Published in Nature on January 10, 2002
The Database of Interacting Proteins: 2004 update. Nucleic Acids Res (2004) 23.67
BioGRID: a general repository for interaction datasets. Nucleic Acids Res (2006) 22.41
BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res (2003) 18.75
A map of the interactome network of the metazoan C. elegans. Science (2004) 15.60
An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics (2003) 15.42
IntAct: an open source molecular interaction database. Nucleic Acids Res (2004) 15.02
Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res (2003) 14.79
Defining the human deubiquitinating enzyme interaction landscape. Cell (2009) 11.39
High-quality binary protein interaction map of the yeast interactome network. Science (2008) 10.65
STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res (2005) 10.44
Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci U S A (2003) 9.03
The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res (2004) 8.79
Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol Syst Biol (2007) 8.16
FunSpec: a web-based cluster interpreter for yeast. BMC Bioinformatics (2002) 8.01
Subcellular localization of the yeast proteome. Genes Dev (2002) 7.93
Conserved patterns of protein interaction in multiple species. Proc Natl Acad Sci U S A (2005) 7.48
Toward the structural genomics of complexes: crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis. Proc Natl Acad Sci U S A (2006) 7.29
Interactome networks and human disease. Cell (2011) 7.16
Transcriptional regulation of protein complexes within and across species. Proc Natl Acad Sci U S A (2007) 7.07
BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals. Nat Methods (2008) 6.51
Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoS Biol (2004) 6.38
Modular organization of cellular networks. Proc Natl Acad Sci U S A (2003) 6.24
Osprey: a network visualization system. Genome Biol (2003) 6.23
Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes Dev (2005) 6.14
Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. Am J Hum Genet (2006) 6.10
Recognition of trimethylated histone H3 lysine 4 facilitates the recruitment of transcription postinitiation factors and pre-mRNA splicing. Mol Cell (2007) 5.78
Large-scale proteomic analysis of the human spliceosome. Genome Res (2002) 5.75
The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol (2007) 5.63
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J Biol (2006) 5.57
Systematic interpretation of genetic interactions using protein networks. Nat Biotechnol (2005) 5.38
Genome-wide dynamics of Htz1, a histone H2A variant that poises repressed/basal promoters for activation through histone loss. Cell (2005) 5.36
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res (2004) 5.26
A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. Proc Natl Acad Sci U S A (2006) 5.24
FlyMine: an integrated database for Drosophila and Anopheles genomics. Genome Biol (2007) 5.23
Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8. Genes Dev (2003) 5.13
Protein kinase CK2: structure, regulation and role in cellular decisions of life and death. Biochem J (2003) 5.11
Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc Natl Acad Sci U S A (2007) 5.09
A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin. PLoS Biol (2004) 5.02
Phosphorylation of RNA polymerase II CTD regulates H3 methylation in yeast. Genes Dev (2003) 4.93
Activation of yeast Snf1 and mammalian AMP-activated protein kinase by upstream kinases. Proc Natl Acad Sci U S A (2003) 4.87
Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics (2006) 4.85
Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc Natl Acad Sci U S A (2003) 4.68
Assessing experimentally derived interactions in a small world. Proc Natl Acad Sci U S A (2003) 4.53
Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science (2008) 4.36
Noise minimization in eukaryotic gene expression. PLoS Biol (2004) 4.36
Structural and functional conservation of the NuA4 histone acetyltransferase complex from yeast to humans. Mol Cell Biol (2004) 4.31
Efficient biotinylation and single-step purification of tagged transcription factors in mammalian cells and transgenic mice. Proc Natl Acad Sci U S A (2003) 4.28
Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res (2006) 4.25
Literature-curated protein interaction datasets. Nat Methods (2009) 4.21
Global topological features of cancer proteins in the human interactome. Bioinformatics (2006) 4.17
Protein interaction mapping: a Drosophila case study. Genome Res (2005) 4.15
Mechanisms that specify promoter nucleosome location and identity. Cell (2009) 4.14
