Published in Nat Methods on August 01, 2006
Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature (2012) 4.35
Evolvability and hierarchy in rewired bacterial gene networks. Nature (2008) 3.43
Adaptive prediction of environmental changes by microorganisms. Nature (2009) 3.19
Ciprofloxacin causes persister formation by inducing the TisB toxin in Escherichia coli. PLoS Biol (2010) 3.12
Translational control and target recognition by Escherichia coli small RNAs in vivo. Nucleic Acids Res (2007) 3.06
Diverse two-dimensional input functions control bacterial sugar genes. Mol Cell (2008) 2.60
Regulatory activity revealed by dynamic correlations in gene expression noise. Nat Genet (2008) 2.49
Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence. Proc Natl Acad Sci U S A (2010) 2.32
Nonoptimal microbial response to antibiotics underlies suppressive drug interactions. Cell (2009) 2.27
The incoherent feed-forward loop can generate non-monotonic input functions for genes. Mol Syst Biol (2008) 2.13
Quantitative estimation of activity and quality for collections of functional genetic elements. Nat Methods (2013) 2.03
Bacterial adaptation through loss of function. PLoS Genet (2013) 1.99
Discretely calibrated regulatory loops controlled by ppGpp partition gene induction across the 'feast to famine' gradient in Escherichia coli. Mol Microbiol (2010) 1.82
Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using engineered Escherichia coli. Proc Natl Acad Sci U S A (2011) 1.75
Resolution of gene regulatory conflicts caused by combinations of antibiotics. Mol Cell (2011) 1.65
HipBA-promoter structures reveal the basis of heritable multidrug tolerance. Nature (2015) 1.53
Condition-dependent cell volume and concentration of Escherichia coli to facilitate data conversion for systems biology modeling. PLoS One (2011) 1.50
Duplex-specific nuclease efficiently removes rRNA for prokaryotic RNA-seq. Nucleic Acids Res (2011) 1.48
ATP-Dependent Persister Formation in Escherichia coli. MBio (2017) 1.46
A Highly Conserved Bacterial D-Serine Uptake System Links Host Metabolism and Virulence. PLoS Pathog (2016) 1.45
The conserved nhaAR operon is drastically divergent between B2 and non-B2 Escherichia coli and is involved in extra-intestinal virulence. PLoS One (2014) 1.44
Inference of quantitative models of bacterial promoters from time-series reporter gene data. PLoS Comput Biol (2015) 1.44
Role of oxidative stress in persister tolerance. Antimicrob Agents Chemother (2012) 1.40
Engineering dynamic pathway regulation using stress-response promoters. Nat Biotechnol (2013) 1.27
Functioning of a metabolic flux sensor in Escherichia coli. Proc Natl Acad Sci U S A (2012) 1.26
Promoters maintain their relative activity levels under different growth conditions. Mol Syst Biol (2013) 1.26
Invariant distribution of promoter activities in Escherichia coli. PLoS Comput Biol (2009) 1.24
Bacteria-surface interactions. Soft Matter (2013) 1.22
Dissecting specific and global transcriptional regulation of bacterial gene expression. Mol Syst Biol (2013) 1.17
Single-cell dynamics reveals sustained growth during diauxic shifts. PLoS One (2013) 1.16
Phenotypic bistability in Escherichia coli's central carbon metabolism. Mol Syst Biol (2014) 1.15
Identification of ZapD as a cell division factor that promotes the assembly of FtsZ in Escherichia coli. J Bacteriol (2012) 1.14
A genome-wide analysis of promoter-mediated phenotypic noise in Escherichia coli. PLoS Genet (2012) 1.14
Repurposing endogenous type I CRISPR-Cas systems for programmable gene repression. Nucleic Acids Res (2014) 1.13
Biogenesis and structure of a type VI secretion membrane core complex. Nature (2015) 1.12
Antibiotic resistance acquired through a DNA damage-inducible response in Acinetobacter baumannii. J Bacteriol (2013) 1.10
An SOS-regulated type 2 toxin-antitoxin system. J Bacteriol (2009) 1.09
Negative auto-regulation increases the input dynamic-range of the arabinose system of Escherichia coli. BMC Syst Biol (2011) 1.07
