Published in Science on February 06, 2004
Integration of biological networks and gene expression data using Cytoscape. Nat Protoc (2007) 27.10
BioGRID: a general repository for interaction datasets. Nucleic Acids Res (2006) 22.41
SNPs3D: candidate gene and SNP selection for association studies. BMC Bioinformatics (2006) 21.54
The genetic landscape of a cell. Science (2010) 16.52
Epistasis--the essential role of gene interactions in the structure and evolution of genetic systems. Nat Rev Genet (2008) 9.26
The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science (2008) 8.52
Transcriptional regulation of protein complexes within and across species. Proc Natl Acad Sci U S A (2007) 7.07
Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes Dev (2005) 6.14
Protein networks in disease. Genome Res (2008) 5.65
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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
A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. Proc Natl Acad Sci U S A (2006) 5.24
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Comprehensive characterization of genes required for protein folding in the endoplasmic reticulum. Science (2009) 4.58
A strategy for extracting and analyzing large-scale quantitative epistatic interaction data. Genome Biol (2006) 4.49
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Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science (2008) 4.36
Yeast Rtt109 promotes genome stability by acetylating histone H3 on lysine 56. Science (2007) 4.07
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Gene connectivity, function, and sequence conservation: predictions from modular yeast co-expression networks. BMC Genomics (2006) 3.87
RTEL1 maintains genomic stability by suppressing homologous recombination. Cell (2008) 3.84
Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome. Genome Biol (2005) 3.79
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A global view of pleiotropy and phenotypically derived gene function in yeast. Mol Syst Biol (2005) 3.70
Defining genetic interaction. Proc Natl Acad Sci U S A (2008) 3.67
The Forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle. Genes Dev (2006) 3.58
Chromatid cohesion defects may underlie chromosome instability in human colorectal cancers. Proc Natl Acad Sci U S A (2008) 3.52
'Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucleic Acids Res (2004) 3.50
Inferring cellular networks--a review. BMC Bioinformatics (2007) 3.49
Synergistic drug combinations tend to improve therapeutically relevant selectivity. Nat Biotechnol (2009) 3.49
Stratus not altocumulus: a new view of the yeast protein interaction network. PLoS Biol (2006) 3.44
VisANT: data-integrating visual framework for biological networks and modules. Nucleic Acids Res (2005) 3.24
Histone H2B ubiquitylation is associated with elongating RNA polymerase II. Mol Cell Biol (2005) 3.20
Combining biological networks to predict genetic interactions. Proc Natl Acad Sci U S A (2004) 3.18
High-throughput, quantitative analyses of genetic interactions in E. coli. Nat Methods (2008) 3.17
Cell wall assembly in Saccharomyces cerevisiae. Microbiol Mol Biol Rev (2006) 3.08
Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity. Nat Genet (2009) 3.06
A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing. Mol Cell (2008) 2.96
A Drosophila protein-interaction map centered on cell-cycle regulators. Genome Biol (2004) 2.95
An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae. PLoS One (2007) 2.84
System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench top Orbitrap. Mol Cell Proteomics (2011) 2.77
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Derivation of genetic interaction networks from quantitative phenotype data. Genome Biol (2005) 2.74
Epistasis and quantitative traits: using model organisms to study gene-gene interactions. Nat Rev Genet (2013) 2.73
Why are there still over 1000 uncharacterized yeast genes? Genetics (2007) 2.71
Molecular determinants and genetic modifiers of aggregation and toxicity for the ALS disease protein FUS/TLS. PLoS Biol (2011) 2.70
Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network. J Biol (2005) 2.68
Quantitative analysis of fitness and genetic interactions in yeast on a genome scale. Nat Methods (2010) 2.67
Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species. PLoS Biol (2009) 2.67
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther (2013) 2.64
Genome-wide analysis of Rad52 foci reveals diverse mechanisms impacting recombination. PLoS Genet (2007) 2.63
Yeast Rmi1/Nce4 controls genome stability as a subunit of the Sgs1-Top3 complex. Mol Cell Biol (2005) 2.49
Network hubs buffer environmental variation in Saccharomyces cerevisiae. PLoS Biol (2008) 2.47
iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. Database (Oxford) (2010) 2.47
An Arabidopsis gene network based on the graphical Gaussian model. Genome Res (2007) 2.45
Yeast Mph1 helicase dissociates Rad51-made D-loops: implications for crossover control in mitotic recombination. Genes Dev (2009) 2.43
Chemical combination effects predict connectivity in biological systems. Mol Syst Biol (2007) 2.42
Prevalence of epistasis in the evolution of influenza A surface proteins. PLoS Genet (2011) 2.41
Drug interactions and the evolution of antibiotic resistance. Nat Rev Microbiol (2009) 2.40
Plasticity of genetic interactions in metabolic networks of yeast. Proc Natl Acad Sci U S A (2007) 2.40
Iron behaving badly: inappropriate iron chelation as a major contributor to the aetiology of vascular and other progressive inflammatory and degenerative diseases. BMC Med Genomics (2009) 2.36
RMI1/NCE4, a suppressor of genome instability, encodes a member of the RecQ helicase/Topo III complex. EMBO J (2005) 2.34
Assessing the limits of genomic data integration for predicting protein networks. Genome Res (2005) 2.33
A comprehensive genetic characterization of bacterial motility. PLoS Genet (2007) 2.33
A decade of systems biology. Annu Rev Cell Dev Biol (2010) 2.30
Kinase requirements in human cells: III. Altered kinase requirements in VHL-/- cancer cells detected in a pilot synthetic lethal screen. Proc Natl Acad Sci U S A (2008) 2.27
Modeling complex genetic interactions in a simple eukaryotic genome: actin displays a rich spectrum of complex haploinsufficiencies. Genes Dev (2006) 2.26
Inviability of a DNA2 deletion mutant is due to the DNA damage checkpoint. Cell Cycle (2011) 2.25
Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms. Nat Rev Microbiol (2013) 2.22
The million mutation project: a new approach to genetics in Caenorhabditis elegans. Genome Res (2013) 2.20
Saccharomyces cerevisiae Sae2- and Tel1-dependent single-strand DNA formation at DNA break promotes microhomology-mediated end joining. Genetics (2007) 2.19
Origins of regulated cell-to-cell variability. Nat Rev Mol Cell Biol (2011) 2.15
Ubiquitin-related modifier Urm1 acts as a sulphur carrier in thiolation of eukaryotic transfer RNA. Nature (2009) 2.14
Gene function prediction from congruent synthetic lethal interactions in yeast. Mol Syst Biol (2005) 2.04
Validation and refinement of gene-regulatory pathways on a network of physical interactions. Genome Biol (2005) 2.03
Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes. Proc Natl Acad Sci U S A (2008) 2.01
A comprehensive synthetic genetic interaction network governing yeast histone acetylation and deacetylation. Genes Dev (2008) 2.01
Systematic phenotyping of a large-scale Candida glabrata deletion collection reveals novel antifungal tolerance genes. PLoS Pathog (2014) 1.98
KNL1/Spc105 recruits PP1 to silence the spindle assembly checkpoint. Curr Biol (2011) 1.98
Swf1-dependent palmitoylation of the SNARE Tlg1 prevents its ubiquitination and degradation. EMBO J (2005) 1.97
Complex genetic interactions in a quantitative trait locus. PLoS Genet (2006) 1.95
Activation of the DNA damage checkpoint in yeast lacking the histone chaperone anti-silencing function 1. Mol Cell Biol (2004) 1.94
The BAR domain proteins: molding membranes in fission, fusion, and phagy. Microbiol Mol Biol Rev (2006) 1.94
Molecular chaperone Hsp90 stabilizes Pih1/Nop17 to maintain R2TP complex activity that regulates snoRNA accumulation. J Cell Biol (2008) 1.92
Global network analysis of phenotypic effects: protein networks and toxicity modulation in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2004) 1.90
Systematic genome instability screens in yeast and their potential relevance to cancer. Proc Natl Acad Sci U S A (2007) 1.90
Analysis of beta-1,3-glucan assembly in Saccharomyces cerevisiae using a synthetic interaction network and altered sensitivity to caspofungin. Genetics (2004) 1.89
Systematic exploration of synergistic drug pairs. Mol Syst Biol (2011) 1.89
Hierarchical modularity and the evolution of genetic interactomes across species. Mol Cell (2012) 1.88
The S. cerevisiae Rrm3p DNA helicase moves with the replication fork and affects replication of all yeast chromosomes. Genes Dev (2006) 1.87
From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II. Cell (2013) 1.87
Genome-wide mRNA surveillance is coupled to mRNA export. Genes Dev (2004) 1.83
Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks. Mol Syst Biol (2007) 1.83
Toward predictive models of mammalian cells. Annu Rev Biophys Biomol Struct (2005) 1.82
Applications of high-throughput RNA interference screens to problems in cell and developmental biology. Genetics (2007) 1.82
Shadows of complexity: what biological networks reveal about epistasis and pleiotropy. Bioessays (2009) 1.82
