Published in Nat Biotechnol on August 01, 2007
IntAct--open source resource for molecular interaction data. Nucleic Acids Res (2006) 13.82
The BioGRID Interaction Database: 2008 update. Nucleic Acids Res (2007) 11.83
Big data: The future of biocuration. Nature (2008) 10.81
The IntAct molecular interaction database in 2010. Nucleic Acids Res (2009) 9.85
The BioGRID Interaction Database: 2011 update. Nucleic Acids Res (2010) 8.46
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol (2007) 8.03
The IntAct molecular interaction database in 2012. Nucleic Acids Res (2011) 7.49
MINT, the molecular interaction database: 2009 update. Nucleic Acids Res (2009) 7.19
Overview of the protein-protein interaction annotation extraction task of BioCreative II. Genome Biol (2008) 6.38
iRefIndex: a consolidated protein interaction database with provenance. BMC Bioinformatics (2008) 5.77
MINT, the molecular interaction database: 2012 update. Nucleic Acids Res (2011) 5.25
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries. Nucleic Acids Res (2008) 4.73
InnateDB: facilitating systems-level analyses of the mammalian innate immune response. Mol Syst Biol (2008) 4.61
The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res (2013) 4.39
Literature-curated protein interaction datasets. Nat Methods (2009) 4.21
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat Methods (2012) 3.17
A gene-centric human proteome project: HUPO--the Human Proteome organization. Mol Cell Proteomics (2010) 3.05
The mzIdentML data standard for mass spectrometry-based proteomics results. Mol Cell Proteomics (2012) 2.82
InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curation. Nucleic Acids Res (2012) 2.66
The European Bioinformatics Institute's data resources. Nucleic Acids Res (2009) 2.55
iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. Database (Oxford) (2010) 2.47
VirusMINT: a viral protein interaction database. Nucleic Acids Res (2008) 2.30
ProHits: integrated software for mass spectrometry-based interaction proteomics. Nat Biotechnol (2010) 2.22
The FEBS Letters/BioCreative II.5 experiment: making biological information accessible. Nat Biotechnol (2010) 2.18
BioTorrents: a file sharing service for scientific data. PLoS One (2010) 2.15
Integrating and annotating the interactome using the MiMI plugin for cytoscape. Bioinformatics (2008) 2.04
MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions. Bioinformatics (2009) 1.96
Interactome3D: adding structural details to protein networks. Nat Methods (2012) 1.89
DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila. Nucleic Acids Res (2010) 1.86
MatrixDB, the extracellular matrix interaction database. Nucleic Acids Res (2010) 1.79
Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins. PLoS Biol (2009) 1.78
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
Protein-protein interactions essentials: key concepts to building and analyzing interactome networks. PLoS Comput Biol (2010) 1.67
Tumor suppressor density-enhanced phosphatase-1 (DEP-1) inhibits the RAS pathway by direct dephosphorylation of ERK1/2 kinases. J Biol Chem (2009) 1.66
Minimum information about a bioactive entity (MIABE). Nat Rev Drug Discov (2011) 1.44
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Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop. Stand Genomic Sci (2010) 1.35
The Biomolecular Interaction Network Database in PSI-MI 2.5. Database (Oxford) (2011) 1.34
Literature curation of protein interactions: measuring agreement across major public databases. Database (Oxford) (2010) 1.33
Curating the innate immunity interactome. BMC Syst Biol (2010) 1.30
The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics. Mol Cell Proteomics (2013) 1.28
Analyzing protein-protein interactions from affinity purification-mass spectrometry data with SAINT. Curr Protoc Bioinformatics (2012) 1.20
Functional and genomic context in pathway analysis of GWAS data. Trends Genet (2014) 1.18
Nucleoside diphosphate kinase (NDPK, NM23, AWD): recent regulatory advances in endocytosis, metastasis, psoriasis, insulin release, fetal erythroid lineage and heart failure; translational medicine exemplified. Mol Cell Biochem (2009) 1.17
Mostly, your results matter to others. Nat Genet (2009) 1.14
Visualization and biochemical analyses of the emerging mammalian 14-3-3-phosphoproteome. Mol Cell Proteomics (2011) 1.11
A new reference implementation of the PSICQUIC web service. Nucleic Acids Res (2013) 1.11
Minimum information about a protein affinity reagent (MIAPAR). Nat Biotechnol (2010) 1.10
Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases. BMC Bioinformatics (2011) 1.09
