Published in Bioinformatics on December 09, 2009
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
Using biological pathway data with paxtools. PLoS Comput Biol (2013) 1.50
SubMAP: aligning metabolic pathways with subnetwork mappings. J Comput Biol (2011) 1.24
Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations. Genome Biol (2015) 1.14
NetSlim: high-confidence curated signaling maps. Database (Oxford) (2011) 1.09
A Network Map of FGF-1/FGFR Signaling System. J Signal Transduct (2014) 1.02
Extended LineSets: a visualization technique for the interactive inspection of biological pathways. BMC Proc (2015) 1.00
A comprehensive manually curated reaction map of RANKL/RANK-signaling pathway. Database (Oxford) (2011) 0.99
Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles. Bioinformatics (2014) 0.99
ReactionFlow: an interactive visualization tool for causality analysis in biological pathways. BMC Proc (2015) 0.97
Integrating biological pathways and genomic profiles with ChiBE 2. BMC Genomics (2014) 0.94
PathwayMatrix: visualizing binary relationships between proteins in biological pathways. BMC Proc (2015) 0.93
TSLP signaling pathway map: a platform for analysis of TSLP-mediated signaling. Database (Oxford) (2014) 0.93
Pattern search in BioPAX models. Bioinformatics (2013) 0.93
Inferring the functional effect of gene expression changes in signaling pathways. Nucleic Acids Res (2013) 0.92
Representing physiological processes and their participants with PhysioMaps. J Biomed Semantics (2013) 0.92
A comprehensive curated resource for follicle stimulating hormone signaling. BMC Res Notes (2011) 0.88
Differential ligand-signaling network of CCL19/CCL21-CCR7 system. Database (Oxford) (2015) 0.81
PINT: Pathways INtegration Tool. Nucleic Acids Res (2010) 0.80
BioASF: a framework for automatically generating executable pathway models specified in BioPAX. Bioinformatics (2016) 0.75
A taxonomy of visualization tasks for the analysis of biological pathway data. BMC Bioinformatics (2017) 0.75
KEGG for linking genomes to life and the environment. Nucleic Acids Res (2007) 49.37
Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res (2008) 15.69
The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res (2007) 10.62
The Systems Biology Graphical Notation. Nat Biotechnol (2009) 8.53
Pathguide: a pathway resource list. Nucleic Acids Res (2006) 6.05
VisANT: an integrative framework for networks in systems biology. Brief Bioinform (2008) 2.85
An ontology for collaborative construction and analysis of cellular pathways. Bioinformatics (2004) 2.66
PathCase: pathways database system. Bioinformatics (2008) 2.10
Knowledge representation of signal transduction pathways. Bioinformatics (2001) 1.63
A graph layout algorithm for drawing metabolic pathways. Bioinformatics (2001) 1.57
High quality visualization of biochemical pathways in BioPath. In Silico Biol (2002) 1.48
Exploring biological networks with Cytoscape software. Curr Protoc Bioinformatics (2008) 1.30
A new dynamical layout algorithm for complex biochemical reaction networks. BMC Bioinformatics (2005) 1.20
PATIKAmad: putting microarray data into pathway context. Proteomics (2008) 0.92
Human MicroRNA targets. PLoS Biol (2004) 34.51
A mammalian microRNA expression atlas based on small RNA library sequencing. Cell (2007) 34.03
Integration of biological networks and gene expression data using Cytoscape. Nat Protoc (2007) 27.10
The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov (2012) 26.98
Integrative genomic profiling of human prostate cancer. Cancer Cell (2010) 23.61
MicroRNA targets in Drosophila. Genome Biol (2003) 23.59
Global mapping of the yeast genetic interaction network. Science (2004) 21.34
International network of cancer genome projects. Nature (2010) 20.35
Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal (2013) 19.54
The microRNA.org resource: targets and expression. Nucleic Acids Res (2007) 16.26
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol (2004) 16.08
Characterizing gene sets with FuncAssociate. Bioinformatics (2003) 14.10
