Published in PLoS Comput Biol on December 04, 2009
Logic-based models for the analysis of cell signaling networks. Biochemistry (2010) 2.21
Crowdsourcing network inference: the DREAM predictive signaling network challenge. Sci Signal (2011) 1.83
CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms. BMC Syst Biol (2012) 1.60
Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli. PLoS Comput Biol (2011) 1.53
A new approach for prediction of tumor sensitivity to targeted drugs based on functional data. BMC Bioinformatics (2013) 1.05
Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. Bioinformatics (2013) 1.02
Detecting and removing inconsistencies between experimental data and signaling network topologies using integer linear programming on interaction graphs. PLoS Comput Biol (2013) 1.01
Understanding disease mechanisms with models of signaling pathway activities. BMC Syst Biol (2014) 1.00
An ensemble based top performing approach for NCI-DREAM drug sensitivity prediction challenge. PLoS One (2014) 0.99
Reconstructing Boolean models of signaling. J Comput Biol (2013) 0.93
Combined logical and data-driven models for linking signalling pathways to cellular response. BMC Syst Biol (2011) 0.91
A Boolean approach to linear prediction for signaling network modeling. PLoS One (2010) 0.91
Protein expression signatures for inhibition of epidermal growth factor receptor-mediated signaling. Mol Cell Proteomics (2011) 0.86
MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. BMC Bioinformatics (2014) 0.86
A network-based multi-target computational estimation scheme for anticoagulant activities of compounds. PLoS One (2011) 0.84
Characterization of p38 MAPK isoforms for drug resistance study using systems biology approach. Bioinformatics (2014) 0.84
Network based elucidation of drug response: from modulators to targets. BMC Syst Biol (2013) 0.83
A crowd-sourcing approach for the construction of species-specific cell signaling networks. Bioinformatics (2014) 0.82
Non Linear Programming (NLP) formulation for quantitative modeling of protein signal transduction pathways. PLoS One (2012) 0.82
Designing Experiments to Discriminate Families of Logic Models. Front Bioeng Biotechnol (2015) 0.81
Integrating genomics and proteomics data to predict drug effects using binary linear programming. PLoS One (2014) 0.81
Experimental design schemes for learning Boolean network models. Bioinformatics (2014) 0.81
Construction of the influenza A virus infection-induced cell-specific inflammatory regulatory network based on mutual information and optimization. BMC Syst Biol (2013) 0.80
Generalized logical model based on network topology to capture the dynamical trends of cellular signaling pathways. BMC Syst Biol (2016) 0.79
Leveraging systems biology approaches in clinical pharmacology. Biopharm Drug Dispos (2013) 0.77
A Copula Based Approach for Design of Multivariate Random Forests for Drug Sensitivity Prediction. PLoS One (2015) 0.77
Network reconstruction based on proteomic data and prior knowledge of protein connectivity using graph theory. PLoS One (2015) 0.77
Combination of a proteomics approach and reengineering of meso scale network models for prediction of mode-of-action for tyrosine kinase inhibitors. PLoS One (2013) 0.76
Erlotinib and gefitinib, epidermal growth factor receptor kinase inhibitors, may treat non-cancer-related tumor necrosis factor-α mediated inflammatory diseases. Oncologist (2013) 0.76
Sig2GRN: a software tool linking signaling pathway with gene regulatory network for dynamic simulation. BMC Syst Biol (2016) 0.75
High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes. Oncotarget (2016) 0.75
Systemic modeling myeloma-osteoclast interactions under normoxic/hypoxic condition using a novel computational approach. Sci Rep (2015) 0.75
Mathematical and Computational Modeling in Complex Biological Systems. Biomed Res Int (2017) 0.75
Power-Law Modeling of Cancer Cell Fates Driven by Signaling Data to Reveal Drug Effects. PLoS One (2016) 0.75
Identification of signaling pathways related to drug efficacy in hepatocellular carcinoma via integration of phosphoproteomic, genomic and clinical data. Proc IEEE Int Symp Bioinformatics Bioeng (2013) 0.75
Inference of dynamic biological networks based on responses to drug perturbations. EURASIP J Bioinform Syst Biol (2014) 0.75
Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res (2003) 103.76
Causal protein-signaling networks derived from multiparameter single-cell data. Science (2005) 34.28
The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science (2006) 25.99
Towards a proteome-scale map of the human protein-protein interaction network. Nature (2005) 24.76
BAY 43-9006 exhibits broad spectrum oral antitumor activity and targets the RAF/MEK/ERK pathway and receptor tyrosine kinases involved in tumor progression and angiogenesis. Cancer Res (2004) 21.36
A quantitative analysis of kinase inhibitor selectivity. Nat Biotechnol (2008) 14.74
Metabolic stability and epigenesis in randomly constructed genetic nets. J Theor Biol (1969) 13.14
A small molecule-kinase interaction map for clinical kinase inhibitors. Nat Biotechnol (2005) 12.22
A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science (2003) 12.07
