Published in J Mol Biol on October 15, 2004
An allosteric model for heterogeneous receptor complexes: understanding bacterial chemotaxis responses to multiple stimuli. Proc Natl Acad Sci U S A (2005) 2.44
Modeling the chemotactic response of Escherichia coli to time-varying stimuli. Proc Natl Acad Sci U S A (2008) 2.41
Physical responses of bacterial chemoreceptors. J Mol Biol (2006) 1.67
Effects of adaptation in maintaining high sensitivity over a wide range of backgrounds for Escherichia coli chemotaxis. Biophys J (2007) 1.67
Receptor-receptor coupling in bacterial chemotaxis: evidence for strongly coupled clusters. Biophys J (2006) 1.43
Quantitative modeling of bacterial chemotaxis: signal amplification and accurate adaptation. Annu Rev Biophys (2013) 1.32
Excitation and adaptation in bacteria-a model signal transduction system that controls taxis and spatial pattern formation. Int J Mol Sci (2013) 0.83
An agent-based model of signal transduction in bacterial chemotaxis. PLoS One (2010) 0.81
A "trimer of dimers"-based model for the chemotactic signal transduction network in bacterial chemotaxis. Bull Math Biol (2012) 0.81
The relation of signal transduction to the sensitivity and dynamic range of bacterial chemotaxis. Biophys J (2012) 0.80
Differential affinity and catalytic activity of CheZ in E. coli chemotaxis. PLoS Comput Biol (2009) 0.80
Site-specific methylation in Bacillus subtilis chemotaxis: effect of covalent modifications to the chemotaxis receptor McpB. Microbiology (2010) 0.79
Information processing in bacteria: memory, computation, and statistical physics: a key issues review. Rep Prog Phys (2016) 0.75
Characterization of the adaptation module of the signaling network in bacterial chemotaxis by measurement of step responses. Biophys J (2012) 0.75
Functional profiling of the Saccharomyces cerevisiae genome. Nature (2002) 36.10
FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One (2010) 26.15
FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol (2009) 15.15
Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell (2013) 13.43
Control, exploitation and tolerance of intracellular noise. Nature (2002) 6.81
Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity. Cell (2005) 5.71
Chemogenomic profiling: identifying the functional interactions of small molecules in yeast. Proc Natl Acad Sci U S A (2004) 5.10
A novel method for accurate operon predictions in all sequenced prokaryotes. Nucleic Acids Res (2005) 4.68
The MicrobesOnline Web site for comparative genomics. Genome Res (2005) 4.48
MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Res (2009) 4.32
Environmentally controlled invasion of cancer cells by engineered bacteria. J Mol Biol (2005) 4.25
Genetic "code": representations and dynamical models of genetic components and networks. Annu Rev Genomics Hum Genet (2002) 4.23
Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Proc Natl Acad Sci U S A (2011) 3.30
Environmental signal integration by a modular AND gate. Mol Syst Biol (2007) 3.25
Detailed simulations of cell biology with Smoldyn 2.1. PLoS Comput Biol (2010) 2.72
Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations. Proc Natl Acad Sci U S A (2005) 2.71
Precise and reliable gene expression via standard transcription and translation initiation elements. Nat Methods (2013) 2.61
Motifs, modules and games in bacteria. Curr Opin Microbiol (2003) 2.58
Diversity in times of adversity: probabilistic strategies in microbial survival games. J Theor Biol (2005) 2.55
RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res (2009) 2.53
Biological networks. Curr Opin Struct Biol (2003) 2.43
Genome-wide requirements for resistance to functionally distinct DNA-damaging agents. PLoS Genet (2005) 2.32
BglBricks: A flexible standard for biological part assembly. J Biol Eng (2010) 2.32
Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks. PLoS Comput Biol (2005) 2.27
Overview of the Alliance for Cellular Signaling. Nature (2002) 2.15
Quantitative estimation of activity and quality for collections of functional genetic elements. Nat Methods (2013) 2.03
Environmental genomics reveals a single-species ecosystem deep within Earth. Science (2008) 1.98
Versatile RNA-sensing transcriptional regulators for engineering genetic networks. Proc Natl Acad Sci U S A (2011) 1.93
RNA processing enables predictable programming of gene expression. Nat Biotechnol (2012) 1.92
The life-cycle of operons. PLoS Genet (2006) 1.91
RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. Nucleic Acids Res (2010) 1.81
Indirect and suboptimal control of gene expression is widespread in bacteria. Mol Syst Biol (2013) 1.81
Design and diversity in bacterial chemotaxis: a comparative study in Escherichia coli and Bacillus subtilis. PLoS Biol (2004) 1.78
The evolution of genetic regulatory systems in bacteria. Nat Rev Genet (2004) 1.73
Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach. J Bacteriol (2006) 1.68
Rationally designed families of orthogonal RNA regulators of translation. Nat Chem Biol (2012) 1.66
Regulation of transcription by unnatural amino acids. Nat Biotechnol (2011) 1.64
Operon formation is driven by co-regulation and not by horizontal gene transfer. Genome Res (2005) 1.64
RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria. BMC Genomics (2013) 1.61
Orthologous transcription factors in bacteria have different functions and regulate different genes. PLoS Comput Biol (2007) 1.58
Toward scalable parts families for predictable design of biological circuits. Curr Opin Microbiol (2008) 1.56
Substrate-free gas-phase synthesis of graphene sheets. Nano Lett (2008) 1.54
Composability of regulatory sequences controlling transcription and translation in Escherichia coli. Proc Natl Acad Sci U S A (2013) 1.53
Control of stochastic gene expression by host factors at the HIV promoter. PLoS Pathog (2009) 1.50
