Multiscale models of cell signaling.

Models of signalling networks - what cell biologists can gain from them and give to them. J Cell Sci (2013) 0.99

Computational modeling of cardiac fibroblasts and fibrosis. J Mol Cell Cardiol (2015) 0.80

Contextualization procedure and modeling of monocyte specific TLR signaling. PLoS One (2012) 0.77

Integrating Multiscale Modeling with Drug Effects for Cancer Treatment. Cancer Inform (2016) 0.76

Late-phase synthesis of IκBα insulates the TLR4-activated canonical NF-κB pathway from noncanonical NF-κB signaling in macrophages. Sci Signal (2016) 0.75

Computational Models of Reactive Oxygen Species as Metabolic Byproducts and Signal-Transduction Modulators. Front Pharmacol (2016) 0.75

Causal protein-signaling networks derived from multiparameter single-cell data. Science (2005) 34.28

RAF inhibitors transactivate RAF dimers and ERK signalling in cells with wild-type BRAF. Nature (2010) 17.31

Oncogenic kinase signalling. Nature (2001) 16.30

Using Bayesian networks to analyze expression data. J Comput Biol (2000) 15.98

Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res (2003) 15.74

RAF inhibitors prime wild-type RAF to activate the MAPK pathway and enhance growth. Nature (2010) 15.63

Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science (2011) 15.45

The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation. Science (2002) 13.86

Robustness in bacterial chemotaxis. Nature (1999) 12.55

The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. Science (1998) 10.83

STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res (2005) 10.44

Emergent properties of networks of biological signaling pathways. Science (1999) 9.93

A new approach to decoding life: systems biology. Annu Rev Genomics Hum Genet (2001) 7.79

Systematic and quantitative assessment of the ubiquitin-modified proteome. Mol Cell (2011) 7.30

Systematic discovery of in vivo phosphorylation networks. Cell (2007) 6.94

Use of an oriented peptide library to determine the optimal substrates of protein kinases. Curr Biol (1994) 6.04

A comprehensive pathway map of epidermal growth factor receptor signaling. Mol Syst Biol (2005) 5.68

Stimulus specificity of gene expression programs determined by temporal control of IKK activity. Science (2005) 5.14

A rapid method for determining protein kinase phosphorylation specificity. Nat Methods (2004) 5.04

The roles of APC and Axin derived from experimental and theoretical analysis of the Wnt pathway. PLoS Biol (2003) 4.89

A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis. Science (2005) 4.75

Modeling T cell antigen discrimination based on feedback control of digital ERK responses. PLoS Biol (2005) 4.26

Quantification of short term signaling by the epidermal growth factor receptor. J Biol Chem (1999) 4.19

Tumor morphology and phenotypic evolution driven by selective pressure from the microenvironment. Cell (2006) 4.07

Probing cellular protein complexes using single-molecule pull-down. Nature (2011) 3.92

Gene expression and the myth of the average cell. Trends Cell Biol (2003) 3.78

Control of beta-catenin stability: reconstitution of the cytoplasmic steps of the wnt pathway in Xenopus egg extracts. Mol Cell (2000) 3.65

The response of human epithelial cells to TNF involves an inducible autocrine cascade. Cell (2006) 3.57

Do morphogen gradients arise by diffusion? Dev Cell (2002) 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

Linking a genetic defect to its cellular phenotype in a cardiac arrhythmia. Nature (1999) 3.41

The incoherent feedforward loop can provide fold-change detection in gene regulation. Mol Cell (2009) 3.38

A fourth IkappaB protein within the NF-kappaB signaling module. Cell (2007) 3.34

BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains. Bioinformatics (2004) 3.32

Automatic generation of cellular reaction networks with Moleculizer 1.0. Nat Biotechnol (2005) 3.26

Data-driven modelling of signal-transduction networks. Nat Rev Mol Cell Biol (2006) 3.18

Global identification of modular cullin-RING ligase substrates. Cell (2011) 3.13

Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Mol Syst Biol (2009) 2.98

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

Unlimited multistability in multisite phosphorylation systems. Nature (2009) 2.57

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

Will the ubiquitin system furnish as many drug targets as protein kinases? Cell (2010) 2.23

Autophosphorylation of FGFR1 kinase is mediated by a sequential and precisely ordered reaction. Mol Cell (2006) 2.21

A compendium of signals and responses triggered by prodeath and prosurvival cytokines. Mol Cell Proteomics (2005) 2.20

Common effector processing mediates cell-specific responses to stimuli. Nature (2007) 2.20

Overview of the Alliance for Cellular Signaling. Nature (2002) 2.15

Identifying single-cell molecular programs by stochastic profiling. Nat Methods (2010) 2.11

Self-organizing and stochastic behaviors during the regeneration of hair stem cells. Science (2011) 1.96

Isoelectric focusing technology quantifies protein signaling in 25 cells. Proc Natl Acad Sci U S A (2006) 1.89

