Published in J Mol Biol on August 29, 2003
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Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence. Proc Natl Acad Sci U S A (2010) 2.32
DNA twisting flexibility and the formation of sharply looped protein-DNA complexes. Proc Natl Acad Sci U S A (2005) 2.00
Diffusion of transcription factors can drastically enhance the noise in gene expression. Biophys J (2006) 1.92
Modeling the Lac repressor-operator assembly: the influence of DNA looping on Lac repressor conformation. Proc Natl Acad Sci U S A (2006) 1.75
Deciphering a transcriptional regulatory code: modeling short-range repression in the Drosophila embryo. Mol Syst Biol (2010) 1.66
Effect of promoter architecture on the cell-to-cell variability in gene expression. PLoS Comput Biol (2011) 1.37
Transcriptional control of noise in gene expression. Proc Natl Acad Sci U S A (2008) 1.36
The transcription factor titration effect dictates level of gene expression. Cell (2014) 1.30
Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping. PLoS One (2006) 1.30
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Quantitative dissection of the simple repression input-output function. Proc Natl Acad Sci U S A (2011) 1.23
Coordinate control of gene expression noise and interchromosomal interactions in a MAP kinase pathway. Nat Cell Biol (2010) 1.22
Spatial and topological organization of DNA chains induced by gene co-localization. PLoS Comput Biol (2010) 1.21
Inferring the in vivo looping properties of DNA. Proc Natl Acad Sci U S A (2005) 1.21
First-principles calculation of DNA looping in tethered particle experiments. Phys Biol (2009) 1.20
Mathematical modeling of gene expression: a guide for the perplexed biologist. Crit Rev Biochem Mol Biol (2011) 1.15
Stochastic simulations of the origins and implications of long-tailed distributions in gene expression. Proc Natl Acad Sci U S A (2005) 1.12
DNA looping provides stability and robustness to the bacteriophage lambda switch. Proc Natl Acad Sci U S A (2009) 1.06
Promoter architecture dictates cell-to-cell variability in gene expression. Science (2014) 1.05
Operator sequence alters gene expression independently of transcription factor occupancy in bacteria. Cell Rep (2012) 1.05
Noise management by molecular networks. PLoS Comput Biol (2009) 1.05
DNA looping in prokaryotes: experimental and theoretical approaches. J Bacteriol (2013) 1.03
3D reconstruction and comparison of shapes of DNA minicircles observed by cryo-electron microscopy. Nucleic Acids Res (2006) 1.02
DNA looping by two-site restriction endonucleases: heterogeneous probability distributions for loop size and unbinding force. Nucleic Acids Res (2006) 1.02
Multilevel deconstruction of the In vivo behavior of looped DNA-protein complexes. PLoS One (2007) 1.02
Stochastic dynamics of macromolecular-assembly networks. Mol Syst Biol (2006) 1.00
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The effect of nonspecific binding of lambda repressor on DNA looping dynamics. Biophys J (2012) 0.98
Transcription-factor-mediated DNA looping probed by high-resolution, single-molecule imaging in live E. coli cells. PLoS Biol (2013) 0.96
Progesterone-dependent deoxyribonucleic acid looping between RUSH/SMARCA3 and Egr-1 mediates repression by c-Rel. Mol Endocrinol (2008) 0.94
Transcription by the numbers redux: experiments and calculations that surprise. Trends Cell Biol (2010) 0.91
An optimal number of molecules for signal amplification and discrimination in a chemical cascade. Biophys J (2006) 0.91
General transfer matrix formalism to calculate DNA-protein-drug binding in gene regulation: application to OR operator of phage lambda. Nucleic Acids Res (2007) 0.90
Quantitation of the DNA tethering effect in long-range DNA looping in vivo and in vitro using the Lac and λ repressors. Proc Natl Acad Sci U S A (2013) 0.89
PreCisIon: PREdiction of CIS-regulatory elements improved by gene's positION. Nucleic Acids Res (2012) 0.88
Regulation of expression of the divergent ulaG and ulaABCDEF operons involved in LaAscorbate dissimilation in Escherichia coli. J Bacteriol (2004) 0.88
Statistical mechanical model of coupled transcription from multiple promoters due to transcription factor titration. Phys Rev E Stat Nonlin Soft Matter Phys (2014) 0.87
Dimerization of the human papillomavirus type 16 E2 N terminus results in DNA looping within the upstream regulatory region. J Virol (2008) 0.86
