Published in J Cell Sci on May 01, 2013
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A comprehensive pathway map of epidermal growth factor receptor signaling. Mol Syst Biol (2005) 5.68
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The roles of APC and Axin derived from experimental and theoretical analysis of the Wnt pathway. PLoS Biol (2003) 4.89
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Growth factor-induced MAPK network topology shapes Erk response determining PC-12 cell fate. Nat Cell Biol (2007) 4.75
A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis. Science (2005) 4.75
Robust, tunable biological oscillations from interlinked positive and negative feedback loops. Science (2008) 4.45
A module of negative feedback regulators defines growth factor signaling. Nat Genet (2007) 4.35
Physicochemical modelling of cell signalling pathways. Nat Cell Biol (2006) 4.34
Modeling T cell antigen discrimination based on feedback control of digital ERK responses. PLoS Biol (2005) 4.26
Prediction and validation of the distinct dynamics of transient and sustained ERK activation. Nat Cell Biol (2005) 4.13
Tumor morphology and phenotypic evolution driven by selective pressure from the microenvironment. Cell (2006) 4.07
Dynamic reprogramming of the kinome in response to targeted MEK inhibition in triple-negative breast cancer. Cell (2012) 3.77
Assessing TP53 status in human tumours to evaluate clinical outcome. Nat Rev Cancer (2001) 3.61
The response of human epithelial cells to TNF involves an inducible autocrine cascade. Cell (2006) 3.57
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Input-output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data. Mol Syst Biol (2009) 3.50
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Reconstruction of cellular signalling networks and analysis of their properties. Nat Rev Mol Cell Biol (2005) 3.46
The incoherent feedforward loop can provide fold-change detection in gene regulation. Mol Cell (2009) 3.38
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Understanding bistability in complex enzyme-driven reaction networks. Proc Natl Acad Sci U S A (2006) 3.21
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A comprehensive map of the toll-like receptor signaling network. Mol Syst Biol (2006) 2.89
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Mathematical modeling reveals threshold mechanism in CD95-induced apoptosis. J Cell Biol (2004) 2.70
Modeling a snap-action, variable-delay switch controlling extrinsic cell death. PLoS Biol (2008) 2.63
Therapeutically targeting ErbB3: a key node in ligand-induced activation of the ErbB receptor-PI3K axis. Sci Signal (2009) 2.57
Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters. Nat Biotechnol (2012) 2.49
Regulatory activity revealed by dynamic correlations in gene expression noise. Nat Genet (2008) 2.49
Dynamics and variability of ERK2 response to EGF in individual living cells. Mol Cell (2009) 2.42
A global analysis of cross-talk in a mammalian cellular signalling network. Nat Cell Biol (2006) 2.39
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Fluctuations of intracellular forces during cell protrusion. Nat Cell Biol (2008) 2.13
Evidence that fold-change, and not absolute level, of beta-catenin dictates Wnt signaling. Mol Cell (2009) 2.11
Identifying single-cell molecular programs by stochastic profiling. Nat Methods (2010) 2.11
Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks. Sci Signal (2009) 2.04
Systems analysis of Ran transport. Science (2002) 1.94
Cell-specific information processing in segregating populations of Eph receptor ephrin-expressing cells. Science (2009) 1.91
Ensemble modeling for analysis of cell signaling dynamics. Nat Biotechnol (2007) 1.84
Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics. Cell (2010) 1.82
Protein dynamics in drug combinations: a linear superposition of individual-drug responses. Cell (2010) 1.75
Modeling HER2 effects on cell behavior from mass spectrometry phosphotyrosine data. PLoS Comput Biol (2006) 1.74
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Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling. PLoS Comput Biol (2009) 1.69
A quantitative model of transcriptional regulation reveals the influence of binding location on expression. PLoS Comput Biol (2010) 1.66
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Strong negative feedback from Erk to Raf confers robustness to MAPK signalling. Mol Syst Biol (2011) 1.65
A comprehensive map of the mTOR signaling network. Mol Syst Biol (2010) 1.59
Collecting and organizing systematic sets of protein data. Nat Rev Mol Cell Biol (2006) 1.58
Rapid phospho-turnover by receptor tyrosine kinases impacts downstream signaling and drug binding. Mol Cell (2011) 1.55
Autocrine loops with positive feedback enable context-dependent cell signaling. Am J Physiol Cell Physiol (2002) 1.55
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
Protein kinase A governs a RhoA-RhoGDI protrusion-retraction pacemaker in migrating cells. Nat Cell Biol (2011) 1.51
Cell-cell interaction networks regulate blood stem and progenitor cell fate. Mol Syst Biol (2009) 1.49
Modeling and computational analysis of EGF receptor-mediated cell communication in Drosophila oogenesis. Development (2002) 1.47
