Published in Nat Biotechnol on May 01, 2007
STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res (2008) 20.62
Visualization of omics data for systems biology. Nat Methods (2010) 4.59
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
Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network. Genome Biol (2009) 2.43
A global analysis of genetic interactions in Caenorhabditis elegans. J Biol (2007) 1.78
Unraveling protein networks with power graph analysis. PLoS Comput Biol (2008) 1.77
Genome Projector: zoomable genome map with multiple views. BMC Bioinformatics (2009) 1.73
VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies. Nucleic Acids Res (2013) 1.71
How to visually interpret biological data using networks. Nat Biotechnol (2009) 1.66
Finding the right questions: exploratory pathway analysis to enhance biological discovery in large datasets. PLoS Biol (2010) 1.33
The evolving transcriptome of head and neck squamous cell carcinoma: a systematic review. PLoS One (2008) 1.18
xiNET: cross-link network maps with residue resolution. Mol Cell Proteomics (2015) 1.03
Extended LineSets: a visualization technique for the interactive inspection of biological pathways. BMC Proc (2015) 1.00
NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. BMC Syst Biol (2013) 0.96
Semantic integration of data on transcriptional regulation. Bioinformatics (2010) 0.94
Genome-wide analysis of PDZ domain binding reveals inherent functional overlap within the PDZ interaction network. PLoS One (2011) 0.93
Properties of metabolic graphs: biological organization or representation artifacts? BMC Bioinformatics (2011) 0.91
Consistent design schematics for biological systems: standardization of representation in biological engineering. J R Soc Interface (2009) 0.89
VANLO--interactive visual exploration of aligned biological networks. BMC Bioinformatics (2009) 0.86
POLAR MAPPER: a computational tool for integrated visualization of protein interaction networks and mRNA expression data. J R Soc Interface (2008) 0.83
The BioIntelligence Framework: a new computational platform for biomedical knowledge computing. J Am Med Inform Assoc (2012) 0.83
Network architecture of signaling from uncoupled helicase-polymerase to cell cycle checkpoints and trans-lesion DNA synthesis. Cell Cycle (2009) 0.82
Interactive, multiscale navigation of large and complicated biological networks. Bioinformatics (2011) 0.81
Functional characterization of breast cancer using pathway profiles. BMC Med Genomics (2014) 0.78
Xtalk: a path-based approach for identifying crosstalk between signaling pathways. Bioinformatics (2015) 0.78
MINER: exploratory analysis of gene interaction networks by machine learning from expression data. BMC Genomics (2009) 0.77
Using VisANT to Analyze Networks. Curr Protoc Bioinformatics (2014) 0.77
Signaling hypergraphs. Trends Biotechnol (2014) 0.76
Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0. PLoS Comput Biol (2016) 0.76
Mimoza: web-based semantic zooming and navigation in metabolic networks. BMC Syst Biol (2015) 0.75
Reverse engineering molecular hypergraphs. IEEE/ACM Trans Comput Biol Bioinform (2014) 0.75
Cell cycle kinases predicted from conserved biophysical properties. Proteins (2009) 0.75
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol (2006) 30.90
KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res (2007) 29.46
International network of cancer genome projects. Nature (2010) 20.35
Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. J Am Chem Soc (2003) 15.30
LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Res (2002) 13.61
Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions. J Am Chem Soc (2004) 11.50
The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet (2013) 11.29
KEGG as a glycome informatics resource. Glycobiology (2005) 11.05
Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics (2010) 8.44
Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature (2002) 8.32
Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature (2012) 8.03
Network-based analysis and characterization of adverse drug-drug interactions. J Chem Inf Model (2011) 7.92
Systematic analysis of enzyme-catalyzed reaction patterns and prediction of microbial biodegradation pathways. J Chem Inf Model (2007) 7.70
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