Adaptive evolution of the lactose utilization network in experimentally evolved populations of Escherichia coli. PLoS Genet (2012) 1.07
Interspecific bacterial sensing through airborne signals modulates locomotion and drug resistance. Nat Commun (2013) 1.06
Metabolic suppression identifies new antibacterial inhibitors under nutrient limitation. Nat Chem Biol (2013) 1.04
HipA-triggered growth arrest and β-lactam tolerance in Escherichia coli are mediated by RelA-dependent ppGpp synthesis. J Bacteriol (2013) 1.03
Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria. BMC Syst Biol (2010) 1.02
A 'resource allocator' for transcription based on a highly fragmented T7 RNA polymerase. Mol Syst Biol (2014) 1.01
Bayesian network expansion identifies new ROS and biofilm regulators. PLoS One (2010) 1.00
Bacterial sugar utilization gives rise to distinct single-cell behaviours. Mol Microbiol (2014) 0.99
Promoter activity dynamics in the lag phase of Escherichia coli. BMC Syst Biol (2013) 0.99
Malate-mediated carbon catabolite repression in Bacillus subtilis involves the HPrK/CcpA pathway. J Bacteriol (2011) 0.93
Strategies for enhancing bioluminescent bacterial sensor performance by promoter region manipulation. Microb Biotechnol (2009) 0.92
The last generation of bacterial growth in limiting nutrient. BMC Syst Biol (2013) 0.91
Transcription by the numbers redux: experiments and calculations that surprise. Trends Cell Biol (2010) 0.91
Design of synthetic yeast promoters via tuning of nucleosome architecture. Nat Commun (2014) 0.91
Hierarchy of non-glucose sugars in Escherichia coli. BMC Syst Biol (2014) 0.91
Promoter swapping unveils the role of the Citrobacter rodentium CTS1 type VI secretion system in interbacterial competition. Appl Environ Microbiol (2012) 0.91
Single-cell time-lapse analysis of depletion of the universally conserved essential protein YgjD. BMC Microbiol (2011) 0.91
Correcting direct effects of ethanol on translation and transcription machinery confers ethanol tolerance in bacteria. Proc Natl Acad Sci U S A (2014) 0.90
The Highly Conserved Escherichia coli Transcription Factor YhaJ Regulates Aromatic Compound Degradation. Front Microbiol (2016) 0.90
Transcriptional occlusion caused by overlapping promoters. Proc Natl Acad Sci U S A (2014) 0.89
Bioreactor mixing efficiency modulates the activity of a prpoS::GFP reporter gene in E. coli. Microb Cell Fact (2009) 0.88
Quantifying selective pressures driving bacterial evolution using lineage analysis. Phys Rev X (2015) 0.88
Transcription of the Escherichia coli fatty acid synthesis operon fabHDG is directly activated by FadR and inhibited by ppGpp. J Bacteriol (2013) 0.88
Dynamic characterization of growth and gene expression using high-throughput automated flow cytometry. Nat Methods (2014) 0.87
Expression of a Yersinia pseudotuberculosis Type VI Secretion System Is Responsive to Envelope Stresses through the OmpR Transcriptional Activator. PLoS One (2013) 0.87
Trade-offs in engineering sugar utilization pathways for titratable control. ACS Synth Biol (2014) 0.86
H-NS silences gfp, the green fluorescent protein gene: gfpTCD is a genetically Remastered gfp gene with reduced susceptibility to H-NS-mediated transcription silencing and with enhanced translation. J Bacteriol (2010) 0.86
Negative feedback and transcriptional overshooting in a regulatory network for horizontal gene transfer. PLoS Genet (2014) 0.85
Discriminating tastes: physiological contributions of the Hfq-binding small RNA Spot 42 to catabolite repression. RNA Biol (2011) 0.85
Metabolic engineering of strains: from industrial-scale to lab-scale chemical production. J Ind Microbiol Biotechnol (2014) 0.85
Live cell imaging and systems biology. Wiley Interdiscip Rev Syst Biol Med (2010) 0.85
Expression noise facilitates the evolution of gene regulation. Elife (2015) 0.85
Stochastic activation of a DNA damage response causes cell-to-cell mutation rate variation. Science (2016) 0.84
