Published in Chem Rev on July 18, 2007
RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res (2009) 2.53
Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children. Science (2016) 2.29
A novel class of modular transporters for vitamins in prokaryotes. J Bacteriol (2008) 2.16
RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. Nucleic Acids Res (2010) 1.81
Comparative genomic analysis of T-box regulatory systems in bacteria. RNA (2008) 1.75
RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria. BMC Genomics (2013) 1.61
Genomic reconstruction of Shewanella oneidensis MR-1 metabolism reveals a previously uncharacterized machinery for lactate utilization. Proc Natl Acad Sci U S A (2009) 1.58
Carbohydrate metabolism in Bifidobacteria. Genes Nutr (2011) 1.50
OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains. BMC Syst Biol (2010) 1.47
Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria. J Bacteriol (2008) 1.45
Transcriptional regulation of central carbon and energy metabolism in bacteria by redox-responsive repressor Rex. J Bacteriol (2011) 1.31
A subset of the diverse COG0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life. BMC Genomics (2009) 1.28
Genomic encyclopedia of sugar utilization pathways in the Shewanella genus. BMC Genomics (2010) 1.26
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
The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence. BMC Genomics (2010) 1.24
A generic approach to identify Transcription Factor-specific operator motifs; Inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1. BMC Genomics (2008) 1.23
Complete genome sequence of Corynebacterium variabile DSM 44702 isolated from the surface of smear-ripened cheeses and insights into cheese ripening and flavor generation. BMC Genomics (2011) 1.23
Transcriptional regulation of NAD metabolism in bacteria: NrtR family of Nudix-related regulators. Nucleic Acids Res (2008) 1.21
Inference of the transcriptional regulatory network in Staphylococcus aureus by integration of experimental and genomics-based evidence. J Bacteriol (2011) 1.15
Positively regulated bacterial expression systems. Microb Biotechnol (2008) 1.14
A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate. Chem Biol (2010) 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
Regulation by transcription factors in bacteria: beyond description. FEMS Microbiol Rev (2009) 1.12
Transcriptional regulation of NAD metabolism in bacteria: genomic reconstruction of NiaR (YrxA) regulon. Nucleic Acids Res (2008) 1.12
Reconstruction of xylose utilization pathway and regulons in Firmicutes. BMC Genomics (2010) 1.11
Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides. Science (2015) 1.09
Glycerate 2-kinase of Thermotoga maritima and genomic reconstruction of related metabolic pathways. J Bacteriol (2007) 1.09
Control of proteobacterial central carbon metabolism by the HexR transcriptional regulator: a case study in Shewanella oneidensis. J Biol Chem (2011) 1.08
Comparative analyses imply that the enigmatic Sigma factor 54 is a central controller of the bacterial exterior. BMC Genomics (2011) 1.07
RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics. Nucleic Acids Res (2012) 1.06
Shrinking the metabolic solution space using experimental datasets. PLoS Comput Biol (2012) 1.04
Genomic reconstruction of the transcriptional regulatory network in Bacillus subtilis. J Bacteriol (2013) 1.03
Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima. Front Microbiol (2013) 1.00
Fur controls iron homeostasis and oxidative stress defense in the oligotrophic alpha-proteobacterium Caulobacter crescentus. Nucleic Acids Res (2009) 0.98
The constancy of global regulation across a species: the concentrations of ppGpp and RpoS are strain-specific in Escherichia coli. BMC Microbiol (2011) 0.97
Functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe. J Bacteriol (2014) 0.97
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Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks. BMC Genomics (2013) 0.97
Zinc-independent folate biosynthesis: genetic, biochemical, and structural investigations reveal new metal dependence for GTP cyclohydrolase IB. J Bacteriol (2009) 0.94
Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria. BMC Genomics (2013) 0.92
Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum. Nucleic Acids Res (2012) 0.92
Comparative genomic analysis of the hexuronate metabolism genes and their regulation in gammaproteobacteria. J Bacteriol (2011) 0.92
MGcV: the microbial genomic context viewer for comparative genome analysis. BMC Genomics (2013) 0.92
Comparative genomics and evolution of regulons of the LacI-family transcription factors. Front Microbiol (2014) 0.92
Tagaturonate-fructuronate epimerase UxaE, a novel enzyme in the hexuronate catabolic network in Thermotoga maritima. Environ Microbiol (2012) 0.91
Premature terminator analysis sheds light on a hidden world of bacterial transcriptional attenuation. Genome Biol (2010) 0.91
Network inference and network response identification: moving genome-scale data to the next level of biological discovery. Mol Biosyst (2009) 0.91
Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria. BMC Genomics (2013) 0.91
Ribulokinase and transcriptional regulation of arabinose metabolism in Clostridium acetobutylicum. J Bacteriol (2011) 0.91
The transcriptional response of Listeria monocytogenes during adaptation to growth on lactate and diacetate includes synergistic changes that increase fermentative acetoin production. Appl Environ Microbiol (2011) 0.90
