Published in Nucleic Acids Res on January 01, 2002
STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res (2005) 10.44
STRING: a database of predicted functional associations between proteins. Nucleic Acids Res (2003) 9.45
The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol (2006) 5.22
Prolinks: a database of protein functional linkages derived from coevolution. Genome Biol (2004) 4.07
Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome. Genome Biol (2005) 3.79
HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. BMC Bioinformatics (2005) 3.75
How complete are current yeast and human protein-interaction networks? Genome Biol (2006) 3.50
VisANT: data-integrating visual framework for biological networks and modules. Nucleic Acids Res (2005) 3.24
Whole-genome annotation by using evidence integration in functional-linkage networks. Proc Natl Acad Sci U S A (2004) 2.93
VisANT: an online visualization and analysis tool for biological interaction data. BMC Bioinformatics (2004) 2.88
VisANT: an integrative framework for networks in systems biology. Brief Bioinform (2008) 2.85
An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae. PLoS One (2007) 2.84
VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology. Nucleic Acids Res (2009) 2.71
Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. BMC Bioinformatics (2006) 2.57
VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. Nucleic Acids Res (2007) 2.17
Genome evolution reveals biochemical networks and functional modules. Proc Natl Acad Sci U S A (2003) 2.08
Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes. Genome Biol (2007) 1.73
VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies. Nucleic Acids Res (2013) 1.71
PrePPI: a structure-informed database of protein-protein interactions. Nucleic Acids Res (2012) 1.59
Predicting genetic modifier loci using functional gene networks. Genome Res (2010) 1.59
The society of genes: networks of functional links between genes from comparative genomics. Genome Biol (2002) 1.55
Phydbac "Gene Function Predictor": a gene annotation tool based on genomic context analysis. BMC Bioinformatics (2005) 1.54
Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment. BMC Bioinformatics (2007) 1.47
Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps. Nucleic Acids Res (2003) 1.31
Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1. Genome Biol (2004) 1.25
FusionDB: a database for in-depth analysis of prokaryotic gene fusion events. Nucleic Acids Res (2004) 1.24
Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes. Nucleic Acids Res (2004) 1.24
Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution. J R Soc Interface (2008) 1.24
Comparative assessment of performance and genome dependence among phylogenetic profiling methods. BMC Bioinformatics (2006) 1.22
VIRGO: computational prediction of gene functions. Nucleic Acids Res (2006) 1.09
MCL-CAw: a refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure. BMC Bioinformatics (2010) 1.09
A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila. BMC Bioinformatics (2006) 1.03
Multi-species integrative biclustering. Genome Biol (2010) 0.99
Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions. Anal Chem (2012) 0.98
Annotation of the M. tuberculosis hypothetical orfeome: adding functional information to more than half of the uncharacterized proteins. PLoS One (2012) 0.95
Prediction of novel archaeal enzymes from sequence-derived features. Protein Sci (2002) 0.95
Construction and analysis of protein-protein interaction networks. Autom Exp (2010) 0.94
ELISA: structure-function inferences based on statistically significant and evolutionarily inspired observations. BMC Bioinformatics (2003) 0.94
Integrated inference and analysis of regulatory networks from multi-level measurements. Methods Cell Biol (2012) 0.88
Predicting protein linkages in bacteria: which method is best depends on task. BMC Bioinformatics (2008) 0.88
Assessing and combining reliability of protein interaction sources. Pac Symp Biocomput (2007) 0.88
Cross-species cluster co-conservation: a new method for generating protein interaction networks. Genome Biol (2007) 0.87
EvoCor: a platform for predicting functionally related genes using phylogenetic and expression profiles. Nucleic Acids Res (2014) 0.85
In Silico screening for functional candidates amongst hypothetical proteins. BMC Bioinformatics (2009) 0.83
Functional association networks as priors for gene regulatory network inference. Bioinformatics (2014) 0.82
