Published in Phys Rev E Stat Nonlin Soft Matter Phys on September 26, 2006
Specificity and stability in topology of protein networks. Science (2002) 21.07
Defining network topologies that can achieve biochemical adaptation. Cell (2009) 5.49
Modularity and extreme edges of the internet. Phys Rev Lett (2003) 3.34
Theoretical analysis of epigenetic cell memory by nucleosome modification. Cell (2007) 3.17
IRE1α induces thioredoxin-interacting protein to activate the NLRP3 inflammasome and promote programmed cell death under irremediable ER stress. Cell Metab (2012) 2.80
Real-time redox measurements during endoplasmic reticulum stress reveal interlinked protein folding functions. Cell (2008) 2.53
Stability puzzles in phage lambda. Phys Rev E Stat Nonlin Soft Matter Phys (2002) 2.25
Hierarchy measures in complex networks. Phys Rev Lett (2004) 1.76
Minimal model of spiky oscillations in NF-kappaB signaling. Proc Natl Acad Sci U S A (2006) 1.68
Toolbox model of evolution of prokaryotic metabolic networks and their regulation. Proc Natl Acad Sci U S A (2009) 1.60
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Efficient degradation and expression prioritization with small RNAs. Phys Biol (2007) 1.33
Single-cell analysis of lambda immunity regulation. J Mol Biol (2003) 1.28
Genetic regulation of fluxes: iron homeostasis of Escherichia coli. Nucleic Acids Res (2006) 1.25
Signal integration in the galactose network of Escherichia coli. Mol Microbiol (2007) 1.25
Dynamic instabilities induced by asymmetric influence: prisoners' dilemma game in small-world networks. Phys Rev E Stat Nonlin Soft Matter Phys (2002) 1.23
Dynamic features of gene expression control by small regulatory RNAs. Proc Natl Acad Sci U S A (2009) 1.23
Ribosome collisions and translation efficiency: optimization by codon usage and mRNA destabilization. J Mol Biol (2008) 1.15
Coexistence of phage and bacteria on the boundary of self-organized refuges. Proc Natl Acad Sci U S A (2012) 1.14
Combinatorics of feedback in cellular uptake and metabolism of small molecules. Proc Natl Acad Sci U S A (2007) 1.11
Computational architecture of the yeast regulatory network. Phys Biol (2005) 1.10
Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res (2012) 1.06
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Localization of denaturation bubbles in random DNA sequences. Proc Natl Acad Sci U S A (2003) 1.01
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The generation of promoter-mediated transcriptional noise in bacteria. PLoS Comput Biol (2008) 0.99
Targeted bacterial immunity buffers phage diversity. J Virol (2011) 0.98
Sustainability of virulence in a phage-bacterial ecosystem. J Virol (2010) 0.95
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Prisoners' dilemma in real-world acquaintance networks: spikes and quasiequilibria induced by the interplay between structure and dynamics. Phys Rev E Stat Nonlin Soft Matter Phys (2003) 0.95
Modelling transcriptional interference and DNA looping in gene regulation. J Mol Biol (2007) 0.93
Structure and function of negative feedback loops at the interface of genetic and metabolic networks. Nucleic Acids Res (2006) 0.93
Quorum sensing regulation in Aeromonas hydrophila. J Mol Biol (2010) 0.92
Modeling oscillatory control in NF-κB, p53 and Wnt signaling. Curr Opin Genet Dev (2010) 0.92
Modeling the two-hybrid detector: experimental bias on protein interaction networks. Biophys J (2007) 0.92
Theory for the stability and regulation of epigenetic landscapes. Phys Biol (2010) 0.92
Direct and indirect effects in the regulation of overlapping promoters. Nucleic Acids Res (2011) 0.91
Dominant negative autoregulation limits steady-state repression levels in gene networks. J Bacteriol (2009) 0.91
Functional alignment of regulatory networks: a study of temperate phages. PLoS Comput Biol (2005) 0.91
Relation of intracellular signal levels and promoter activities in the gal regulon of Escherichia coli. J Mol Biol (2009) 0.90
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Labyrinthine clustering in a spatial rock-paper-scissors ecosystem. Phys Rev E Stat Nonlin Soft Matter Phys (2013) 0.88
Network models of phage-bacteria coevolution. Phys Rev E Stat Nonlin Soft Matter Phys (2006) 0.88
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Ecosystems with mutually exclusive interactions self-organize to a state of high diversity. Phys Rev Lett (2011) 0.87
Resampling effects on significance analysis of network clustering and ranking. PLoS One (2013) 0.86
The functional half-life of an mRNA depends on the ribosome spacing in an early coding region. J Mol Biol (2011) 0.86