Perturbation of iron homeostasis promotes the evolution of antibiotic resistance. Mol Biol Evol (2014) 0.84
Comparison and calibration of different reporters for quantitative analysis of gene expression. Biophys J (2011) 0.84
The CRISPR RNA-guided surveillance complex in Escherichia coli accommodates extended RNA spacers. Nucleic Acids Res (2016) 0.84
Systematic discovery of drug interaction mechanisms. Mol Syst Biol (2015) 0.84
An active site aromatic triad in Escherichia coli DNA Pol IV coordinates cell survival and mutagenesis in different DNA damaging agents. PLoS One (2011) 0.84
Tight regulation of the intS gene of the KplE1 prophage: a new paradigm for integrase gene regulation. PLoS Genet (2010) 0.83
Evidence that the supE44 mutation of Escherichia coli is an amber suppressor allele of glnX and that it also suppresses ochre and opal nonsense mutations. J Bacteriol (2010) 0.83
Linear superposition and prediction of bacterial promoter activity dynamics in complex conditions. PLoS Comput Biol (2014) 0.83
Vectors for ligation-independent construction of lacZ gene fusions and cloning of PCR products using a nicking endonuclease. Plasmid (2011) 0.83
Repression of flagellar genes in exponential phase by CsgD and CpxR, two crucial modulators of Escherichia coli biofilm formation. J Bacteriol (2013) 0.83
The sensory histidine kinases TorS and EvgS tend to form clusters in Escherichia coli cells. PLoS One (2013) 0.83
Systems-level response to point mutations in a core metabolic enzyme modulates genotype-phenotype relationship. Cell Rep (2015) 0.83
Glucose becomes one of the worst carbon sources for E.coli on poor nitrogen sources due to suboptimal levels of cAMP. Sci Rep (2016) 0.83
Negative regulation of bacterial quorum sensing tunes public goods cooperation. ISME J (2013) 0.83
RNA Futile Cycling in Model Persisters Derived from MazF Accumulation. MBio (2015) 0.83
The expression of stlA in Photorhabdus luminescens is controlled by nutrient limitation. PLoS One (2013) 0.83
Resveratrol induced inhibition of Escherichia coli proceeds via membrane oxidation and independent of diffusible reactive oxygen species generation. Redox Biol (2014) 0.82
Environmental dependence of stationary-phase metabolism in Bacillus subtilis and Escherichia coli. Appl Environ Microbiol (2014) 0.82
Transcriptional responses of uropathogenic Escherichia coli to increased environmental osmolality caused by salt or urea. Infect Immun (2012) 0.82
Metal binding properties of Escherichia coli YjiA, a member of the metal homeostasis-associated COG0523 family of GTPases. Biochemistry (2013) 0.82
The weak shall inherit: bacteriocin-mediated interactions in bacterial populations. PLoS One (2013) 0.81
Engineering scalable biological systems. Bioeng Bugs (2011) 0.81
Noise genetics: inferring protein function by correlating phenotype with protein levels and localization in individual human cells. PLoS Genet (2014) 0.81
Gene regulatory network inference using fused LASSO on multiple data sets. Sci Rep (2016) 0.81
Monitoring of dynamic microbiological processes using real-time flow cytometry. PLoS One (2013) 0.81
YfgM is an ancillary subunit of the SecYEG translocon in Escherichia coli. J Biol Chem (2014) 0.81
Metagenomic scaffolds enable combinatorial lignin transformation. Proc Natl Acad Sci U S A (2014) 0.81
ArcB1, a homolog of Escherichia coli ArcB, regulates dimethyl sulfoxide reduction in Shewanella oneidensis MR-1. J Bacteriol (2010) 0.80
Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet (2002) 19.57
Gene regulation at the single-cell level. Science (2005) 11.52
Dynamics of the p53-Mdm2 feedback loop in individual cells. Nat Genet (2004) 8.30
Superfamilies of evolved and designed networks. Science (2004) 8.12
A catalog of reference genomes from the human microbiome. Science (2010) 8.10
Functional atlas of the integrin adhesome. Nat Cell Biol (2007) 6.89
Negative autoregulation speeds the response times of transcription networks. J Mol Biol (2002) 6.32
Variability and memory of protein levels in human cells. Nature (2006) 6.15