Network portal: a database for storage, analysis and visualization of biological networks. Nucleic Acids Res (2013) 0.81
Protein functional links in Trypanosoma brucei, identified by gene fusion analysis. BMC Evol Biol (2011) 0.80
Effects of subminimum inhibitory concentrations of antibiotics on the Pasteurella multocida proteome: a systems approach. Comp Funct Genomics (2008) 0.78
On the detection of functionally coherent groups of protein domains with an extension to protein annotation. BMC Bioinformatics (2007) 0.78
Comparative microbial modules resource: generation and visualization of multi-species biclusters. PLoS Comput Biol (2011) 0.78
Using VisANT to Analyze Networks. Curr Protoc Bioinformatics (2014) 0.77
Rationalising the role of Keratin 9 as a biomarker for Alzheimer's disease. Sci Rep (2016) 0.75
Integrating in silico resources to map a signaling network. Methods Mol Biol (2014) 0.75
Molecular mechanisms of OLIG2 transcription factor in brain cancer. Oncotarget (2016) 0.75
InterWeaver: interaction reports for discovering potential protein interaction partners with online evidence. Nucleic Acids Res (2004) 0.75
Basic local alignment search tool. J Mol Biol (1990) 659.07
KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res (2000) 117.00
Creating the gene ontology resource: design and implementation. Genome Res (2001) 55.73
A genomic perspective on protein families. Science (1997) 50.51
A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature (2000) 47.15
A novel genetic system to detect protein-protein interactions. Nature (1989) 43.83
The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res (2001) 43.17
A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A (2001) 33.71
Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci U S A (1999) 22.80
Detecting protein function and protein-protein interactions from genome sequences. Science (1999) 18.69
Protein interaction maps for complete genomes based on gene fusion events. Nature (1999) 16.48
The use of gene clusters to infer functional coupling. Proc Natl Acad Sci U S A (1999) 16.35
Automated genome sequence analysis and annotation. Bioinformatics (1999) 13.92
BIND--The Biomolecular Interaction Network Database. Nucleic Acids Res (2001) 11.74
DIP: the database of interacting proteins. Nucleic Acids Res (2000) 10.06
A combined algorithm for genome-wide prediction of protein function. Nature (1999) 9.99
Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem Sci (1998) 9.94
The protein-protein interaction map of Helicobacter pylori. Nature (2001) 8.71
Protein function in the post-genomic era. Nature (2000) 7.00
Measuring genome evolution. Proc Natl Acad Sci U S A (1998) 6.97
STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res (2000) 5.68
Mining literature for protein-protein interactions. Bioinformatics (2001) 5.18
Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res (2000) 5.14
Who's your neighbor? New computational approaches for functional genomics. Nat Biotechnol (2000) 4.04
Constructing multigenome views of whole microbial genomes. Microb Comp Genomics (1998) 3.60
Automated extraction of information in molecular biology. FEBS Lett (2000) 3.28
Genes linked by fusion events are generally of the same functional category: a systematic analysis of 30 microbial genomes. Proc Natl Acad Sci U S A (2001) 2.95
Exploitation of gene context. Curr Opin Struct Biol (2000) 2.65
Indigo: a World-Wide-Web review of genomes and gene functions. FEMS Microbiol Rev (1998) 2.11
Computational genetics: finding protein function by nonhomology methods. Curr Opin Struct Biol (2000) 2.07
CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. Cell Rep (2012) 5.17
Ubiquitin-like protein involved in the proteasome pathway of Mycobacterium tuberculosis. Science (2008) 4.15
A protein complex network of Drosophila melanogaster. Cell (2011) 3.31
Rewiring of the yeast transcriptional network through the evolution of motif usage. Science (2005) 3.10
A protein-protein docking benchmark. Proteins (2003) 2.90
VisANT: an online visualization and analysis tool for biological interaction data. BMC Bioinformatics (2004) 2.88
VisANT: an integrative framework for networks in systems biology. Brief Bioinform (2008) 2.85
VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology. Nucleic Acids Res (2009) 2.71
Protein-protein docking benchmark version 3.0. Proteins (2008) 2.54