Dynamics of single DNA looping and cleavage by Sau3AI and effect of tension applied to the DNA. Biophys J (2006) 0.85
Accurate prediction of gene expression by integration of DNA sequence statistics with detailed modeling of transcription regulation. Biophys J (2010) 0.84
Comparison and calibration of different reporters for quantitative analysis of gene expression. Biophys J (2011) 0.84
DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation. Phys Biol (2013) 0.84
Theoretical and experimental dissection of DNA loop-mediated repression. Phys Rev Lett (2013) 0.82
Control of gene expression by modulated self-assembly. Nucleic Acids Res (2011) 0.80
Systems biophysics of gene expression. Biophys J (2013) 0.80
Perspectives: using polymer modeling to understand the formation and function of nuclear compartments. Chromosome Res (2017) 0.79
Do femtonewton forces affect genetic function? A review. J Biol Phys (2006) 0.79
Comparison of the theoretical and real-world evolutionary potential of a genetic circuit. Phys Biol (2014) 0.78
Deterministic and stochastic population-level simulations of an artificial lac operon genetic network. BMC Bioinformatics (2011) 0.78
Biological Sources of Intrinsic and Extrinsic Noise in cI Expression of Lysogenic Phage Lambda. Sci Rep (2015) 0.78
From multiple pathogenicity islands to a unique organized pathogenicity archipelago. Sci Rep (2016) 0.76
Effect of Interaction between Chromatin Loops on Cell-to-Cell Variability in Gene Expression. PLoS Comput Biol (2016) 0.76
Protein distributions from a stochastic model of the lac operon of E. coli with DNA looping: analytical solution and comparison with experiments. PLoS One (2014) 0.76
Modeling the effect of transcriptional noise on switching in gene networks in a genetic bistable switch. J Biol Phys (2015) 0.75
Using synthetic biology to make cells tomorrow's test tubes. Integr Biol (Camb) (2016) 0.75
Guidance for data collection and computational modelling of regulatory networks. Methods Mol Biol (2009) 0.75
Effect of transcription factor resource sharing on gene expression noise. PLoS Comput Biol (2017) 0.75
Self-consistent theory of transcriptional control in complex regulatory architectures. PLoS One (2017) 0.75
Tailor-made transcriptional biosensors for optimizing microbial cell factories. J Ind Microbiol Biotechnol (2016) 0.75
Bacterial persistence as a phenotypic switch. Science (2004) 15.80
Phenotypic diversity, population growth, and information in fluctuating environments. Science (2005) 8.21
Combinatorial synthesis of genetic networks. Science (2002) 5.91
Establishment of developmental precision and proportions in the early Drosophila embryo. Nature (2002) 5.55
Resilient circadian oscillator revealed in individual cyanobacteria. Nature (2004) 3.84
Mechanisms of noise-resistance in genetic oscillators. Proc Natl Acad Sci U S A (2002) 3.78
Protein sectors: evolutionary units of three-dimensional structure. Cell (2009) 3.76
Dynamic persistence of antibiotic-stressed mycobacteria. Science (2013) 3.34
Bacterial persistence: a model of survival in changing environments. Genetics (2005) 2.97
Simpson's paradox in a synthetic microbial system. Science (2009) 2.97
Modeling network dynamics: the lac operon, a case study. J Cell Biol (2003) 2.03
Environmental stresses can alleviate the average deleterious effect of mutations. J Biol (2003) 1.76
An interdomain sector mediating allostery in Hsp70 molecular chaperones. Mol Syst Biol (2010) 1.42
Contingency and statistical laws in replicate microbial closed ecosystems. Cell (2012) 1.23
Cooperation and Hamilton's rule in a simple synthetic microbial system. Mol Syst Biol (2010) 1.22
Neuronal couplings between retinal ganglion cells inferred by efficient inverse statistical physics methods. Proc Natl Acad Sci U S A (2009) 1.20
Quantitation of cellular dynamics in growing Arabidopsis roots with light sheet microscopy. PLoS One (2011) 1.10
Speed, dissipation, and error in kinetic proofreading. Proc Natl Acad Sci U S A (2012) 0.97
Printing multistrain bacterial patterns with a piezoelectric inkjet printer. PLoS One (2007) 0.95
Microbial population dynamics by digital in-line holographic microscopy. Rev Sci Instrum (2010) 0.91
Behavioral diversity in microbes and low-dimensional phenotypic spaces. Proc Natl Acad Sci U S A (2013) 0.86
Polymer-population mapping and localization in the space of phenotypes. Phys Rev Lett (2006) 0.82