Comprehensive analysis of distinctive polyketide and nonribosomal peptide structural motifs encoded in microbial genomes. J Mol Biol (2007) 6.59
PharmGKB: the Pharmacogenetics Knowledge Base. Nucleic Acids Res (2002) 6.40
Prediction of glycan structures from gene expression data based on glycosyltransferase reactions. Bioinformatics (2005) 5.76
The commonality of protein interaction networks determined in neurodegenerative disorders (NDDs). Bioinformatics (2007) 5.63
Subtype and pathway specific responses to anticancer compounds in breast cancer. Proc Natl Acad Sci U S A (2011) 4.55
AAindex: amino acid index database, progress report 2008. Nucleic Acids Res (2007) 4.21
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
Modular architecture of metabolic pathways revealed by conserved sequences of reactions. J Chem Inf Model (2013) 3.58
The UCSC Cancer Genomics Browser: update 2011. Nucleic Acids Res (2010) 3.37
Predictome: a database of putative functional links between proteins. Nucleic Acids Res (2002) 3.32
VisANT: data-integrating visual framework for biological networks and modules. Nucleic Acids Res (2005) 3.24
Prediction of drug-target interaction networks from the integration of chemical and genomic spaces. Bioinformatics (2008) 2.96
E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs. Bioinformatics (2009) 2.88
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
The repertoire of desaturases and elongases reveals fatty acid variations in 56 eukaryotic genomes. J Lipid Res (2007) 2.65
The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies. BMC Bioinformatics (2008) 2.54
iPath2.0: interactive pathway explorer. Nucleic Acids Res (2011) 2.50
High expression of lymphocyte-associated genes in node-negative HER2+ breast cancers correlates with lower recurrence rates. Cancer Res (2007) 2.48
The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult. Cell Rep (2012) 2.45
Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs. Bioinformatics (2003) 2.45
Gene expression in lung adenocarcinomas of smokers and nonsmokers. Am J Respir Cell Mol Biol (2003) 2.45
Comprehensive analysis of glycosyltransferases in eukaryotic genomes for structural and functional characterization of glycans. Carbohydr Res (2009) 2.40
Association of leukocyte telomere length with breast cancer risk: nested case-control findings from the Shanghai Women's Health Study. Am J Epidemiol (2013) 2.34
Identification of functional links between genes using phylogenetic profiles. Bioinformatics (2003) 2.33
Loss of Bif-1 suppresses Bax/Bak conformational change and mitochondrial apoptosis. Mol Cell Biol (2005) 2.31
Extraction and analysis of chemical modification patterns in drug development. J Chem Inf Model (2009) 2.28
VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. Nucleic Acids Res (2007) 2.17
Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework. Bioinformatics (2010) 2.14
Identification of a new cryptochrome class. Structure, function, and evolution. Mol Cell (2003) 2.11
Gene annotation and pathway mapping in KEGG. Methods Mol Biol (2007) 2.09
Hierarchical organization in the hemostatic response and its relationship to the platelet-signaling network. Blood (2013) 2.05
Voltage-gated Na+ channel SCN5A is a key regulator of a gene transcriptional network that controls colon cancer invasion. Cancer Res (2010) 2.01
Discovery of a novel shp2 protein tyrosine phosphatase inhibitor. Mol Pharmacol (2006) 1.98
Potent inhibition of platelet-derived growth factor-induced responses in vascular smooth muscle cells by BMS-354825 (dasatinib). Mol Pharmacol (2006) 1.95
Identifying functional links between genes using conserved chromosomal proximity. Trends Genet (2002) 1.91
Gene set enrichment analysis: performance evaluation and usage guidelines. Brief Bioinform (2011) 1.84
Regulated surface expression and shedding support a dual role for semaphorin 4D in platelet responses to vascular injury. Proc Natl Acad Sci U S A (2007) 1.83
Global analysis of circadian expression in the cyanobacterium Synechocystis sp. strain PCC 6803. J Bacteriol (2005) 1.80
Functional fingerprints of folds: evidence for correlated structure-function evolution. J Mol Biol (2003) 1.80
Noonan syndrome-associated SHP2/PTPN11 mutants cause EGF-dependent prolonged GAB1 binding and sustained ERK2/MAPK1 activation. Hum Mutat (2004) 1.80
A global analysis of genetic interactions in Caenorhabditis elegans. J Biol (2007) 1.78
EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments. Nucleic Acids Res (2006) 1.75
The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships. Bioinformatics (2005) 1.75
Effect of atorvastatin on SR-BI expression and HDL-induced cholesterol efflux in adipocytes of hypercholesterolemic rabbits. Clin Chim Acta (2005) 1.71
Systemic spread and propagation of a plant-pathogenic virus in European honeybees, Apis mellifera. MBio (2014) 1.71
Roles of Gab1 and SHP2 in paxillin tyrosine dephosphorylation and Src activation in response to epidermal growth factor. J Biol Chem (2003) 1.68
Alteration of gene expression in human hepatocellular carcinoma with integrated hepatitis B virus DNA. Clin Cancer Res (2005) 1.64
ODB: a database of operons accumulating known operons across multiple genomes. Nucleic Acids Res (2006) 1.58
Perilipin 5 improves hepatic lipotoxicity by inhibiting lipolysis. Hepatology (2015) 1.55
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
PathPred: an enzyme-catalyzed metabolic pathway prediction server. Nucleic Acids Res (2010) 1.49
Functional rundown of gamma-aminobutyric acid(A) receptors in human hypothalamic hamartomas. Ann Neurol (2011) 1.48
Problematic Internet Use in high school students in Guangdong Province, China. PLoS One (2011) 1.47
Cross-priming amplification for rapid detection of Mycobacterium tuberculosis in sputum specimens. J Clin Microbiol (2008) 1.47
Regulation of the mitogen-activated protein kinase signaling pathway by SHP2. J Biol Chem (2002) 1.47
Molecular signatures of quiescent, mobilized and leukemia-initiating hematopoietic stem cells. PLoS One (2010) 1.46
DNA microarray analysis of redox-responsive genes in the genome of the cyanobacterium Synechocystis sp. strain PCC 6803. J Bacteriol (2003) 1.46
PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis. Bioinformatics (2012) 1.43
KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains. Nucleic Acids Res (2004) 1.43
The phosphorylation of EphB2 receptor regulates migration and invasion of human glioma cells. Cancer Res (2004) 1.42
Hydroxamic acid analogue histone deacetylase inhibitors attenuate estrogen receptor-alpha levels and transcriptional activity: a result of hyperacetylation and inhibition of chaperone function of heat shock protein 90. Clin Cancer Res (2007) 1.42
3D coordination framework with uncommon two-fold interpenetrated {3(3)5(9)6(3)}-lcy net and coordinated anion exchange. Chemistry (2009) 1.40
A computational framework for optimal masking in the synthesis of oligonucleotide microarrays. Nucleic Acids Res (2002) 1.40
Positive regulation of sugar catabolic pathways in the cyanobacterium Synechocystis sp. PCC 6803 by the group 2 sigma factor sigE. J Biol Chem (2005) 1.40
Towards the identification of essential genes using targeted genome sequencing and comparative analysis. BMC Genomics (2006) 1.39
Inhibition of Bcr-Abl kinase activity by PD180970 blocks constitutive activation of Stat5 and growth of CML cells. Oncogene (2002) 1.38
KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters. Nucleic Acids Res (2012) 1.36
Combined effects of novel tyrosine kinase inhibitor AMN107 and histone deacetylase inhibitor LBH589 against Bcr-Abl-expressing human leukemia cells. Blood (2006) 1.36
Impact of cigarette smoking in type 2 diabetes development. Acta Pharmacol Sin (2009) 1.34
A novel nicotinic acetylcholine receptor subtype in basal forebrain cholinergic neurons with high sensitivity to amyloid peptides. J Neurosci (2009) 1.33
The KEGG databases and tools facilitating omics analysis: latest developments involving human diseases and pharmaceuticals. Methods Mol Biol (2012) 1.33
Identification of a signalling molecule involved in bacterial intergeneric communication. Microbiology (2007) 1.32
Extracting active pathways from gene expression data. Bioinformatics (2003) 1.31
Prediction of estrogen receptor binding for 58,000 chemicals using an integrated system of a tree-based model with structural alerts. Environ Health Perspect (2002) 1.31
Flow shear stress stimulates Gab1 tyrosine phosphorylation to mediate protein kinase B and endothelial nitric-oxide synthase activation in endothelial cells. J Biol Chem (2005) 1.31
Supervised enzyme network inference from the integration of genomic data and chemical information. Bioinformatics (2005) 1.28