Published in Nucleic Acids Res on November 25, 2008
International network of cancer genome projects. Nature (2010) 20.35
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res (2010) 18.73
Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res (2011) 18.50
The UCSC Genome Browser database: update 2010. Nucleic Acids Res (2009) 16.58
Transcriptome genetics using second generation sequencing in a Caucasian population. Nature (2010) 14.85
Ensembl 2012. Nucleic Acids Res (2011) 14.55
Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res (2010) 11.32
Ensembl's 10th year. Nucleic Acids Res (2009) 10.82
The IntAct molecular interaction database in 2010. Nucleic Acids Res (2009) 9.85
De novo assembly and analysis of RNA-seq data. Nat Methods (2010) 9.69
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res (2009) 9.14
BioMart Central Portal--unified access to biological data. Nucleic Acids Res (2009) 9.06
Ensembl 2015. Nucleic Acids Res (2014) 8.30
Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines. Cell (2011) 8.21
ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Res (2010) 7.67
Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science (2010) 7.41
MINT, the molecular interaction database: 2009 update. Nucleic Acids Res (2009) 7.19
The evolution of gene expression levels in mammalian organs. Nature (2011) 7.16
Savant: genome browser for high-throughput sequencing data. Bioinformatics (2010) 6.51
iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol (2010) 5.98
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res (2009) 5.90
genenames.org: the HGNC resources in 2011. Nucleic Acids Res (2010) 5.77
A guide to the Proteomics Identifications Database proteomics data repository. Proteomics (2009) 5.63
Deep proteome and transcriptome mapping of a human cancer cell line. Mol Syst Biol (2011) 5.48
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief Bioinform (2009) 5.44
MEROPS: the peptidase database. Nucleic Acids Res (2009) 5.33
WormBase: a comprehensive resource for nematode research. Nucleic Acids Res (2009) 5.20
Ensembl Genomes: extending Ensembl across the taxonomic space. Nucleic Acids Res (2009) 5.09
Alternative expression analysis by RNA sequencing. Nat Methods (2010) 5.02
Gene expression atlas at the European bioinformatics institute. Nucleic Acids Res (2009) 4.99
Characterising and predicting haploinsufficiency in the human genome. PLoS Genet (2010) 4.85
A ChIP-seq defined genome-wide map of vitamin D receptor binding: associations with disease and evolution. Genome Res (2010) 4.77
A database and API for variation, dense genotyping and resequencing data. BMC Bioinformatics (2010) 4.68
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Res (2009) 4.55
The Proteomics Identifications database: 2010 update. Nucleic Acids Res (2009) 4.47
starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res (2013) 4.33
Fast and efficient searching of biological data resources--using EB-eye. Brief Bioinform (2010) 4.19
GenomeGraphs: integrated genomic data visualization with R. BMC Bioinformatics (2009) 4.16
Insights into hominid evolution from the gorilla genome sequence. Nature (2012) 4.12
MicroScope: a platform for microbial genome annotation and comparative genomics. Database (Oxford) (2009) 3.87
WormBase 2012: more genomes, more data, new website. Nucleic Acids Res (2011) 3.87
Web services at the European Bioinformatics Institute-2009. Nucleic Acids Res (2009) 3.78
Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nat Protoc (2009) 3.77
The characterization of twenty sequenced human genomes. PLoS Genet (2010) 3.72
Effects of thymic selection of the T-cell repertoire on HLA class I-associated control of HIV infection. Nature (2010) 3.57
FRT-seq: amplification-free, strand-specific transcriptome sequencing. Nat Methods (2010) 3.55
A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data. Nucleic Acids Res (2009) 3.50
A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Mol Cell Proteomics (2011) 3.37
RATT: Rapid Annotation Transfer Tool. Nucleic Acids Res (2011) 3.29
Massively parallel sequencing and rare disease. Hum Mol Genet (2010) 3.28
Genetic analysis of complex traits in the emerging Collaborative Cross. Genome Res (2011) 3.25
Genome-wide association of hypoxia-inducible factor (HIF)-1alpha and HIF-2alpha DNA binding with expression profiling of hypoxia-inducible transcripts. J Biol Chem (2009) 3.23
