Published in J Theor Biol on March 19, 2005
Predicting essential components of signal transduction networks: a dynamic model of guard cell abscisic acid signaling. PLoS Biol (2006) 3.53
Robustness can evolve gradually in complex regulatory gene networks with varying topology. PLoS Comput Biol (2007) 3.09
Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Mol Syst Biol (2009) 2.98
Network model of survival signaling in large granular lymphocyte leukemia. Proc Natl Acad Sci U S A (2008) 2.60
A logical model provides insights into T cell receptor signaling. PLoS Comput Biol (2007) 2.25
Boolean network simulations for life scientists. Source Code Biol Med (2008) 2.05
The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data. PLoS Comput Biol (2009) 1.88
Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling. BMC Syst Biol (2009) 1.78
Dynamic simulation of regulatory networks using SQUAD. BMC Bioinformatics (2007) 1.75
Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling. PLoS Comput Biol (2009) 1.69
Multi-level modeling of light-induced stomatal opening offers new insights into its regulation by drought. PLoS Comput Biol (2014) 1.63
Modeling systems-level regulation of host immune responses. PLoS Comput Biol (2007) 1.56
Dynamical and structural analysis of a T cell survival network identifies novel candidate therapeutic targets for large granular lymphocyte leukemia. PLoS Comput Biol (2011) 1.51
Monotone and near-monotone biochemical networks. Syst Synth Biol (2007) 1.29
Shape, size, and robustness: feasible regions in the parameter space of biochemical networks. PLoS Comput Biol (2009) 1.25
Visual setup of logical models of signaling and regulatory networks with ProMoT. BMC Bioinformatics (2006) 1.22
The signaling petri net-based simulator: a non-parametric strategy for characterizing the dynamics of cell-specific signaling networks. PLoS Comput Biol (2008) 1.19
Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks. Cell Commun Signal (2013) 1.17
Mathematical modeling of gene expression: a guide for the perplexed biologist. Crit Rev Biochem Mol Biol (2011) 1.15
Modeling reveals bistability and low-pass filtering in the network module determining blood stem cell fate. PLoS Comput Biol (2010) 1.12
Biological switches and clocks. J R Soc Interface (2008) 1.08
Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with desired expression levels in prokaryotes. BMC Syst Biol (2010) 1.04
Absence of Tec family kinases interleukin-2 inducible T cell kinase (Itk) and Bruton's tyrosine kinase (Btk) severely impairs Fc epsilonRI-dependent mast cell responses. J Biol Chem (2011) 1.03
Host-pathogen systems biology: logical modelling of hepatocyte growth factor and Helicobacter pylori induced c-Met signal transduction. BMC Syst Biol (2008) 1.01
Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome. PLoS Comput Biol (2015) 0.99
Deterministic and stochastic models of genetic regulatory networks. Methods Enzymol (2009) 0.98
Geometry and topology of parameter space: investigating measures of robustness in regulatory networks. J Math Biol (2008) 0.97
Logic-based models in systems biology: a predictive and parameter-free network analysis method. Integr Biol (Camb) (2012) 0.90
Boolean network model predicts knockout mutant phenotypes of fission yeast. PLoS One (2013) 0.89
Autonomous Boolean modelling of developmental gene regulatory networks. J R Soc Interface (2012) 0.89
Dynamical modeling of the cholesterol regulatory pathway with Boolean networks. BMC Syst Biol (2008) 0.88
A tutorial on analysis and simulation of boolean gene regulatory network models. Curr Genomics (2009) 0.88
The effect of negative feedback loops on the dynamics of boolean networks. Biophys J (2008) 0.88
Combining network modeling and gene expression microarray analysis to explore the dynamics of Th1 and Th2 cell regulation. PLoS Comput Biol (2010) 0.87
Boolean approach to signalling pathway modelling in HGF-induced keratinocyte migration. Bioinformatics (2012) 0.86
Network model of immune responses reveals key effectors to single and co-infection dynamics by a respiratory bacterium and a gastrointestinal helminth. PLoS Comput Biol (2012) 0.85
Timing robustness in the budding and fission yeast cell cycles. PLoS One (2010) 0.85
Continuous time Boolean modeling for biological signaling: application of Gillespie algorithm. BMC Syst Biol (2012) 0.84
Logical Modeling and Dynamical Analysis of Cellular Networks. Front Genet (2016) 0.84
Canalization and control in automata networks: body segmentation in Drosophila melanogaster. PLoS One (2013) 0.84
An algebra-based method for inferring gene regulatory networks. BMC Syst Biol (2014) 0.83
