Published in Science on February 04, 2005
Integration of biological networks and gene expression data using Cytoscape. Nat Protoc (2007) 27.10
STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res (2008) 20.62
Transcriptional regulation of protein complexes within and across species. Proc Natl Acad Sci U S A (2007) 7.07
Network-based prediction of protein function. Mol Syst Biol (2007) 6.13
Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nat Biotechnol (2009) 5.41
Visualization of omics data for systems biology. Nat Methods (2010) 4.59
Global topological features of cancer proteins in the human interactome. Bioinformatics (2006) 4.17
Differential network biology. Mol Syst Biol (2012) 3.74
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
Tissue specificity and the human protein interaction network. Mol Syst Biol (2009) 3.20
Cell wall assembly in Saccharomyces cerevisiae. Microbiol Mol Biol Rev (2006) 3.08
Identification of functional modules using network topology and high-throughput data. BMC Syst Biol (2007) 3.00
A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. BMC Bioinformatics (2007) 2.51
Widespread reorganization of metabolic enzymes into reversible assemblies upon nutrient starvation. Proc Natl Acad Sci U S A (2009) 2.39
Genome-wide functional analysis of human cell-cycle regulators. Proc Natl Acad Sci U S A (2006) 2.31
Conserved principles of mammalian transcriptional regulation revealed by RNA half-life. Nucleic Acids Res (2009) 2.26
Integrative approaches for finding modular structure in biological networks. Nat Rev Genet (2013) 2.19
HURP controls spindle dynamics to promote proper interkinetochore tension and efficient kinetochore capture. J Cell Biol (2006) 2.14
Evolution of biomolecular networks: lessons from metabolic and protein interactions. Nat Rev Mol Cell Biol (2009) 2.09
Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks. BMC Syst Biol (2008) 2.02
Review and application of group theory to molecular systems biology. Theor Biol Med Model (2011) 2.00
Prediction of yeast protein-protein interaction network: insights from the Gene Ontology and annotations. Nucleic Acids Res (2006) 1.93
Toward the dynamic interactome: it's about time. Brief Bioinform (2010) 1.91
Plk1- and beta-TrCP-dependent degradation of Bora controls mitotic progression. J Cell Biol (2008) 1.81
The origins and evolution of functional modules: lessons from protein complexes. Philos Trans R Soc Lond B Biol Sci (2006) 1.71
Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae. Nucleic Acids Res (2006) 1.65
Clusters of temporal discordances reveal distinct embryonic patterning mechanisms in Drosophila and anopheles. PLoS Biol (2011) 1.65
Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines. Mol Syst Biol (2013) 1.63
Current approaches to gene regulatory network modelling. BMC Bioinformatics (2007) 1.60
It's the machine that matters: Predicting gene function and phenotype from protein networks. J Proteomics (2010) 1.57
Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastasis. BMC Bioinformatics (2006) 1.57
Revealing static and dynamic modular architecture of the eukaryotic protein interaction network. Mol Syst Biol (2007) 1.53
Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis. Mol Syst Biol (2007) 1.53
High-resolution transcription atlas of the mitotic cell cycle in budding yeast. Genome Biol (2010) 1.51
The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast. Genome Res (2008) 1.44
Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium. Mol Syst Biol (2012) 1.44
Modelling the network of cell cycle transcription factors in the yeast Saccharomyces cerevisiae. BMC Bioinformatics (2006) 1.41
VistaClara: an expression browser plug-in for Cytoscape. Bioinformatics (2008) 1.41
Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes. Genome Biol (2008) 1.40
Modularity and dynamics of cellular networks. PLoS Comput Biol (2006) 1.37
Functional modules in the Arabidopsis core cell cycle binary protein-protein interaction network. Plant Cell (2010) 1.35
High-resolution timing of cell cycle-regulated gene expression. Proc Natl Acad Sci U S A (2007) 1.35
Assessing systems properties of yeast mitochondria through an interaction map of the organelle. PLoS Genet (2006) 1.31
Construction of a large extracellular protein interaction network and its resolution by spatiotemporal expression profiling. Mol Cell Proteomics (2010) 1.22
The Modular Organization of Protein Interactions in Escherichia coli. PLoS Comput Biol (2009) 1.20
A comparison of the functional modules identified from time course and static PPI network data. BMC Bioinformatics (2011) 1.20
Transcriptional analysis of the Candida albicans cell cycle. Mol Biol Cell (2009) 1.18
Adding protein context to the human protein-protein interaction network to reveal meaningful interactions. PLoS Comput Biol (2013) 1.10
An integrated approach to identify causal network modules of complex diseases with application to colorectal cancer. J Am Med Inform Assoc (2012) 1.10