Knowledge management for systems biology a general and visually driven framework applied to translational medicine. BMC Syst Biol (2011) 1.01
Making a new technology work: the standardization and regulation of microarrays. Yale J Biol Med (2007) 0.97
Short time-series microarray analysis: methods and challenges. BMC Syst Biol (2008) 0.97
Using biological networks to integrate, visualize and analyze genomics data. Genet Sel Evol (2016) 0.96
Development of data representation standards by the human proteome organization proteomics standards initiative. J Am Med Inform Assoc (2015) 0.96
Bioinformatics and molecular modeling in glycobiology. Cell Mol Life Sci (2010) 0.95
From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase. Cell Mol Life Sci (2009) 0.95
Fundamentals of protein interaction network mapping. Mol Syst Biol (2015) 0.93
Using ProHits to store, annotate, and analyze affinity purification-mass spectrometry (AP-MS) data. Curr Protoc Bioinformatics (2012) 0.92
A general pipeline for quality and statistical assessment of protein interaction data using R and Bioconductor. Nat Protoc (2009) 0.92
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
Mass spectrometry-based immuno-precipitation proteomics - the user's guide. Proteomics (2011) 0.91
The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative. Proteomics (2010) 0.91
Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study. Database (Oxford) (2015) 0.88
Capturing cooperative interactions with the PSI-MI format. Database (Oxford) (2013) 0.86
pISTil: a pipeline for yeast two-hybrid Interaction Sequence Tags identification and analysis. BMC Res Notes (2009) 0.86
MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities. Nucleic Acids Res (2014) 0.85
DIPSBC--data integration platform for systems biology collaborations. BMC Bioinformatics (2012) 0.84
Getting a grip on complexes. Curr Genomics (2009) 0.84
From evidence to inference: probing the evolution of protein interaction networks. HFSP J (2009) 0.84
Quality assessment and optimization of purified protein samples: why and how? Microb Cell Fact (2014) 0.82
Guidelines for managing data and processes in bone and cartilage tissue engineering. BMC Bioinformatics (2014) 0.82
A visual review of the interactome of LRRK2: Using deep-curated molecular interaction data to represent biology. Proteomics (2015) 0.82
Enabling BioSharing - a report on the Annual Spring Workshop of the HUPO-PSI April 11-13, 2011, EMBL-Heidelberg, Germany. Proteomics (2011) 0.81
Computational Prediction of Protein-Protein Interaction Networks: Algo-rithms and Resources. Curr Genomics (2013) 0.81
Steps towards a repertoire of comprehensive maps of human protein interaction networks: the Human Proteotheque Initiative (HuPI). Biochem Cell Biol (2008) 0.81
APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks. Nucleic Acids Res (2016) 0.81
Swimming upstream: identifying proteomic signals that drive transcriptional changes using the interactome and multiple "-omics" datasets. Methods Cell Biol (2012) 0.79
Data standards for Omics data: the basis of data sharing and reuse. Methods Mol Biol (2011) 0.78
BISC: binary subcomplexes in proteins database. Nucleic Acids Res (2010) 0.78
A semantic proteomics dashboard (SemPoD) for data management in translational research. BMC Syst Biol (2012) 0.78
The human plasma membrane peripherome: visualization and analysis of interactions. Biomed Res Int (2014) 0.78
Glycosaminoglycanomics: where we are. Glycoconj J (2016) 0.77
Minireview: progress and challenges in proteomics data management, sharing, and integration. Mol Endocrinol (2012) 0.76
Detecting modules in biological networks by edge weight clustering and entropy significance. Front Genet (2015) 0.76
CellWhere: graphical display of interaction networks organized on subcellular localizations. Nucleic Acids Res (2015) 0.75
Data integration in biological research: an overview. J Biol Res (Thessalon) (2015) 0.75
Application of Functional Genomics for Bovine Respiratory Disease Diagnostics. Bioinform Biol Insights (2015) 0.75
Guidelines for information about therapy experiments: a proposal on best practice for recording experimental data on cancer therapy. BMC Res Notes (2012) 0.75
HPIDB 2.0: a curated database for host-pathogen interactions. Database (Oxford) (2016) 0.75
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res (2003) 52.80
The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) 48.99
Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature (2002) 45.19
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature (2002) 37.66
