Published in PLoS Biol on January 01, 2007
Wisdom of crowds for robust gene network inference. Nat Methods (2012) 6.91
Revealing strengths and weaknesses of methods for gene network inference. Proc Natl Acad Sci U S A (2010) 5.41
Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol (2008) 5.36
A validated regulatory network for Th17 cell specification. Cell (2012) 4.82
How antibiotics kill bacteria: from targets to networks. Nat Rev Microbiol (2010) 4.65
Mistranslation of membrane proteins and two-component system activation trigger antibiotic-mediated cell death. Cell (2008) 4.47
CellNet: network biology applied to stem cell engineering. Cell (2014) 4.10
Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coli. Mol Syst Biol (2007) 3.98
Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. Nucleic Acids Res (2007) 3.80
Inferring regulatory networks from expression data using tree-based methods. PLoS One (2010) 3.37
Multidimensional annotation of the Escherichia coli K-12 genome. Nucleic Acids Res (2007) 3.34
Network link prediction by global silencing of indirect correlations. Nat Biotechnol (2013) 3.27
minet: A R/Bioconductor package for inferring large transcriptional networks using mutual information. BMC Bioinformatics (2008) 3.15
Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol (2009) 3.03
Advantages and limitations of current network inference methods. Nat Rev Microbiol (2010) 2.97
The transcription unit architecture of the Escherichia coli genome. Nat Biotechnol (2009) 2.85
Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. Nat Biotechnol (2009) 2.79
Hydroxyurea induces hydroxyl radical-mediated cell death in Escherichia coli. Mol Cell (2009) 2.74
TonB-dependent transporters: regulation, structure, and function. Annu Rev Microbiol (2010) 2.72
Information-theoretic inference of large transcriptional regulatory networks. EURASIP J Bioinform Syst Biol (2007) 2.65
Transcriptional regulatory circuits: predicting numbers from alphabets. Science (2009) 2.61
Cross-species regulatory network analysis identifies a synergistic interaction between FOXM1 and CENPF that drives prostate cancer malignancy. Cancer Cell (2014) 2.60
Comprehensive literature review and statistical considerations for microarray meta-analysis. Nucleic Acids Res (2012) 2.54
Software for systems biology: from tools to integrated platforms. Nat Rev Genet (2011) 2.42
Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chem Rev (2007) 2.40
Systems analysis of EGF receptor signaling dynamics with microwestern arrays. Nat Methods (2010) 2.20
Network deconvolution as a general method to distinguish direct dependencies in networks. Nat Biotechnol (2013) 2.05
Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli. Proc Natl Acad Sci U S A (2008) 1.99
The transcriptional landscape of hematopoietic stem cell ontogeny. Cell Stem Cell (2012) 1.96
microRNA regulatory network inference identifies miR-34a as a novel regulator of TGF-β signaling in glioblastoma. Cancer Discov (2012) 1.94
A multiply redundant genetic switch 'locks in' the transcriptional signature of regulatory T cells. Nat Immunol (2012) 1.93
Heterogeneity of tumor-induced gene expression changes in the human metabolic network. Nat Biotechnol (2013) 1.91
DREAM4: Combining genetic and dynamic information to identify biological networks and dynamical models. PLoS One (2010) 1.89
Integrating multiple evidence sources to predict transcription factor binding in the human genome. Genome Res (2010) 1.84
TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach. BMC Bioinformatics (2010) 1.82
TIGRESS: Trustful Inference of Gene REgulation using Stability Selection. BMC Syst Biol (2012) 1.77
Evaluating the consistency of gene sets used in the analysis of bacterial gene expression data. BMC Bioinformatics (2012) 1.72
Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling. PLoS Comput Biol (2009) 1.69
The impact of multifunctional genes on "guilt by association" analysis. PLoS One (2011) 1.69
Modeling gene expression regulatory networks with the sparse vector autoregressive model. BMC Syst Biol (2007) 1.69
Gene network inference via structural equation modeling in genetical genomics experiments. Genetics (2008) 1.68