Towards the identification of protein complexes and functional modules by integrating PPI network and gene expression data. BMC Bioinformatics (2012) 1.10
Towards inferring time dimensionality in protein-protein interaction networks by integrating structures: the p53 example. Mol Biosyst (2009) 1.09
Network crosstalk dynamically changes during neutrophil polarization. Cell (2012) 1.09
Reverse engineering dynamic temporal models of biological processes and their relationships. Proc Natl Acad Sci U S A (2010) 1.09
A simple principle concerning the robustness of protein complex activity to changes in gene expression. BMC Syst Biol (2008) 1.09
CellCircuits: a database of protein network models. Nucleic Acids Res (2006) 1.08
Germinal center B cell-like (GCB) and activated B cell-like (ABC) type of diffuse large B cell lymphoma (DLBCL): analysis of molecular predictors, signatures, cell cycle state and patient survival. Cancer Inform (2007) 1.03
Phosphosite mapping of P-type plasma membrane H+-ATPase in homologous and heterologous environments. J Biol Chem (2011) 1.02
Cell cycle regulation by feed-forward loops coupling transcription and phosphorylation. Mol Syst Biol (2009) 1.01
Ashbya Genome Database 3.0: a cross-species genome and transcriptome browser for yeast biologists. BMC Genomics (2007) 1.01
Biological process linkage networks. PLoS One (2009) 1.00
The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process. Genome Biol (2009) 1.00
Simultaneous clustering of multiple gene expression and physical interaction datasets. PLoS Comput Biol (2010) 0.99
Spatiotemporal 16p11.2 protein network implicates cortical late mid-fetal brain development and KCTD13-Cul3-RhoA pathway in psychiatric diseases. Neuron (2015) 0.98
Core and periphery structures in protein interaction networks. BMC Bioinformatics (2009) 0.97
Metabolic engineering in the -omics era: elucidating and modulating regulatory networks. Microbiol Mol Biol Rev (2005) 0.97
Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions. Protein Sci (2011) 0.96
How to cluster gene expression dynamics in response to environmental signals. Brief Bioinform (2011) 0.96
Temporal dynamics of protein complexes in PPI networks: a case study using yeast cell cycle dynamics. BMC Bioinformatics (2012) 0.96
Complex fate of paralogs. BMC Evol Biol (2008) 0.95
Functional organization of the yeast proteome by a yeast interactome map. Proc Natl Acad Sci U S A (2009) 0.95
Physical protein-protein interactions predicted from microarrays. Bioinformatics (2008) 0.94
Patterns of human gene expression variance show strong associations with signaling network hierarchy. BMC Syst Biol (2010) 0.93
GO-Diff: mining functional differentiation between EST-based transcriptomes. BMC Bioinformatics (2006) 0.92
Detection of transcriptional triggers in the dynamics of microbial growth: application to the respiratorily versatile bacterium Shewanella oneidensis. Nucleic Acids Res (2012) 0.91
Yeast Protein Interactome topology provides framework for coordinated-functionality. Nucleic Acids Res (2006) 0.90
Predicting housekeeping genes based on Fourier analysis. PLoS One (2011) 0.90
Modelling in molecular biology: describing transcription regulatory networks at different scales. Philos Trans R Soc Lond B Biol Sci (2006) 0.89
Effect of reference genome selection on the performance of computational methods for genome-wide protein-protein interaction prediction. PLoS One (2012) 0.89
Spatiotemporal variation of mammalian protein complex stoichiometries. Genome Biol (2016) 0.87
Combinatorial complexity and compositional drift in protein interaction networks. PLoS One (2012) 0.87
Dynamic circadian protein-protein interaction networks predict temporal organization of cellular functions. PLoS Genet (2013) 0.87
Chronic rejection of a lung transplant is characterized by a profile of specific autoantibodies. Immunology (2010) 0.86
Module discovery by exhaustive search for densely connected, co-expressed regions in biomolecular interaction networks. PLoS One (2010) 0.86
Structural basis for K(V)7.1-KCNE(x) interactions in the I(Ks) channel complex. Heart Rhythm (2009) 0.86
Modeling disease progression using dynamics of pathway connectivity. Bioinformatics (2014) 0.86
Dynamic networks from hierarchical bayesian graph clustering. PLoS One (2010) 0.86
Human protein interaction networks across tissues and diseases. Front Genet (2015) 0.86
Efficiency of complex production in changing environment. BMC Syst Biol (2009) 0.84
Protein evolution in yeast transcription factor subnetworks. Nucleic Acids Res (2010) 0.84
Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression. BMC Syst Biol (2009) 0.84
Differential evolutionary conservation of motif modes in the yeast protein interaction network. BMC Genomics (2006) 0.84
POLAR MAPPER: a computational tool for integrated visualization of protein interaction networks and mRNA expression data. J R Soc Interface (2008) 0.83
MyProteinNet: build up-to-date protein interaction networks for organisms, tissues and user-defined contexts. Nucleic Acids Res (2015) 0.83
