Published in BMC Bioinformatics on November 09, 2011
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Biological network exploration with cytoscape 3. Curr Protoc Bioinformatics (2014) 1.14
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The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. Nucleic Acids Res (2016) 1.02
BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats. BMC Syst Biol (2013) 1.02
Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions. Nat Protoc (2014) 0.92
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Identification and characterization of three chemosensory receptor families in the cotton bollworm Helicoverpa armigera. BMC Genomics (2014) 0.91
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Cadmium-induced proteome remodeling regulated by Spc1/Sty1 and Zip1 in fission yeast. Toxicol Sci (2012) 0.83
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A Module Analysis Approach to Investigate Molecular Mechanism of TCM Formula: A Trial on Shu-feng-jie-du Formula. Evid Based Complement Alternat Med (2013) 0.80
A network-based approach to dissect the cilia/centrosome complex interactome. BMC Genomics (2014) 0.80
Transcriptional landscapes of emerging autoimmunity: transient aberrations in the targeted tissue's extracellular milieu precede immune responses in Sjögren's syndrome. Arthritis Res Ther (2013) 0.80
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Community-based network study of protein-carbohydrate interactions in plant lectins using glycan array data. PLoS One (2014) 0.78
Revealing the Molecular Portrait of Triple Negative Breast Tumors in an Understudied Population through Omics Analysis of Formalin-Fixed and Paraffin-Embedded Tissues. PLoS One (2015) 0.78
The human plasma membrane peripherome: visualization and analysis of interactions. Biomed Res Int (2014) 0.78
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Seasonal Succession of Free-Living Bacterial Communities in Coastal Waters of the Western Antarctic Peninsula. Front Microbiol (2016) 0.78
Expression-based network biology identifies immune-related functional modules involved in plant defense. BMC Genomics (2014) 0.78
Identification of a nutrient-sensing transcriptional network in monocytes by using inbred rat models on a cafeteria diet. Dis Model Mech (2016) 0.78
Ecogenomic perspectives on domains of unknown function: correlation-based exploration of marine metagenomes. PLoS One (2013) 0.78
Network Analysis for the Identification of Differentially Expressed Hub Genes Using Myogenin Knock-down Muscle Satellite Cells. PLoS One (2015) 0.77
FunMod: a Cytoscape plugin for identifying functional modules in undirected protein-protein networks. Genomics Proteomics Bioinformatics (2014) 0.77
Inferring plant microRNA functional similarity using a weighted protein-protein interaction network. BMC Bioinformatics (2015) 0.77
Evidence for the Induction of Key Components of the NOTCH Signaling Pathway via Deltamethrin and Azamethiphos Treatment in the Sea Louse Caligus rogercresseyi. Int J Mol Sci (2016) 0.77
SCUDO: a tool for signature-based clustering of expression profiles. Nucleic Acids Res (2015) 0.77
Identification of potential therapeutic targets for papillary thyroid carcinoma by bioinformatics analysis. Oncol Lett (2015) 0.77
Integrative systems analysis of diet-induced obesity identified a critical transition in the transcriptomes of the murine liver and epididymal white adipose tissue. Int J Obes (Lond) (2015) 0.77
Systems biology analysis of the proteomic alterations induced by MPP(+), a Parkinson's disease-related mitochondrial toxin. Front Cell Neurosci (2015) 0.76
Evolutionarily Dynamic, but Robust, Targeting of Resistance Genes by the miR482/2118 Gene Family in the Solanaceae. Genome Biol Evol (2015) 0.76
Transcriptome analysis reveals regulatory networks underlying differential susceptibility to Botrytis cinerea in response to nitrogen availability in Solanum lycopersicum. Front Plant Sci (2015) 0.76
Cancer Transcriptome Dataset Analysis: Comparing Methods of Pathway and Gene Regulatory Network-Based Cluster Identification. OMICS (2017) 0.75
Classification of Beta-lactamases and penicillin binding proteins using ligand-centric network models. PLoS One (2015) 0.75
