupled homologous and nonhomologous recombination. PMID:16380909
Systematic genome-wide annotation of spliceosomal proteins reveals differential gene family expansion. PMID:16344558
Abundant novel transcriptional units and unconventional gene pairs on human chromosome 22. PMID:16344557
Mapping and characterization of the amplicon near APOA2 in 1q23 in human sarcomas by FISH and array CGH. PMID:16274472
Emergence of young human genes after a burst of retroposition in primates. PMID:16201836
Diversification of stem cell molecular repertoire by alternative splicing. PMID:16183747
Functional coverage of the human genome by existing structures, structural genomics targets, and homology models. PMID:16118666
A sequence sub-sampling algorithm increases the power to detect distant homologues. PMID:16006623
Structural genomics of human proteins--target selection and generation of a public catalogue of expression clones. PMID:15998469
FACT--a framework for the functional interpretation of high-throughput experiments. PMID:15985174
RPBS: a web resource for structural bioinformatics. PMID:15980507
PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families. PMID:15980440
Substantial regional variation in substitution rates in the human genome: importance of GC content, gene density, and telomere-specific effects. PMID:15959677
Protein length in eukaryotic and prokaryotic proteomes. PMID:15951512
Satellog: a database for the identification and prioritization of satellite repeats in disease association studies. PMID:15949044
Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals. PMID:15882449
Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser. PMID:15826305
NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence. PMID:15760844
FISH analysis of hematological neoplasias with 1p36 rearrangements allows the definition of a cluster of 2.5 Mb included in the minimal region deleted in 1p36 deletion syndrome. PMID:15744521
Gene expression profiling in murine autoimmune arthritis during the initiation and progression of joint inflammation. PMID:15743466
Protein coding potential of retroviruses and other transposable elements in vertebrate genomes. PMID:15716312
Characterization of a centromeric marker on mouse chromosome 11 and its introgression in a domesticus/musculus hybrid zone. PMID:15672596
Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases. PMID:15642112
Significant expansion of exon-bordering protein domains during animal proteome evolution. PMID:15640447
Gene and alternative splicing annotation with AIR. PMID:15632090
The Rat Genome Database (RGD): developments towards a phenome database. PMID:15608243
The Universal Protein Resource (UniProt). PMID:15608167
PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization. PMID:15608166
Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics. PMID:15601538
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
Consensus clustering and functional interpretation of gene-expression data. PMID:15535870
Systematic recovery and analysis of full-ORF human cDNA clones. PMID:15489330
Divergence of spatial gene expression profiles following species-specific gene duplications in human and mouse. PMID:15466287
A comprehensive transcript index of the human genome generated using microarrays and computational approaches. PMID:15461792
Fast and effective prediction of microRNA/target duplexes. PMID:15383676
What can we learn from noncoding regions of similarity between genomes? PMID:15369604
Genetic analysis of X-linked hybrid sterility in the house mouse. PMID:15366371
Organization and evolution of a gene-rich region of the mouse genome: a 12.7-Mb region deleted in the Del(13)Svea36H mouse. PMID:15364904
A catalog of human cDNA expression clones and its application to structural genomics. PMID:15345055
Effects of G-protein mutations on skin color. PMID:15322542
The Alternative Splicing Gallery (ASG): bridging the gap between genome and transcriptome. PMID:15292448
C-type lectin-like domains in Fugu rubripes. PMID:15285787
Global survey of chromatin accessibility using DNA microarrays. PMID:15231753
Low number of mitochondrial pseudogenes in the chicken (Gallus gallus) nuclear genome: implications for molecular inference of population history and phylogenetics. PMID:15219233
Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations. PMID:15215412
ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes. PMID:15215395
POBO, transcription factor binding site verification with bootstrapping. PMID:15215385
ASmodeler: gene modeling of alternative splicing from genomic alignment of mRNA, EST and protein sequences. PMID:15215376
SNPbox: web-based high-throughput primer design from gene to genome. PMID:15215373
Public web-based services from the European Bioinformatics Institute. PMID:15215339
Structure-function evolution of the transforming acidic coiled coil genes revealed by analysis of phylogenetically diverse organisms. PMID:15207008
Genome-wide identification of genes likely to be involved in human genetic disease. PMID:15181176
eShadow: a tool for comparing closely related sequences. PMID:15173121
Genomic regionality in rates of evolution is not explained by clustering of genes of comparable expression profile. PMID:15173108
