Published in Mol Microbiol on July 01, 2007
Regulatory activity revealed by dynamic correlations in gene expression noise. Nat Genet (2008) 2.49
The incoherent feed-forward loop can generate non-monotonic input functions for genes. Mol Syst Biol (2008) 2.13
Mechanisms and evolution of control logic in prokaryotic transcriptional regulation. Microbiol Mol Biol Rev (2009) 1.25
Dynamic features of gene expression control by small regulatory RNAs. Proc Natl Acad Sci U S A (2009) 1.23
Deciphering the transcriptional regulatory logic of amino acid metabolism. Nat Chem Biol (2011) 1.22
Genetic flexibility of regulatory networks. Proc Natl Acad Sci U S A (2010) 1.20
Combinatorics of feedback in cellular uptake and metabolism of small molecules. Proc Natl Acad Sci U S A (2007) 1.11
Engineering transcription factors with novel DNA-binding specificity using comparative genomics. Nucleic Acids Res (2009) 1.06
Glucose transport in Escherichia coli mutant strains with defects in sugar transport systems. J Bacteriol (2012) 0.96
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
Genome-wide screening of genes whose enhanced expression affects glycogen accumulation in Escherichia coli. DNA Res (2010) 0.90
Timing of gene transcription in the galactose utilization system of Escherichia coli. J Biol Chem (2010) 0.87
Tn5AraOut mutagenesis for the identification of Yersinia pestis genes involved in resistance towards cationic antimicrobial peptides. Microb Pathog (2011) 0.85
The effect of LacI autoregulation on the performance of the lactose utilization system in Escherichia coli. Nucleic Acids Res (2013) 0.85
Structure and function of the D-galactose network in enterobacteria. MBio (2011) 0.82
Dynamics of uptake and metabolism of small molecules in cellular response systems. PLoS One (2009) 0.80
Mutations in transcriptional regulators allow selective engineering of signal integration logic. MBio (2014) 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
The transcriptional regulator GalR self-assembles to form highly regular tubular structures. Sci Rep (2016) 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
Switches in bacteriophage lambda development. Annu Rev Genet (2005) 3.24
Theoretical analysis of epigenetic cell memory by nucleosome modification. Cell (2007) 3.17
Bacteriophage therapy rescues mice bacteremic from a clinical isolate of vancomycin-resistant Enterococcus faecium. Infect Immun (2002) 2.52
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
On the role of Cro in lambda prophage induction. Proc Natl Acad Sci U S A (2005) 1.65
Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping. Proc Natl Acad Sci U S A (2003) 1.63
Toolbox model of evolution of prokaryotic metabolic networks and their regulation. Proc Natl Acad Sci U S A (2009) 1.60
Direct demonstration and quantification of long-range DNA looping by the lambda bacteriophage repressor. Nucleic Acids Res (2009) 1.49
Toward a live microbial microbicide for HIV: commensal bacteria secreting an HIV fusion inhibitor peptide. Proc Natl Acad Sci U S A (2005) 1.39
Upstream plasticity and downstream robustness in evolution of molecular networks. BMC Evol Biol (2004) 1.36
High-sensitivity bacterial detection using biotin-tagged phage and quantum-dot nanocomplexes. Proc Natl Acad Sci U S A (2006) 1.36
A gamut of loops: meandering DNA. Trends Biochem Sci (2005) 1.33
Efficient degradation and expression prioritization with small RNAs. Phys Biol (2007) 1.33
Simplified models of biological networks. Annu Rev Biophys (2010) 1.33
Escherichia coli K1's capsule is a barrier to bacteriophage T7. Appl Environ Microbiol (2005) 1.31
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
Axiom of determining transcription start points by RNA polymerase in Escherichia coli. Mol Microbiol (2004) 1.27
Genetic regulation of fluxes: iron homeostasis of Escherichia coli. Nucleic Acids Res (2006) 1.25
Bacteriophage infection is targeted to cellular poles. Mol Microbiol (2008) 1.25
Three-stage regulation of the amphibolic gal operon: from repressosome to GalR-free DNA. J Mol Biol (2006) 1.25
Recognition of the tumor suppressor protein p53 and other protein targets by the calcium-binding protein S100B. Biochim Biophys Acta (2006) 1.24
Dynamic features of gene expression control by small regulatory RNAs. Proc Natl Acad Sci U S A (2009) 1.23