Functional profiling of the Saccharomyces cerevisiae genome. Nature (2002) 36.10
The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol (2008) 31.04
Integration of biological networks and gene expression data using Cytoscape. Nat Protoc (2007) 27.10
InterPro: the integrative protein signature database. Nucleic Acids Res (2008) 25.07
Towards a proteome-scale map of the human protein-protein interaction network. Nature (2005) 24.76
The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res (2003) 24.72
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature (2006) 24.29
The Database of Interacting Proteins: 2004 update. Nucleic Acids Res (2004) 23.67
The Universal Protein Resource (UniProt). Nucleic Acids Res (2005) 23.66
The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res (2006) 22.70
BioGRID: a general repository for interaction datasets. Nucleic Acids Res (2006) 22.41
Global mapping of the yeast genetic interaction network. Science (2004) 21.34
Proteome survey reveals modularity of the yeast cell machinery. Nature (2006) 20.77
International network of cancer genome projects. Nature (2010) 20.35
Landscape of transcription in human cells. Nature (2012) 20.18
The human disease network. Proc Natl Acad Sci U S A (2007) 19.58
GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res (2004) 18.75
Toll-like receptor triggering of a vitamin D-mediated human antimicrobial response. Science (2006) 18.74
Global identification of human transcribed sequences with genome tiling arrays. Science (2004) 17.85
InterPro, progress and status in 2005. Nucleic Acids Res (2005) 17.53
MINT: a Molecular INTeraction database. FEBS Lett (2002) 17.21
The genetic landscape of a cell. Science (2010) 16.52
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol (2004) 16.08
DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res (2002) 15.70
Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res (2008) 15.69
A map of the interactome network of the metazoan C. elegans. Science (2004) 15.60
Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics (2009) 15.08
IntAct: an open source molecular interaction database. Nucleic Acids Res (2004) 15.02
The International Protein Index: an integrated database for proteomics experiments. Proteomics (2004) 14.67
Functional impact of global rare copy number variation in autism spectrum disorders. Nature (2010) 14.66
COT drives resistance to RAF inhibition through MAP kinase pathway reactivation. Nature (2010) 14.62
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol (2007) 13.99
A mitochondrial protein compendium elucidates complex I disease biology. Cell (2008) 13.51
InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res (2011) 13.45
Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature (2004) 13.27
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
The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. Genome Res (2003) 12.81
New developments in the InterPro database. Nucleic Acids Res (2007) 12.49
Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell (2012) 12.32
Prepublication data sharing. Nature (2009) 12.24
The Protein Information Resource: an integrated public resource of functional annotation of proteins. Nucleic Acids Res (2002) 12.20
A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science (2003) 12.07
UniProt archive. Bioinformatics (2004) 11.92
MINT: the Molecular INTeraction database. Nucleic Acids Res (2006) 11.90
The BioGRID Interaction Database: 2008 update. Nucleic Acids Res (2007) 11.83
Structure of the cross-beta spine of amyloid-like fibrils. Nature (2005) 11.56
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
Drug-target network. Nat Biotechnol (2007) 11.15
The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res (2010) 10.97
High-quality binary protein interaction map of the yeast interactome network. Science (2008) 10.65
The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol (2007) 10.24
The GOA database in 2009--an integrated Gene Ontology Annotation resource. Nucleic Acids Res (2008) 10.21
Cytoscape Web: an interactive web-based network browser. Bioinformatics (2010) 10.03
Atomic structures of amyloid cross-beta spines reveal varied steric zippers. Nature (2007) 10.02
EMBL Nucleotide Sequence Database in 2006. Nucleic Acids Res (2006) 9.72
Somatic mutations of calreticulin in myeloproliferative neoplasms. N Engl J Med (2013) 9.65
Genomic analysis of regulatory network dynamics reveals large topological changes. Nature (2004) 9.32
Drug target identification using side-effect similarity. Science (2008) 9.24
The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19