Published in Nature on November 14, 2002
Control of stochasticity in eukaryotic gene expression. Science (2004) 12.85
Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science (2010) 11.37
Cellular decision making and biological noise: from microbes to mammals. Cell (2011) 4.44
Detailed map of a cis-regulatory input function. Proc Natl Acad Sci U S A (2003) 4.30
Growth rate-dependent global effects on gene expression in bacteria. Cell (2009) 3.57
Predicting essential components of signal transduction networks: a dynamic model of guard cell abscisic acid signaling. PLoS Biol (2006) 3.53
Bistability in the Bacillus subtilis K-state (competence) system requires a positive feedback loop. Mol Microbiol (2005) 3.37
A stress-sensitive reporter predicts longevity in isogenic populations of Caenorhabditis elegans. Nat Genet (2005) 3.29
Tissue architecture: the ultimate regulator of breast epithelial function. Curr Opin Cell Biol (2003) 2.92
Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations. Proc Natl Acad Sci U S A (2005) 2.71
Delay-induced stochastic oscillations in gene regulation. Proc Natl Acad Sci U S A (2005) 2.47
Negative autoregulation linearizes the dose-response and suppresses the heterogeneity of gene expression. Proc Natl Acad Sci U S A (2009) 2.45
Combinatorial promoter design for engineering noisy gene expression. Proc Natl Acad Sci U S A (2007) 2.40
Emergence of large-scale cell morphology and movement from local actin filament growth dynamics. PLoS Biol (2007) 2.30
Noisy signal amplification in ultrasensitive signal transduction. Proc Natl Acad Sci U S A (2004) 2.29
Strategies for cellular decision-making. Mol Syst Biol (2009) 2.29
Microfluidic high-throughput encapsulation and hydrodynamic self-sorting of single cells. Proc Natl Acad Sci U S A (2008) 2.22
Boolean network models of cellular regulation: prospects and limitations. J R Soc Interface (2008) 2.13
Distributed biological computation with multicellular engineered networks. Nature (2010) 2.13
Heritable stochastic switching revealed by single-cell genealogy. PLoS Biol (2007) 2.11
Frequency domain analysis of noise in autoregulated gene circuits. Proc Natl Acad Sci U S A (2003) 2.10
Transcriptional dynamics of the embryonic stem cell switch. PLoS Comput Biol (2006) 2.06
Determination of cell fate selection during phage lambda infection. Proc Natl Acad Sci U S A (2008) 2.05
Modeling network dynamics: the lac operon, a case study. J Cell Biol (2003) 2.03
Noise propagation and signaling sensitivity in biological networks: a role for positive feedback. PLoS Comput Biol (2007) 1.94
Diffusion of transcription factors can drastically enhance the noise in gene expression. Biophys J (2006) 1.92
Regulated noise in the epigenetic landscape of development and disease. Cell (2012) 1.79
Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol (2009) 1.73
Predicting stochastic gene expression dynamics in single cells. Proc Natl Acad Sci U S A (2006) 1.70
Dynamics of single-cell gene expression. Mol Syst Biol (2006) 1.69
Fold-change detection and scalar symmetry of sensory input fields. Proc Natl Acad Sci U S A (2010) 1.67
Optimal noise filtering in the chemotactic response of Escherichia coli. PLoS Comput Biol (2006) 1.61
The sonic hedgehog signaling system as a bistable genetic switch. Biophys J (2004) 1.61
Topology of biological networks and reliability of information processing. Proc Natl Acad Sci U S A (2005) 1.54
Tuning and controlling gene expression noise in synthetic gene networks. Nucleic Acids Res (2010) 1.52
Transcriptional infidelity promotes heritable phenotypic change in a bistable gene network. PLoS Biol (2009) 1.48
Cellular asymmetry and individuality in directional sensing. Proc Natl Acad Sci U S A (2006) 1.47
Precise developmental gene expression arises from globally stochastic transcriptional activity. Cell (2013) 1.47
An information-theoretic characterization of the optimal gradient sensing response of cells. PLoS Comput Biol (2007) 1.45