Interactive XCMS Online: simplifying advanced metabolomic data processing and subsequent statistical analyses. Anal Chem (2014) 1.49
Modeling and automation of sequencing-based characterization of RNA structure. Proc Natl Acad Sci U S A (2011) 1.49
Design and construction of a double inversion recombination switch for heritable sequential genetic memory. PLoS One (2008) 1.49
Deviant effects in molecular reaction pathways. Nat Biotechnol (2006) 1.48
The histidine operon is ancient. J Mol Evol (2006) 1.44
Complexity in bacterial cell-cell communication: quorum signal integration and subpopulation signaling in the Bacillus subtilis phosphorelay. Proc Natl Acad Sci U S A (2009) 1.42
From fluctuations to phenotypes: the physiology of noise. Sci STKE (2006) 1.41
Combinatorial latency reactivation for HIV-1 subtypes and variants. J Virol (2010) 1.40
Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli. Genome Biol (2008) 1.40
The electron transfer system of syntrophically grown Desulfovibrio vulgaris. J Bacteriol (2009) 1.35
A tightly regulated inducible expression system utilizing the fim inversion recombination switch. Biotechnol Bioeng (2006) 1.35
Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough, inferred from global transcriptional analysis. Appl Environ Microbiol (2006) 1.35
Theoretical design of a gene therapy to prevent AIDS but not human immunodeficiency virus type 1 infection. J Virol (2003) 1.34
Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions. PLoS Genet (2011) 1.33
Stochasticity, succession, and environmental perturbations in a fluidic ecosystem. Proc Natl Acad Sci U S A (2014) 1.31
Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibrio vulgaris Hildenborough. Appl Environ Microbiol (2007) 1.31
HIV promoter integration site primarily modulates transcriptional burst size rather than frequency. PLoS Comput Biol (2010) 1.30
Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. BMC Genomics (2011) 1.26
Sequencing of multiple clostridial genomes related to biomass conversion and biofuel production. J Bacteriol (2010) 1.25
Development of a low bias method for characterizing viral populations using next generation sequencing technology. PLoS One (2010) 1.25
The Bacillus subtilis sin operon: an evolvable network motif. Genetics (2004) 1.24
Complete genome sequence of "Enterobacter lignolyticus" SCF1. Stand Genomic Sci (2011) 1.24
Memory in microbes: quantifying history-dependent behavior in a bacterium. PLoS One (2008) 1.22
Interruptions in gene expression drive highly expressed operons to the leading strand of DNA replication. Nucleic Acids Res (2005) 1.22
A dual receptor crosstalk model of G-protein-coupled signal transduction. PLoS Comput Biol (2008) 1.20
A mechanical explanation for cytoskeletal rings and helices in bacteria. Biophys J (2007) 1.20
Rational and evolutionary engineering approaches uncover a small set of genetic changes efficient for rapid xylose fermentation in Saccharomyces cerevisiae. PLoS One (2013) 1.18
Measurement and modeling of intrinsic transcription terminators. Nucleic Acids Res (2013) 1.18
How sulphate-reducing microorganisms cope with stress: lessons from systems biology. Nat Rev Microbiol (2011) 1.16
Identification of genes involved in the toxic response of Saccharomyces cerevisiae against iron and copper overload by parallel analysis of deletion mutants. Toxicol Sci (2007) 1.16
Cell-wide responses to low-oxygen exposure in Desulfovibrio vulgaris Hildenborough. J Bacteriol (2007) 1.14
RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes. BMC Genomics (2013) 1.13
Response of Desulfovibrio vulgaris to alkaline stress. J Bacteriol (2007) 1.11
A universal TagModule collection for parallel genetic analysis of microorganisms. Nucleic Acids Res (2010) 1.11
A latent variable model for chemogenomic profiling. Bioinformatics (2005) 1.10
Fifteen minutes of fim: control of type 1 pili expression in E. coli. OMICS (2002) 1.10
OpWise: operons aid the identification of differentially expressed genes in bacterial microarray experiments. BMC Bioinformatics (2006) 1.10
Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation. Appl Environ Microbiol (2009) 1.10
Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals. Nucleic Acids Res (2012) 1.08
Varying virulence: epigenetic control of expression noise and disease processes. Trends Biotechnol (2011) 1.07
FastBLAST: homology relationships for millions of proteins. PLoS One (2008) 1.06
RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics. Nucleic Acids Res (2012) 1.06
Engineering robust control of two-component system phosphotransfer using modular scaffolds. Proc Natl Acad Sci U S A (2012) 1.04
Global analysis of host response to induction of a latent bacteriophage. BMC Microbiol (2007) 1.03
Phosphatase localization in bacterial chemotaxis: divergent mechanisms, convergent principles. Phys Biol (2005) 1.02
Microbial community succession during lactate amendment and electron acceptor limitation reveals a predominance of metal-reducing Pelosinus spp. Appl Environ Microbiol (2012) 1.01
Snapshot of iron response in Shewanella oneidensis by gene network reconstruction. BMC Genomics (2009) 1.01
Sequestration-based bistability enables tuning of the switching boundaries and design of a latch. Mol Syst Biol (2012) 0.99
Transcript level and sequence determinants of protein abundance and noise in Escherichia coli. Nucleic Acids Res (2014) 0.99
Microfluidic fluorescence in situ hybridization and flow cytometry (μFlowFISH). Lab Chip (2011) 0.98
Simulating cell biology. Curr Biol (2006) 0.98
Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough. Environ Microbiol (2010) 0.97
Model discrimination using data collaboration. J Phys Chem A (2006) 0.97
Modularity of stress response evolution. Proc Natl Acad Sci U S A (2008) 0.97
A microbial modified prisoner's dilemma game: how frequency-dependent selection can lead to random phase variation. J Theor Biol (2005) 0.97