The Neurospora Transcription Factor ADV-1 Transduces Light Signals and Temporal Information to Control Rhythmic Expression of Genes Involved in Cell-Fusion. G3 (Bethesda) (2016) 0.75
The amyloid interactome: Exploring protein aggregation. PLoS One (2017) 0.75
VennPainter: A Tool for the Comparison and Identification of Candidate Genes Based on Venn Diagrams. PLoS One (2016) 0.75
Detecting non-uniform clusters in large-scale interaction graphs. J Comput Biol (2013) 0.75
Regulatory modules controlling early shade avoidance response in maize seedlings. BMC Genomics (2016) 0.75
CyAnimator: Simple Animations of Cytoscape Networks. F1000Res (2015) 0.75
Systems Analysis of the Complement-Induced Priming Phase of Liver Regeneration. J Immunol (2016) 0.75
The last enzyme of the de novo purine synthesis pathway 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase (ATIC) plays a central role in insulin signaling and the Golgi/endosomes protein network. Mol Cell Proteomics (2015) 0.75
Control of Neuronal Network in Caenorhabditis elegans. PLoS One (2015) 0.75
In silico analysis of the molecular mechanism of postmenopausal osteoporosis. Mol Med Rep (2015) 0.75
MORO: a Cytoscape app for relationship analysis between modularity and robustness in large-scale biological networks. BMC Syst Biol (2016) 0.75
In silico identification of essential proteins in Corynebacterium pseudotuberculosis based on protein-protein interaction networks. BMC Syst Biol (2016) 0.75
Structure-Activity Relationship in TLR4 Mutations: Atomistic Molecular Dynamics Simulations and Residue Interaction Network Analysis. Sci Rep (2017) 0.75
Network-Based Protein Biomarker Discovery Platforms. Genomics Inform (2016) 0.75
A comprehensive platform for the analysis of ubiquitin-like protein modifications using in vivo biotinylation. Sci Rep (2017) 0.75
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Visualization of network target crosstalk optimizes drug synergism in myocardial ischemia. PLoS One (2014) 0.75
Identification and Characterization of miRNA differentially expressed in macrophages exposed to Porphyromonas gingivalis infection. Infect Immun (2017) 0.75
Semi-Quantitative Mass Spectrometry in AML Cells Identifies New Non-Genomic Targets of the EZH2 Methyltransferase. Int J Mol Sci (2017) 0.75
CytoCluster: A Cytoscape Plugin for Cluster Analysis and Visualization of Biological Networks. Int J Mol Sci (2017) 0.75
Differential Tissue-specific and Pathway-specific Anti-obesity Effects of Green Tea and Taeumjowitang, a Traditional Korean Medicine, in Mice. J Cancer Prev (2017) 0.75
NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium-scale biological networks. BMC Res Notes (2017) 0.75
Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis. Adv Bioinformatics (2017) 0.75
Cleaning by clustering: methodology for addressing data quality issues in biomedical metadata. BMC Bioinformatics (2017) 0.75
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A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature (2000) 47.15
TM4: a free, open-source system for microarray data management and analysis. Biotechniques (2003) 38.02
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature (2002) 37.66
Integration of biological networks and gene expression data using Cytoscape. Nat Protoc (2007) 27.10
An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res (2002) 25.81
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature (2006) 24.29
Finding and evaluating community structure in networks. Phys Rev E Stat Nonlin Soft Matter Phys (2004) 24.12
Java Treeview--extensible visualization of microarray data. Bioinformatics (2004) 24.12
BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics (2005) 24.04
Proteome survey reveals modularity of the yeast cell machinery. Nature (2006) 20.77
PIRSF: family classification system at the Protein Information Resource. Nucleic Acids Res (2004) 19.62
The genetic landscape of a cell. Science (2010) 16.52
Clustering by passing messages between data points. Science (2007) 15.45
An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics (2003) 15.42
TM4 microarray software suite. Methods Enzymol (2006) 13.78
Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics (2002) 12.88
Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc Natl Acad Sci U S A (2000) 10.98
Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Cell (2005) 10.41
Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature (2007) 9.25
Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics (2001) 9.11
Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol Cell Proteomics (2007) 7.93
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CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins. Nucleic Acids Res (2001) 4.59
Protein complex prediction via cost-based clustering. Bioinformatics (2004) 4.30
ProtoMap: automatic classification of protein sequences and hierarchy of protein families. Nucleic Acids Res (2000) 3.97
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Expression analysis of G Protein-Coupled Receptors in mouse macrophages. Immunome Res (2008) 3.54
Exploration of uncharted regions of the protein universe. PLoS Biol (2009) 3.41
Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes. Nucleic Acids Res (2001) 3.26
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
Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database. Biochemistry (2006) 2.65
GeneRAGE: a robust algorithm for sequence clustering and domain detection. Bioinformatics (2000) 2.64
ProtoNet: hierarchical classification of the protein space. Nucleic Acids Res (2003) 1.88
Clustering of proximal sequence space for the identification of protein families. Bioinformatics (2002) 1.87
Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing. BMC Bioinformatics (2007) 1.71
SYSTERS, GeneNest, SpliceNest: exploring sequence space from genome to protein. Nucleic Acids Res (2002) 1.65
Markov clustering versus affinity propagation for the partitioning of protein interaction graphs. BMC Bioinformatics (2009) 1.44
Computational cluster validation for microarray data analysis: experimental assessment of Clest, Consensus Clustering, Figure of Merit, Gap Statistics and Model Explorer. BMC Bioinformatics (2008) 1.38
AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number. BMC Bioinformatics (2010) 1.37
Mechanistic diversity in a metalloenzyme superfamily. Biochemistry (2000) 1.28
Comprehensive cluster analysis with Transitivity Clustering. Nat Protoc (2011) 1.28
Sequence clustering strategies improve remote homology recognitions while reducing search times. Protein Eng (2002) 1.25
GLay: community structure analysis of biological networks. Bioinformatics (2010) 1.24
Partitioning biological data with transitivity clustering. Nat Methods (2010) 1.23
jClust: a clustering and visualization toolbox. Bioinformatics (2009) 1.20
Clustering and analysis of protein families. Curr Opin Struct Biol (2001) 1.14
Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution. Bioinformatics (2010) 1.09
SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale. BMC Bioinformatics (2010) 0.96
Identification of protein functions using a machine-learning approach based on sequence-derived properties. Proteome Sci (2009) 0.90
A mouse protein interactome through combined literature mining with multiple sources of interaction evidence. Amino Acids (2009) 0.86
A split-ubiquitin-based assay detects the influence of mutations on the conformational stability of the p53 DNA binding domain in vivo. FEBS Lett (2002) 0.78
Homology-free prediction of functional class of proteins and peptides by support vector machines. Curr Protein Pept Sci (2008) 0.78
Using support vector machines to distinguish enzymes: approached by incorporating wavelet transform. J Theor Biol (2008) 0.78
UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem (2004) 112.47
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature (2002) 37.66
Integration of biological networks and gene expression data using Cytoscape. Nat Protoc (2007) 27.10
Global mapping of the yeast genetic interaction network. Science (2004) 21.34
International network of cancer genome projects. Nature (2010) 20.35
The genetic landscape of a cell. Science (2010) 16.52
Functional impact of global rare copy number variation in autism spectrum disorders. Nature (2010) 14.66
The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res (2010) 10.97