High expression of lymphocyte-associated genes in node-negative HER2+ breast cancers correlates with lower recurrence rates. Cancer Res (2007) 2.48
Gene expression in lung adenocarcinomas of smokers and nonsmokers. Am J Respir Cell Mol Biol (2003) 2.45
Are protein-protein interfaces more conserved in sequence than the rest of the protein surface? Protein Sci (2004) 2.38
Developmental milestones punctuate gene expression in the Caenorhabditis embryo. Dev Cell (2012) 2.37
Phosphoproteome analysis of Drosophila melanogaster embryos. J Proteome Res (2008) 2.33
Identification of functional links between genes using phylogenetic profiles. Bioinformatics (2003) 2.33
Towards zoomable multidimensional maps of the cell. Nat Biotechnol (2007) 2.20
VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. Nucleic Acids Res (2007) 2.17
GeneAnnot: comprehensive two-way linking between oligonucleotide array probesets and GeneCards genes. Bioinformatics (2004) 1.92
Identifying functional links between genes using conserved chromosomal proximity. Trends Genet (2002) 1.91
The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI. Proteins (2007) 1.85
Gene set enrichment analysis: performance evaluation and usage guidelines. Brief Bioinform (2011) 1.84
Functional fingerprints of folds: evidence for correlated structure-function evolution. J Mol Biol (2003) 1.80
Widespread ectopic expression of olfactory receptor genes. BMC Genomics (2006) 1.80
Prokaryotic ubiquitin-like protein (Pup) proteome of Mycobacterium tuberculosis [corrected] . PLoS One (2010) 1.65
ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5. Proteins (2005) 1.61
Alternative splicing and gene duplication are inversely correlated evolutionary mechanisms. Nat Genet (2005) 1.60
Optimal clustering for detecting near-native conformations in protein docking. Biophys J (2005) 1.59
The society of genes: networks of functional links between genes from comparative genomics. Genome Biol (2002) 1.55
The importance of thermodynamic equilibrium for high throughput gene expression arrays. Biophys J (2003) 1.50
A computational framework for optimal masking in the synthesis of oligonucleotide microarrays. Nucleic Acids Res (2002) 1.40
Towards the identification of essential genes using targeted genome sequencing and comparative analysis. BMC Genomics (2006) 1.39
Sexual dimorphism of rat liver gene expression: regulatory role of growth hormone revealed by deoxyribonucleic Acid microarray analysis. Mol Endocrinol (2003) 1.30
Identification of functional modules that correlate with phenotypic difference: the influence of network topology. Genome Biol (2010) 1.25
Getting started in gene expression microarray analysis. PLoS Comput Biol (2009) 1.25
The COMBREX project: design, methodology, and initial results. PLoS Biol (2013) 1.24
Comparative assessment of performance and genome dependence among phylogenetic profiling methods. BMC Bioinformatics (2006) 1.22
ZDOCK predictions for the CAPRI challenge. Proteins (2003) 1.18
Portraits of breast cancer progression. BMC Bioinformatics (2007) 1.17
Integrating genomic data to predict transcription factor binding. Genome Inform (2005) 1.15
Label-free microarray imaging for direct detection of DNA hybridization and single-nucleotide mismatches. Biosens Bioelectron (2010) 1.15
Core promoter T-blocks correlate with gene expression levels in C. elegans. Genome Res (2011) 1.14
Photoreactive stapled BH3 peptides to dissect the BCL-2 family interactome. Chem Biol (2010) 1.11
GeneAnnot: interfacing GeneCards with high-throughput gene expression compendia. Brief Bioinform (2003) 1.10
Using functional signatures to identify repositioned drugs for breast, myelogenous leukemia and prostate cancer. PLoS Comput Biol (2012) 1.06
Pathway-based classification of cancer subtypes. Biol Direct (2012) 1.05
A novel lineage of myoviruses infecting cyanobacteria is widespread in the oceans. Proc Natl Acad Sci U S A (2012) 1.03
Modular genes with metazoan-specific domains have increased tissue specificity. Trends Genet (2005) 1.02
Analyzing networks with VisANT. Curr Protoc Bioinformatics (2004) 1.01
BLIND ordering of large-scale transcriptomic developmental timecourses. Development (2014) 1.00
Gene annotation and network inference by phylogenetic profiling. BMC Bioinformatics (2006) 0.98
Spatial localization of co-regulated genes exceeds genomic gene clustering in the Saccharomyces cerevisiae genome. Nucleic Acids Res (2013) 0.97
The genomic determinants of genotype × environment interactions in gene expression. Trends Genet (2013) 0.95
