Published in BMC Syst Biol on March 22, 2011
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther (2013) 2.64
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
Integrating pathways of Parkinson's disease in a molecular interaction map. Mol Neurobiol (2013) 1.34
Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks. BMC Syst Biol (2012) 1.28
Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks. Cell Commun Signal (2013) 1.17
Dysregulated signaling hubs of liver lipid metabolism reveal hepatocellular carcinoma pathogenesis. Nucleic Acids Res (2016) 0.89
Angiogenic activity of breast cancer patients' monocytes reverted by combined use of systems modeling and experimental approaches. PLoS Comput Biol (2015) 0.88
Control of complex networks requires both structure and dynamics. Sci Rep (2016) 0.85
Some perspectives on network modeling in therapeutic target prediction. Biomed Eng Comput Biol (2013) 0.84
Systems medicine: evolution of systems biology from bench to bedside. Wiley Interdiscip Rev Syst Biol Med (2015) 0.83
Perturbation centrality and turbine: a novel centrality measure obtained using a versatile network dynamics tool. PLoS One (2013) 0.81
Nonparametric simulation of signal transduction networks with semi-synchronized update. PLoS One (2012) 0.78
Identification of core T cell network based on immunome interactome. BMC Syst Biol (2014) 0.77
Quantitative analysis of intracellular communication and signaling errors in signaling networks. BMC Syst Biol (2014) 0.77
A flood-based information flow analysis and network minimization method for gene regulatory networks. BMC Bioinformatics (2013) 0.76
Combining Chemical Profiling and Network Analysis to Investigate the Pharmacology of Complex Prescriptions in Traditional Chinese Medicine. Sci Rep (2017) 0.75
Manatee invariants reveal functional pathways in signaling networks. BMC Syst Biol (2017) 0.75
Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (2002) 43.52
Network biology: understanding the cell's functional organization. Nat Rev Genet (2004) 36.62
Lethality and centrality in protein networks. Nature (2001) 29.64
The large-scale organization of metabolic networks. Nature (2000) 27.57
A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat Biotechnol (2000) 6.74
Metabolic network structure determines key aspects of functionality and regulation. Nature (2002) 6.64
Scale-free networks in cell biology. J Cell Sci (2005) 6.08
The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster. J Theor Biol (2003) 5.85
Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Syst Biol (2007) 4.52
Edgetic perturbation models of human inherited disorders. Mol Syst Biol (2009) 3.96
A methodology for the structural and functional analysis of signaling and regulatory networks. BMC Bioinformatics (2006) 3.55
Predicting essential components of signal transduction networks: a dynamic model of guard cell abscisic acid signaling. PLoS Biol (2006) 3.53
Genomic analysis of essentiality within protein networks. Trends Genet (2004) 3.52
Formation of regulatory patterns during signal propagation in a Mammalian cellular network. Science (2005) 3.48
Combinatorial control of gene expression. Nat Struct Mol Biol (2004) 2.66
Network model of survival signaling in large granular lymphocyte leukemia. Proc Natl Acad Sci U S A (2008) 2.60
Bacterial strategies for overcoming host innate and adaptive immune responses. Nat Immunol (2002) 2.33
A logical model provides insights into T cell receptor signaling. PLoS Comput Biol (2007) 2.25
The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data. PLoS Comput Biol (2009) 1.88
Pregenomic comparative analysis between bordetella bronchiseptica RB50 and Bordetella pertussis tohama I in murine models of respiratory tract infection. Infect Immun (1999) 1.83
Role of antibodies in immunity to Bordetella infections. Infect Immun (2003) 1.71
Modeling systems-level regulation of host immune responses. PLoS Comput Biol (2007) 1.56
ON/OFF and beyond--a boolean model of apoptosis. PLoS Comput Biol (2009) 1.53
Low degree metabolites explain essential reactions and enhance modularity in biological networks. BMC Bioinformatics (2006) 1.28
Functional essentiality from topology features in metabolic networks: a case study in yeast. FEBS Lett (2005) 1.25
Using the topology of metabolic networks to predict viability of mutant strains. Biophys J (2006) 1.24
Insights into the organization of biochemical regulatory networks using graph theory analyses. J Biol Chem (2008) 1.22
Fault diagnosis engineering of digital circuits can identify vulnerable molecules in complex cellular pathways. Sci Signal (2008) 1.16
How to identify essential genes from molecular networks? BMC Syst Biol (2009) 1.09
Discrete dynamic modeling of cellular signaling networks. Methods Enzymol (2009) 1.05
Identification of a topological characteristic responsible for the biological robustness of regulatory networks. PLoS Comput Biol (2009) 1.01
A weighted communicability measure applied to complex brain networks. J R Soc Interface (2009) 1.00
Proximity of intracellular regulatory networks to monotone systems. IET Syst Biol (2008) 0.97
Computing combinatorial intervention strategies and failure modes in signaling networks. J Comput Biol (2010) 0.94
Genome-wide system analysis reveals stable yet flexible network dynamics in yeast. IET Syst Biol (2009) 0.92
The pairwise disconnectivity index as a new metric for the topological analysis of regulatory networks. BMC Bioinformatics (2008) 0.90
Quantifying the relevance of different mediators in the human immune cell network. Bioinformatics (2004) 0.84
An approach to evaluate the topological significance of motifs and other patterns in regulatory networks. BMC Syst Biol (2009) 0.82
Determination of critical network interactions: an augmented Boolean pseudo-dynamics approach. IET Syst Biol (2008) 0.80
Expansion of signal transduction networks. Syst Biol (Stevenage) (2006) 0.80
Modeling signal transduction in enzyme cascades with the concept of elementary flux modes. J Comput Biol (2009) 0.80
SigFlux: a novel network feature to evaluate the importance of proteins in signal transduction networks. BMC Bioinformatics (2006) 0.79
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
Network model of survival signaling in large granular lymphocyte leukemia. Proc Natl Acad Sci U S A (2008) 2.60
Robustness and fragility of Boolean models for genetic regulatory networks. J Theor Biol (2005) 2.51
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
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
Activation of neural progenitor cells in human eyes with proliferative vitreoretinopathy. Exp Eye Res (2012) 1.46
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
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
Border control--a membrane-linked interactome of Arabidopsis. Science (2014) 1.10
A network model for plant-pollinator community assembly. Proc Natl Acad Sci U S A (2010) 1.05
NET-SYNTHESIS: a software for synthesis, inference and simplification of signal transduction networks. Bioinformatics (2007) 1.02
Bacteriophage-mediated competition in Bordetella bacteria. Proc Biol Sci (2006) 0.99
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
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
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
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 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
Why Do CD8+ T Cells become Indifferent to Tumors: A Dynamic Modeling Approach. Front Physiol (2011) 0.83
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
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
Shaping specificity in signaling networks. Nat Genet (2007) 0.77
Studying the effect of cell division on expression patterns of the segment polarity genes. J R Soc Interface (2008) 0.77
Effects of community structure on the dynamics of random threshold networks. Phys Rev E Stat Nonlin Soft Matter Phys (2013) 0.76