Monotonicity, frustration, and ordered response: an analysis of the energy landscape of perturbed large-scale biological networks. BMC Syst Biol (2010) 0.83
Identifying dynamical modules from genetic regulatory systems: applications to the segment polarity network. BMC Bioinformatics (2007) 0.83
A Boolean model of the Pseudomonas syringae hrp regulon predicts a tightly regulated system. PLoS One (2010) 0.83
Inferring the Effects of Honokiol on the Notch Signaling Pathway in SW480 Colon Cancer Cells. Cancer Inform (2014) 0.82
A computational paradigm for dynamic logic-gates in neuronal activity. Front Comput Neurosci (2014) 0.81
Recent advances in intervention in markovian regulatory networks. Curr Genomics (2009) 0.81
Wine glasses and hourglasses: Non-adaptive complexity of vesicle traffic in microbial eukaryotes. Mol Biochem Parasitol (2016) 0.81
Stacking the odds for Golgi cisternal maturation. Elife (2016) 0.80
A checkpoints capturing timing-robust Boolean model of the budding yeast cell cycle regulatory network. BMC Syst Biol (2012) 0.79
Robustness in regulatory interaction networks. A generic approach with applications at different levels: physiologic, metabolic and genetic. Int J Mol Sci (2009) 0.78
Network modelling reveals the mechanism underlying colitis-associated colon cancer and identifies novel combinatorial anti-cancer targets. Sci Rep (2015) 0.78
Network class superposition analyses. PLoS One (2013) 0.78
Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord. PLoS One (2014) 0.77
MONOMIALS AND BASIN CYLINDERS FOR NETWORK DYNAMICS. SIAM J Appl Dyn Syst (2015) 0.77
Studying the effect of cell division on expression patterns of the segment polarity genes. J R Soc Interface (2008) 0.77
Fanconi anemia cells with unrepaired DNA damage activate components of the checkpoint recovery process. Theor Biol Med Model (2015) 0.76
An Extended, Boolean Model of the Septation Initiation Network in S.Pombe Provides Insights into Its Regulation. PLoS One (2015) 0.76
Boolean modeling of gene regulatory networks: Driesch redux. Proc Natl Acad Sci U S A (2012) 0.75
Causality analysis detects the regulatory role of maternal effect genes in the early Drosophila embryo. Genom Data (2016) 0.75
Mathematical and Computational Modeling in Complex Biological Systems. Biomed Res Int (2017) 0.75
Analysis of signaling networks distributed over intracellular compartments based on protein-protein interactions. BMC Genomics (2014) 0.75
COMPUTATIONAL METHODS FOR ASYNCHRONOUS BASINS. Discrete Continuous Dyn Syst Ser B (2016) 0.75
Systemic modeling myeloma-osteoclast interactions under normoxic/hypoxic condition using a novel computational approach. Sci Rep (2015) 0.75
Building a cell cycle oscillator: hysteresis and bistability in the activation of Cdc2. Nat Cell Biol (2003) 5.86
Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems. Proc Natl Acad Sci U S A (2004) 4.63
Predicting essential components of signal transduction networks: a dynamic model of guard cell abscisic acid signaling. PLoS Biol (2006) 3.53
Near linear time algorithm to detect community structures in large-scale networks. Phys Rev E Stat Nonlin Soft Matter Phys (2007) 3.19
Modular cell biology: retroactivity and insulation. Mol Syst Biol (2008) 3.11
Network model of survival signaling in large granular lymphocyte leukemia. Proc Natl Acad Sci U S A (2008) 2.60
Boolean network simulations for life scientists. Source Code Biol Med (2008) 2.05
Boolean modeling in systems biology: an overview of methodology and applications. Phys Biol (2012) 1.88
Load-induced modulation of signal transduction networks. Sci Signal (2011) 1.67
Modeling systems-level regulation of host immune responses. PLoS Comput Biol (2007) 1.56
Computational aspects of feedback in neural circuits. PLoS Comput Biol (2006) 1.54
Dynamical and structural analysis of a T cell survival network identifies novel candidate therapeutic targets for large granular lymphocyte leukemia. PLoS Comput Biol (2011) 1.51
Activation of neural progenitor cells in human eyes with proliferative vitreoretinopathy. Exp Eye Res (2012) 1.46
On the number of steady states in a multiple futile cycle. J Math Biol (2007) 1.39
Conserved network motifs allow protein-protein interaction prediction. Bioinformatics (2004) 1.31
Attractor analysis of asynchronous Boolean models of signal transduction networks. J Theor Biol (2010) 1.28
Shape, size, and robustness: feasible regions in the parameter space of biochemical networks. PLoS Comput Biol (2009) 1.25
Boolean modeling of transcriptome data reveals novel modes of heterotrimeric G-protein action. Mol Syst Biol (2010) 1.23
Common and unique elements of the ABA-regulated transcriptome of Arabidopsis guard cells. BMC Genomics (2011) 1.21