In silico pathway reconstruction: Iron-sulfur cluster biogenesis in Saccharomyces cerevisiae. BMC Syst Biol (2007) 0.83
A bacterial two-hybrid system based on the twin-arginine transporter pathway of E. coli. Protein Sci (2007) 0.83
Network biology concepts in complex disease comorbidities. Nat Rev Genet (2016) 0.82
Comparative gene expression between two yeast species. BMC Genomics (2013) 0.82
Investigating the validity of current network analysis on static conglomerate networks by protein network stratification. BMC Bioinformatics (2010) 0.81
Cellular plasticity enables adaptation to unforeseen cell-cycle rewiring challenges. PLoS One (2012) 0.81
Evidence for the additions of clustered interacting nodes during the evolution of protein interaction networks from network motifs. BMC Evol Biol (2011) 0.80
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
Improved prediction of signal peptides: SignalP 3.0. J Mol Biol (2004) 48.40
Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature (2002) 45.19
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods (2011) 33.90
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
Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc (2007) 19.50
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
A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol (2007) 9.90
SMART 6: recent updates and new developments. Nucleic Acids Res (2008) 9.80
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
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
Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci Signal (2010) 8.61
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res (2006) 8.36
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
Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics (2004) 7.76
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol (2011) 7.53
Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature (2010) 7.51
Alternative splicing and genome complexity. Nat Genet (2001) 7.30
The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc Natl Acad Sci U S A (2002) 7.21
A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biol (2002) 7.12
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
Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci (2003) 6.85
A side effect resource to capture phenotypic effects of drugs. Mol Syst Biol (2010) 6.75
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature (2008) 6.69
The ecoresponsive genome of Daphnia pulex. Science (2011) 6.55
The genome of the model beetle and pest Tribolium castaneum. Nature (2008) 6.50
Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites. Glycobiology (2004) 6.13
Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci (2003) 5.94
Association of genes to genetically inherited diseases using data mining. Nat Genet (2002) 5.78
Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science (2010) 5.56
Immunity-related genes and gene families in Anopheles gambiae. Science (2002) 5.47
Analysis and prediction of leucine-rich nuclear export signals. Protein Eng Des Sel (2004) 5.15
STITCH: interaction networks of chemicals and proteins. Nucleic Acids Res (2007) 4.88
Genomes in flux: the evolution of archaeal and proteobacterial gene content. Genome Res (2002) 4.85
eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Res (2007) 4.84
An Aboriginal Australian genome reveals separate human dispersals into Asia. Science (2011) 4.84
Transcriptome complexity in a genome-reduced bacterium. Science (2009) 4.64
Feature-based prediction of non-classical and leaderless protein secretion. Protein Eng Des Sel (2004) 4.54
Mining electronic health records: towards better research applications and clinical care. Nat Rev Genet (2012) 4.42
Update on XplorMed: A web server for exploring scientific literature. Nucleic Acids Res (2003) 4.42
Genomic variation landscape of the human gut microbiome. Nature (2012) 4.38
Genome-wide experimental determination of barriers to horizontal gene transfer. Science (2007) 4.37
A genome-wide survey of human pseudogenes. Genome Res (2003) 4.34
KEGG Atlas mapping for global analysis of metabolic pathways. Nucleic Acids Res (2008) 4.14
iPath: interactive exploration of biochemical pathways and networks. Trends Biochem Sci (2008) 4.03
Proteome organization in a genome-reduced bacterium. Science (2009) 3.97
Molecular eco-systems biology: towards an understanding of community function. Nat Rev Microbiol (2008) 3.95
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res (2011) 3.94
The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93
Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing. Genes Dev (2007) 3.92
SuperTarget and Matador: resources for exploring drug-target relationships. Nucleic Acids Res (2007) 3.82
eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res (2013) 3.77
Linear motif atlas for phosphorylation-dependent signaling. Sci Signal (2008) 3.77
Medusa: a simple tool for interaction graph analysis. Bioinformatics (2005) 3.74