The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium. Nucleic Acids Res (2010) 3.23
Noisy splicing drives mRNA isoform diversity in human cells. PLoS Genet (2010) 3.19
Ensembl variation resources. BMC Genomics (2010) 3.17
A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs. Nat Protoc (2012) 3.17
Next generation software for functional trend analysis. Bioinformatics (2009) 3.01
Defining the transcriptome and proteome in three functionally different human cell lines. Mol Syst Biol (2010) 3.00
Genomic distribution and inter-sample variation of non-CpG methylation across human cell types. PLoS Genet (2011) 2.98
A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling. BMC Genomics (2010) 2.95
BioMart: a data federation framework for large collaborative projects. Database (Oxford) (2011) 2.90
Global survey of escape from X inactivation by RNA-sequencing in mouse. Genome Res (2010) 2.87
Hippocampal atrophy as a quantitative trait in a genome-wide association study identifying novel susceptibility genes for Alzheimer's disease. PLoS One (2009) 2.85
REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila. Nucleic Acids Res (2010) 2.84
Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nat Genet (2013) 2.76
Gitools: analysis and visualisation of genomic data using interactive heat-maps. PLoS One (2011) 2.74
The Microbe browser for comparative genomics. Nucleic Acids Res (2009) 2.71
Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proc Biol Sci (2012) 2.68
PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci. BMC Bioinformatics (2010) 2.65
Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biol (2010) 2.60
eHive: an artificial intelligence workflow system for genomic analysis. BMC Bioinformatics (2010) 2.52
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. Nucleic Acids Res (2010) 2.41
Xenbase: gene expression and improved integration. Nucleic Acids Res (2009) 2.38
Gene3D: merging structure and function for a Thousand genomes. Nucleic Acids Res (2009) 2.34
Conserved principles of mammalian transcriptional regulation revealed by RNA half-life. Nucleic Acids Res (2009) 2.26
A genome-wide characterization of microRNA genes in maize. PLoS Genet (2009) 2.23
The completion of the Mammalian Gene Collection (MGC). Genome Res (2009) 2.21
EMAGE mouse embryo spatial gene expression database: 2010 update. Nucleic Acids Res (2009) 2.16
Deep sequencing of RNA from immune cell-derived vesicles uncovers the selective incorporation of small non-coding RNA biotypes with potential regulatory functions. Nucleic Acids Res (2012) 2.15
SyMAP v3.4: a turnkey synteny system with application to plant genomes. Nucleic Acids Res (2011) 2.08
Dalliance: interactive genome viewing on the web. Bioinformatics (2011) 2.07
Mapping the human membrane proteome: a majority of the human membrane proteins can be classified according to function and evolutionary origin. BMC Biol (2009) 2.07
The mouse Gene Expression Database (GXD): 2011 update. Nucleic Acids Res (2010) 2.07
MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons. PLoS One (2011) 2.06
HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology. Mol Syst Biol (2010) 2.05
The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. BMC Bioinformatics (2010) 2.03
Using caching and optimization techniques to improve performance of the Ensembl website. BMC Bioinformatics (2010) 1.95
Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme. Genome Med (2010) 1.94
Annotating genes and genomes with DNA sequences extracted from biomedical articles. Bioinformatics (2011) 1.91
GenomeView: a next-generation genome browser. Nucleic Acids Res (2011) 1.91
The origins and evolution of the p53 family of genes. Cold Spring Harb Perspect Biol (2009) 1.90
A pipeline for RNA-seq data processing and quality assessment. Bioinformatics (2011) 1.85
i-GSEA4GWAS: a web server for identification of pathways/gene sets associated with traits by applying an improved gene set enrichment analysis to genome-wide association study. Nucleic Acids Res (2010) 1.83
NAViGaTing the micronome--using multiple microRNA prediction databases to identify signalling pathway-associated microRNAs. PLoS One (2011) 1.80
deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res (2009) 1.78