Optimality and evolutionary tuning of the expression level of a protein. Nature (2005) 5.94
Slug and Sox9 cooperatively determine the mammary stem cell state. Cell (2012) 4.77
Oscillations and variability in the p53 system. Mol Syst Biol (2006) 4.59
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol (2008) 4.55
Spontaneous evolution of modularity and network motifs. Proc Natl Acad Sci U S A (2005) 4.49
Communication in bacteria: an ecological and evolutionary perspective. Nat Rev Microbiol (2006) 4.44
Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis. Science (2012) 4.41
A module of negative feedback regulators defines growth factor signaling. Nat Genet (2007) 4.35
Just-in-time transcription program in metabolic pathways. Nat Genet (2004) 4.30
Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics. Proc Natl Acad Sci U S A (2002) 4.20
The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent '+4' cell markers. EMBO J (2012) 3.70
Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. Proc Natl Acad Sci U S A (2004) 3.60
The incoherent feedforward loop can provide fold-change detection in gene regulation. Mol Cell (2009) 3.38
Proteome half-life dynamics in living human cells. Science (2011) 3.34
Programming gene expression with combinatorial promoters. Mol Syst Biol (2007) 3.29
A polymicrobial perspective of pulmonary infections exposes an enigmatic pathogen in cystic fibrosis patients. Proc Natl Acad Sci U S A (2008) 3.28
Transcriptional modulation of bacterial gene expression by subinhibitory concentrations of antibiotics. Proc Natl Acad Sci U S A (2002) 3.25
Plasticity of the cis-regulatory input function of a gene. PLoS Biol (2006) 3.22
Modulation of Pseudomonas aeruginosa gene expression by host microflora through interspecies communication. Mol Microbiol (2003) 3.09
Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins. Nat Methods (2006) 2.94
A conserved role for a GATA transcription factor in regulating epithelial innate immune responses. Proc Natl Acad Sci U S A (2006) 2.91
Diverse two-dimensional input functions control bacterial sugar genes. Mol Cell (2008) 2.60
The genetic code is nearly optimal for allowing additional information within protein-coding sequences. Genome Res (2007) 2.56
The moderately efficient enzyme: evolutionary and physicochemical trends shaping enzyme parameters. Biochemistry (2011) 2.42
Dynamics and variability of ERK2 response to EGF in individual living cells. Mol Cell (2009) 2.42
Using a quantitative blueprint to reprogram the dynamics of the flagella gene network. Cell (2004) 2.41
Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism. Science (2012) 2.38
Input output robustness in simple bacterial signaling systems. Proc Natl Acad Sci U S A (2007) 2.17
Cost of unneeded proteins in E. coli is reduced after several generations in exponential growth. Mol Cell (2010) 2.17
Response delays and the structure of transcription networks. J Mol Biol (2003) 2.15
The incoherent feed-forward loop can generate non-monotonic input functions for genes. Mol Syst Biol (2008) 2.13
Expander: from expression microarrays to networks and functions. Nat Protoc (2010) 2.12
Discerning the complexity of community interactions using a Drosophila model of polymicrobial infections. PLoS Pathog (2008) 2.09
Systems biology standards--the community speaks. Nat Biotechnol (2007) 2.09
Central carbon metabolism as a minimal biochemical walk between precursors for biomass and energy. Mol Cell (2010) 2.08
A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli. Mol Syst Biol (2005) 1.97
Genetic and phenotypic diversity in breast tumor metastases. Cancer Res (2014) 1.96
Environmental variability and modularity of bacterial metabolic networks. BMC Evol Biol (2007) 1.88
Genomic profiling of iron-responsive genes in Salmonella enterica serovar typhimurium by high-throughput screening of a random promoter library. J Bacteriol (2003) 1.88
Precise temporal modulation in the response of the SOS DNA repair network in individual bacteria. PLoS Biol (2005) 1.84