Comprehensive analysis of the base composition around the transcription start site in Metazoa. PMID:15171795
Complete MHC haplotype sequencing for common disease gene mapping. PMID:15140828
eL-DASionator: an LDAS upload file generator. PMID:15132760
Sockeye: a 3D environment for comparative genomics. PMID:15123592
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PMID:15103394
Pegasys: software for executing and integrating analyses of biological sequences. PMID:15096276
Visualization of multiple genome annotations and alignments with the K-BROWSER. PMID:15060015
Automated whole-genome multiple alignment of rat, mouse, and human. PMID:15060011
Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing. PMID:15060008
Evolution and comparative genomics of odorant- and pheromone-associated genes in rodents. PMID:15060000
Occurrence and consequences of coding sequence insertions and deletions in Mammalian genomes. PMID:15059996
The DNA sequence and analysis of human chromosome 13. PMID:15057823
Identifying transcriptional regulatory sites in the human genome using an integrated system. PMID:15051813
FRAGS: estimation of coding sequence substitution rates from fragmentary data. PMID:15005802
Diverse and specific gene expression responses to stresses in cultured human cells. PMID:15004229
A functional domain of Dof that is required for fibroblast growth factor signaling. PMID:14993266
Identification of biochemical adaptations in hyper- or hypocontractile hearts from phospholamban mutant mice by expression proteomics. PMID:14982994
Numerous novel annotations of the human genome sequence supported by a 5'-end-enriched cDNA collection. PMID:14962985
Genomic shotgun array: a procedure linking large-scale DNA sequencing with regional transcript mapping. PMID:14960710
The bioinformatics challenges in comparative analysis of cereal genomes-an overview. PMID:14770300
Gene structure conservation aids similarity based gene prediction. PMID:14764925
Large-scale identification of disease genes involved in acute myeloid leukemia. PMID:14747562
MicroRNA targets in Drosophila. PMID:14709173
EnsMart: a generic system for fast and flexible access to biological data. PMID:14707178
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
The mouse Gene Expression Database (GXD): updates and enhancements. PMID:14681482
The Centre for Modeling Human Disease Gene Trap resource. PMID:14681480
SNP500Cancer: a public resource for sequence validation and assay development for genetic variation in candidate genes. PMID:14681474
HGVbase: a curated resource describing human DNA variation and phenotype relationships. PMID:14681471
BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics. PMID:14681438
UniProt: the Universal Protein knowledgebase. PMID:14681372
A genome-wide survey of human pseudogenes. PMID:14656963
Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. PMID:14656962
The German cDNA network: cDNAs, functional genomics and proteomics. PMID:14649292
The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PMID:14624247
Bioinformatics Resources for In Silico Proteome Analysis. PMID:14615630
Fugu ESTs: new resources for transcription analysis and genome annotation. PMID:14613980
Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates. PMID:14611660
GeneViTo: visualizing gene-product functional and structural features in genomic datasets. PMID:14594459
Exegesis: a procedure to improve gene predictions and its use to find immunoglobulin superfamily proteins in the human and mouse genomes. PMID:14576296
Functionality of system components: conservation of protein function in protein feature space. PMID:14559779
Single nucleotide variation analysis in 65 candidate genes for CNS disorders in a representative sample of the European population. PMID:14525928
Transposon mutagenesis of the mouse germline. PMID:14504232
cDNA2Genome: a tool for mapping and annotating cDNAs. PMID:12964951
Fugu rubripes possesses genes for the entire set of the ITAM-bearing transmembrane signal subunits. PMID:12955357
GANESH: software for customized annotation of genome regions. PMID:12952886
Different evolutionary patterns between young duplicate genes in the human genome. PMID:12952535
Computational identification of protein coding potential of conserved sequence tags through cross-species evolutionary analysis. PMID:12888525
Biopipe: a flexible framework for protocol-based bioinformatics analysis. PMID:12869579
The 2R hypothesis and the human genome sequence. PMID:12836689
OntoBlast function: From sequence similarities directly to potential functional annotations by ontology terms. PMID:12824422
FIE2: A program for the extraction of genomic DNA sequences around the start and translation initiation site of human genes. PMID:12824363
GenePublisher: Automated analysis of DNA microarray data. PMID:12824347
Connecting sequence and biology in the laboratory mouse. PMID:12819150
GeneLynx mouse: integrated portal to the mouse genome. PMID:12819149
Identification and analysis of chromodomain-containing proteins encoded in the mouse transcriptome. PMID:12819141
Mouse proteome analysis. PMID:12819131
Cytokine-related genes identified from the RIKEN full-length mouse cDNA data set. PMID:12819128
Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs. PMID:12783626
Human-mouse gene identification by comparative evidence integration and evolutionary analysis. PMID:12743024
Conservation of human alternative splice events in mouse. PMID:12736303
Duplication and selection in the evolution of primate beta-defensin genes. PMID:12734011
DAVID: Database for Annotation, Visualization, and Integrated Discovery. PMID:12734009
Otubains: a new family of cysteine proteases in the ubiquitin pathway. PMID:12704427
ProSplicer: a database of putative alternative splicing information derived from protein, mRNA and expressed sequence tag sequence data. PMID:12702210
Comparative genomic tools and databases: providing insights into the human genome. PMID:12697725
GALA, a database for genomic sequence alignments and annotations. PMID:12671007
The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. PMID:12654719
Toucan: deciphering the cis-regulatory logic of coregulated genes. PMID:12626717
The transcriptional activity of human Chromosome 22. PMID:12600945
Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes. PMID:12552088
Apollo: a sequence annotation editor. PMID:12537571
Strategies and tools for whole-genome alignments. PMID:12529308
Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map. PMID:12529305
Cross-species sequence comparisons: a review of methods and available resources. PMID:12529301
The Proteome Analysis database: a tool for the in silico analysis of whole proteomes. PMID:12520037
SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. PMID:12519986
MOsDB: an integrated information resource for rice genomics. PMID:12519979
Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE. PMID:12519968
The SNP Consortium website: past, present and future. PMID:12519964
MTID: a database of Sleeping Beauty transposon insertions in mice. PMID:12519952
ParaDB: a tool for paralogy mapping in vertebrate genomes. PMID:12519948
CORG: a database for COmparative Regulatory Genomics. PMID:12519946
The UCSC Genome Browser Database. PMID:12519945
The European Bioinformatics Institute's data resources. PMID:12519944
Ensembl 2002: accommodating comparative genomics. PMID:12519943
The EMBL Nucleotide Sequence Database: major new developments. PMID:12519939
SeqVISTA: a graphical tool for sequence feature visualization and comparison. PMID:12513700
Cynomolgus monkey testicular cDNAs for discovery of novel human genes in the human genome sequence. PMID:12498619
ORFer--retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files. PMID:12493080
Functional second genes generated by retrotransposition of the X-linked ribosomal protein genes. PMID:12490704
Genomic expansion and clustering of ZAD-containing C2H2 zinc-finger genes in Drosophila. PMID:12446571
Signatures of domain shuffling in the human genome. PMID:12421750
A major susceptibility locus for systemic lupus erythemathosus maps to chromosome 1q31. PMID:12373647
The Bioperl toolkit: Perl modules for the life sciences. PMID:12368254
The generic genome browser: a building block for a model organism system database. PMID:12368253
Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. PMID:12368239
Current methods of gene prediction, their strengths and weaknesses. PMID:12364589
Genomic rearrangements resulting in PLP1 deletion occur by nonhomologous end joining and cause different dysmyelinating phenotypes in males and females. PMID:12297985
Prediction of MHC class I binding peptides, using SVMHC. PMID:12225620
Sushi gets serious: the draft genome sequence of the pufferfish Fugu rubripes. PMID:12225591
Impact of the presence of paralogs on sequence divergence in a set of mouse-human orthologs. PMID:12213774
Exploring alternative models for sex-linked quantitative trait loci in outbred populations: application to an iberian x landrace pig intercross. PMID:12196405
Large-scale protein annotation through gene ontology. PMID:11997345
Search and retrieve. Large-scale data generation is becoming increasingly important in biological research. But how good are the tools to make sense of the data? PMID:11991940
The EMBL Nucleotide Sequence Database. PMID:11752244
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sequence assembly
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:42.880153
whole genome sequencing
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:42.880153
genomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:42.880153
human biology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:42.880153
gene transcripts
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:42.880153
Tags
More detailed information about this field from each metasource.
sequence assembly
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:42.880153
whole genome sequencing
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:42.880153
genomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:42.880153
human biology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:42.880153
gene transcripts
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:42.880153
sequence assembly whole genome sequencing genomics human gene transcripts
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