Published in Database (Oxford) on October 19, 2011
International Cancer Genome Consortium Data Portal--a one-stop shop for cancer genomics data. Database (Oxford) (2011) 4.53
BioMart: driving a paradigm change in biological data management. Database (Oxford) (2011) 4.32
BioMart Central Portal: an open database network for the biological community. Database (Oxford) (2011) 3.03
BioMart: a data federation framework for large collaborative projects. Database (Oxford) (2011) 2.90
The InterPro BioMart: federated query and web service access to the InterPro Resource. Database (Oxford) (2011) 1.75
Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations. Database (Oxford) (2011) 1.32
Genomic analyses with biofilter 2.0: knowledge driven filtering, annotation, and model development. BioData Min (2013) 1.15
BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology. Nucleic Acids Res (2015) 1.07
Integrative variable selection via Bayesian model uncertainty. Stat Med (2013) 1.00
Profiling microRNAs in lung tissue from pigs infected with Actinobacillus pleuropneumoniae. BMC Genomics (2012) 0.96
Genome-wide analysis of LXRα activation reveals new transcriptional networks in human atherosclerotic foam cells. Nucleic Acids Res (2013) 0.95
Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments. Mol Cell Proteomics (2012) 0.92
Mismatch repair deficiency endows tumors with a unique mutation signature and sensitivity to DNA double-strand breaks. Elife (2014) 0.82
Development of an undergraduate bioinformatics degree program at a liberal arts college. Yale J Biol Med (2012) 0.77
Reconstruction of Danio rerio metabolic model accounting for subcellular compartmentalisation. PLoS One (2012) 0.75
In silico analysis of the transportome in human pancreatic ductal adenocarcinoma. Eur Biophys J (2016) 0.75
Bioconductor: open software development for computational biology and bioinformatics. Genome Biol (2004) 143.19
Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res (2003) 103.76
A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39
KEGG for linking genomes to life and the environment. Nucleic Acids Res (2007) 49.37
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol (2010) 39.63
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics (2003) 32.92
COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res (2010) 25.55
International network of cancer genome projects. Nature (2010) 20.35
Reactome: a knowledgebase of biological pathways. Nucleic Acids Res (2005) 20.05
The UCSC Genome Browser database: update 2011. Nucleic Acids Res (2010) 16.24
Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res (2008) 15.69
Ensembl 2011. Nucleic Acids Res (2010) 14.68
Reactome: a knowledge base of biologic pathways and processes. Genome Biol (2007) 13.36
The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res (2009) 11.49
A new bioinformatics analysis tools framework at EMBL-EBI. Nucleic Acids Res (2010) 11.42
Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res (2010) 11.23
BioMart--biological queries made easy. BMC Genomics (2009) 11.06
BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics (2005) 9.84
The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19
Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res (2010) 9.09
BioMart Central Portal--unified access to biological data. Nucleic Acids Res (2009) 9.06
Infrastructure for the life sciences: design and implementation of the UniProt website. BMC Bioinformatics (2009) 8.87
The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species. PLoS Comput Biol (2009) 7.95
PubMed: bridging the information gap. CMAJ (2001) 6.49
International Cancer Genome Consortium Data Portal--a one-stop shop for cancer genomics data. Database (Oxford) (2011) 4.53
VectorBase: a data resource for invertebrate vector genomics. Nucleic Acids Res (2008) 3.73
The PSI-MOD community standard for representation of protein modification data. Nat Biotechnol (2008) 3.38
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
BioMart Central Portal: an open database network for the biological community. Database (Oxford) (2011) 3.03
BioMart: a data federation framework for large collaborative projects. Database (Oxford) (2011) 2.90
Data mining using the Catalogue of Somatic Mutations in Cancer BioMart. Database (Oxford) (2011) 2.84
Protégé-2000: an open-source ontology-development and knowledge-acquisition environment. AMIA Annu Symp Proc (2003) 2.73
Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations. Database (Oxford) (2011) 1.32
ChEBI: an open bioinformatics and cheminformatics resource. Curr Protoc Bioinformatics (2009) 1.24
The systematic annotation of the three main GPCR families in Reactome. Database (Oxford) (2010) 1.09
BioMart as an integration solution for the International Knockout Mouse Consortium. Database (Oxford) (2011) 0.96
PRIDE: Data submission and analysis. Curr Protoc Protein Sci (2010) 0.87
A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39
The Bioperl toolkit: Perl modules for the life sciences. Genome Res (2002) 58.63
The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol (2008) 31.04
International network of cancer genome projects. Nature (2010) 20.35
Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27
Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat Genet (2010) 16.96
Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res (2008) 15.69
Reactome: a knowledge base of biologic pathways and processes. Genome Biol (2007) 13.36
The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol (2003) 13.32
The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res (2012) 13.14
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol (2008) 12.96
Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39
A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol (2004) 11.42
Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res (2010) 11.23
The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol (2007) 10.24