Emergence of complex dynamics in a simple model of signaling networks. Proc Natl Acad Sci U S A (2004) 1.45
Signaling through receptors and scaffolds: independent interactions reduce combinatorial complexity. Biophys J (2005) 1.44
Noise in gene expression is coupled to growth rate. Genome Res (2015) 1.44
Recurrent design patterns in the feedback regulation of the mammalian signalling network. Mol Syst Biol (2008) 1.41
Chromosome-specific and noisy IFNB1 transcription in individual virus-infected human primary dendritic cells. Nucleic Acids Res (2007) 1.40
Signaling in small subcellular volumes. I. Stochastic and diffusion effects on individual pathways. Biophys J (2004) 1.36
Bridging the gap between stochastic and deterministic regimes in the kinetic simulations of the biochemical reaction networks. Biophys J (2004) 1.36
Biology by design: reduction and synthesis of cellular components and behaviour. J R Soc Interface (2007) 1.33
Biochemical simulations: stochastic, approximate stochastic and hybrid approaches. Brief Bioinform (2009) 1.31
Stochastic regulation in early immune response. Biophys J (2005) 1.31
Positive selection for elevated gene expression noise in yeast. Mol Syst Biol (2009) 1.30
Determinants of beat-to-beat variability of repolarization duration in the canine ventricular myocyte: a computational analysis. PLoS Comput Biol (2013) 1.30
Network inference, analysis, and modeling in systems biology. Plant Cell (2007) 1.27
Interdependence of behavioural variability and response to small stimuli in bacteria. Nature (2010) 1.26
A computational systems biology software platform for multiscale modeling and simulation: integrating whole-body physiology, disease biology, and molecular reaction networks. Front Physiol (2011) 1.26
Trading the micro-world of combinatorial complexity for the macro-world of protein interaction domains. Biosystems (2005) 1.26
Epigenetic chromatin silencing: bistability and front propagation. Phys Biol (2007) 1.25
Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent. BMC Syst Biol (2010) 1.24
The Bacillus subtilis sin operon: an evolvable network motif. Genetics (2004) 1.24
Solving the chemical master equation using sliding windows. BMC Syst Biol (2010) 1.24
Ras nanoclusters: combining digital and analog signaling. Cell Cycle (2007) 1.21
Gene expression noise in spatial patterning: hunchback promoter structure affects noise amplitude and distribution in Drosophila segmentation. PLoS Comput Biol (2011) 1.21
Bet-hedging during bacterial diauxic shift. Proc Natl Acad Sci U S A (2014) 1.21
Classical versus stochastic kinetics modeling of biochemical reaction systems. Biophys J (2007) 1.18
The stochastic dynamics of filopodial growth. Biophys J (2008) 1.17
The slow-scale linear noise approximation: an accurate, reduced stochastic description of biochemical networks under timescale separation conditions. BMC Syst Biol (2012) 1.16
A genome-wide analysis of promoter-mediated phenotypic noise in Escherichia coli. PLoS Genet (2012) 1.14
Modeling of the role of a Bax-activation switch in the mitochondrial apoptosis decision. Biophys J (2007) 1.14
Integration of metabolomic and proteomic phenotypes: analysis of data covariance dissects starch and RFO metabolism from low and high temperature compensation response in Arabidopsis thaliana. Mol Cell Proteomics (2008) 1.13
Noise reduction by diffusional dissipation in a minimal quorum sensing motif. PLoS Comput Biol (2008) 1.12
Computational approaches for modeling regulatory cellular networks. Trends Cell Biol (2004) 1.11
Dynamics of a minimal model of interlocked positive and negative feedback loops of transcriptional regulation by cAMP-response element binding proteins. Biophys J (2007) 1.10
Spatial stochastic dynamics enable robust cell polarization. PLoS Comput Biol (2013) 1.08