ELISA: structure-function inferences based on statistically significant and evolutionarily inspired observations. BMC Bioinformatics (2003) 0.94
The NIH National Center for Integrative Biomedical Informatics (NCIBI). J Am Med Inform Assoc (2011) 0.94
Identification of novel epigenetic markers for clear cell renal cell carcinoma. J Urol (2008) 0.92
Identification and characterization of renal cell carcinoma gene markers. Cancer Inform (2007) 0.92
A genomic bias for genotype-environment interactions in C. elegans. Mol Syst Biol (2012) 0.90
Structure-based discovery of novel amide-containing nicotinamide phosphoribosyltransferase (nampt) inhibitors. J Med Chem (2013) 0.89
Inferring protein-protein interactions in viral proteins by co-evolution of conserved side chains. Genome Inform (2006) 0.89
Protein-protein docking: overview and performance analysis. Methods Mol Biol (2008) 0.87
Structure-based identification of ureas as novel nicotinamide phosphoribosyltransferase (Nampt) inhibitors. J Med Chem (2013) 0.86
High-precision high-coverage functional inference from integrated data sources. BMC Bioinformatics (2008) 0.85
Mycobacterium tuberculosis prokaryotic ubiquitin-like protein-deconjugating enzyme is an unusual aspartate amidase. J Biol Chem (2012) 0.85
TATA binding proteins can recognize nontraditional DNA sequences. Biophys J (2012) 0.84
New type of polyubiquitin-like genes with intein-like autoprocessing domains. Trends Genet (2004) 0.82
Binding site graphs: a new graph theoretical framework for prediction of transcription factor binding sites. PLoS Comput Biol (2007) 0.82
Deciphering protein network organization using phylogenetic profile groups. Genome Inform (2005) 0.81
Drosophila protein interaction map (DPiM): a paradigm for metazoan protein complex interactions. Fly (Austin) (2012) 0.81
Protein therapeutics: promises and challenges for the 21st century. Trends Biotechnol (2002) 0.81
Identification of amides derived from 1H-pyrazolo[3,4-b]pyridine-5-carboxylic acid as potent inhibitors of human nicotinamide phosphoribosyltransferase (NAMPT). Bioorg Med Chem Lett (2013) 0.81
Phenotypic connections in surprising places. Genome Biol (2010) 0.79
PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes. Nucleic Acids Res (2005) 0.79
Simple discriminant functions identify small sets of genes that distinguish cancer phenotype from normal. Genome Inform (2005) 0.79
ELOPER: elongation of paired-end reads as a pre-processing tool for improved de novo genome assembly. Bioinformatics (2013) 0.78
Positional clustering improves computational binding site detection and identifies novel cis-regulatory sites in mammalian GABAA receptor subunit genes. Nucleic Acids Res (2007) 0.78
Condition specific transcription factor binding site characterization in Saccharomyces cerevisiae. Bioinformatics (2002) 0.78
An introduction to high-throughput sequencing experiments: design and bioinformatics analysis. Methods Mol Biol (2013) 0.78
Assessing transcription factor motif drift from noisy decoy sequences. Genome Inform (2005) 0.78
Classifying transcription factor targets and discovering relevant biological features. Biol Direct (2008) 0.78
Discovery of potent and efficacious urea-containing nicotinamide phosphoribosyltransferase (NAMPT) inhibitors with reduced CYP2C9 inhibition properties. Bioorg Med Chem Lett (2013) 0.77
Revealing developmental networks by comparative transcriptomics. Transcription (2010) 0.77
Genome-wide association studies. Methods Mol Biol (2013) 0.77
Seeing is believing: new methods for in situ single-cell transcriptomics. Genome Biol (2014) 0.76
In silico regulatory analysis for exploring human disease progression. Biol Direct (2008) 0.76
Selecting stable molecular targets for treatment and prevention of AIDS. Genome Inform (2005) 0.76
The interaction map of yeast: terra incognita? J Biol (2006) 0.75
Systems biology, the second time around. Environ Health Perspect (2004) 0.75
Toward an unbiased evolutionary platform for unraveling Xenopus developmental gene networks. Genesis (2012) 0.75
An equilibrium partitioning model connecting gene expression and cis-motif content. Bioinformatics (2006) 0.75
Clustering of domains of functionally related enzymes in the interaction database PRECISE by the generation of primary sequence patterns. J Mol Graph Model (2005) 0.75
Identifying functional links between genes by evolutionary transcriptomics. Mol Biosyst (2012) 0.75