Printing proteins as microarrays for high-throughput function determination. Science (2000) 10.77
Literature mining for the biologist: from information retrieval to biological discovery. Nat Rev Genet (2006) 8.23
Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors. Nat Biotechnol (2007) 6.56
A unique structure for epidermal growth factor receptor bound to GW572016 (Lapatinib): relationships among protein conformation, inhibitor off-rate, and receptor activity in tumor cells. Cancer Res (2004) 6.53
Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle. Mol Cell (2008) 5.38
Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Syst Biol (2007) 4.52
Features of selective kinase inhibitors. Chem Biol (2005) 4.07
Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nat Biotechnol (2005) 3.89
Anti-tumor activity of GW572016: a dual tyrosine kinase inhibitor blocks EGF activation of EGFR/erbB2 and downstream Erk1/2 and AKT pathways. Oncogene (2002) 3.87
Identifying the proteins to which small-molecule probes and drugs bind in cells. Proc Natl Acad Sci U S A (2009) 2.94
Therapeutically targeting ErbB3: a key node in ligand-induced activation of the ErbB receptor-PI3K axis. Sci Signal (2009) 2.57
Models from experiments: combinatorial drug perturbations of cancer cells. Mol Syst Biol (2008) 2.33
A compendium of signals and responses triggered by prodeath and prosurvival cytokines. Mol Cell Proteomics (2005) 2.20
A method for the generation of standardized qualitative dynamical systems of regulatory networks. Theor Biol Med Model (2006) 2.14
High-throughput kinase profiling as a platform for drug discovery. Nat Rev Drug Discov (2008) 2.12
Mass spectrometry-based functional proteomics: from molecular machines to protein networks. Nat Methods (2007) 2.06
The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data. PLoS Comput Biol (2009) 1.88
Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling. PLoS Comput Biol (2009) 1.69
A high-throughput quantitative multiplex kinase assay for monitoring information flow in signaling networks: application to sepsis-apoptosis. Mol Cell Proteomics (2003) 1.61
Cue-signal-response analysis of TNF-induced apoptosis by partial least squares regression of dynamic multivariate data. J Comput Biol (2004) 1.61
Hypergraphs and cellular networks. PLoS Comput Biol (2009) 1.58
Flexible informatics for linking experimental data to mathematical models via DataRail. Bioinformatics (2008) 1.45
Can cell systems biology rescue drug discovery? Nat Rev Drug Discov (2005) 1.45
ZD1839 ('Iressa') as an anticancer agent. Drugs (2000) 1.29
Identifying network of drug mode of action by gene expression profiling. J Comput Biol (2009) 1.21
Boolean network analysis of a neurotransmitter signaling pathway. J Theor Biol (2006) 1.13
Review article: pharmacological therapy for hepatocellular carcinoma with sorafenib and other oral agents. Aliment Pharmacol Ther (2008) 1.12
The mode-of-action by network identification (MNI) algorithm: a network biology approach for molecular target identification. Nat Protoc (2006) 0.91
Fishing for targets: novel approaches using small molecule baits. Drug Discov Today Technol (2004) 0.90
Logic integer programming models for signaling networks. J Comput Biol (2009) 0.88
BAY-43-9006 Bayer/Onyx. Curr Opin Investig Drugs (2003) 0.87
Off-target decoding of a multitarget kinase inhibitor by chemical proteomics. Chembiochem (2009) 0.84
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Chemoproteomics-driven drug discovery: addressing high attrition rates. Drug Discov Today (2006) 0.80
Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature (2012) 15.91
Towards a rigorous assessment of systems biology models: the DREAM3 challenges. PLoS One (2010) 4.94
Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Syst Biol (2007) 4.52
A methodology for the structural and functional analysis of signaling and regulatory networks. BMC Bioinformatics (2006) 3.55
Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Mol Syst Biol (2009) 2.98
Evaluation of methods for modeling transcription factor sequence specificity. Nat Biotechnol (2013) 2.34
Determination of the Poisson's ratio of the cell: recovery properties of chondrocytes after release from complete micropipette aspiration. J Biomech (2005) 2.29
Logic-based models for the analysis of cell signaling networks. Biochemistry (2010) 2.21
The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data. PLoS Comput Biol (2009) 1.88
Crowdsourcing network inference: the DREAM predictive signaling network challenge. Sci Signal (2011) 1.83
Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling. BMC Syst Biol (2009) 1.78
Networks inferred from biochemical data reveal profound differences in toll-like receptor and inflammatory signaling between normal and transformed hepatocytes. Mol Cell Proteomics (2010) 1.77
The pericellular matrix as a transducer of biomechanical and biochemical signals in articular cartilage. Ann N Y Acad Sci (2006) 1.71
Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling. PLoS Comput Biol (2009) 1.69
CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms. BMC Syst Biol (2012) 1.60
Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli. PLoS Comput Biol (2011) 1.53
A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks. BMC Bioinformatics (2006) 1.53
Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties. PLoS One (2013) 1.50
Synergistic drug-cytokine induction of hepatocellular death as an in vitro approach for the study of inflammation-associated idiosyncratic drug hepatotoxicity. Toxicol Appl Pharmacol (2009) 1.49
Flexible informatics for linking experimental data to mathematical models via DataRail. Bioinformatics (2008) 1.45
Comparing signaling networks between normal and transformed hepatocytes using discrete logical models. Cancer Res (2011) 1.45
Transcriptional data: a new gateway to drug repositioning? Drug Discov Today (2012) 1.40
Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Syst Biol (2013) 1.29
Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks. BMC Syst Biol (2012) 1.28
Verification of systems biology research in the age of collaborative competition. Nat Biotechnol (2011) 1.28
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Syst Biol (2013) 1.20
Zonal uniformity in mechanical properties of the chondrocyte pericellular matrix: micropipette aspiration of canine chondrons isolated by cartilage homogenization. Ann Biomed Eng (2005) 1.19
Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach. BMC Syst Biol (2014) 1.06
Cytokine-associated drug toxicity in human hepatocytes is associated with signaling network dysregulation. Mol Biosyst (2010) 1.04
DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data. Bioinformatics (2012) 1.04
Integrating literature-constrained and data-driven inference of signalling networks. Bioinformatics (2012) 1.03
Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. Bioinformatics (2013) 1.02
State-time spectrum of signal transduction logic models. Phys Biol (2012) 1.02
Dynamics of proximal signaling events after TCR/CD8-mediated induction of proliferation or apoptosis in mature CD8+ T cells. J Immunol (2008) 1.02
Detecting and removing inconsistencies between experimental data and signaling network topologies using integer linear programming on interaction graphs. PLoS Comput Biol (2013) 1.01
Large-scale network models of IL-1 and IL-6 signalling and their hepatocellular specification. Mol Biosyst (2011) 0.99
Construction of large signaling pathways using an adaptive perturbation approach with phosphoproteomic data. Mol Biosyst (2012) 0.99
Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models. Mol Biosyst (2013) 0.98
CySBGN: a Cytoscape plug-in to integrate SBGN maps. BMC Bioinformatics (2013) 0.94
Modeling signaling networks using high-throughput phospho-proteomics. Adv Exp Med Biol (2012) 0.92
Combined logical and data-driven models for linking signalling pathways to cellular response. BMC Syst Biol (2011) 0.91
IL-1beta decreases the elastic modulus of human tenocytes. J Appl Physiol (1985) (2006) 0.90
Prediction of human population responses to toxic compounds by a collaborative competition. Nat Biotechnol (2015) 0.88
A rapidly reversible chemical dimerizer system to study lipid signaling in living cells. Angew Chem Int Ed Engl (2014) 0.87
MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. BMC Bioinformatics (2014) 0.86
Mapping the human phosphatome on growth pathways. Mol Syst Biol (2012) 0.85
Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors. Genome Biol (2013) 0.85
A multipathway phosphoproteomic signaling network model of idiosyncratic drug- and inflammatory cytokine-induced toxicity in human hepatocytes. Conf Proc IEEE Eng Med Biol Soc (2009) 0.85
BioServices: a common Python package to access biological Web Services programmatically. Bioinformatics (2013) 0.84
Network based elucidation of drug response: from modulators to targets. BMC Syst Biol (2013) 0.83
Setting the standards for signal transduction research. Sci Signal (2011) 0.82
Non Linear Programming (NLP) formulation for quantitative modeling of protein signal transduction pathways. PLoS One (2012) 0.82
PIP₃ induces the recycling of receptor tyrosine kinases. Sci Signal (2014) 0.81
Cancer develops, progresses and responds to therapies through restricted perturbation of the protein-protein interaction network. Integr Biol (Camb) (2012) 0.80
Identification of drug-specific pathways based on gene expression data: application to drug induced lung injury. Integr Biol (Camb) (2015) 0.80
Modeling signaling networks with different formalisms: a preview. Methods Mol Biol (2013) 0.79
Leveraging systems biology approaches in clinical pharmacology. Biopharm Drug Dispos (2013) 0.77
Corrigendum: Fumarate is an epigenetic modifier that elicits epithelial-to-mesenchymal transition. Nature (2016) 0.77
Construction of cell type-specific logic models of signaling networks using CellNOpt. Methods Mol Biol (2013) 0.75
Integrative approaches for signalling and metabolic networks. Integr Biol (Camb) (2015) 0.75
Construction of signaling pathways and identification of drug effects on the liver cancer cell HepG2. Conf Proc IEEE Eng Med Biol Soc (2010) 0.75
Modeling signaling pathways in articular cartilage. Conf Proc IEEE Eng Med Biol Soc (2011) 0.75
Benchmarking substrate-based kinase activity inference using phosphoproteomic data. Bioinformatics (2017) 0.75
Erratum: Prediction of human population responses to toxic compounds by a collaborative competition. Nat Biotechnol (2015) 0.75