Predicting disease genes using protein-protein interactions. J Med Genet (2006) 4.10
The GRID: the General Repository for Interaction Datasets. Genome Biol (2003) 4.09
Probing cellular protein complexes using single-molecule pull-down. Nature (2011) 3.92
A census of human soluble protein complexes. Cell (2012) 3.90
Mixed Membership Stochastic Blockmodels. J Mach Learn Res (2008) 3.88
Dimethylation of histone H3 at lysine 36 demarcates regulatory and nonregulatory chromatin genome-wide. Mol Cell Biol (2005) 3.83
Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network. Genome Biol (2003) 3.80
Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome. Genome Biol (2005) 3.79
Evaluation of different biological data and computational classification methods for use in protein interaction prediction. Proteins (2006) 3.78
HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. BMC Bioinformatics (2005) 3.75
A global view of pleiotropy and phenotypically derived gene function in yeast. Mol Syst Biol (2005) 3.70
Estimating the size of the human interactome. Proc Natl Acad Sci U S A (2008) 3.66
A first-draft human protein-interaction map. Genome Biol (2004) 3.64
60S pre-ribosome formation viewed from assembly in the nucleolus until export to the cytoplasm. EMBO J (2002) 3.62
A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes. Proc Natl Acad Sci U S A (2008) 3.57
A systematic mammalian genetic interaction map reveals pathways underlying ricin susceptibility. Cell (2013) 3.53
Phosphoproteomics of the Arabidopsis plasma membrane and a new phosphorylation site database. Plant Cell (2004) 3.51
Genomic analysis of the hierarchical structure of regulatory networks. Proc Natl Acad Sci U S A (2006) 3.51
How common are extraribosomal functions of ribosomal proteins? Mol Cell (2009) 3.51
How complete are current yeast and human protein-interaction networks? Genome Biol (2006) 3.50
Transitions in RNA polymerase II elongation complexes at the 3' ends of genes. EMBO J (2004) 3.50
Phosphotyrosine interactome of the ErbB-receptor kinase family. Mol Syst Biol (2005) 3.48
The Paf1 complex physically and functionally associates with transcription elongation factors in vivo. EMBO J (2002) 3.44
Stratus not altocumulus: a new view of the yeast protein interaction network. PLoS Biol (2006) 3.44
Protein factors in pre-mRNA 3'-end processing. Cell Mol Life Sci (2008) 3.44
The putative cancer stem cell marker USP22 is a subunit of the human SAGA complex required for activated transcription and cell-cycle progression. Mol Cell (2008) 3.42
Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality. PLoS Comput Biol (2008) 3.41
The path from nucleolar 90S to cytoplasmic 40S pre-ribosomes. EMBO J (2003) 3.38
Analyzing chromatin remodeling complexes using shotgun proteomics and normalized spectral abundance factors. Methods (2006) 3.37
Human ORFeome version 1.1: a platform for reverse proteomics. Genome Res (2004) 3.36
Diversity of protein-protein interactions. EMBO J (2003) 3.35
Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system. Genome Biol (2006) 3.34
Why do hubs tend to be essential in protein networks? PLoS Genet (2006) 3.29
Chromatin remodeling protein Chd1 interacts with transcription elongation factors and localizes to transcribed genes. EMBO J (2003) 3.26
Dead-box proteins: a family affair--active and passive players in RNP-remodeling. Nucleic Acids Res (2006) 3.26
VisANT: data-integrating visual framework for biological networks and modules. Nucleic Acids Res (2005) 3.24
Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics. Proc Natl Acad Sci U S A (2008) 3.23
ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nat Rev Genet (2012) 3.23
Phosphoinositides: tiny lipids with giant impact on cell regulation. Physiol Rev (2013) 3.21
PathBLAST: a tool for alignment of protein interaction networks. Nucleic Acids Res (2004) 3.20
Mechanism of the eukaryotic chaperonin: protein folding in the chamber of secrets. Trends Cell Biol (2004) 3.18
Combining biological networks to predict genetic interactions. Proc Natl Acad Sci U S A (2004) 3.18
Widespread cytoplasmic mRNA transport in yeast: identification of 22 bud-localized transcripts using DNA microarray analysis. Proc Natl Acad Sci U S A (2003) 3.16
Comprehensive interaction map of the Arabidopsis MADS Box transcription factors. Plant Cell (2005) 3.12
The landscape of human proteins interacting with viruses and other pathogens. PLoS Pathog (2008) 3.11
Proteomics of the eukaryotic transcription machinery: identification of proteins associated with components of yeast TFIID by multidimensional mass spectrometry. Mol Cell Biol (2002) 3.10