Tracking, tuning, and terminating microbial physiology using synthetic riboregulators. Proc Natl Acad Sci U S A (2010) 1.66
A general co-expression network-based approach to gene expression analysis: comparison and applications. BMC Syst Biol (2010) 1.63
Prevalence of transcription promoters within archaeal operons and coding sequences. Mol Syst Biol (2009) 1.62
Coordinated regulation of virulence during systemic infection of Salmonella enterica serovar Typhimurium. PLoS Pathog (2009) 1.58
Orthologous transcription factors in bacteria have different functions and regulate different genes. PLoS Comput Biol (2007) 1.58
Inferring the conservative causal core of gene regulatory networks. BMC Syst Biol (2010) 1.53
OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains. BMC Syst Biol (2010) 1.47
Comparison of co-expression measures: mutual information, correlation, and model based indices. BMC Bioinformatics (2012) 1.47
From knockouts to networks: establishing direct cause-effect relationships through graph analysis. PLoS One (2010) 1.47
Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs. Mol Syst Biol (2011) 1.45
Single-Cell Transcriptomics Reveals that Differentiation and Spatial Signatures Shape Epidermal and Hair Follicle Heterogeneity. Cell Syst (2016) 1.44
Inferring protein modulation from gene expression data using conditional mutual information. PLoS One (2014) 1.44
A synthetic gene network for tuning protein degradation in Saccharomyces cerevisiae. Mol Syst Biol (2007) 1.42
Suppressed expression of T-box transcription factors is involved in senescence in chronic obstructive pulmonary disease. PLoS Comput Biol (2012) 1.41
A comparative evaluation of data-merging and meta-analysis methods for reconstructing gene-gene interactions. BMC Bioinformatics (2016) 1.41
Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks. BMC Syst Biol (2009) 1.40
A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli. PLoS Comput Biol (2008) 1.40
Inferring interaction type in gene regulatory networks using co-expression data. Algorithms Mol Biol (2015) 1.39
DREAM3: network inference using dynamic context likelihood of relatedness and the inferelator. PLoS One (2010) 1.39
Reverse engineering and identification in systems biology: strategies, perspectives and challenges. J R Soc Interface (2013) 1.38
Bagging statistical network inference from large-scale gene expression data. PLoS One (2012) 1.38
Network inference algorithms elucidate Nrf2 regulation of mouse lung oxidative stress. PLoS Comput Biol (2008) 1.38
A gene expression signature of emphysema-related lung destruction and its reversal by the tripeptide GHK. Genome Med (2012) 1.38
DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli. Genome Biol (2009) 1.36
Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites. Elife (2015) 1.36
An Interspecies Regulatory Network Inferred from Simultaneous RNA-seq of Candida albicans Invading Innate Immune Cells. Front Microbiol (2012) 1.35
Transcriptional gene network inference from a massive dataset elucidates transcriptome organization and gene function. Nucleic Acids Res (2011) 1.31
Lag phase is a distinct growth phase that prepares bacteria for exponential growth and involves transient metal accumulation. J Bacteriol (2011) 1.31
Quantitative and logic modelling of molecular and gene networks. Nat Rev Genet (2015) 1.30
Statistical inference and reverse engineering of gene regulatory networks from observational expression data. Front Genet (2012) 1.30
Gene regulatory network reconstruction using conditional mutual information. EURASIP J Bioinform Syst Biol (2008) 1.30
Beyond differential expression: the quest for causal mutations and effector molecules. BMC Genomics (2012) 1.29
Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. BMC Genomics (2011) 1.26
Mechanisms and evolution of control logic in prokaryotic transcriptional regulation. Microbiol Mol Biol Rev (2009) 1.25
Expression, circulation, and excretion profile of microRNA-21, -155, and -18a following acute kidney injury. Toxicol Sci (2012) 1.24
Coordinated activation of cellulose and repression of lignin biosynthesis pathways in rice. Plant Physiol (2010) 1.23
Deciphering the transcriptional regulatory logic of amino acid metabolism. Nat Chem Biol (2011) 1.22
