Published in Biochemistry on September 14, 2012
Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems. Wiley Interdiscip Rev Syst Biol Med (2013) 1.04
Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. Bioinformatics (2013) 1.02
Deciphering the mechanism behind Fibroblast Growth Factor (FGF) induced biphasic signal-response profiles. Cell Commun Signal (2014) 0.86
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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
A chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations. Cell (2010) 11.20
The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. Science (1998) 10.83
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Oscillations in NF-kappaB signaling control the dynamics of gene expression. Science (2004) 8.44
Dynamics of the p53-Mdm2 feedback loop in individual cells. Nat Genet (2004) 8.30
Seventeen-colour flow cytometry: unravelling the immune system. Nat Rev Immunol (2004) 7.37
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Functional roles for noise in genetic circuits. Nature (2010) 6.96
Coordination of Rho GTPase activities during cell protrusion. Nature (2009) 6.54
Metastasis results from preexisting variant cells within a malignant tumor. Science (1977) 6.47
Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell (2012) 5.62
Dynamic proteomics of individual cancer cells in response to a drug. Science (2008) 5.43
Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing. Nature (2010) 5.27
Transcription factor profiling in individual hematopoietic progenitors by digital RT-PCR. Proc Natl Acad Sci U S A (2006) 5.21
Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell (2012) 5.16
Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis. Cell Stem Cell (2010) 4.97
Oscillations and variability in the p53 system. Mol Syst Biol (2006) 4.59
Notch signaling: the core pathway and its posttranslational regulation. Dev Cell (2009) 4.49
Localized and reversible TGFbeta signalling switches breast cancer cells from cohesive to single cell motility. Nat Cell Biol (2009) 4.39
Physicochemical modelling of cell signalling pathways. Nat Cell Biol (2006) 4.34
Pulsatile stimulation determines timing and specificity of NF-kappaB-dependent transcription. Science (2009) 4.14
Identification and testing of a gene expression signature of invasive carcinoma cells within primary mammary tumors. Cancer Res (2004) 4.04
Image-based multivariate profiling of drug responses from single cells. Nat Methods (2007) 3.90
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Using gene expression noise to understand gene regulation. Science (2012) 3.49
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Data-driven modelling of signal-transduction networks. Nat Rev Mol Cell Biol (2006) 3.18
A deep profiler's guide to cytometry. Trends Immunol (2012) 3.14
Information transduction capacity of noisy biochemical signaling networks. Science (2011) 2.95
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Measurement of single-cell dynamics. Nature (2010) 2.55
High-content single-cell drug screening with phosphospecific flow cytometry. Nat Chem Biol (2007) 2.54
Simultaneous measurement of multiple active kinase states using polychromatic flow cytometry. Nat Biotechnol (2002) 2.43
A multiplexed homogeneous fluorescence-based assay for protein kinase activity in cell lysates. Nat Methods (2005) 2.39
Direct observation of mammalian cell growth and size regulation. Nat Methods (2012) 2.34
Coordinated regulation of pathways for enhanced cell motility and chemotaxis is conserved in rat and mouse mammary tumors. Cancer Res (2007) 2.24
Single-cell genomics. Nat Methods (2011) 2.24
Logic-based models for the analysis of cell signaling networks. Biochemistry (2010) 2.21
Cellular noise regulons underlie fluctuations in Saccharomyces cerevisiae. Mol Cell (2012) 2.16
Origins of regulated cell-to-cell variability. Nat Rev Mol Cell Biol (2011) 2.15
Identifying single-cell molecular programs by stochastic profiling. Nat Methods (2010) 2.11
Measuring and modeling apoptosis in single cells. Cell (2011) 2.10
Transient IkappaB kinase activity mediates temporal NF-kappaB dynamics in response to a wide range of tumor necrosis factor-alpha doses. J Biol Chem (2005) 2.08
Characterizing heterogeneous cellular responses to perturbations. Proc Natl Acad Sci U S A (2008) 2.03
Stimulus-dependent dynamics of p53 in single cells. Mol Syst Biol (2011) 2.02
Measurement of kinase activation in single mammalian cells. Nat Biotechnol (2000) 1.85
Parallel picoliter rt-PCR assays using microfluidics. Anal Chem (2006) 1.84
Profiling metabolites and peptides in single cells. Nat Methods (2011) 1.79
Understanding NF-kappaB signaling via mathematical modeling. Mol Syst Biol (2008) 1.79
Patterns of basal signaling heterogeneity can distinguish cellular populations with different drug sensitivities. Mol Syst Biol (2010) 1.77
Single-cell proteomic chip for profiling intracellular signaling pathways in single tumor cells. Proc Natl Acad Sci U S A (2011) 1.76
High-throughput single copy DNA amplification and cell analysis in engineered nanoliter droplets. Anal Chem (2008) 1.71
Population robustness arising from cellular heterogeneity. Proc Natl Acad Sci U S A (2010) 1.66
Collecting and organizing systematic sets of protein data. Nat Rev Mol Cell Biol (2006) 1.58
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
Heterogeneity in the physiological states and pharmacological responses of differentiating 3T3-L1 preadipocytes. J Cell Biol (2009) 1.51
Computational approaches for analyzing information flow in biological networks. Sci Signal (2012) 1.49
Imaging the coordination of multiple signalling activities in living cells. Nat Rev Mol Cell Biol (2011) 1.47
Physiological levels of TNFalpha stimulation induce stochastic dynamics of NF-kappaB responses in single living cells. J Cell Sci (2010) 1.38
