Published in Proc Natl Acad Sci U S A on July 17, 2012
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Population cycles and species diversity in dynamic Kill-the-Winner model of microbial ecosystems. Sci Rep (2017) 0.75
Pseudo-chaotic oscillations in CRISPR-virus coevolution predicted by bifurcation analysis. Biol Direct (2014) 0.75
Modelling and parameter inference of predator-prey dynamics in heterogeneous environments using the direct integral approach. J R Soc Interface (2017) 0.75
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Elevated abundance of bacteriophage infecting bacteria in soil. Appl Environ Microbiol (2003) 1.50
Spatial heterogeneity and the stability of host-parasite coexistence. J Evol Biol (2006) 1.35
The use of phages for the removal of infectious biofilms. Curr Pharm Biotechnol (2008) 1.25
Bacteriophage T4 multiplication in a glucose-limited Escherichia coli biofilm. Can J Microbiol (2001) 1.11
Asymmetry in host and parasitoid diffuse coevolution: when the red queen has to keep a finger in more than one pie. Front Zool (2005) 1.04
Bacterial debris-an ecological mechanism for coexistence of bacteria and their viruses. J Theor Biol (2003) 1.04
Sustainability of virulence in a phage-bacterial ecosystem. J Virol (2010) 0.95
Space, time, and host evolution facilitate coexistence of competing bacteriophages: theory and experiment. Am Nat (2009) 0.95
Bacteriophage T4 development in Escherichia coli is growth rate dependent. J Theor Biol (2002) 0.94
Pseudomonas fluorescens infection by bacteriophage PhiS1: the influence of temperature, host growth phase and media. FEMS Microbiol Lett (2004) 0.94
Ecology and evolution in microbial systems: the generation and maintenance of diversity in phage-host interactions. Res Microbiol (2008) 0.93
Stochastic receptor expression allows sensitive bacteria to evade phage attack. Part I: experiments. Biophys J (2008) 0.89
Network models of phage-bacteria coevolution. Phys Rev E Stat Nonlin Soft Matter Phys (2006) 0.88
Prey-predator models in spatially heterogeneous environments. J Theor Biol (1974) 0.81
Specificity and stability in topology of protein networks. Science (2002) 21.07
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
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
Upstream plasticity and downstream robustness in evolution of molecular networks. BMC Evol Biol (2004) 1.36
Efficient degradation and expression prioritization with small RNAs. Phys Biol (2007) 1.33
Simplified models of biological networks. Annu Rev Biophys (2010) 1.33
Single-cell analysis of lambda immunity regulation. J Mol Biol (2003) 1.28
Low degree metabolites explain essential reactions and enhance modularity in biological networks. BMC Bioinformatics (2006) 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 features of gene expression control by small regulatory RNAs. Proc Natl Acad Sci U S A (2009) 1.23
Genetic flexibility of regulatory networks. Proc Natl Acad Sci U S A (2010) 1.20
Ribosome collisions and translation efficiency: optimization by codon usage and mRNA destabilization. J Mol Biol (2008) 1.15
Oscillation patterns in negative feedback loops. Proc Natl Acad Sci U S A (2007) 1.15
Combinatorics of feedback in cellular uptake and metabolism of small molecules. Proc Natl Acad Sci U S A (2007) 1.11
Large extinctions in an evolutionary model: the role of innovation and keystone species. Proc Natl Acad Sci U S A (2002) 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
Protein interaction networks beyond artifacts. FEBS Lett (2002) 1.04
Why do phage play dice? J Virol (2009) 1.03
Localization of denaturation bubbles in random DNA sequences. Proc Natl Acad Sci U S A (2003) 1.01
Stress-specific response of the p53-Mdm2 feedback loop. BMC Syst Biol (2010) 0.99
Spatial structure and Lamarckian adaptation explain extreme genetic diversity at CRISPR locus. MBio (2012) 0.99
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
Context-dependent conservation of DNA methyltransferases in bacteria. Nucleic Acids Res (2012) 0.96
Sustainability of virulence in a phage-bacterial ecosystem. J Virol (2010) 0.95