Identification of microRNAs of the herpesvirus family. Nat Methods (2005) 12.98
Identification of virus-encoded microRNAs. Science (2004) 12.56
The somatic genomic landscape of glioblastoma. Cell (2013) 11.73
The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet (2013) 11.29
Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res (2011) 10.99
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
A novel class of small RNAs bind to MILI protein in mouse testes. Nature (2006) 8.80
The Systems Biology Graphical Notation. Nat Biotechnol (2009) 8.53
Mutual exclusivity analysis identifies oncogenic network modules. Genome Res (2011) 7.22
Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol (2010) 7.15
Cellular cofactors affecting hepatitis C virus infection and replication. Proc Natl Acad Sci U S A (2007) 6.79
(V600E)BRAF is associated with disabled feedback inhibition of RAF-MEK signaling and elevated transcriptional output of the pathway. Proc Natl Acad Sci U S A (2009) 6.78
Genome sequencing identifies a basis for everolimus sensitivity. Science (2012) 6.71
Emerging landscape of oncogenic signatures across human cancers. Nat Genet (2013) 6.48
miR-122, a mammalian liver-specific microRNA, is processed from hcr mRNA and may downregulate the high affinity cationic amino acid transporter CAT-1. RNA Biol (2004) 6.44
Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy. Nat Genet (2010) 6.10
Pathguide: a pathway resource list. Nucleic Acids Res (2006) 6.05
Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med (2015) 5.71
Cooperativity of TMPRSS2-ERG with PI3-kinase pathway activation in prostate oncogenesis. Nat Genet (2009) 5.31
MicroRNA profiling of the murine hematopoietic system. Genome Biol (2005) 4.94
Protein 3D structure computed from evolutionary sequence variation. PLoS One (2011) 4.71
Genetic dissection of the miR-17~92 cluster of microRNAs in Myc-induced B-cell lymphomas. Genes Dev (2009) 4.43
Evaluating cell lines as tumour models by comparison of genomic profiles. Nat Commun (2013) 4.35
Functional copy-number alterations in cancer. PLoS One (2008) 4.27
Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci U S A (2011) 4.08
Antisense-mediated depletion reveals essential and specific functions of microRNAs in Drosophila development. Cell (2005) 3.95
Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat Biotechnol (2009) 3.66
Quantitative technologies establish a novel microRNA profile of chronic lymphocytic leukemia. Blood (2007) 3.64
Automated network analysis identifies core pathways in glioblastoma. PLoS One (2010) 3.64
A series of PDB related databases for everyday needs. Nucleic Acids Res (2010) 3.60
Determinants of protein function revealed by combinatorial entropy optimization. Genome Biol (2007) 3.46
The nuclear deubiquitinase BAP1 is commonly inactivated by somatic mutations and 3p21.1 losses in malignant pleural mesothelioma. Nat Genet (2011) 3.41
Target mRNA abundance dilutes microRNA and siRNA activity. Mol Syst Biol (2010) 3.37
Characterization of small RNAs in Aplysia reveals a role for miR-124 in constraining synaptic plasticity through CREB. Neuron (2009) 3.27
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
Three-dimensional structures of membrane proteins from genomic sequencing. Cell (2012) 3.02
CancerGenes: a gene selection resource for cancer genome projects. Nucleic Acids Res (2006) 3.00
Pathway information for systems biology. FEBS Lett (2005) 2.97
The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes Dev (2005) 2.94
Introducing meta-services for biomedical information extraction. Genome Biol (2008) 2.78
A role for neuronal piRNAs in the epigenetic control of memory-related synaptic plasticity. Cell (2012) 2.72
Evaluation of annotation strategies using an entire genome sequence. Bioinformatics (2003) 2.66
NetPath: a public resource of curated signal transduction pathways. Genome Biol (2010) 2.62
The amino-acid mutational spectrum of human genetic disease. Genome Biol (2003) 2.55