BioQuali Cytoscape plugin: analysing the global consistency of regulatory networks. BMC Genomics (2009) 1.19
Transcriptome analysis identifies regulators of hematopoietic stem and progenitor cells. Stem Cell Reports (2013) 1.19
On the impact of entropy estimation on transcriptional regulatory network inference based on mutual information. EURASIP J Bioinform Syst Biol (2009) 1.19
FACS purification and transcriptome analysis of drosophila neural stem cells reveals a role for Klumpfuss in self-renewal. Cell Rep (2012) 1.19
Predicting gene targets of perturbations via network-based filtering of mRNA expression compendia. Bioinformatics (2008) 1.18
Reverse engineering cellular networks with information theoretic methods. Cells (2013) 1.18
Efficient reverse-engineering of a developmental gene regulatory network. PLoS Comput Biol (2012) 1.16
Bioinformatics resources for the study of gene regulation in bacteria. J Bacteriol (2008) 1.16
Supervised, semi-supervised and unsupervised inference of gene regulatory networks. Brief Bioinform (2013) 1.15
Global probabilistic annotation of metabolic networks enables enzyme discovery. Nat Chem Biol (2012) 1.15
Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context. BMC Bioinformatics (2007) 1.15
Inference of the transcriptional regulatory network in Staphylococcus aureus by integration of experimental and genomics-based evidence. J Bacteriol (2011) 1.15
Learning gene regulatory networks from only positive and unlabeled data. BMC Bioinformatics (2010) 1.14
Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content. J Bacteriol (2009) 1.14
Gene regulatory network inference: evaluation and application to ovarian cancer allows the prioritization of drug targets. Genome Med (2012) 1.14
Principles of transcriptional regulation and evolution of the metabolic system in E. coli. Genome Res (2008) 1.14
Functional characterization of bacterial sRNAs using a network biology approach. Proc Natl Acad Sci U S A (2011) 1.14
A genome-wide regulatory network identifies key transcription factors for memory CD8⁺ T-cell development. Nat Commun (2013) 1.13
Computational prediction and experimental verification of the gene encoding the NAD+/NADP+-dependent succinate semialdehyde dehydrogenase in Escherichia coli. J Bacteriol (2007) 1.13
Regulation by transcription factors in bacteria: beyond description. FEMS Microbiol Rev (2009) 1.12
Fast Bayesian inference for gene regulatory networks using ScanBMA. BMC Syst Biol (2014) 1.11
The role of DNA-binding specificity in the evolution of bacterial regulatory networks. J Mol Biol (2008) 1.11
Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A (1998) 192.97
One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A (2000) 96.90
Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci U S A (2001) 68.44
Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res (2003) 52.74
Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (2002) 43.52
Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol (1994) 37.96
Transcriptional regulatory code of a eukaryotic genome. Nature (2004) 27.21
Systematic determination of genetic network architecture. Nat Genet (1999) 25.45
Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science (2001) 17.11
Using Bayesian networks to analyze expression data. J Comput Biol (2000) 15.98
Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet (2003) 14.56
ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics (2006) 14.49
Reverse engineering of regulatory networks in human B cells. Nat Genet (2005) 13.16
EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res (2005) 11.01
Genomic analysis of regulatory network dynamics reveals large topological changes. Nature (2004) 9.32
Inferring genetic networks and identifying compound mode of action via expression profiling. Science (2003) 9.10
Predicting gene expression from sequence. Cell (2004) 8.12
Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pac Symp Biocomput (2000) 8.02
Integrating high-throughput and computational data elucidates bacterial networks. Nature (2004) 7.72
Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Proc Natl Acad Sci U S A (2000) 6.87
Computational discovery of gene modules and regulatory networks. Nat Biotechnol (2003) 6.55