Mechanism-independent method for predicting response to multidrug combinations in bacteria. Proc Natl Acad Sci U S A (2012) 1.17
Global entrainment of transcriptional systems to periodic inputs. PLoS Comput Biol (2010) 1.08
A Petri net approach to the study of persistence in chemical reaction networks. Math Biosci (2007) 1.08
A network model for plant-pollinator community assembly. Proc Natl Acad Sci U S A (2010) 1.05
Elementary signaling modes predict the essentiality of signal transduction network components. BMC Syst Biol (2011) 1.04
NET-SYNTHESIS: a software for synthesis, inference and simplification of signal transduction networks. Bioinformatics (2007) 1.02
Steady-states of receptor-ligand dynamics: a theoretical framework. J Theor Biol (2004) 1.00
Bacteriophage-mediated competition in Bordetella bacteria. Proc Biol Sci (2006) 0.99
Minimization of thermodynamic costs in cancer cell invasion. Proc Natl Acad Sci U S A (2013) 0.98
Geometry and topology of parameter space: investigating measures of robustness in regulatory networks. J Math Biol (2008) 0.97
Global stability in a chemostat with multiple nutrients. J Math Biol (2006) 0.96
Discrete dynamic modeling with asynchronous update, or how to model complex systems in the absence of quantitative information. Methods Mol Biol (2009) 0.95
Boolean modeling of biological regulatory networks: a methodology tutorial. Methods (2012) 0.95
Variation in host susceptibility and infectiousness generated by co-infection: the myxoma-Trichostrongylus retortaeformis case in wild rabbits. J R Soc Interface (2007) 0.94
Generating super-shedders: co-infection increases bacterial load and egg production of a gastrointestinal helminth. J R Soc Interface (2012) 0.93
A characterization of scale invariant responses in enzymatic networks. PLoS Comput Biol (2012) 0.93
Topology of plant-pollinator networks that are vulnerable to collapse from species extinction. Phys Rev E Stat Nonlin Soft Matter Phys (2012) 0.92
Stabilization of perturbed Boolean network attractors through compensatory interactions. BMC Syst Biol (2014) 0.91
Elucidation of directionality for co-expressed genes: predicting intra-operon termination sites. Bioinformatics (2005) 0.91
On the stability of a model of testosterone dynamics. J Math Biol (2004) 0.91
An effective network reduction approach to find the dynamical repertoire of discrete dynamic networks. Chaos (2013) 0.91
Dynamic models of immune responses: what is the ideal level of detail? Theor Biol Med Model (2010) 0.89
Constraint-based network model of pathogen-immune system interactions. J R Soc Interface (2008) 0.89
Network model of immune responses reveals key effectors to single and co-infection dynamics by a respiratory bacterium and a gastrointestinal helminth. PLoS Comput Biol (2012) 0.85
Boolean modeling: a logic-based dynamic approach for understanding signaling and regulatory networks and for making useful predictions. Wiley Interdiscip Rev Syst Biol Med (2014) 0.85
Network analysis reveals cross-links of the immune pathways activated by bacteria and allergen. Phys Rev E Stat Nonlin Soft Matter Phys (2011) 0.83
Why Do CD8+ T Cells become Indifferent to Tumors: A Dynamic Modeling Approach. Front Physiol (2011) 0.83
The energy costs of insulators in biochemical networks. Biophys J (2013) 0.82
On predator-prey systems and small-gain theorems. Math Biosci Eng (2005) 0.82
Modeling proximal tubule cell homeostasis: tracking changes in luminal flow. Bull Math Biol (2009) 0.82
Discrete dynamic modeling of signal transduction networks. Methods Mol Biol (2012) 0.81
Disease Dynamics in a Dynamic Social Network. Physica A (2010) 0.80
Comparison of upstream regulators in human ex vivo cultured cornea limbal epithelial stem cells and differentiated corneal epithelial cells. BMC Genomics (2013) 0.78
A passivity-based stability criterion for a class of biochemical reaction networks. Math Biosci Eng (2008) 0.77
Shaping specificity in signaling networks. Nat Genet (2007) 0.77
Conditions for Global Stability of Monotone Tridiagonal Systems with Negative Feedback. Syst Control Lett (2010) 0.77
Studying the effect of cell division on expression patterns of the segment polarity genes. J R Soc Interface (2008) 0.77
Oscillations in multi-stable monotone systems with slowly varying feedback. J Differ Equ (2007) 0.77
Effects of community structure on the dynamics of random threshold networks. Phys Rev E Stat Nonlin Soft Matter Phys (2013) 0.76
Logarithmic Lipschitz norms and diffusion-induced instability. Nonlinear Anal Theory Methods Appl (2013) 0.75
Chemical networks with inflows and outflows: a positive linear differential inclusions approach. Biotechnol Prog (2009) 0.75