The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19
The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics (2006) 8.68
The Reactome pathway knowledgebase. Nucleic Acids Res (2013) 8.56
Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes. Nature (2012) 8.31
The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol (2007) 8.24
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol (2007) 8.03
PRIDE: the proteomics identifications database. Proteomics (2005) 7.52
The IntAct molecular interaction database in 2012. Nucleic Acids Res (2011) 7.49
Calling on a million minds for community annotation in WikiProteins. Genome Biol (2008) 7.11
WormBase: better software, richer content. Nucleic Acids Res (2006) 6.78
JBrowse: a next-generation genome browser. Genome Res (2009) 6.77
Integrating biological data--the Distributed Annotation System. BMC Bioinformatics (2008) 6.56
The International HapMap Project Web site. Genome Res (2005) 5.96
A guide to the Proteomics Identifications Database proteomics data repository. Proteomics (2009) 5.63
WormBase: a cross-species database for comparative genomics. Nucleic Acids Res (2003) 5.28
WormBase: a comprehensive resource for nematode research. Nucleic Acids Res (2009) 5.20
PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat Methods (2011) 5.01
mzML--a community standard for mass spectrometry data. Mol Cell Proteomics (2010) 4.81
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries. Nucleic Acids Res (2008) 4.73
Toward interoperable bioscience data. Nat Genet (2012) 4.72
The Proteomics Identifications database: 2010 update. Nucleic Acids Res (2009) 4.47
PRIDE: new developments and new datasets. Nucleic Acids Res (2007) 4.42
The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res (2013) 4.39
PRIDE: a public repository of protein and peptide identifications for the proteomics community. Nucleic Acids Res (2006) 4.19
WormBase: a multi-species resource for nematode biology and genomics. Nucleic Acids Res (2004) 4.14
WormBase: new content and better access. Nucleic Acids Res (2006) 4.01
The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases. BMC Bioinformatics (2007) 3.97
The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93
WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. Nucleic Acids Res (2005) 3.82
The proteomics standards initiative. Proteomics (2003) 3.78
Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles. J Proteome Res (2009) 3.77
The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible. Expert Rev Proteomics (2006) 3.74
The Protein Ontology: a structured representation of protein forms and complexes. Nucleic Acids Res (2010) 3.74
Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO-Proteomics Standards Initiative April 23-25, 2007 Ecole Nationale Supérieure (ENS), Lyon, France. Proteomics (2007) 3.69
WormBase 2007. Nucleic Acids Res (2007) 3.69
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nat Biotechnol (2007) 3.55
Dasty2, an Ajax protein DAS client. Bioinformatics (2008) 3.26
Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals. PLoS Genet (2012) 3.21
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat Methods (2012) 3.17
Gramene, a tool for grass genomics. Plant Physiol (2002) 3.14
BioMart Central Portal: an open database network for the biological community. Database (Oxford) (2011) 3.03
Clinical proteomics: A need to define the field and to begin to set adequate standards. Proteomics Clin Appl (2007) 2.84
The mzIdentML data standard for mass spectrometry-based proteomics results. Mol Cell Proteomics (2012) 2.82
Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition. Proteomics (2007) 2.74
Dasty and UniProt DAS: a perfect pair for protein feature visualization. Bioinformatics (2005) 2.74
InterPro: an integrated documentation resource for protein families, domains and functional sites. Brief Bioinform (2002) 2.66
BioJS: an open source JavaScript framework for biological data visualization. Bioinformatics (2013) 2.53
Arabidopsis reactome: a foundation knowledgebase for plant systems biology. Plant Cell (2008) 2.50
The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI). OMICS (2006) 2.38
Annotating cancer variants and anti-cancer therapeutics in reactome. Cancers (Basel) (2012) 2.35
The Protein Feature Ontology: a tool for the unification of protein feature annotations. Bioinformatics (2008) 2.33
The use of common ontologies and controlled vocabularies to enable data exchange and deposition for complex proteomic experiments. Pac Symp Biocomput (2005) 2.29
The Ontology Lookup Service: bigger and better. Nucleic Acids Res (2010) 2.27
modMine: flexible access to modENCODE data. Nucleic Acids Res (2011) 2.18
The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium. Mol Cell Proteomics (2012) 2.10
PRIDE Inspector: a tool to visualize and validate MS proteomics data. Nat Biotechnol (2012) 2.10
Gramene 2013: comparative plant genomics resources. Nucleic Acids Res (2013) 2.08
The SNP Consortium website: past, present and future. Nucleic Acids Res (2003) 2.08
Cystin, a novel cilia-associated protein, is disrupted in the cpk mouse model of polycystic kidney disease. J Clin Invest (2002) 2.07
Human genome: end of the beginning. Nature (2004) 2.06
ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome. Nat Methods (2007) 2.04
The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Plant Physiol (2006) 2.03
MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data. Genome Biol (2008) 1.76
A genome-wide association search for type 2 diabetes genes in African Americans. PLoS One (2012) 1.72
WormBook: the online review of Caenorhabditis elegans biology. Nucleic Acids Res (2006) 1.71
Common interchange standards for proteomics data: Public availability of tools and schema. Proteomics (2004) 1.68
Dasty3, a WEB framework for DAS. Bioinformatics (2011) 1.67
Computational approaches to identify functional genetic variants in cancer genomes. Nat Methods (2013) 1.64