Published in PLoS Biol on July 22, 2008
Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res (2010) 11.23
BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol (2009) 11.17
The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2011) 8.62
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2012) 8.41
A travel guide to Cytoscape plugins. Nat Methods (2012) 6.53
WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013. Nucleic Acids Res (2013) 6.17
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2013) 5.25
WikiPathways: building research communities on biological pathways. Nucleic Acids Res (2011) 4.78
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics (2013) 4.73
Visualization of omics data for systems biology. Nat Methods (2010) 4.59
Presenting and exploring biological pathways with PathVisio. BMC Bioinformatics (2008) 4.34
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2014) 3.55
The Gene Wiki: community intelligence applied to human gene annotation. Nucleic Acids Res (2009) 3.51
Seeking health information online: does Wikipedia matter? J Am Med Inform Assoc (2009) 3.28
SMPDB: The Small Molecule Pathway Database. Nucleic Acids Res (2009) 3.18
NetPath: a public resource of curated signal transduction pathways. Genome Biol (2010) 2.62
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2015) 2.44
Software for systems biology: from tools to integrated platforms. Nat Rev Genet (2011) 2.42
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. Nucleic Acids Res (2010) 2.41
Mass-spectrometry-based metabolomics: limitations and recommendations for future progress with particular focus on nutrition research. Metabolomics (2009) 2.21
Mining biological pathways using WikiPathways web services. PLoS One (2009) 2.17
Pathway databases and tools for their exploitation: benefits, current limitations and challenges. Mol Syst Biol (2009) 2.03
The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. BMC Bioinformatics (2010) 2.03
Capture of microRNA-bound mRNAs identifies the tumor suppressor miR-34a as a regulator of growth factor signaling. PLoS Genet (2011) 2.00
EnrichNet: network-based gene set enrichment analysis. Bioinformatics (2012) 1.92
A systems approach identifies HIPK2 as a key regulator of kidney fibrosis. Nat Med (2012) 1.83
PDBWiki: added value through community annotation of the Protein Data Bank. Database (Oxford) (2010) 1.72
Pathway signature and cellular differentiation in clear cell renal cell carcinoma. PLoS One (2010) 1.70
Time-resolved and tissue-specific systems analysis of the pathogenesis of insulin resistance. PLoS One (2010) 1.64
Identification and pathway analysis of microRNAs with no previous involvement in breast cancer. PLoS One (2012) 1.57
Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API. PLoS One (2009) 1.57
Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors. PLoS Comput Biol (2009) 1.57
MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity. BMC Bioinformatics (2012) 1.56
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Methods and approaches in the topology-based analysis of biological pathways. Front Physiol (2013) 1.48
SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system. Nucleic Acids Res (2008) 1.42
Role of Mitochondrial Metabolism in the Control of Early Lineage Progression and Aging Phenotypes in Adult Hippocampal Neurogenesis. Neuron (2017) 1.40
Detection of gene-environment interactions in the presence of linkage disequilibrium and noise by using genetic risk scores with internal weights from elastic net regression. BMC Genet (2017) 1.37
Ten simple rules for editing Wikipedia. PLoS Comput Biol (2010) 1.36
WikiPathways: capturing the full diversity of pathway knowledge. Nucleic Acids Res (2015) 1.35
LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. Nucleic Acids Res (2014) 1.34
Finding the right questions: exploratory pathway analysis to enhance biological discovery in large datasets. PLoS Biol (2010) 1.33
The Cell Collective: toward an open and collaborative approach to systems biology. BMC Syst Biol (2012) 1.33
The PluriNetWork: an electronic representation of the network underlying pluripotency in mouse, and its applications. PLoS One (2010) 1.33
Savant Genome Browser 2: visualization and analysis for population-scale genomics. Nucleic Acids Res (2012) 1.32