Somatic mutations of the Parkinson's disease-associated gene PARK2 in glioblastoma and other human malignancies. Nat Genet (2009) 2.51
Protein structure prediction from sequence variation. Nat Biotechnol (2012) 2.50
DGCR8-dependent microRNA biogenesis is essential for skin development. Proc Natl Acad Sci U S A (2008) 2.49
RNA targets of wild-type and mutant FET family proteins. Nat Struct Mol Biol (2011) 2.46
Gene expression profiling of liposarcoma identifies distinct biological types/subtypes and potential therapeutic targets in well-differentiated and dedifferentiated liposarcoma. Cancer Res (2007) 2.44
Models from experiments: combinatorial drug perturbations of cancer cells. Mol Syst Biol (2008) 2.33
Adverse outcomes in clear cell renal cell carcinoma with mutations of 3p21 epigenetic regulators BAP1 and SETD2: a report by MSKCC and the KIRC TCGA research network. Clin Cancer Res (2013) 2.26
The tyrosine phosphatase PTPRD is a tumor suppressor that is frequently inactivated and mutated in glioblastoma and other human cancers. Proc Natl Acad Sci U S A (2009) 2.09
Prevalence and co-occurrence of actionable genomic alterations in high-grade bladder cancer. J Clin Oncol (2013) 1.92
Frequent alterations and epigenetic silencing of differentiation pathway genes in structurally rearranged liposarcomas. Cancer Discov (2011) 1.85
The mutational landscape of adenoid cystic carcinoma. Nat Genet (2013) 1.83
An Integrated Metabolic Atlas of Clear Cell Renal Cell Carcinoma. Cancer Cell (2016) 1.79
Integrated analyses of microRNAs demonstrate their widespread influence on gene expression in high-grade serous ovarian carcinoma. PLoS One (2012) 1.76
Identification of PHLPP1 as a tumor suppressor reveals the role of feedback activation in PTEN-mutant prostate cancer progression. Cancer Cell (2011) 1.74
Distinct patterns of dysregulated expression of enzymes involved in androgen synthesis and metabolism in metastatic prostate cancer tumors. Cancer Res (2012) 1.71
Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinformatics (2012) 1.69
Computational approaches to identify functional genetic variants in cancer genomes. Nat Methods (2013) 1.64
Pattern discovery and cancer gene identification in integrated cancer genomic data. Proc Natl Acad Sci U S A (2013) 1.60
Prediction of human microRNA targets. Methods Mol Biol (2006) 1.60
Tumor genetic analyses of patients with metastatic renal cell carcinoma and extended benefit from mTOR inhibitor therapy. Clin Cancer Res (2014) 1.57
Genome-wide identification of microRNA targets in human ES cells reveals a role for miR-302 in modulating BMP response. Genes Dev (2011) 1.55
Signal processing in the TGF-beta superfamily ligand-receptor network. PLoS Comput Biol (2006) 1.54
Using biological pathway data with paxtools. PLoS Comput Biol (2013) 1.50
Genomic complexity and AKT dependence in serous ovarian cancer. Cancer Discov (2012) 1.50
miR-34a repression in proneural malignant gliomas upregulates expression of its target PDGFRA and promotes tumorigenesis. PLoS One (2012) 1.44
An epidemiologic and genomic investigation into the obesity paradox in renal cell carcinoma. J Natl Cancer Inst (2013) 1.42
Analysis of microRNA-target interactions across diverse cancer types. Nat Struct Mol Biol (2013) 1.41
Small RNA sequencing and functional characterization reveals MicroRNA-143 tumor suppressor activity in liposarcoma. Cancer Res (2011) 1.40
MYC cooperates with AKT in prostate tumorigenesis and alters sensitivity to mTOR inhibitors. PLoS One (2011) 1.38
Genomic and transcriptomic hallmarks of poorly differentiated and anaplastic thyroid cancers. J Clin Invest (2016) 1.36
18F-fluorodeoxy-glucose positron emission tomography marks MYC-overexpressing human basal-like breast cancers. Cancer Res (2011) 1.36
Computational analysis of mouse piRNA sequence and biogenesis. PLoS Comput Biol (2007) 1.36
Superoxide dismutase 1 (SOD1) is a target for a small molecule identified in a screen for inhibitors of the growth of lung adenocarcinoma cell lines. Proc Natl Acad Sci U S A (2011) 1.30