Finding function: evaluation methods for functional genomic data. BMC Genomics (2006) 3.10
From genes to functional classes in the study of biological systems. BMC Bioinformatics (2007) 3.09
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
A method and server for predicting damaging missense mutations. Nat Methods (2010) 78.53
Human non-synonymous SNPs: server and survey. Nucleic Acids Res (2002) 50.45
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
Comparative metagenomics of microbial communities. Science (2005) 25.88
InterPro: the integrative protein signature database. Nucleic Acids Res (2008) 25.07
Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res (2002) 25.06
The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res (2003) 24.72
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
Enterotypes of the human gut microbiome. Nature (2011) 24.36
Comparative assessment of large-scale data sets of protein-protein interactions. Nature (2002) 24.25
Proteome survey reveals modularity of the yeast cell machinery. Nature (2006) 20.77
STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res (2008) 20.62
The genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36
SMART 4.0: towards genomic data integration. Nucleic Acids Res (2004) 19.37
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res (2010) 18.73
STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res (2012) 18.26
InterPro, progress and status in 2005. Nucleic Acids Res (2005) 17.53
SMART 5: domains in the context of genomes and networks. Nucleic Acids Res (2006) 17.13
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol (2004) 16.08
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics (2006) 14.96
Toward automatic reconstruction of a highly resolved tree of life. Science (2006) 14.96
InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res (2011) 13.45
New developments in the InterPro database. Nucleic Acids Res (2007) 12.49
STRING 7--recent developments in the integration and prediction of protein interactions. Nucleic Acids Res (2006) 12.16
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res (2011) 10.82
STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res (2005) 10.44
SMART 6: recent updates and new developments. Nucleic Acids Res (2008) 9.80
Somatic mutations of calreticulin in myeloproliferative neoplasms. N Engl J Med (2013) 9.65
STRING: a database of predicted functional associations between proteins. Nucleic Acids Res (2003) 9.45
Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science (2002) 9.43
Drug target identification using side-effect similarity. Science (2008) 9.24
Tankyrase inhibition stabilizes axin and antagonizes Wnt signalling. Nature (2009) 9.15
SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res (2011) 9.15
Bioinformatics in the post-sequence era. Nat Genet (2003) 8.83
mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes. Genes Dev (2006) 8.78
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res (2006) 8.36
Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia. Nature (2011) 8.29
The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol (2007) 8.24
Literature mining for the biologist: from information retrieval to biological discovery. Nat Rev Genet (2006) 8.23
Protein disorder prediction: implications for structural proteomics. Structure (2003) 7.93
An orthogonal proteomic-genomic screen identifies AIM2 as a cytoplasmic DNA sensor for the inflammasome. Nat Immunol (2009) 7.93
Computational prediction of proteotypic peptides for quantitative proteomics. Nat Biotechnol (2006) 7.56
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol (2011) 7.53
Alternative splicing and genome complexity. Nat Genet (2001) 7.30
A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway. Nat Cell Biol (2004) 7.23
The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc Natl Acad Sci U S A (2002) 7.21
Systematic discovery of in vivo phosphorylation networks. Cell (2007) 6.94
Richness of human gut microbiome correlates with metabolic markers. Nature (2013) 6.93
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res (2003) 6.86
Quantitative mass spectrometry in proteomics: a critical review. Anal Bioanal Chem (2007) 6.80
A side effect resource to capture phenotypic effects of drugs. Mol Syst Biol (2010) 6.75
Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet (2006) 6.74
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature (2008) 6.69
Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors. Nat Biotechnol (2007) 6.56