MicroRNAs profiling in murine models of acute and chronic asthma: a relationship with mRNAs targets. PLoS One (2011) 1.31
A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki. Database (Oxford) (2009) 1.30
Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Syst Biol (2013) 1.29
A genome-wide siRNA screen identifies proteasome addiction as a vulnerability of basal-like triple-negative breast cancer cells. Cancer Cell (2013) 1.29
SMPDB 2.0: big improvements to the Small Molecule Pathway Database. Nucleic Acids Res (2013) 1.29
IntPath--an integrated pathway gene relationship database for model organisms and important pathogens. BMC Syst Biol (2012) 1.28
Human papillomavirus deregulates the response of a cellular network comprising of chemotactic and proinflammatory genes. PLoS One (2011) 1.26
Public domain databases for medicinal chemistry. J Med Chem (2012) 1.23
Systems toxicology: from basic research to risk assessment. Chem Res Toxicol (2014) 1.23
LIN28B promotes growth and tumorigenesis of the intestinal epithelium via Let-7. Genes Dev (2013) 1.23
HPD: an online integrated human pathway database enabling systems biology studies. BMC Bioinformatics (2009) 1.21
PathText: a text mining integrator for biological pathway visualizations. Bioinformatics (2010) 1.20
TOPSAN: a collaborative annotation environment for structural genomics. BMC Bioinformatics (2010) 1.19
CyTargetLinker: a cytoscape app to integrate regulatory interactions in network analysis. PLoS One (2013) 1.19
The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons. Nucleic Acids Res (2011) 1.18
Gene set analysis exploiting the topology of a pathway. BMC Syst Biol (2010) 1.16
Aggregating data for computational toxicology applications: The U.S. Environmental Protection Agency (EPA) Aggregated Computational Toxicology Resource (ACToR) System. Int J Mol Sci (2012) 1.16
Proteomic analysis of acquired tamoxifen resistance in MCF-7 cells reveals expression signatures associated with enhanced migration. Breast Cancer Res (2012) 1.14
Comparative analysis and assessment of M. tuberculosis H37Rv protein-protein interaction datasets. BMC Genomics (2011) 1.14
Metagenome annotation using a distributed grid of undergraduate students. PLoS Biol (2008) 1.14
Integrated enrichment analysis of variants and pathways in genome-wide association studies indicates central role for IL-2 signaling genes in type 1 diabetes, and cytokine signaling genes in Crohn's disease. PLoS Genet (2013) 1.14
Linking genes to diseases with a SNPedia-Gene Wiki mashup. J Biomed Semantics (2012) 1.12
A zebrafish high throughput screening system used for Staphylococcus epidermidis infection marker discovery. BMC Genomics (2013) 1.11
Critical assessment of human metabolic pathway databases: a stepping stone for future integration. BMC Syst Biol (2011) 1.10
Extending biochemical databases by metabolomic surveys. J Biol Chem (2011) 1.09
hiPathDB: a human-integrated pathway database with facile visualization. Nucleic Acids Res (2011) 1.08
Network-based pipeline for analyzing MS data: an application toward liver cancer. J Proteome Res (2011) 1.07
Biomarkers of NAFLD progression: a lipidomics approach to an epidemic. J Lipid Res (2015) 1.07
CMS: a web-based system for visualization and analysis of genome-wide methylation data of human cancers. PLoS One (2013) 1.07
t4 workshop report: Pathways of Toxicity. ALTEX (2013) 1.06
The Micronutrient Genomics Project: a community-driven knowledge base for micronutrient research. Genes Nutr (2010) 1.06
Comparison of human cell signaling pathway databases--evolution, drawbacks and challenges. Database (Oxford) (2015) 1.06
Wikis and collaborative writing applications in health care: a scoping review. J Med Internet Res (2013) 1.05
Assessing quality and completeness of human transcriptional regulatory pathways on a genome-wide scale. Biol Direct (2011) 1.04
NDEx, the Network Data Exchange. Cell Syst (2015) 1.03
Integrating literature-constrained and data-driven inference of signalling networks. Bioinformatics (2012) 1.03
Payao: a community platform for SBML pathway model curation. Bioinformatics (2010) 1.02
The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways. Bioinformatics (2011) 1.02
e!DAL--a framework to store, share and publish research data. BMC Bioinformatics (2014) 1.02