Sensitivity of OR in phage lambda. Biophys J (2004) 0.95
DNA supercoiling enhances cooperativity and efficiency of an epigenetic switch. Proc Natl Acad Sci U S A (2013) 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
Functional alignment of regulatory networks: a study of temperate phages. PLoS Comput Biol (2005) 0.91
Stop-and-go kinetics in amyloid fibrillation. Phys Rev E Stat Nonlin Soft Matter Phys (2010) 0.91
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
Relation of intracellular signal levels and promoter activities in the gal regulon of Escherichia coli. J Mol Biol (2009) 0.90
UV-induced mutagenesis in Escherichia coli SOS response: a quantitative model. PLoS Comput Biol (2007) 0.89
A Wnt oscillator model for somitogenesis. Biophys J (2010) 0.89
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
Competition between diffusion and fragmentation: an important evolutionary process of nature. Phys Rev Lett (2003) 0.88
Ecosystems with mutually exclusive interactions self-organize to a state of high diversity. Phys Rev Lett (2011) 0.87
Timing of gene transcription in the galactose utilization system of Escherichia coli. J Biol Chem (2010) 0.87
Variability-based sequence alignment identifies residues responsible for functional differences in alpha and beta tubulin. Protein Sci (2004) 0.86
Modeling the NF-κB mediated inflammatory response predicts cytokine waves in tissue. BMC Syst Biol (2011) 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
Economy of operon formation: cotranscription minimizes shortfall in protein complexes. MBio (2010) 0.86
The effect of LacI autoregulation on the performance of the lactose utilization system in Escherichia coli. Nucleic Acids Res (2013) 0.85
Crashes, recoveries, and "core shifts" in a model of evolving networks. Phys Rev E Stat Nonlin Soft Matter Phys (2002) 0.85
Barriers and silencers: a theoretical toolkit for control and containment of nucleosome-based epigenetic states. J Mol Biol (2011) 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
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
Degree landscapes in scale-free networks. Phys Rev E Stat Nonlin Soft Matter Phys (2006) 0.82
Differentiation of developing olfactory neurons analysed in terms of coupled epigenetic landscapes. Nucleic Acids Res (2013) 0.82
Quantifying the benefits of translation regulation in the unfolded protein response. Phys Biol (2004) 0.82
Repressor lattice: feedback, commensurability, and dynamical frustration. Phys Rev Lett (2009) 0.82
Structure and function of the D-galactose network in enterobacteria. MBio (2011) 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
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
Dynamics of uptake and metabolism of small molecules in cellular response systems. PLoS One (2009) 0.80
Spreading out of perturbations in reversible reaction networks. New J Phys (2007) 0.80
Symbolic dynamics of biological feedback networks. Phys Rev Lett (2009) 0.80
Genomic analysis reveals epistatic silencing of "expensive" genes in Escherichia coli K-12. Mol Biosyst (2013) 0.79
Modeling the spatial dynamics of culture spreading in the presence of cultural strongholds. Phys Rev E Stat Nonlin Soft Matter Phys (2011) 0.79
Inducing phase-locking and chaos in cellular oscillators by modulating the driving stimuli. FEBS Lett (2012) 0.79
Dickkopf1--a new player in modelling the Wnt pathway. PLoS One (2011) 0.78
Emergence of diversity in a model ecosystem. Phys Rev E Stat Nonlin Soft Matter Phys (2012) 0.78
Information spreading and development of cultural centers. Phys Rev E Stat Nonlin Soft Matter Phys (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
Switching between oscillations and homeostasis in competing negative and positive feedback motifs. J Theor Biol (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
Key players in the genetic switch of bacteriophage TP901-1. Biophys J (2011) 0.75
Protein localization with flexible DNA or RNA. PLoS One (2012) 0.75
Effects of growth and mutation on pattern formation in tissues. PLoS One (2012) 0.75