Cytokinesis and the contractile ring in fission yeast: towards a systems-level understanding. Trends Microbiol (2009) 1.08
Inferring Drosophila gap gene regulatory network: a parameter sensitivity and perturbation analysis. BMC Syst Biol (2009) 1.08
Dose response relationship in anti-stress gene regulatory networks. PLoS Comput Biol (2006) 1.07
Computational models of the Notch network elucidate mechanisms of context-dependent signaling. PLoS Comput Biol (2009) 1.07
Phenotypic variability of growing cellular populations. Proc Natl Acad Sci U S A (2007) 1.07
Toward a complete in silico, multi-layered embryonic stem cell regulatory network. Wiley Interdiscip Rev Syst Biol Med (2010) 1.06
Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks. PLoS One (2011) 1.05
Exact results for the evolution of stochastic switching in variable asymmetric environments. Genetics (2010) 1.05
On the attenuation and amplification of molecular noise in genetic regulatory networks. BMC Bioinformatics (2006) 1.04
Translational repression contributes greater noise to gene expression than transcriptional repression. Biophys J (2009) 1.03
DNA looping in prokaryotes: experimental and theoretical approaches. J Bacteriol (2013) 1.03
A mathematical tool for exploring the dynamics of biological networks. Proc Natl Acad Sci U S A (2007) 1.02
Quantifying the contribution of chromatin dynamics to stochastic gene expression reveals long, locus-dependent periods between transcriptional bursts. BMC Biol (2013) 1.02
Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria. BMC Syst Biol (2010) 1.02
Stochastic processes influence stationary-phase decisions in Bacillus subtilis. J Bacteriol (2004) 1.02
Stochastic binding of Ca2+ ions in the dyadic cleft; continuous versus random walk description of diffusion. Biophys J (2008) 1.01
Listeria monocytogenes actin-based motility varies depending on subcellular location: a kinematic probe for cytoarchitecture. Mol Biol Cell (2004) 0.99
Transcript level and sequence determinants of protein abundance and noise in Escherichia coli. Nucleic Acids Res (2014) 0.99
Noise-limited frequency signal transmission in gene circuits. Biophys J (2007) 0.99
Neuronal homeostasis: time for a change? J Physiol (2011) 0.99
Stochastic simulations of minimal self-reproducing cellular systems. Philos Trans R Soc Lond B Biol Sci (2007) 0.99
A critical quantity for noise attenuation in feedback systems. PLoS Comput Biol (2010) 0.98
A closure scheme for chemical master equations. Proc Natl Acad Sci U S A (2013) 0.98
Deterministic and stochastic models of genetic regulatory networks. Methods Enzymol (2009) 0.98
Modeling stochasticity and robustness in gene regulatory networks. Bioinformatics (2009) 0.97
Dosage compensation on the active X chromosome minimizes transcriptional noise of X-linked genes in mammals. Genome Biol (2009) 0.97
Measuring retroactivity from noise in gene regulatory networks. Biophys J (2011) 0.97
Synthetic control of a fitness tradeoff in yeast nitrogen metabolism. J Biol Eng (2009) 0.96
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
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
Subtype and pathway specific responses to anticancer compounds in breast cancer. Proc Natl Acad Sci U S A (2011) 4.55
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
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 mechanical explanation for cytoskeletal rings and helices in bacteria. Biophys J (2007) 1.20
A dual receptor crosstalk model of G-protein-coupled signal transduction. PLoS Comput Biol (2008) 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
A universal TagModule collection for parallel genetic analysis of microorganisms. Nucleic Acids Res (2010) 1.11
Response of Desulfovibrio vulgaris to alkaline stress. J Bacteriol (2007) 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
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
Modularity of stress response evolution. Proc Natl Acad Sci U S A (2008) 0.97