In vitro repression of the gal promoters by GalR and HU depends on the proper helical phasing of the two operators. J Biol Chem (2001) 1.22
A mutant spacer sequence between -35 and -10 elements makes the Plac promoter hyperactive and cAMP receptor protein-independent. Proc Natl Acad Sci U S A (2004) 1.22
Operator-bound GalR dimers close DNA loops by direct interaction: tetramerization and inducer binding. EMBO J (2002) 1.21
A-tract clusters may facilitate DNA packaging in bacterial nucleoid. Nucleic Acids Res (2005) 1.21
Genetic flexibility of regulatory networks. Proc Natl Acad Sci U S A (2010) 1.20
Nucleoid remodeling by an altered HU protein: reorganization of the transcription program. Proc Natl Acad Sci U S A (2005) 1.20
Spiral structure of Escherichia coli HUalphabeta provides foundation for DNA supercoiling. Proc Natl Acad Sci U S A (2007) 1.18
Multilevel autoregulation of λ repressor protein CI by DNA looping in vitro. Proc Natl Acad Sci U S A (2011) 1.18
"Antiparallel" DNA loop in gal repressosome visualized by atomic force microscopy. J Mol Biol (2003) 1.17
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
Coexistence of phage and bacteria on the boundary of self-organized refuges. Proc Natl Acad Sci U S A (2012) 1.14
Effect of varying the supercoiling of DNA on transcription and its regulation. Biochemistry (2003) 1.12
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
Cellular stress created by intermediary metabolite imbalances. Proc Natl Acad Sci U S A (2009) 1.09
DNA trajectory in the Gal repressosome. Genes Dev (2004) 1.08
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
The antiparallel loops in gal DNA. Nucleic Acids Res (2008) 1.02
Right-handed DNA supercoiling by an octameric form of histone-like protein HU: modulation of cellular transcription. J Biol Chem (2006) 1.02
Localization of denaturation bubbles in random DNA sequences. Proc Natl Acad Sci U S A (2003) 1.01
Identification of host receptor and receptor-binding module of a newly sequenced T5-like phage EPS7. FEMS Microbiol Lett (2008) 1.00
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
Genetic instability favoring transversions associated with ErbB2-induced mammary tumorigenesis. Proc Natl Acad Sci U S A (2002) 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
GalR represses galP1 by inhibiting the rate-determining open complex formation through RNA polymerase contact: a GalR negative control mutant. J Mol Biol (2004) 0.98
Genetic analysis of GalR tetramerization in DNA looping during repressosome assembly. J Biol Chem (2002) 0.97
Ribosomal protein S1 promotes transcriptional cycling. RNA (2006) 0.97
Host responses influence on the induction of lambda prophage. Mol Microbiol (2008) 0.97
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
Bacteriophage SP6 is closely related to phages K1-5, K5, and K1E but encodes a tail protein very similar to that of the distantly related P22. J Bacteriol (2002) 0.94
Conversion of commensal Escherichia coli K-12 to an invasive form via expression of a mutant histone-like protein. MBio (2011) 0.94
Asynchronous basepair openings in transcription initiation: CRP enhances the rate-limiting step. EMBO J (2004) 0.94
Architectural organization in E. coli nucleoid. Biochim Biophys Acta (2012) 0.94
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
High-density functional display of proteins on bacteriophage lambda. J Mol Biol (2003) 0.93
Noncoding RNAs binding to the nucleoid protein HU in Escherichia coli. J Bacteriol (2012) 0.93
Modeling oscillatory control in NF-κB, p53 and Wnt signaling. Curr Opin Genet Dev (2010) 0.92
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
Galactose repressor mediated intersegmental chromosomal connections in Escherichia coli. Proc Natl Acad Sci U S A (2012) 0.92
An amino acid substitution in a capsid protein enhances phage survival in mouse circulatory system more than a 1000-fold. Virus Res (2005) 0.91
Stop-and-go kinetics in amyloid fibrillation. Phys Rev E Stat Nonlin Soft Matter Phys (2010) 0.91
Functional alignment of regulatory networks: a study of temperate phages. PLoS Comput Biol (2005) 0.91
Evolution of DNA binding motifs and operators. Gene (2002) 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
An unsubstituted C2 hydrogen of adenine is critical and sufficient at the -11 position of a promoter to signal base pair deformation. J Biol Chem (2004) 0.89
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