Modeling the NF-κB mediated inflammatory response predicts cytokine waves in tissue. BMC Syst Biol (2011) 0.86
Variability-based sequence alignment identifies residues responsible for functional differences in alpha and beta tubulin. Protein Sci (2004) 0.86
Significant communities in large sparse networks. PLoS One (2012) 0.86
Barriers and silencers: a theoretical toolkit for control and containment of nucleosome-based epigenetic states. J Mol Biol (2011) 0.84
A network-based approach to visualize prevalence and progression of metabolic syndrome components. PLoS One (2012) 0.84
Modeling of the genetic switch of bacteriophage TP901-1: A heteromer of CI and MOR ensures robust bistability. J Mol Biol (2009) 0.84
Optimization and scale-freeness for complex networks. Chaos (2007) 0.84
Dynamical analysis on gene activity in the presence of repressors and an interfering promoter. Biophys J (2008) 0.83
Collaboration between CpG sites is needed for stable somatic inheritance of DNA methylation states. Nucleic Acids Res (2013) 0.83
Quantifying the benefits of translation regulation in the unfolded protein response. Phys Biol (2004) 0.82
Differentiation of developing olfactory neurons analysed in terms of coupled epigenetic landscapes. Nucleic Acids Res (2013) 0.82
Minimal gene regulatory circuits for a lysis-lysogeny choice in the presence of noise. PLoS One (2010) 0.81
Detection of topological patterns in protein networks. Genet Eng (N Y) (2004) 0.81
Conditional cooperativity of toxin - antitoxin regulation can mediate bistability between growth and dormancy. PLoS Comput Biol (2013) 0.81
Clonal selection prevents tragedy of the commons when neighbors compete in a rock-paper-scissors game. Phys Rev E Stat Nonlin Soft Matter Phys (2012) 0.81
Spreading out of perturbations in reversible reaction networks. New J Phys (2007) 0.80
Dynamics of uptake and metabolism of small molecules in cellular response systems. PLoS One (2009) 0.80
Longevity of orders is related to the longevity of their constituent genera rather than genus richness. Theory Biosci (2008) 0.80
Spreading of multiple epidemics with cross immunization. Phys Rev E Stat Nonlin Soft Matter Phys (2012) 0.80
Modeling the spatial dynamics of culture spreading in the presence of cultural strongholds. Phys Rev E Stat Nonlin Soft Matter Phys (2011) 0.79
Two portable recombination enhancers direct donor choice in fission yeast heterochromatin. PLoS Genet (2013) 0.79
Emergence of diversity in a model ecosystem. Phys Rev E Stat Nonlin Soft Matter Phys (2012) 0.78
Dynamics of the DNA repair proteins WRN and BLM in the nucleoplasm and nucleoli. Eur Biophys J (2014) 0.77
Analyzing inflammatory response as excitable media. Phys Rev E Stat Nonlin Soft Matter Phys (2011) 0.77
Fragile DNA repair mechanism reduces ageing in multicellular model. PLoS One (2012) 0.77
Specific contacts of the -35 region of the galP1 promoter by RNA polymerase inhibit GalR-mediated DNA looping repression. Nucleic Acids Res (2012) 0.77
Information spreading and development of cultural centers. Phys Rev E Stat Nonlin Soft Matter Phys (2012) 0.77
Short-range growth inhibitory signals from the epithelium can drive non-stereotypic branching in the pancreas. Phys Biol (2016) 0.76
Genetic regulatory networks that count to 3. J Theor Biol (2013) 0.76
Aging mechanism as the "down side" of adaptation: a network approach. J Theor Biol (2007) 0.76
Noisy transcription factor NF-κB oscillations stabilize and sensitize cytokine signaling in space. Phys Rev E Stat Nonlin Soft Matter Phys (2013) 0.76
Protein localization with flexible DNA or RNA. PLoS One (2012) 0.75
Key players in the genetic switch of bacteriophage TP901-1. Biophys J (2011) 0.75
One hub-one process: a tool based view on regulatory network topology. BMC Syst Biol (2008) 0.75
Replicator dynamics with turnover of players. Phys Rev E Stat Nonlin Soft Matter Phys (2013) 0.75
Quality control system response to stochastic growth of amyloid fibrils. FEBS Lett (2013) 0.75
Circuit architecture explains functional similarity of bacterial heat shock responses. Phys Biol (2012) 0.75
Flow improvement caused by agents who ignore traffic rules. Phys Rev E Stat Nonlin Soft Matter Phys (2009) 0.75
Locally self-organized quasicritical percolation in a multiple-disease model. Phys Rev E Stat Nonlin Soft Matter Phys (2011) 0.75
Modeling dynamics of information networks. Phys Rev Lett (2003) 0.75
Visualization of large-scale correlations in gene expressions. Funct Integr Genomics (2004) 0.75
Dynamics of the recovery from sRNA-mediated gene silencing. Cell Cycle (2009) 0.75
Organizational structure and communication networks in a university environment. Phys Rev E Stat Nonlin Soft Matter Phys (2010) 0.75