Published in Bioinformatics on May 01, 2005
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
A method for the generation of standardized qualitative dynamical systems of regulatory networks. Theor Biol Med Model (2006) 2.14
Cell surface restriction of EGFR by a tenascin cytotactin-encoded EGF-like repeat is preferential for motility-related signaling. J Cell Physiol (2008) 1.34
Targeting tumor cell motility as a strategy against invasion and metastasis. Trends Pharmacol Sci (2013) 1.19
m-Calpain activation is regulated by its membrane localization and by its binding to phosphatidylinositol 4,5-bisphosphate. J Biol Chem (2010) 1.07
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
Proteome-wide prediction of signal flow direction in protein interaction networks based on interacting domains. Mol Cell Proteomics (2009) 0.97
Controlling multipotent stromal cell migration by integrating "course-graining" materials and "fine-tuning" small molecules via decision tree signal-response modeling. Biomaterials (2011) 0.87
Non-linear dimensionality reduction of signaling networks. BMC Syst Biol (2007) 0.85
Traction stresses and translational distortion of the nucleus during fibroblast migration on a physiologically relevant ECM mimic. Biophys J (2009) 0.84
Towards a quantitative representation of the cell signaling mechanisms of hallucinogens: measurement and mathematical modeling of 5-HT1A and 5-HT2A receptor-mediated ERK1/2 activation. Neuropharmacology (2008) 0.81
Computational modeling of cardiac fibroblasts and fibrosis. J Mol Cell Cardiol (2015) 0.80
Envisioning migration: mathematics in both experimental analysis and modeling of cell behavior. Curr Opin Cell Biol (2013) 0.78
Multiscale analysis of the murine intestine for modeling human diseases. Integr Biol (Camb) (2015) 0.76
Decision-tree based model analysis for efficient identification of parameter relations leading to different signaling states. PLoS One (2013) 0.75
An integrated framework to model cellular phenotype as a component of biochemical networks. Adv Bioinformatics (2011) 0.75
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
Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Mol Syst Biol (2009) 2.98
Computational modeling of the EGF-receptor system: a paradigm for systems biology. Trends Cell Biol (2003) 2.85
A Mena invasion isoform potentiates EGF-induced carcinoma cell invasion and metastasis. Dev Cell (2008) 2.65
Modeling a snap-action, variable-delay switch controlling extrinsic cell death. PLoS Biol (2008) 2.63
Addressing genetic tumor heterogeneity through computationally predictive combination therapy. Cancer Discov (2013) 2.59
Mechanotransduction through growth-factor shedding into the extracellular space. Nature (2004) 2.48
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
Breast carcinoma cells re-express E-cadherin during mesenchymal to epithelial reverting transition. Mol Cancer (2010) 2.31
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
Common effector processing mediates cell-specific responses to stimuli. Nature (2007) 2.20
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
Mesenchymal-epithelial transition (MET) as a mechanism for metastatic colonisation in breast cancer. Cancer Metastasis Rev (2012) 2.08
Tethered epidermal growth factor provides a survival advantage to mesenchymal stem cells. Stem Cells (2007) 2.03
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
Glu-Leu-Arg-negative CXC chemokine interferon gamma inducible protein-9 as a mediator of epidermal-dermal communication during wound repair. J Invest Dermatol (2003) 1.89
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
Epidermal growth factor as a candidate for ex vivo expansion of bone marrow-derived mesenchymal stem cells. Stem Cells (2005) 1.66
Activation of m-calpain (calpain II) by epidermal growth factor is limited by protein kinase A phosphorylation of m-calpain. Mol Cell Biol (2002) 1.64
A high-throughput quantitative multiplex kinase assay for monitoring information flow in signaling networks: application to sepsis-apoptosis. Mol Cell Proteomics (2003) 1.61
IP-10 blocks vascular endothelial growth factor-induced endothelial cell motility and tube formation via inhibition of calpain. Circ Res (2006) 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
Erythropoietin-mediated activation of JAK-STAT signaling contributes to cellular invasion in head and neck squamous cell carcinoma. Oncogene (2005) 1.56
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
Control of self-assembling oligopeptide matrix formation through systematic variation of amino acid sequence. Biomaterials (2002) 1.52
Bayesian analysis of signaling networks governing embryonic stem cell fate decisions. Bioinformatics (2004) 1.52
Effects of Bcl-2 levels on Fas signaling-induced caspase-3 activation: molecular genetic tests of computational model predictions. J Immunol (2005) 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
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
Extracellular matrix signaling through growth factor receptors during wound healing. Wound Repair Regen (2004) 1.39
Growth factor regulation of proliferation and survival of multipotential stromal cells. Stem Cell Res Ther (2010) 1.39
IP-10 induces dissociation of newly formed blood vessels. J Cell Sci (2009) 1.38
Delayed and deficient dermal maturation in mice lacking the CXCR3 ELR-negative CXC chemokine receptor. Am J Pathol (2007) 1.38
In vivo systems analysis identifies spatial and temporal aspects of the modulation of TNF-α-induced apoptosis and proliferation by MAPKs. Sci Signal (2011) 1.37
Partial mesenchymal to epithelial reverting transition in breast and prostate cancer metastases. Cancer Microenviron (2011) 1.37
Cardiomyocyte hypertrophy and degradation of connexin43 through spatially restricted autocrine/paracrine heparin-binding EGF. Proc Natl Acad Sci U S A (2005) 1.36
Interferon-inducible protein 9 (CXCL11)-induced cell motility in keratinocytes requires calcium flux-dependent activation of mu-calpain. Mol Cell Biol (2005) 1.35
Growth factor-induced cell motility in tumor invasion. Acta Oncol (2002) 1.34
Cell surface restriction of EGFR by a tenascin cytotactin-encoded EGF-like repeat is preferential for motility-related signaling. J Cell Physiol (2008) 1.34
Spatial localization of m-calpain to the plasma membrane by phosphoinositide biphosphate binding during epidermal growth factor receptor-mediated activation. Mol Cell Biol (2006) 1.31
Loss of profilin-1 expression enhances breast cancer cell motility by Ena/VASP proteins. J Cell Physiol (2009) 1.30
An inducible autocrine cascade regulates rat hepatocyte proliferation and apoptosis responses to tumor necrosis factor-alpha. Hepatology (2008) 1.30
ELR-negative CXC chemokine CXCL11 (IP-9/I-TAC) facilitates dermal and epidermal maturation during wound repair. Am J Pathol (2008) 1.29
Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks. BMC Syst Biol (2012) 1.28
Profilin1 regulates PI(3,4)P2 and lamellipodin accumulation at the leading edge thus influencing motility of MDA-MB-231 cells. Proc Natl Acad Sci U S A (2010) 1.28
DU145 human prostate carcinoma invasiveness is modulated by urokinase receptor (uPAR) downstream of epidermal growth factor receptor (EGFR) signaling. Exp Cell Res (2004) 1.28
Epidermal growth factor induces acute matrix contraction and subsequent calpain-modulated relaxation. Wound Repair Regen (2002) 1.27
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
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
2D protrusion but not motility predicts growth factor-induced cancer cell migration in 3D collagen. J Cell Biol (2012) 1.26
Novel three-dimensional organotypic liver bioreactor to directly visualize early events in metastatic progression. Adv Cancer Res (2007) 1.25
Ligand accumulation in autocrine cell cultures. Biophys J (2005) 1.25
Curriculum content and evaluation of resident competency in clinical pathology (laboratory medicine): a proposal. Clin Chem (2006) 1.22
Interleukin-7 receptor signaling network: an integrated systems perspective. Cell Mol Immunol (2008) 1.22