Comparing signaling networks between normal and transformed hepatocytes using discrete logical models. Cancer Res (2011) 1.45
Stochastic model of autocrine and paracrine signals in cell culture assays. Biophys J (2003) 1.39
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Quantitative analysis of the EGF receptor autocrine system reveals cryptic regulation of cell response by ligand capture. J Cell Sci (2001) 1.35
Pairwise agonist scanning predicts cellular signaling responses to combinatorial stimuli. Nat Biotechnol (2010) 1.31
An inducible autocrine cascade regulates rat hepatocyte proliferation and apoptosis responses to tumor necrosis factor-alpha. Hepatology (2008) 1.30
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Quantitative network signal combinations downstream of TCR activation can predict IL-2 production response. J Immunol (2007) 1.26
Intersection of FOXO- and RUNX1-mediated gene expression programs in single breast epithelial cells during morphogenesis and tumor progression. Proc Natl Acad Sci U S A (2011) 1.26
Combined experimental and computational analysis of DNA damage signaling reveals context-dependent roles for Erk in apoptosis and G1/S arrest after genotoxic stress. Mol Syst Biol (2012) 1.20
The specificity of innate immune responses is enforced by repression of interferon response elements by NF-κB p50. Sci Signal (2011) 1.18
Linear combinations of docking affinities explain quantitative differences in RTK signaling. Mol Syst Biol (2009) 1.16
RUNX1 and its understudied role in breast cancer. Cell Cycle (2011) 1.16
Robust network topologies for generating switch-like cellular responses. PLoS Comput Biol (2011) 1.12
Multi-scale in vivo systems analysis reveals the influence of immune cells on TNF-α-induced apoptosis in the intestinal epithelium. PLoS Biol (2012) 1.10
Causal protein-signaling networks derived from multiparameter single-cell data. Science (2005) 34.28
Migration of tumor cells in 3D matrices is governed by matrix stiffness along with cell-matrix adhesion and proteolysis. Proc Natl Acad Sci U S A (2006) 7.48
Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks. Proc Natl Acad Sci U S A (2007) 4.80
A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis. Science (2005) 4.75
Physicochemical modelling of cell signalling pathways. Nat Cell Biol (2006) 4.34
Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules. Mol Cell Proteomics (2005) 4.33
Quantitative analysis of pathways controlling extrinsic apoptosis in single cells. Mol Cell (2008) 3.88
The response of human epithelial cells to TNF involves an inducible autocrine cascade. Cell (2006) 3.57
Input-output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data. Mol Syst Biol (2009) 3.50
Effects of HER2 overexpression on cell signaling networks governing proliferation and migration. Mol Syst Biol (2006) 3.01
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Computational modeling of the EGF-receptor system: a paradigm for systems biology. Trends Cell Biol (2003) 2.85
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Co-regulation of cell adhesion by nanoscale RGD organization and mechanical stimulus. J Cell Sci (2002) 2.42
A multiplexed homogeneous fluorescence-based assay for protein kinase activity in cell lysates. Nat Methods (2005) 2.39
Cutting to the chase: calpain proteases in cell motility. Trends Cell Biol (2002) 2.38
Cancer systems biology: a network modeling perspective. Carcinogenesis (2009) 2.22
Logic-based models for the analysis of cell signaling networks. Biochemistry (2010) 2.21
A compendium of signals and responses triggered by prodeath and prosurvival cytokines. Mol Cell Proteomics (2005) 2.20
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Systems analysis of EGF receptor signaling dynamics with microwestern arrays. Nat Methods (2010) 2.20
Rational cytokine design for increased lifetime and enhanced potency using pH-activated "histidine switching". Nat Biotechnol (2002) 2.09
Computational model for cell migration in three-dimensional matrices. Biophys J (2005) 2.09
Mena invasive (MenaINV) promotes multicellular streaming motility and transendothelial migration in a mouse model of breast cancer. J Cell Sci (2011) 2.00
Polyfunctional responses by human T cells result from sequential release of cytokines. Proc Natl Acad Sci U S A (2011) 2.00
Bayesian network approach to cell signaling pathway modeling. Sci STKE (2002) 1.96
Microfluidic shear devices for quantitative analysis of cell adhesion. Anal Chem (2004) 1.95
The receptor AXL diversifies EGFR signaling and limits the response to EGFR-targeted inhibitors in triple-negative breast cancer cells. Sci Signal (2013) 1.92
Global network analysis of phenotypic effects: protein networks and toxicity modulation in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2004) 1.90
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
Modeling HER2 effects on cell behavior from mass spectrometry phosphotyrosine data. PLoS Comput Biol (2006) 1.74
A biological approach to computational models of proteomic networks. Curr Opin Chem Biol (2006) 1.73
Directional persistence of EGF-induced cell migration is associated with stabilization of lamellipodial protrusions. Biophys J (2005) 1.70
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
Microarchitecture of three-dimensional scaffolds influences cell migration behavior via junction interactions. Biophys J (2008) 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
CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms. BMC Syst Biol (2012) 1.60
Collecting and organizing systematic sets of protein data. Nat Rev Mol Cell Biol (2006) 1.58
Rapid phospho-turnover by receptor tyrosine kinases impacts downstream signaling and drug binding. Mol Cell (2011) 1.55
Epidermal growth factor induces fibroblast contractility and motility via a protein kinase C delta-dependent pathway. J Biol Chem (2004) 1.55
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
Bayesian analysis of signaling networks governing embryonic stem cell fate decisions. Bioinformatics (2004) 1.52
Control of self-assembling oligopeptide matrix formation through systematic variation of amino acid sequence. Biomaterials (2002) 1.52
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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
The Na+/H+ exchanger regulatory factor stabilizes epidermal growth factor receptors at the cell surface. Mol Biol Cell (2004) 1.48
Modeling and computational analysis of EGF receptor-mediated cell communication in Drosophila oogenesis. Development (2002) 1.47
Combination antibody treatment down-regulates epidermal growth factor receptor by inhibiting endosomal recycling. Proc Natl Acad Sci U S A (2010) 1.46
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
Parsing ERK activation reveals quantitatively equivalent contributions from epidermal growth factor receptor and HER2 in human mammary epithelial cells. J Biol Chem (2004) 1.41
EGF-receptor-mediated mammary epithelial cell migration is driven by sustained ERK signaling from autocrine stimulation. J Cell Sci (2007) 1.40
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Epidermal growth factor-induced enhancement of glioblastoma cell migration in 3D arises from an intrinsic increase in speed but an extrinsic matrix- and proteolysis-dependent increase in persistence. Mol Biol Cell (2008) 1.27
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A mammalian functional-genetic approach to characterizing cancer therapeutics. Nat Chem Biol (2010) 1.26
Quantitative network signal combinations downstream of TCR activation can predict IL-2 production response. J Immunol (2007) 1.26
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Proteolytic Activity Matrix Analysis (PrAMA) for simultaneous determination of multiple protease activities. Integr Biol (Camb) (2010) 1.20
Defining principles of combination drug mechanisms of action. Proc Natl Acad Sci U S A (2012) 1.19
Multipathway model enables prediction of kinase inhibitor cross-talk effects on migration of Her2-overexpressing mammary epithelial cells. Mol Pharmacol (2008) 1.18
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Autocrine EGF receptor activation mediates endothelial cell migration and vascular morphogenesis induced by VEGF under interstitial flow. Exp Cell Res (2005) 1.15
Calpain proteases in cell adhesion and motility. Int Rev Cytol (2005) 1.14
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Calpain-2 as a target for limiting prostate cancer invasion. Cancer Res (2003) 1.14
PTMScout, a Web resource for analysis of high throughput post-translational proteomics studies. Mol Cell Proteomics (2010) 1.13
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Multipathway kinase signatures of multipotent stromal cells are predictive for osteogenic differentiation: tissue-specific stem cells. Stem Cells (2009) 1.11
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Understanding effects of matrix protease and matrix organization on directional persistence and translational speed in three-dimensional cell migration. Ann Biomed Eng (2006) 1.11
Multi-scale in vivo systems analysis reveals the influence of immune cells on TNF-α-induced apoptosis in the intestinal epithelium. PLoS Biol (2012) 1.10
Applying computational modeling to drug discovery and development. Drug Discov Today (2006) 1.08
Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogene-induced signaling. PLoS Comput Biol (2013) 1.06
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Marrow-derived stem cell motility in 3D synthetic scaffold is governed by geometry along with adhesivity and stiffness. Biotechnol Bioeng (2011) 1.05
Cytokine-associated drug toxicity in human hepatocytes is associated with signaling network dysregulation. Mol Biosyst (2010) 1.04
Adenoviral vector saturates Akt pro-survival signaling and blocks insulin-mediated rescue of tumor necrosis-factor-induced apoptosis. J Cell Sci (2006) 1.04
Decision tree modeling predicts effects of inhibiting contractility signaling on cell motility. BMC Syst Biol (2007) 1.03
Integrated mechanistic and data-driven modelling for multivariate analysis of signalling pathways. J R Soc Interface (2006) 1.02
ADAM-10 and -17 regulate endometriotic cell migration via concerted ligand and receptor shedding feedback on kinase signaling. Proc Natl Acad Sci U S A (2013) 1.02
Sustained epidermal growth factor receptor levels and activation by tethered ligand binding enhances osteogenic differentiation of multi-potent marrow stromal cells. J Cell Physiol (2009) 1.02
Affinity regulates spatial range of EGF receptor autocrine ligand binding. Dev Biol (2002) 1.01
Integrating cell-level kinetic modeling into the design of engineered protein therapeutics. Nat Biotechnol (2005) 1.01