Modeling beta-adrenergic control of cardiac myocyte contractility in silico. J Biol Chem (2003) 1.84

Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics. Cell (2010) 1.82

Systems-level interactions between insulin-EGF networks amplify mitogenic signaling. Mol Syst Biol (2009) 1.77

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

A biological approach to computational models of proteomic networks. Curr Opin Chem Biol (2006) 1.73

Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling. PLoS Comput Biol (2009) 1.69

Cytokine-induced signaling networks prioritize dynamic range over signal strength. Cell (2008) 1.65

Spatial exclusivity combined with positive and negative selection of phosphorylation motifs is the basis for context-dependent mitotic signaling. Sci Signal (2011) 1.62

Collecting and organizing systematic sets of protein data. Nat Rev Mol Cell Biol (2006) 1.58

The ins and outs of signalling. Nature (2001) 1.50

Kinetic analysis of platelet-derived growth factor receptor/phosphoinositide 3-kinase/Akt signaling in fibroblasts. J Biol Chem (2003) 1.43

Multicellular simulation predicts microvascular patterning and in silico tissue assembly. FASEB J (2004) 1.34

Pairwise agonist scanning predicts cellular signaling responses to combinatorial stimuli. Nat Biotechnol (2010) 1.31

Combinatorial complexity and dynamical restriction of network flows in signal transduction. Syst Biol (Stevenage) (2005) 1.27

Quantitative network signal combinations downstream of TCR activation can predict IL-2 production response. J Immunol (2007) 1.26

Phosphoproteomics: unraveling the signaling web. Mol Cell (2008) 1.18

Linear combinations of docking affinities explain quantitative differences in RTK signaling. Mol Syst Biol (2009) 1.16

Elongation, proliferation & migration differentiate endothelial cell phenotypes and determine capillary sprouting. BMC Syst Biol (2009) 1.10

Normal morphogenesis of epithelial tissues and progression of epithelial tumors. Wiley Interdiscip Rev Syst Biol Med (2011) 1.10

Multiscale modeling of diffusion in the early Drosophila embryo. Proc Natl Acad Sci U S A (2010) 1.07

Deciphering signaling outcomes from a system of complex networks. Sci Signal (2009) 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

Capturing cell-fate decisions from the molecular signatures of a receptor-dependent signaling response. Mol Syst Biol (2007) 1.02

Pairwise network mechanisms in the host signaling response to coxsackievirus B3 infection. Proc Natl Acad Sci U S A (2010) 0.97

The complexity of cell signaling and the need for a new mechanics. Sci Signal (2009) 0.92

'On-the-fly' or 'generate-first' modeling? Nat Biotechnol (2005) 0.89

Ensuring congruency in multiscale modeling: towards linking agent based and continuum biomechanical models of arterial adaptation. Ann Biomed Eng (2011) 0.89

Robustness portraits of diverse biological networks conserved despite order-of-magnitude parameter uncertainty. Bioinformatics (2011) 0.78

Paring down signaling complexity. Nat Biotechnol (2010) 0.78

A multiplexed homogeneous fluorescence-based assay for protein kinase activity in cell lysates. Nat Methods (2005) 2.39

A compendium of signals and responses triggered by prodeath and prosurvival cytokines. Mol Cell Proteomics (2005) 2.20

Common effector processing mediates cell-specific responses to stimuli. Nature (2007) 2.20

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

Normal morphogenesis of epithelial tissues and progression of epithelial tumors. Wiley Interdiscip Rev Syst Biol Med (2011) 1.10

Applying computational modeling to drug discovery and development. Drug Discov Today (2006) 1.08

Adenoviral vector saturates Akt pro-survival signaling and blocks insulin-mediated rescue of tumor necrosis-factor-induced apoptosis. J Cell Sci (2006) 1.04

Parameterizing cell-to-cell regulatory heterogeneities via stochastic transcriptional profiles. Proc Natl Acad Sci U S A (2014) 1.01

Pairwise network mechanisms in the host signaling response to coxsackievirus B3 infection. Proc Natl Acad Sci U S A (2010) 0.97

An ERK-p38 subnetwork coordinates host cell apoptosis and necrosis during coxsackievirus B3 infection. Cell Host Microbe (2013) 0.92

Simultaneous profiling of 194 distinct receptor transcripts in human cells. Sci Signal (2013) 0.90

Stochastic profiling of transcriptional regulatory heterogeneities in tissues, tumors and cultured cells. Nat Protoc (2013) 0.88

Modeling the latent dimensions of multivariate signaling datasets. Phys Biol (2012) 0.82

Paring down signaling complexity. Nat Biotechnol (2010) 0.78

A high-throughput assay for phosphoprotein-specific phosphatase activity in cellular extracts. Mol Cell Proteomics (2012) 0.77

Bringing systems biology to cancer, immunology and infectious disease. Genome Biol (2014) 0.76