GeneSetDB: A comprehensive meta-database, statistical and visualisation framework for gene set analysis. FEBS Open Bio (2012) 1.01
Systematic approaches towards the development of host-directed antiviral therapeutics. Int J Mol Sci (2011) 1.01
WebLab: a data-centric, knowledge-sharing bioinformatic platform. Nucleic Acids Res (2009) 1.00
The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways. BMC Syst Biol (2010) 0.99
Relating protein adduction to gene expression changes: a systems approach. Mol Biosyst (2011) 0.99
Measuring passive myocardial stiffness in Drosophila melanogaster to investigate diastolic dysfunction. J Cell Mol Med (2012) 0.98
Construction of a large scale integrated map of macrophage pathogen recognition and effector systems. BMC Syst Biol (2010) 0.98
Transcriptional signatures related to glucose and lipid metabolism predict treatment response to the tumor necrosis factor antagonist infliximab in patients with treatment-resistant depression. Brain Behav Immun (2013) 0.98
NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. BMC Syst Biol (2013) 0.96
Small RNA sequencing-microarray analyses in Parkinson leukocytes reveal deep brain stimulation-induced splicing changes that classify brain region transcriptomes. Front Mol Neurosci (2013) 0.94
A network-based gene-weighting approach for pathway analysis. Cell Res (2011) 0.94
Using the reactome database. Curr Protoc Bioinformatics (2012) 0.93
Targeting PBK/TOPK decreases growth and survival of glioma initiating cells in vitro and attenuates tumor growth in vivo. Mol Cancer (2015) 0.93
Signaling network of dendritic cells in response to pathogens: a community-input supported knowledgebase. BMC Syst Biol (2010) 0.92
Collaboratively charting the gene-to-phenotype network of human congenital heart defects. Genome Med (2010) 0.92
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol (2007) 35.41
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics (2003) 32.92
Integration of biological networks and gene expression data using Cytoscape. Nat Protoc (2007) 27.10
Internet encyclopaedias go head to head. Nature (2005) 19.07
Reactome: a knowledge base of biologic pathways and processes. Genome Biol (2007) 13.36
Calling on a million minds for community annotation in WikiProteins. Genome Biol (2008) 7.11
Pathguide: a pathway resource list. Nucleic Acids Res (2006) 6.05
GenMAPP 2: new features and resources for pathway analysis. BMC Bioinformatics (2007) 4.97
Genome re-annotation: a wiki solution? Genome Biol (2007) 4.61
The Molecular Biology Database Collection: 2008 update. Nucleic Acids Res (2007) 2.46
The emerging world of wikis. Science (2008) 1.84
A review of standards for data exchange within systems biology. Proteomics (2007) 1.61
Integration of biological networks and gene expression data using Cytoscape. Nat Protoc (2007) 27.10
MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biol (2003) 20.83
GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat Genet (2002) 14.69
GenMAPP 2: new features and resources for pathway analysis. BMC Bioinformatics (2007) 4.97
WikiPathways: building research communities on biological pathways. Nucleic Acids Res (2011) 4.78
MicroRNA regulation of cell lineages in mouse and human embryonic stem cells. Cell Stem Cell (2008) 4.70
Presenting and exploring biological pathways with PathVisio. BMC Bioinformatics (2008) 4.34
A public gene trap resource for mouse functional genomics. Nat Genet (2004) 3.96
The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse. Nucleic Acids Res (2006) 3.40
Spotted long oligonucleotide arrays for human gene expression analysis. Genome Res (2003) 2.95
Lentiviral vectors and protocols for creation of stable hESC lines for fluorescent tracking and drug resistance selection of cardiomyocytes. PLoS One (2009) 2.62
Canonical Wnt signaling is a positive regulator of mammalian cardiac progenitors. Proc Natl Acad Sci U S A (2007) 2.56
Interfacing silicon nanowires with mammalian cells. J Am Chem Soc (2007) 2.47
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. Nucleic Acids Res (2010) 2.41
Mining biological pathways using WikiPathways web services. PLoS One (2009) 2.17
The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. BMC Bioinformatics (2010) 2.03
Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation. Proc Natl Acad Sci U S A (2010) 1.93
GO-Elite: a flexible solution for pathway and ontology over-representation. Bioinformatics (2012) 1.91
Model for long QT syndrome type 2 using human iPS cells demonstrates arrhythmogenic characteristics in cell culture. Dis Model Mech (2011) 1.87
The emerging world of wikis. Science (2008) 1.84
A system-based approach to interpret dose- and time-dependent microarray data: quantitative integration of gene ontology analysis for risk assessment. Toxicol Sci (2006) 1.74
Time-resolved and tissue-specific systems analysis of the pathogenesis of insulin resistance. PLoS One (2010) 1.64
Obtaining consent for future research with induced pluripotent cells: opportunities and challenges. PLoS Biol (2009) 1.58
Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors. PLoS Comput Biol (2009) 1.57
Constitutive activity of the melanocortin-4 receptor is maintained by its N-terminal domain and plays a role in energy homeostasis in humans. J Clin Invest (2004) 1.55
Gene expression patterns define key transcriptional events in cell-cycle regulation by cAMP and protein kinase A. Proc Natl Acad Sci U S A (2005) 1.52
Regression approaches for microarray data analysis. J Comput Biol (2003) 1.51
Osteoblast expression of an engineered Gs-coupled receptor dramatically increases bone mass. Proc Natl Acad Sci U S A (2008) 1.46
Time- and exercise-dependent gene regulation in human skeletal muscle. Genome Biol (2003) 1.44
SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system. Nucleic Acids Res (2008) 1.42
Derivation conditions impact X-inactivation status in female human induced pluripotent stem cells. Cell Stem Cell (2012) 1.35
Finding the right questions: exploratory pathway analysis to enhance biological discovery in large datasets. PLoS Biol (2010) 1.33
Development of hydrocephalus in mice expressing the G(i)-coupled GPCR Ro1 RASSL receptor in astrocytes. J Neurosci (2007) 1.30
Identifying genetic networks underlying myometrial transition to labor. Genome Biol (2005) 1.28
Gene expression profiles during human CD4+ T cell differentiation. Int Immunol (2004) 1.27
Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases. Bioinformatics (2007) 1.27
Marking embryonic stem cells with a 2A self-cleaving peptide: a NKX2-5 emerald GFP BAC reporter. PLoS One (2008) 1.22
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Syst Biol (2013) 1.20
Mosaic: making biological sense of complex networks. Bioinformatics (2012) 1.19
CyTargetLinker: a cytoscape app to integrate regulatory interactions in network analysis. PLoS One (2013) 1.19
Four selenoproteins, protein biosynthesis, and Wnt signalling are particularly sensitive to limited selenium intake in mouse colon. Mol Nutr Food Res (2009) 1.12
A combined transcriptomics and lipidomics analysis of subcutaneous, epididymal and mesenteric adipose tissue reveals marked functional differences. PLoS One (2010) 1.09
Increased DNA microarray hybridization specificity using sscDNA targets. BMC Genomics (2005) 1.09
Gene expression signatures of cAMP/protein kinase A (PKA)-promoted, mitochondrial-dependent apoptosis. Comparative analysis of wild-type and cAMP-deathless S49 lymphoma cells. J Biol Chem (2007) 1.08
Modifying ligand-induced and constitutive signaling of the human 5-HT4 receptor. PLoS One (2007) 1.04
Alterations in hepatic one-carbon metabolism and related pathways following a high-fat dietary intervention. Physiol Genomics (2011) 1.04
Reporter-based isolation of induced pluripotent stem cell- and embryonic stem cell-derived cardiac progenitors reveals limited gene expression variance. Circ Res (2010) 1.04
Gene-trapped mouse embryonic stem cell-derived cardiac myocytes and human genetics implicate AKAP10 in heart rhythm regulation. Proc Natl Acad Sci U S A (2007) 1.04
Cardiac transgenesis with the tetracycline transactivator changes myocardial function and gene expression. Physiol Genomics (2005) 1.02
PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs). Bioinformatics (2011) 1.01
A robust method to derive functional neural crest cells from human pluripotent stem cells. Am J Stem Cells (2013) 1.01