Reporting from the field: genetically encoded fluorescent reporters uncover signaling dynamics in living biological systems. Annu Rev Biochem (2011) 1.30
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
Massively parallel detection of gene expression in single cells using subnanolitre wells. Lab Chip (2010) 1.22
Protein signaling networks from single cell fluctuations and information theory profiling. Biophys J (2011) 1.21
Sensitive multiplexed analysis of kinase activities and activity-based kinase identification. Nat Biotechnol (2009) 1.21
A microfluidic platform for systems pathology: multiparameter single-cell signaling measurements of clinical brain tumor specimens. Cancer Res (2010) 1.20
Visualization of JNK activity dynamics with a genetically encoded fluorescent biosensor. Proc Natl Acad Sci U S A (2010) 1.20
Cell-to-cell variability in PI3K protein level regulates PI3K-AKT pathway activity in cell populations. Curr Biol (2011) 1.18
Intravital imaging illuminates transforming growth factor beta signaling switches during metastasis. Cancer Res (2010) 1.18
A site-specific, multiplexed kinase activity assay using stable-isotope dilution and high-resolution mass spectrometry. Proc Natl Acad Sci U S A (2009) 1.17
Sources of cell-to-cell variability in canonical nuclear factor-κB (NF-κB) signaling pathway inferred from single cell dynamic images. J Biol Chem (2011) 1.13
Trait variability of cancer cells quantified by high-content automated microscopy of single cells. Methods Enzymol (2009) 1.10
Phospho flow cytometry methods for the analysis of kinase signaling in cell lines and primary human blood samples. Methods Mol Biol (2011) 1.07
Identification of models of heterogeneous cell populations from population snapshot data. BMC Bioinformatics (2011) 1.04
High-density micro-arrays for mass spectrometry. Lab Chip (2010) 1.00
Integrated microfluidic and imaging platform for a kinase activity radioassay to analyze minute patient cancer samples. Cancer Res (2010) 0.98
Microfluidic concentration-enhanced cellular kinase activity assay. J Am Chem Soc (2009) 0.97
Learning signaling network structures with sparsely distributed data. J Comput Biol (2009) 0.95
Cellular imaging: Taking a long, hard look. Nature (2010) 0.95
Class assignment of sequence-unrelated members of enzyme superfamilies by activity-based protein profiling. Angew Chem Int Ed Engl (2005) 0.92
Increasing the sensitivity of enzyme-linked immunosorbent assay using multiplexed electrokinetic concentrator. Anal Chem (2010) 0.89
Predicting cytotoxic T-cell age from multivariate analysis of static and dynamic biomarkers. Mol Cell Proteomics (2010) 0.88
Setting the standards for signal transduction research. Sci Signal (2011) 0.82
Models at the single cell level. Wiley Interdiscip Rev Syst Biol Med (2010) 0.81
BAYESIAN HIERARCHICAL MODELING FOR SIGNALING PATHWAY INFERENCE FROM SINGLE CELL INTERVENTIONAL DATA. Ann Appl Stat (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
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
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
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
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
Cardiomyocyte hypertrophy and degradation of connexin43 through spatially restricted autocrine/paracrine heparin-binding EGF. Proc Natl Acad Sci U S A (2005) 1.36
Growth factor-induced cell motility in tumor invasion. Acta Oncol (2002) 1.34
An inducible autocrine cascade regulates rat hepatocyte proliferation and apoptosis responses to tumor necrosis factor-alpha. Hepatology (2008) 1.30
Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks. BMC Syst Biol (2012) 1.28
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
Epidermal growth factor induces acute matrix contraction and subsequent calpain-modulated relaxation. Wound Repair Regen (2002) 1.27
Modeling of signal-response cascades using decision tree analysis. Bioinformatics (2005) 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
Ligand accumulation in autocrine cell cultures. Biophys J (2005) 1.25
Interleukin-7 receptor signaling network: an integrated systems perspective. Cell Mol Immunol (2008) 1.22
RAS mutations affect tumor necrosis factor-induced apoptosis in colon carcinoma cells via ERK-modulatory negative and positive feedback circuits along with non-ERK pathway effects. Cancer Res (2009) 1.21
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
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
Multivariate proteomic analysis of murine embryonic stem cell self-renewal versus differentiation signaling. Proc Natl Acad Sci U S A (2004) 1.17
Impaired SHP2-mediated extracellular signal-regulated kinase activation contributes to gefitinib sensitivity of lung cancer cells with epidermal growth factor receptor-activating mutations. Cancer Res (2010) 1.16
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
Signaling thresholds govern heterogeneity in IL-7-receptor-mediated responses of naïve CD8(+) T cells. Immunol Cell Biol (2011) 1.14
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
Epithelial and mesenchymal phenotypic switchings modulate cell motility in metastasis. Front Biosci (Landmark Ed) (2011) 1.12
Multipathway kinase signatures of multipotent stromal cells are predictive for osteogenic differentiation: tissue-specific stem cells. Stem Cells (2009) 1.11
Gene delivery properties of end-modified poly(beta-amino ester)s. Bioconjug Chem (2007) 1.11
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
Self-organization of polarized cell signaling via autocrine circuits: computational model analysis. Biophys J (2004) 1.06
Effects of systematic variation of amino acid sequence on the mechanical properties of a self-assembling, oligopeptide biomaterial. J Biomater Sci Polym Ed (2002) 1.05
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