Published in Curr Opin Microbiol on April 01, 2003
Cell-signalling dynamics in time and space. Nat Rev Mol Cell Biol (2006) 7.25
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Stochastic gene expression in fluctuating environments. Genetics (2004) 4.23
An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs. Nucleic Acids Res (2004) 3.44
Uncovering intrinsic modular organization of spontaneous brain activity in humans. PLoS One (2009) 3.43
Dynamic properties of network motifs contribute to biological network organization. PLoS Biol (2005) 2.58
Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network. BMC Bioinformatics (2004) 2.41
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Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach. BMC Bioinformatics (2004) 2.14
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Transcriptional dynamics of the embryonic stem cell switch. PLoS Comput Biol (2006) 2.06
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Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network. Genome Res (2008) 1.71
Quantifying modularity in the evolution of biomolecular systems. Genome Res (2004) 1.67
Deciding fate in adverse times: sporulation and competence in Bacillus subtilis. Proc Natl Acad Sci U S A (2009) 1.65
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Dynamic modelling of oestrogen signalling and cell fate in breast cancer cells. Nat Rev Cancer (2011) 1.51
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Design and implementation of three incoherent feed-forward motif based biological concentration sensors. Syst Synth Biol (2007) 1.37
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Modelling the molecular mechanisms of synaptic plasticity using systems biology approaches. Nat Rev Neurosci (2010) 1.32
Fish and chips: functional genomics of social plasticity in an African cichlid fish. J Exp Biol (2008) 1.32
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Regulatory circuit design and evolution using phage lambda. Genes Dev (2004) 1.02
A primer on regression methods for decoding cis-regulatory logic. PLoS Comput Biol (2009) 1.00
Specialized or flexible feed-forward loop motifs: a question of topology. BMC Syst Biol (2009) 0.95
Large-scale analysis of network bistability for human cancers. PLoS Comput Biol (2010) 0.95
Coordination logic of the sensing machinery in the transcriptional regulatory network of Escherichia coli. Nucleic Acids Res (2007) 0.93
Gene co-expression modules as clinically relevant hallmarks of breast cancer diversity. PLoS One (2014) 0.90
Integration of the Gene Ontology into an object-oriented architecture. BMC Bioinformatics (2005) 0.89
Evolutionary conservation and over-representation of functionally enriched network patterns in the yeast regulatory network. BMC Syst Biol (2007) 0.88
MicroRNA-mediated positive feedback loop and optimized bistable switch in a cancer network Involving miR-17-92. PLoS One (2011) 0.88
Developmental robustness by obligate interaction of class B floral homeotic genes and proteins. PLoS Comput Biol (2009) 0.87
Boosting functionality of synthetic DNA circuits with tailored deactivation. Nat Commun (2016) 0.87
Dynamic changes in subgraph preference profiles of crucial transcription factors. PLoS Comput Biol (2006) 0.87
Network motifs provide signatures that characterize metabolism. Mol Biosyst (2013) 0.85
Simple molecular networks that respond optimally to time-periodic stimulation. BMC Syst Biol (2009) 0.84
LsrR quorum sensing "switch" is revealed by a bottom-up approach. PLoS Comput Biol (2011) 0.83
Noise propagation in gene regulation networks involving interlinked positive and negative feedback loops. PLoS One (2012) 0.82
Control of MarRAB Operon in Escherichia coli via Autoactivation and Autorepression. Biophys J (2015) 0.81
An evolutionarily conserved RNase-based mechanism for repression of transcriptional positive autoregulation. Mol Microbiol (2014) 0.80
Understanding system dynamics of an adaptive enzyme network from globally profiled kinetic parameters. BMC Syst Biol (2014) 0.80
Microscopic agents programmed by DNA circuits. Nat Nanotechnol (2017) 0.78
Evidence for calcium-mediated perception of plant symbiotic signals in aequorin-expressing Mesorhizobium loti. BMC Microbiol (2009) 0.78
Evolution, ecology and the engineered organism: lessons for synthetic biology. Genome Biol (2009) 0.77
Effects of rate-limiting steps in transcription initiation on genetic filter motifs. PLoS One (2013) 0.77
Sparse cliques trump scale-free networks in coordination and competition. Sci Rep (2016) 0.77
A top-down approach to mechanistic biological modeling: application to the single-chain antibody folding pathway. Biophys J (2008) 0.76
A DNA network as an information processing system. Int J Mol Sci (2012) 0.76
Systems level modeling of the cell cycle using budding yeast. Cancer Inform (2007) 0.76
RMOD: a tool for regulatory motif detection in signaling network. PLoS One (2013) 0.75
Evolution of DNA double-strand break repair by gene conversion: coevolution between a phage and a restriction-modification system. Genetics (2007) 0.75
Positive Autoregulation of an Acyl-Homoserine Lactone Quorum-Sensing Circuit Synchronizes the Population Response. MBio (2017) 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
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
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
An allosteric model for transmembrane signaling in bacterial chemotaxis. J Mol Biol (2004) 1.15
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
Fifteen minutes of fim: control of type 1 pili expression in E. coli. OMICS (2002) 1.10
A latent variable model for chemogenomic profiling. Bioinformatics (2005) 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
Transcript level and sequence determinants of protein abundance and noise in Escherichia coli. Nucleic Acids Res (2014) 0.99
Sequestration-based bistability enables tuning of the switching boundaries and design of a latch. Mol Syst Biol (2012) 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
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
Evidence-based annotation of transcripts and proteins in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. J Bacteriol (2011) 0.96
Toward rational design of bacterial genomes. Curr Opin Microbiol (2011) 0.96