Automated Video-Based Analysis of Contractility and Calcium Flux in Human-Induced Pluripotent Stem Cell-Derived Cardiomyocytes Cultured over Different Spatial Scales. Tissue Eng Part C Methods (2015) 1.00
Engineered G protein coupled receptors reveal independent regulation of internalization, desensitization and acute signaling. BMC Biol (2005) 0.99
Engineering the melanocortin-4 receptor to control G(s) signaling in vivo. Ann N Y Acad Sci (2003) 0.96
The NuGO proof of principle study package: a collaborative research effort of the European Nutrigenomics Organisation. Genes Nutr (2008) 0.96
G(i)-coupled GPCR signaling controls the formation and organization of human pluripotent colonies. PLoS One (2009) 0.95
Modeling insertional mutagenesis using gene length and expression in murine embryonic stem cells. PLoS One (2007) 0.95
Induced pluripotent stem cells from patients with human fibrodysplasia ossificans progressiva show increased mineralization and cartilage formation. Orphanet J Rare Dis (2013) 0.94
Identification of novel ER-alpha target genes in breast cancer cells: gene- and cell-selective co-regulator recruitment at target promoters determines the response to 17beta-estradiol and tamoxifen. Mol Cell Endocrinol (2009) 0.93
NOA: a cytoscape plugin for network ontology analysis. Bioinformatics (2013) 0.93
Human induced pluripotent stem cell-based microphysiological tissue models of myocardium and liver for drug development. Stem Cell Res Ther (2013) 0.92
Differential effects of drug interventions and dietary lifestyle in developing type 2 diabetes and complications: a systems biology analysis in LDLr-/- mice. PLoS One (2013) 0.92
Gs G protein-coupled receptor signaling in osteoblasts elicits age-dependent effects on bone formation. J Bone Miner Res (2010) 0.92
Synthetic control of mammalian-cell motility by engineering chemotaxis to an orthogonal bioinert chemical signal. Proc Natl Acad Sci U S A (2014) 0.92
PathVisio-Validator: a rule-based validation plugin for graphical pathway notations. Bioinformatics (2011) 0.89
Exploring pathway interactions in insulin resistant mouse liver. BMC Syst Biol (2011) 0.89
AKAP13 Rho-GEF and PKD-binding domain deficient mice develop normally but have an abnormal response to β-adrenergic-induced cardiac hypertrophy. PLoS One (2013) 0.88
Coordinated and interactive expression of genes of lipid metabolism and inflammation in adipose tissue and liver during metabolic overload. PLoS One (2013) 0.86
Sculpting genomes with a hammer and chisel. Nat Methods (2013) 0.86
Engineering the melanocortin-4 receptor to control constitutive and ligand-mediated G(S) signaling in vivo. PLoS One (2007) 0.85
mGluR2 acts through inhibitory Galpha subunits to regulate transmission and long-term plasticity at hippocampal mossy fiber-CA3 synapses. Proc Natl Acad Sci U S A (2006) 0.84
Network-based integration of molecular and physiological data elucidates regulatory mechanisms underlying adaptation to high-fat diet. Genes Nutr (2015) 0.83
Blockade of receptor-activated G(i) signaling in osteoblasts in vivo leads to site-specific increases in cortical and cancellous bone formation. J Bone Miner Res (2011) 0.83
Ligand-mediated activation of an engineered gs g protein-coupled receptor in osteoblasts increases trabecular bone formation. Mol Endocrinol (2010) 0.83
PathVisio-Faceted Search: an exploration tool for multi-dimensional navigation of large pathways. Bioinformatics (2013) 0.82
Bioinformatics for the NuGO proof of principle study: analysis of gene expression in muscle of ApoE3*Leiden mice on a high-fat diet using PathVisio. Genes Nutr (2008) 0.82
Alperujo extract, hydroxytyrosol, and 3,4-dihydroxyphenylglycol are bioavailable and have antioxidant properties in vitamin E-deficient rats--a proteomics and network analysis approach. Mol Nutr Food Res (2012) 0.81
Systems biology analysis unravels the complementary action of combined rosuvastatin and ezetimibe therapy. Pharmacogenet Genomics (2012) 0.81
AKAP10 (I646V) functional polymorphism predicts heart rate and heart rate variability in apparently healthy, middle-aged European-Americans. Psychophysiology (2009) 0.81
The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1. J Integr Bioinform (2015) 0.80
Constitutive Gs activation using a single-construct tetracycline-inducible expression system in embryonic stem cells and mice. Stem Cell Res Ther (2011) 0.79