Published in J Mol Biol on January 19, 2011
Birth, life and death of nascent polypeptide chains. Biotechnol J (2011) 0.98
Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate. Nucleic Acids Res (2015) 0.89
Synonymous Codons Direct Cotranslational Folding toward Different Protein Conformations. Mol Cell (2016) 0.88
Quantifying the effect of ribosomal density on mRNA stability. PLoS One (2014) 0.79
Occlusion of the Ribosome Binding Site Connects the Translational Initiation Frequency, mRNA Stability and Premature Transcription Termination. Front Microbiol (2017) 0.78
Rapid Curtailing of the Stringent Response by Toxin-Antitoxin Module-Encoded mRNases. J Bacteriol (2016) 0.77
Time-resolved dual RNA-seq reveals extensive rewiring of lung epithelial and pneumococcal transcriptomes during early infection. Genome Biol (2016) 0.76
PROKARYO: an illustrative and interactive computational model of the lactose operon in the bacterium Escherichia coli. BMC Bioinformatics (2015) 0.75
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
Limiting factors in Escherichia coli fed-batch production of recombinant proteins. Biotechnol Bioeng (2003) 1.31
Pseudouridylation of helix 69 of 23S rRNA is necessary for an effective translation termination. Proc Natl Acad Sci U S A (2007) 1.30
Single-cell analysis of lambda immunity regulation. J Mol Biol (2003) 1.28
Apocalmodulin and Ca2+ calmodulin-binding sites on the CaV1.2 channel. Biophys J (2003) 1.26
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
Molecular crowding limits translation and cell growth. Proc Natl Acad Sci U S A (2013) 1.19
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
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
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
Sustainability of virulence in a phage-bacterial ecosystem. J Virol (2010) 0.95
DNA supercoiling enhances cooperativity and efficiency of an epigenetic switch. Proc Natl Acad Sci U S A (2013) 0.95
Sensitivity of OR in phage lambda. Biophys J (2004) 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 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
Dominant negative autoregulation limits steady-state repression levels in gene networks. J Bacteriol (2009) 0.91
Direct and indirect effects in the regulation of overlapping promoters. Nucleic Acids Res (2011) 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
Network models of phage-bacteria coevolution. Phys Rev E Stat Nonlin Soft Matter Phys (2006) 0.88
Labyrinthine clustering in a spatial rock-paper-scissors ecosystem. Phys Rev E Stat Nonlin Soft Matter Phys (2013) 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
Economy of operon formation: cotranscription minimizes shortfall in protein complexes. MBio (2010) 0.86
Oxidative stress promotes ligand-independent and enhanced ligand-dependent tumor necrosis factor receptor signaling. J Biol Chem (2008) 0.86
Variability-based sequence alignment identifies residues responsible for functional differences in alpha and beta tubulin. Protein Sci (2004) 0.86
Nonideal behavior of the intramolecular structure factor of dilute polymers in a theta solvent. Phys Rev E Stat Nonlin Soft Matter Phys (2009) 0.86
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
Collaboration between CpG sites is needed for stable somatic inheritance of DNA methylation states. Nucleic Acids Res (2013) 0.83
Dynamical analysis on gene activity in the presence of repressors and an interfering promoter. Biophys J (2008) 0.83
Differentiation of developing olfactory neurons analysed in terms of coupled epigenetic landscapes. Nucleic Acids Res (2013) 0.82
Degree landscapes in scale-free networks. Phys Rev E Stat Nonlin Soft Matter Phys (2006) 0.82
Quantifying the benefits of translation regulation in the unfolded protein response. Phys Biol (2004) 0.82
Control of ribosome traffic by position-dependent choice of synonymous codons. Phys Biol (2013) 0.81
Conditional cooperativity of toxin - antitoxin regulation can mediate bistability between growth and dormancy. PLoS Comput Biol (2013) 0.81
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
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 of multiple epidemics with cross immunization. Phys Rev E Stat Nonlin Soft Matter Phys (2012) 0.80
Longevity of orders is related to the longevity of their constituent genera rather than genus richness. Theory Biosci (2008) 0.80
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
Modeling the spatial dynamics of culture spreading in the presence of cultural strongholds. Phys Rev E Stat Nonlin Soft Matter Phys (2011) 0.79
Emergence of diversity in a model ecosystem. Phys Rev E Stat Nonlin Soft Matter Phys (2012) 0.78
Multistability with a metastable mixed state. Phys Rev Lett (2012) 0.78
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
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
Protein localization with flexible DNA or RNA. PLoS One (2012) 0.75
One hub-one process: a tool based view on regulatory network topology. BMC Syst Biol (2008) 0.75
Key players in the genetic switch of bacteriophage TP901-1. Biophys J (2011) 0.75
Circuit architecture explains functional similarity of bacterial heat shock responses. Phys Biol (2012) 0.75
Organizational structure and communication networks in a university environment. Phys Rev E Stat Nonlin Soft Matter Phys (2010) 0.75
Visualization of large-scale correlations in gene expressions. Funct Integr Genomics (2004) 0.75
Quality control system response to stochastic growth of amyloid fibrils. FEBS Lett (2013) 0.75
Modeling dynamics of information networks. Phys Rev Lett (2003) 0.75
Fluid dynamics of dilatant fluids. Phys Rev E Stat Nonlin Soft Matter Phys (2012) 0.75
Anomalous fluctuations in sliding motion of cytoskeletal filaments driven by molecular motors: model simulations. J Phys Chem B (2008) 0.75
Locally self-organized quasicritical percolation in a multiple-disease model. Phys Rev E Stat Nonlin Soft Matter Phys (2011) 0.75
Dynamics of the recovery from sRNA-mediated gene silencing. Cell Cycle (2009) 0.75
Loewner driving functions for off-critical percolation clusters. Phys Rev E Stat Nonlin Soft Matter Phys (2009) 0.75