The Zur regulon of Corynebacterium glutamicum ATCC 13032. BMC Genomics (2010) 0.90
Evolution of transcriptional regulation in closely related bacteria. BMC Evol Biol (2012) 0.88
Phenylacetic acid catabolism and its transcriptional regulation in Corynebacterium glutamicum. Appl Environ Microbiol (2012) 0.87
Redox-responsive repressor Rex modulates alcohol production and oxidative stress tolerance in Clostridium acetobutylicum. J Bacteriol (2014) 0.87
N-acetylgalactosamine utilization pathway and regulon in proteobacteria: genomic reconstruction and experimental characterization in Shewanella. J Biol Chem (2012) 0.86
Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes. J Bacteriol (2012) 0.86
Regulation and evolution of malonate and propionate catabolism in proteobacteria. J Bacteriol (2012) 0.83
Transcriptional repression mediated by a TetR family protein, PfmR, from Thermus thermophilus HB8. J Bacteriol (2012) 0.82
GntR Family of Bacterial Transcription Factors and Their DNA Binding Motifs: Structure, Positioning and Co-Evolution. PLoS One (2015) 0.82
Comparative genomics and functional analysis of the NiaP family uncover nicotinate transporters from bacteria, plants, and mammals. Funct Integr Genomics (2011) 0.81
Adaptation to environmental factors shapes the organization of regulatory regions in microbial communities. BMC Genomics (2014) 0.81
Two novel regulators of N-acetyl-galactosamine utilization pathway and distinct roles in bacterial infections. Microbiologyopen (2015) 0.80
Metabolic constraint-based refinement of transcriptional regulatory networks. PLoS Comput Biol (2013) 0.80
Comparative genomics of DtxR family regulons for metal homeostasis in Archaea. J Bacteriol (2014) 0.79
Predicting DNA-binding specificities of eukaryotic transcription factors. PLoS One (2010) 0.79
Characterization of the biotin uptake system encoded by the biotin-inducible bioYMN operon of Corynebacterium glutamicum. BMC Microbiol (2012) 0.79
Systematic genomic analysis reveals the complementary aerobic and anaerobic respiration capacities of the human gut microbiota. Front Microbiol (2014) 0.78
Construction and verification of the transcriptional regulatory response network of Streptococcus mutans upon treatment with the biofilm inhibitor carolacton. BMC Genomics (2014) 0.78
Signal correlations in ecological niches can shape the organization and evolution of bacterial gene regulatory networks. Adv Microb Physiol (2012) 0.78
An integrated approach to reconstructing genome-scale transcriptional regulatory networks. PLoS Comput Biol (2015) 0.78
The nitrogen-regulated response regulator NrrA controls cyanophycin synthesis and glycogen catabolism in the cyanobacterium Synechocystis sp. PCC 6803. J Biol Chem (2013) 0.78
Functional role of pyruvate kinase from Lactobacillus bulgaricus in acid tolerance and identification of its transcription factor by bacterial one-hybrid. Sci Rep (2015) 0.78
Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation. Front Microbiol (2016) 0.77
A Novel Transcriptional Regulator Related to Thiamine Phosphate Synthase Controls Thiamine Metabolism Genes in Archaea. J Bacteriol (2016) 0.77
Comparative genomics of pyridoxal 5'-phosphate-dependent transcription factor regulons in Bacteria. Microb Genom (2016) 0.77
Transcriptional Regulation of Carbohydrate Utilization Pathways in the Bifidobacterium Genus. Front Microbiol (2016) 0.77
Novel Transcriptional Regulons for Autotrophic Cycle Genes in Crenarchaeota. J Bacteriol (2015) 0.77
A novel transcriptional regulator of L-arabinose utilization in human gut bacteria. Nucleic Acids Res (2015) 0.77
Comparative genomics of transcriptional regulation of methionine metabolism in Proteobacteria. PLoS One (2014) 0.77
The architecture of ArgR-DNA complexes at the genome-scale in Escherichia coli. Nucleic Acids Res (2015) 0.76
CMRegNet-An interspecies reference database for corynebacterial and mycobacterial regulatory networks. BMC Genomics (2015) 0.76
Enterococcus faecalis reconfigures its transcriptional regulatory network activation at different copper levels. Metallomics (2014) 0.76
Comparative genomics and evolution of transcriptional regulons in Proteobacteria. Microb Genom (2016) 0.76
Integrated transcriptomic and proteomic analysis of the bile stress response in a centenarian-originated probiotic Bifidobacterium longum BBMN68. Mol Cell Proteomics (2014) 0.76
Nitrogen Fixation and Molecular Oxygen: Comparative Genomic Reconstruction of Transcription Regulation in Alphaproteobacteria. Front Microbiol (2016) 0.75
Cap0037, a Novel Global Regulator of Clostridium acetobutylicum Metabolism. MBio (2016) 0.75
A novel bifunctional transcriptional regulator of riboflavin metabolism in Archaea. Nucleic Acids Res (2017) 0.75
Reconstruction of Transcription Control Networks in Mollicutes by High-Throughput Identification of Promoters. Front Microbiol (2016) 0.75
Elucidation of roles for vitamin B12 in regulation of folate, ubiquinone, and methionine metabolism. Proc Natl Acad Sci U S A (2017) 0.75
Direct Involvement of the Master Nitrogen Metabolism Regulator GlnR in Antibiotic Biosynthesis in Streptomyces. J Biol Chem (2016) 0.75
Identification of Position-Specific Correlations between DNA-Binding Domains and Their Binding Sites. Application to the MerR Family of Transcription Factors. PLoS One (2016) 0.75
Deciphering transcriptional regulations coordinating the response to environmental changes. BMC Bioinformatics (2016) 0.75
Tailor-made transcriptional biosensors for optimizing microbial cell factories. J Ind Microbiol Biotechnol (2016) 0.75
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