Genome sequencing in microfabricated high-density picolitre reactors. Nature (2005) 150.21
A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78
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
Human MicroRNA targets. PLoS Biol (2004) 34.51
A mammalian microRNA expression atlas based on small RNA library sequencing. Cell (2007) 34.03
Integration of biological networks and gene expression data using Cytoscape. Nat Protoc (2007) 27.10
The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov (2012) 26.98
Towards a proteome-scale map of the human protein-protein interaction network. Nature (2005) 24.76
Integrative genomic profiling of human prostate cancer. Cancer Cell (2010) 23.61
MicroRNA targets in Drosophila. Genome Biol (2003) 23.59
International network of cancer genome projects. Nature (2010) 20.35
Guidelines for the use and interpretation of assays for monitoring autophagy. Autophagy (2012) 20.08
Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal (2013) 19.54
The genetic landscape of a cell. Science (2010) 16.52
The microRNA.org resource: targets and expression. Nucleic Acids Res (2007) 16.26
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol (2004) 16.08
A map of the interactome network of the metazoan C. elegans. Science (2004) 15.60
Functional impact of global rare copy number variation in autism spectrum disorders. Nature (2010) 14.66
Characterizing gene sets with FuncAssociate. Bioinformatics (2003) 14.10
Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature (2004) 13.27
Identification of microRNAs of the herpesvirus family. Nat Methods (2005) 12.98
Identification of virus-encoded microRNAs. Science (2004) 12.56
The somatic genomic landscape of glioblastoma. Cell (2013) 11.73
The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet (2013) 11.29
Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res (2011) 10.99
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
Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Cell (2005) 10.41
Cytoscape Web: an interactive web-based network browser. Bioinformatics (2010) 10.03
Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature (2007) 9.25
The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19
Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res (2010) 9.18
A novel class of small RNAs bind to MILI protein in mouse testes. Nature (2006) 8.80
The Systems Biology Graphical Notation. Nat Biotechnol (2009) 8.53
The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol (2007) 8.24
Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature (2005) 8.19
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol (2007) 8.03
Global analysis of protein phosphorylation in yeast. Nature (2005) 7.46
The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. Annu Rev Biochem (2003) 7.22
Mutual exclusivity analysis identifies oncogenic network modules. Genome Res (2011) 7.22
Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell (2005) 7.21
Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol (2010) 7.15
A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science (2001) 7.08
Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol Cell Biol (2003) 6.79
Cellular cofactors affecting hepatitis C virus infection and replication. Proc Natl Acad Sci U S A (2007) 6.79
(V600E)BRAF is associated with disabled feedback inhibition of RAF-MEK signaling and elevated transcriptional output of the pathway. Proc Natl Acad Sci U S A (2009) 6.78
Genome sequencing identifies a basis for everolimus sensitivity. Science (2012) 6.71
Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS One (2010) 6.61
An empirical framework for binary interactome mapping. Nat Methods (2008) 6.59
A travel guide to Cytoscape plugins. Nat Methods (2012) 6.53
Emerging landscape of oncogenic signatures across human cancers. Nat Genet (2013) 6.48
miR-122, a mammalian liver-specific microRNA, is processed from hcr mRNA and may downregulate the high affinity cationic amino acid transporter CAT-1. RNA Biol (2004) 6.44
Mapping pathways and phenotypes by systematic gene overexpression. Mol Cell (2006) 6.42
PreBIND and Textomy--mining the biomedical literature for protein-protein interactions using a support vector machine. BMC Bioinformatics (2003) 6.31
Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy. Nat Genet (2010) 6.10
Pathguide: a pathway resource list. Nucleic Acids Res (2006) 6.05
Human receptors for sweet and umami taste. Proc Natl Acad Sci U S A (2002) 5.91
Ubiquitin-binding domains in Y-family polymerases regulate translesion synthesis. Science (2005) 5.75
Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med (2015) 5.71
Exploring genetic interactions and networks with yeast. Nat Rev Genet (2007) 5.67
Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways. Nat Biotechnol (2003) 5.60