Network component analysis: reconstruction of regulatory signals in biological systems. Proc Natl Acad Sci U S A (2003) 5.64
Independent coordinates for strange attractors from mutual information. Phys Rev A Gen Phys (1986) 5.60
RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. Nucleic Acids Res (2006) 5.57
The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol (2006) 5.22
Identification of additional genes belonging to the LexA regulon in Escherichia coli. Mol Microbiol (2000) 5.08
Engineered riboregulators enable post-transcriptional control of gene expression. Nat Biotechnol (2004) 5.07
Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling. Proc Natl Acad Sci U S A (2003) 4.89
Integrating regulatory motif discovery and genome-wide expression analysis. Proc Natl Acad Sci U S A (2003) 4.74
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
Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nat Biotechnol (2005) 3.89
Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycle. Proc Natl Acad Sci U S A (2002) 3.70
Physiological studies of Escherichia coli strain MG1655: growth defects and apparent cross-regulation of gene expression. J Bacteriol (2003) 3.29
Untangling the wires: a strategy to trace functional interactions in signaling and gene networks. Proc Natl Acad Sci U S A (2002) 3.18
Combining location and expression data for principled discovery of genetic regulatory network models. Pac Symp Biocomput (2002) 3.05
Estimating mutual information using B-spline functions--an improved similarity measure for analysing gene expression data. BMC Bioinformatics (2004) 2.83
pH regulates genes for flagellar motility, catabolism, and oxidative stress in Escherichia coli K-12. J Bacteriol (2005) 2.60
Genome-wide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function. J Bacteriol (2005) 2.56
Reconstruction of microbial transcriptional regulatory networks. Curr Opin Biotechnol (2004) 2.47
Systems biology: its practice and challenges. Cell (2005) 2.20
Genome-scale analysis of the uses of the Escherichia coli genome: model-driven analysis of heterogeneous data sets. J Bacteriol (2003) 2.10
Global transcriptional programs reveal a carbon source foraging strategy by Escherichia coli. J Biol Chem (2005) 2.00
Linking the genes: inferring quantitative gene networks from microarray data. Trends Genet (2002) 1.83
Iron transport and signaling in Escherichia coli. FEBS Lett (2002) 1.63
Elucidation of gene interaction networks through time-lagged correlation analysis of transcriptional data. Genome Res (2004) 1.59
Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data. Bioinformatics (2003) 1.55
Least absolute regression network analysis of the murine osteoblast differentiation network. Bioinformatics (2005) 1.50
Growing genetic regulatory networks from seed genes. Bioinformatics (2004) 1.49
Global transcriptional effects of a suppressor tRNA and the inactivation of the regulator frmR. J Bacteriol (2004) 1.29
Transcriptome profiles for high-cell-density recombinant and wild-type Escherichia coli. Biotechnol Bioeng (2005) 1.20
Amino acid content of recombinant proteins influences the metabolic burden response. Biotechnol Bioeng (2005) 1.18
Genome-wide analysis of lipoprotein expression in Escherichia coli MG1655. J Bacteriol (2004) 1.11
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Stochasticity in gene expression: from theories to phenotypes. Nat Rev Genet (2005) 14.39
Highly efficient reprogramming to pluripotency and directed differentiation of human cells with synthetic modified mRNA. Cell Stem Cell (2010) 14.18
A common mechanism of cellular death induced by bactericidal antibiotics. Cell (2007) 12.92
Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet (2008) 11.17
Inferring genetic networks and identifying compound mode of action via expression profiling. Science (2003) 9.10
Synthetic biology: applications come of age. Nat Rev Genet (2010) 6.96
Wisdom of crowds for robust gene network inference. Nat Methods (2012) 6.91
Sublethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis. Mol Cell (2010) 5.33
Reverse engineering gene networks using singular value decomposition and robust regression. Proc Natl Acad Sci U S A (2002) 5.29