Varying environments can speed up evolution. Proc Natl Acad Sci U S A (2007) 1.81
The mirror game as a paradigm for studying the dynamics of two people improvising motion together. Proc Natl Acad Sci U S A (2011) 1.76
pfs-dependent regulation of autoinducer 2 production in Salmonella enterica serovar Typhimurium. J Bacteriol (2002) 1.76
Glycolytic strategy as a tradeoff between energy yield and protein cost. Proc Natl Acad Sci U S A (2013) 1.75
Protein dynamics in drug combinations: a linear superposition of individual-drug responses. Cell (2010) 1.75
Robust control of nitrogen assimilation by a bifunctional enzyme in E. coli. Mol Cell (2011) 1.70
Coarse-graining and self-dissimilarity of complex networks. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 1.67
Fold-change detection and scalar symmetry of sensory input fields. Proc Natl Acad Sci U S A (2010) 1.67
Individuality in bacteria. Annu Rev Genet (2008) 1.65
Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model. Bioinformatics (2010) 1.65
Annotation and merging of SBML models with semanticSBML. Bioinformatics (2009) 1.62
Search for computational modules in the C. elegans brain. BMC Biol (2004) 1.61
Culture enriched molecular profiling of the cystic fibrosis airway microbiome. PLoS One (2011) 1.61
Environmental selection of the feed-forward loop circuit in gene-regulation networks. Phys Biol (2005) 1.59
Environmental regulation of Pseudomonas aeruginosa PAO1 Las and Rhl quorum-sensing systems. J Bacteriol (2007) 1.58
Mode of regulation and the insulation of bacterial gene expression. Mol Cell (2012) 1.53
Cystic fibrosis: a polymicrobial infectious disease. Future Microbiol (2006) 1.52
Phenotypic heterogeneity of Pseudomonas aeruginosa populations in a cystic fibrosis patient. PLoS One (2013) 1.49
Reconstruction of cell lineage trees in mice. PLoS One (2008) 1.46
Swarm-cell differentiation in Salmonella enterica serovar typhimurium results in elevated resistance to multiple antibiotics. J Bacteriol (2003) 1.45
Accurate prediction of gene feedback circuit behavior from component properties. Mol Syst Biol (2007) 1.45
The immune-body cytokine network defines a social architecture of cell interactions. Biol Direct (2006) 1.41
Mutation rules and the evolution of sparseness and modularity in biological systems. PLoS One (2013) 1.40
The Streptococcus milleri group--an unrecognized cause of disease in cystic fibrosis: a case series and literature review. Pediatr Pulmonol (2008) 1.39
A fluctuation method to quantify in vivo fluorescence data. Biophys J (2006) 1.39
Coding limits on the number of transcription factors. BMC Genomics (2006) 1.38
Multiparametric analysis of focal adhesion formation by RNAi-mediated gene knockdown. J Cell Biol (2009) 1.36
Generation of a fluorescently labeled endogenous protein library in living human cells. Nat Protoc (2007) 1.36
Metabolic differentiation in actively swarming Salmonella. Mol Microbiol (2004) 1.35
A critical role for the Wnt effector Tcf4 in adult intestinal homeostatic self-renewal. Mol Cell Biol (2012) 1.34
Cell lineage analysis of a mouse tumor. Cancer Res (2008) 1.29
Defined order of evolutionary adaptations: experimental evidence. Evolution (2008) 1.26
Promoters maintain their relative activity levels under different growth conditions. Mol Syst Biol (2013) 1.26
Cost-benefit theory and optimal design of gene regulation functions. Phys Biol (2007) 1.25
The utility of paradoxical components in biological circuits. Mol Cell (2013) 1.25
Invariant distribution of promoter activities in Escherichia coli. PLoS Comput Biol (2009) 1.24
Transcriptional modulation induced by ionizing radiation: p53 remains a central player. Mol Oncol (2011) 1.23
The relevance of the polymicrobial nature of airway infection in the acute and chronic management of patients with cystic fibrosis. Curr Opin Investig Drugs (2009) 1.19
Fourier analysis and systems identification of the p53 feedback loop. Proc Natl Acad Sci U S A (2010) 1.19