EMMA--mouse mutant resources for the international scientific community. Nucleic Acids Res (2009) 1.75
Mutations in PCYT1A, encoding a key regulator of phosphatidylcholine metabolism, cause spondylometaphyseal dysplasia with cone-rod dystrophy. Am J Hum Genet (2014) 1.66
In-depth annotation of SNPs arising from resequencing projects using NGS-SNP. Bioinformatics (2011) 1.64
Mechanisms that determine the internal environment of the developing brain: a transcriptomic, functional and ultrastructural approach. PLoS One (2013) 1.64
Birth and expression evolution of mammalian microRNA genes. Genome Res (2012) 1.64
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature (2007) 144.95
High-resolution profiling of histone methylations in the human genome. Cell (2007) 85.74
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res (2006) 48.10
The distributed annotation system. BMC Bioinformatics (2001) 42.98
The Ensembl genome database project. Nucleic Acids Res (2002) 40.87
Population genomics of human gene expression. Nat Genet (2007) 24.49
The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res (2007) 23.13
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2007) 22.53
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol (2008) 21.72
Ensembl 2008. Nucleic Acids Res (2007) 20.67
Ensembl 2007. Nucleic Acids Res (2006) 20.10
Distribution and intensity of constraint in mammalian genomic sequence. Genome Res (2005) 18.85
Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet (2008) 18.28
EnsMart: a generic system for fast and flexible access to biological data. Genome Res (2004) 17.64
The universal protein resource (UniProt). Nucleic Acids Res (2007) 16.33
Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21
GENCODE: producing a reference annotation for ENCODE. Genome Biol (2006) 15.08
Optimized design and assessment of whole genome tiling arrays. Bioinformatics (2007) 11.38
Distinguishing protein-coding and noncoding genes in the human genome. Proc Natl Acad Sci U S A (2007) 8.00
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature (2007) 7.91
The vertebrate genome annotation (Vega) database. Nucleic Acids Res (2007) 7.53
Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Res (2008) 7.35
The HGNC Database in 2008: a resource for the human genome. Nucleic Acids Res (2007) 7.29
EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol (2006) 7.06
TreeFam: 2008 Update. Nucleic Acids Res (2007) 6.63
Integrating biological data--the Distributed Annotation System. BMC Bioinformatics (2008) 6.56
Progress and prospects in rat genetics: a community view. Nat Genet (2008) 6.01
Genome analysis of the platypus reveals unique signatures of evolution. Nature (2008) 5.74
Genome-wide nucleotide-level mammalian ancestor reconstruction. Genome Res (2008) 5.12
An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Res (2008) 4.84
Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res (2007) 4.33
The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93
Detecting amino acid sites under positive selection and purifying selection. Genetics (2005) 3.35
TranscriptSNPView: a genome-wide catalog of mouse coding variation. Nat Genet (2006) 3.10
SNP and haplotype mapping for genetic analysis in the rat. Nat Genet (2008) 2.96
What everybody should know about the rat genome and its online resources. Nat Genet (2008) 1.94
Genome browsing with Ensembl: a practical overview. Brief Funct Genomic Proteomic (2007) 1.93
Initial sequencing and analysis of the human genome. Nature (2001) 212.86
EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet (2000) 69.26
The Pfam protein families database. Nucleic Acids Res (2000) 42.28
The Ensembl genome database project. Nucleic Acids Res (2002) 40.87
Gene-expression profiles in hereditary breast cancer. N Engl J Med (2001) 29.80
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature (2002) 28.79
Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins (1997) 26.91
Comparative genomics of the eukaryotes. Science (2000) 26.62
A colony bank containing synthetic Col El hybrid plasmids representative of the entire E. coli genome. Cell (1976) 26.20
The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res (2001) 24.45
Role of AMP-activated protein kinase in mechanism of metformin action. J Clin Invest (2001) 23.21
Ensembl 2008. Nucleic Acids Res (2007) 20.67
Ensembl 2007. Nucleic Acids Res (2006) 20.10