Engineered riboregulators enable post-transcriptional control of gene expression. Nat Biotechnol (2004) 5.07
Phenotypic consequences of promoter-mediated transcriptional noise. Mol Cell (2006) 4.93
Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling. Proc Natl Acad Sci U S A (2003) 4.89
Programmable cells: interfacing natural and engineered gene networks. Proc Natl Acad Sci U S A (2004) 4.72
How antibiotics kill bacteria: from targets to networks. Nat Rev Microbiol (2010) 4.65
Synthetic gene networks that count. Science (2009) 4.54
Mistranslation of membrane proteins and two-component system activation trigger antibiotic-mediated cell death. Cell (2008) 4.47
Cellular decision making and biological noise: from microbes to mammals. Cell (2011) 4.44
Towards environmental systems biology of Shewanella. Nat Rev Microbiol (2008) 4.37
Metabolite-enabled eradication of bacterial persisters by aminoglycosides. Nature (2011) 4.06
Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coli. Mol Syst Biol (2007) 3.98
Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nat Biotechnol (2005) 3.89
Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nat Biotechnol (2009) 3.86
Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. Nucleic Acids Res (2007) 3.80
Bacterial charity work leads to population-wide resistance. Nature (2010) 3.50
Programmable bacteria detect and record an environmental signal in the mammalian gut. Proc Natl Acad Sci U S A (2014) 3.50
topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association. Nucleic Acids Res (2004) 3.50
Vibrating insoles and balance control in elderly people. Lancet (2003) 3.48
RNA synthetic biology. Nat Biotechnol (2006) 3.37
Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells. Nat Biotechnol (2011) 3.25
Predicting protein function from protein/protein interaction data: a probabilistic approach. Bioinformatics (2003) 3.24
Structural location of disease-associated single-nucleotide polymorphisms. J Mol Biol (2003) 3.20
Next-generation synthetic gene networks. Nat Biotechnol (2009) 3.12
Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature (2013) 3.02
Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy. Proc Natl Acad Sci U S A (2009) 3.01
Signaling-mediated bacterial persister formation. Nat Chem Biol (2012) 2.96
Reprogramming of T cells from human peripheral blood. Cell Stem Cell (2010) 2.93
Whole-genome annotation by using evidence integration in functional-linkage networks. Proc Natl Acad Sci U S A (2004) 2.93
Dispersing biofilms with engineered enzymatic bacteriophage. Proc Natl Acad Sci U S A (2007) 2.87
A tunable genetic switch based on RNAi and repressor proteins for regulating gene expression in mammalian cells. Cell (2007) 2.83
Hydroxyurea induces hydroxyl radical-mediated cell death in Escherichia coli. Mol Cell (2009) 2.74
Oxidation of the guanine nucleotide pool underlies cell death by bactericidal antibiotics. Science (2012) 2.72
Antibiotic-induced bacterial cell death exhibits physiological and biochemical hallmarks of apoptosis. Mol Cell (2012) 2.56
Network-based analysis of affected biological processes in type 2 diabetes models. PLoS Genet (2007) 2.54
Combinatorial promoter design for engineering noisy gene expression. Proc Natl Acad Sci U S A (2007) 2.40
MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium. Proc Natl Acad Sci U S A (2009) 2.37
Synthetic biology moving into the clinic. Science (2011) 2.36
Computational identification of operons in microbial genomes. Genome Res (2002) 2.35
Identification of functional links between genes using phylogenetic profiles. Bioinformatics (2003) 2.33
A synthetic biology framework for programming eukaryotic transcription functions. Cell (2012) 2.32
Oncogenic NRAS signaling differentially regulates survival and proliferation in melanoma. Nat Med (2012) 2.26
Synthetic gene network for entraining and amplifying cellular oscillations. Phys Rev Lett (2002) 2.24
A network biology approach to prostate cancer. Mol Syst Biol (2007) 2.07
Noise-enhanced balance control in patients with diabetes and patients with stroke. Ann Neurol (2006) 2.06
The GacS/GacA signal transduction system of Pseudomonas aeruginosa acts exclusively through its control over the transcription of the RsmY and RsmZ regulatory small RNAs. Mol Microbiol (2009) 1.97