Cytoscape Web: an interactive web-based network browser. Bioinformatics (2010) 10.03
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
The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol (2007) 8.24
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol (2007) 8.03
A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science (2001) 7.08
Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS One (2010) 6.61
A travel guide to Cytoscape plugins. Nat Methods (2012) 6.53
PreBIND and Textomy--mining the biomedical literature for protein-protein interactions using a support vector machine. BMC Bioinformatics (2003) 6.31
Natural variation in human membrane transporter genes reveals evolutionary and functional constraints. Proc Natl Acad Sci U S A (2003) 5.77
Visualizing density maps with UCSF Chimera. J Struct Biol (2006) 5.75
PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat Methods (2011) 5.01
BayGenomics: a resource of insertional mutations in mouse embryonic stem cells. Nucleic Acids Res (2003) 4.83
A large-scale evaluation of computational protein function prediction. Nat Methods (2013) 4.61
MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res (2004) 4.54
Subgroup-specific structural variation across 1,000 medulloblastoma genomes. Nature (2012) 4.13
Comprehensive identification of mutational cancer driver genes across 12 tumor types. Sci Rep (2013) 3.92
The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse. Nucleic Acids Res (2006) 3.40
cPath: open source software for collecting, storing, and querying biological pathways. BMC Bioinformatics (2006) 3.24
A specificity map for the PDZ domain family. PLoS Biol (2008) 3.16
Delineation of two clinically and molecularly distinct subgroups of posterior fossa ependymoma. Cancer Cell (2011) 3.11
Designed divergent evolution of enzyme function. Nature (2006) 3.09
Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. PLoS One (2009) 3.03
Pathway information for systems biology. FEBS Lett (2005) 2.97
ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res (2010) 2.96
Germ-line DNA copy number variation frequencies in a large North American population. Hum Genet (2007) 2.94
Too many roads not taken. Nature (2011) 2.93
SeqHound: biological sequence and structure database as a platform for bioinformatics research. BMC Bioinformatics (2002) 2.84
GeneMANIA prediction server 2013 update. Nucleic Acids Res (2013) 2.74
Quantitative analysis of fitness and genetic interactions in yeast on a genome scale. Nat Methods (2010) 2.67
Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database. Biochemistry (2006) 2.65
NetPath: a public resource of curated signal transduction pathways. Genome Biol (2010) 2.62
Graph-based analysis and visualization of experimental results with ONDEX. Bioinformatics (2006) 2.60
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. Nucleic Acids Res (2010) 2.41
Tools for integrated sequence-structure analysis with UCSF Chimera. BMC Bioinformatics (2006) 2.38
Computational prediction of protein-protein interactions. Mol Biotechnol (2007) 2.35
Positive selection of tyrosine loss in metazoan evolution. Science (2009) 2.28
Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases. Sci Signal (2009) 2.16
Software extensions to UCSF chimera for interactive visualization of large molecular assemblies. Structure (2005) 2.12
UCSF Chimera, MODELLER, and IMP: an integrated modeling system. J Struct Biol (2011) 2.10
Evolutionary conservation predicts function of variants of the human organic cation transporter, OCT1. Proc Natl Acad Sci U S A (2003) 2.03
The genome sequence of the colonial chordate, Botryllus schlosseri. Elife (2013) 1.86
Rapid evolution of functional complexity in a domain family. Sci Signal (2009) 1.85
Genetic correction of Huntington's disease phenotypes in induced pluripotent stem cells. Cell Stem Cell (2012) 1.79
Sequence diversity and haplotype structure in the human ABCB1 (MDR1, multidrug resistance transporter) gene. Pharmacogenetics (2003) 1.79
Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins. PLoS Biol (2009) 1.78
Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers. Mol Syst Biol (2013) 1.78
Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study. J Microbiol Methods (2011) 1.76
Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing. BMC Bioinformatics (2007) 1.71
Identification of a colonial chordate histocompatibility gene. Science (2013) 1.68
How to visually interpret biological data using networks. Nat Biotechnol (2009) 1.66
Compound prioritization methods increase rates of chemical probe discovery in model organisms. Chem Biol (2011) 1.64
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Polymorphisms in a human kidney xenobiotic transporter, OCT2, exhibit altered function. Pharmacogenetics (2002) 1.57
Chromatin is an ancient innovation conserved between Archaea and Eukarya. Elife (2012) 1.56
Evidence for reductive genome evolution and lateral acquisition of virulence functions in two Corynebacterium pseudotuberculosis strains. PLoS One (2011) 1.53
Dynamic interaction networks in a hierarchically organized tissue. Mol Syst Biol (2010) 1.51
The Structure-Function Linkage Database. Nucleic Acids Res (2013) 1.50
Using biological pathway data with paxtools. PLoS Comput Biol (2013) 1.50
Role of organic cation transporter 3 (SLC22A3) and its missense variants in the pharmacologic action of metformin. Pharmacogenet Genomics (2010) 1.48
A comparative transcriptomic analysis reveals conserved features of stem cell pluripotency in planarians and mammals. Stem Cells (2012) 1.48
DRYGIN: a database of quantitative genetic interaction networks in yeast. Nucleic Acids Res (2009) 1.41
A predictive model for drug bioaccumulation and bioactivity in Caenorhabditis elegans. Nat Chem Biol (2010) 1.41
Analysis of quality raw data of second generation sequencers with Quality Assessment Software. BMC Res Notes (2011) 1.40
The mutational landscape of phosphorylation signaling in cancer. Sci Rep (2013) 1.39
Mapping the cellular response to small molecules using chemogenomic fitness signatures. Science (2014) 1.39
WordCloud: a Cytoscape plugin to create a visual semantic summary of networks. Source Code Biol Med (2011) 1.38
Interaction of methotrexate with organic-anion transporting polypeptide 1A2 and its genetic variants. J Pharmacol Exp Ther (2006) 1.38
Cytoscape app store. Bioinformatics (2013) 1.35
B cell exchange across the blood-brain barrier in multiple sclerosis. J Clin Invest (2012) 1.35
Attenuation of miR-126 activity expands HSC in vivo without exhaustion. Cell Stem Cell (2012) 1.35
The biology/disease-driven human proteome project (B/D-HPP): enabling protein research for the life sciences community. J Proteome Res (2012) 1.35
Coevolution of PDZ domain-ligand interactions analyzed by high-throughput phage display and deep sequencing. Mol Biosyst (2010) 1.35
Bringing order to protein disorder through comparative genomics and genetic interactions. Genome Biol (2011) 1.34
The Biomolecular Interaction Network Database in PSI-MI 2.5. Database (Oxford) (2011) 1.34
Functional complexes between YAP2 and ZO-2 are PDZ domain-dependent, and regulate YAP2 nuclear localization and signalling. Biochem J (2010) 1.34
Exploring biological networks with Cytoscape software. Curr Protoc Bioinformatics (2008) 1.30
Comparison of human solute carriers. Protein Sci (2010) 1.29
Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps. Proteomics (2010) 1.29
Comprehensive cluster analysis with Transitivity Clustering. Nat Protoc (2011) 1.28
From bytes to bedside: data integration and computational biology for translational cancer research. PLoS Comput Biol (2007) 1.27
Exact and heuristic algorithms for weighted cluster editing. Comput Syst Bioinformatics Conf (2007) 1.27
Immunologic response to cryoablation of breast cancer. Breast Cancer Res Treat (2005) 1.23
PIPS: pathogenicity island prediction software. PLoS One (2012) 1.23
Genetic and pharmacologic disruption of interleukin-1β signaling inhibits experimental aortic aneurysm formation. Arterioscler Thromb Vasc Biol (2013) 1.23
The human multidrug resistance protein 4 (MRP4, ABCC4): functional analysis of a highly polymorphic gene. J Pharmacol Exp Ther (2008) 1.23
Partitioning biological data with transitivity clustering. Nat Methods (2010) 1.23
An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology. BMC Bioinformatics (2010) 1.21