RankGene: identification of diagnostic genes based on expression data. Bioinformatics (2003) 1.96
The transcriptional landscape of hematopoietic stem cell ontogeny. Cell Stem Cell (2012) 1.96
Deep sequencing of the oral microbiome reveals signatures of periodontal disease. PLoS One (2012) 1.96
Extracting conserved gene expression motifs from gene expression data. Pac Symp Biocomput (2003) 1.95
microRNA regulatory network inference identifies miR-34a as a novel regulator of TGF-β signaling in glioblastoma. Cancer Discov (2012) 1.94
A multiply redundant genetic switch 'locks in' the transcriptional signature of regulatory T cells. Nat Immunol (2012) 1.93
Role of reactive oxygen species in antibiotic action and resistance. Curr Opin Microbiol (2009) 1.92
Aging, muscle activity, and balance control: physiologic changes associated with balance impairment. Gait Posture (2003) 1.84
Genomic functional annotation using co-evolution profiles of gene clusters. Genome Biol (2002) 1.76
COMBREX: a project to accelerate the functional annotation of prokaryotic genomes. Nucleic Acids Res (2010) 1.72
Induction of multipotential hematopoietic progenitors from human pluripotent stem cells via respecification of lineage-restricted precursors. Cell Stem Cell (2013) 1.68
Tracking, tuning, and terminating microbial physiology using synthetic riboregulators. Proc Natl Acad Sci U S A (2010) 1.66
Genetic switchboard for synthetic biology applications. Proc Natl Acad Sci U S A (2012) 1.60
Combination drugs, an emerging option for antibacterial therapy. Trends Biotechnol (2007) 1.59
Potentiating antibacterial activity by predictably enhancing endogenous microbial ROS production. Nat Biotechnol (2013) 1.59
The art of gene function prediction. Nat Biotechnol (2006) 1.56
Complex effects of nucleotide variants in a mammalian cis-regulatory element. Proc Natl Acad Sci U S A (2012) 1.55
Tuning and controlling gene expression noise in synthetic gene networks. Nucleic Acids Res (2010) 1.52
Identification of transcription factor binding sites upstream of human genes regulated by the phosphatidylinositol 3-kinase and MEK/ERK signaling pathways. J Biol Chem (2004) 1.49
Heterogeneous bacterial persisters and engineering approaches to eliminate them. Curr Opin Microbiol (2011) 1.47
Tunable signal processing in synthetic MAP kinase cascades. Cell (2011) 1.45
Systematic discovery of new genes in the Saccharomyces cerevisiae genome. Genome Res (2003) 1.43
A systems biology approach identifies inflammatory abnormalities between mouse strains prior to development of metabolic disease. Diabetes (2010) 1.41
Probabilistic protein function prediction from heterogeneous genome-wide data. PLoS One (2007) 1.41
Antibiotics and the gut microbiota. J Clin Invest (2014) 1.39
Towards the identification of essential genes using targeted genome sequencing and comparative analysis. BMC Genomics (2006) 1.39
Microbial persistence and the road to drug resistance. Cell Host Microbe (2013) 1.37
Immediate-early and delayed primary response genes are distinct in function and genomic architecture. J Biol Chem (2007) 1.37
A Bayesian framework for combining gene predictions. Bioinformatics (2002) 1.37
An aberrant transcription factor network essential for Wnt signaling and stem cell maintenance in glioblastoma. Cell Rep (2013) 1.35
GC/AT-content spikes as genomic punctuation marks. Proc Natl Acad Sci U S A (2004) 1.30
Salmonella typhimurium intercepts Escherichia coli signaling to enhance antibiotic tolerance. Proc Natl Acad Sci U S A (2013) 1.29
MuPlex: multi-objective multiplex PCR assay design. Nucleic Acids Res (2005) 1.28
RimO, a MiaB-like enzyme, methylthiolates the universally conserved Asp88 residue of ribosomal protein S12 in Escherichia coli. Proc Natl Acad Sci U S A (2008) 1.27
Accelerated postnatal growth increases lipogenic gene expression and adipocyte size in low-birth weight mice. Diabetes (2009) 1.25
Biological context networks: a mosaic view of the interactome. Mol Syst Biol (2006) 1.24
The COMBREX project: design, methodology, and initial results. PLoS Biol (2013) 1.24
Transcriptome analysis identifies regulators of hematopoietic stem and progenitor cells. Stem Cell Reports (2013) 1.19