Published in Genome Biol on November 26, 2002
Conserved and variable functions of the sigmaE stress response in related genomes. PLoS Biol (2006) 4.46
Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. BMC Bioinformatics (2006) 2.57
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The mosaic structure of the symbiotic plasmid of Rhizobium etli CFN42 and its relation to other symbiotic genome compartments. Genome Biol (2003) 1.54
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In silico identification and experimental validation of PmrAB targets in Salmonella typhimurium by regulatory motif detection. Genome Biol (2004) 1.16
Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in Sinorhizobium meliloti strain 1021. BMC Genomics (2007) 1.11
Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011. BMC Genomics (2008) 1.09
Promoter and regulon analysis of nitrogen assimilation factor, sigma54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis. Nucleic Acids Res (2009) 1.07
Characterization of the NifA-RpoN regulon in Rhizobium etli in free life and in symbiosis with Phaseolus vulgaris. Appl Environ Microbiol (2010) 0.93
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The NifA-RpoN regulon of Mesorhizobium loti strain R7A and its symbiotic activation by a novel LacI/GalR-family regulator. PLoS One (2013) 0.87
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Expression of the 1-aminocyclopropane-1-carboxylic acid deaminase gene requires symbiotic nitrogen-fixing regulator gene nifA2 in Mesorhizobium loti MAFF303099. Appl Environ Microbiol (2006) 0.83
Pleiotropic effects of a rel mutation on stress survival of Rhizobium etli CNPAF512. BMC Microbiol (2008) 0.82
Sinorhizobium meliloti sigma factors RpoE1 and RpoE4 are activated in stationary phase in response to sulfite. PLoS One (2012) 0.81
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Transcriptional profiling of nitrogen fixation and the role of NifA in the diazotrophic endophyte Azoarcus sp. strain BH72. PLoS One (2014) 0.78
Identification of metabolism pathways directly regulated by sigma(54) factor in Bacillus thuringiensis. Front Microbiol (2015) 0.78
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Regulation of Burkholderia cenocepacia biofilm formation by RpoN and the c-di-GMP effector BerB. Microbiologyopen (2017) 0.75
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Identification and characterization of the Rhizobium meliloti ntrC gene: R. meliloti has separate regulatory pathways for activation of nitrogen fixation genes in free-living and symbiotic cells. J Bacteriol (1987) 2.23
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Potential symbiosis-specific genes uncovered by sequencing a 410-kilobase DNA region of the Bradyrhizobium japonicum chromosome. J Bacteriol (2001) 1.82
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Conservation between coding and regulatory elements of Rhizobium meliloti and Rhizobium leguminosarum dct genes. J Bacteriol (1989) 1.56
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Oxygen as a key developmental regulator of Rhizobium meliloti N2-fixation gene expression within the alfalfa root nodule. Proc Natl Acad Sci U S A (1995) 1.45
The Rhizobium etli rpoN locus: DNA sequence analysis and phenotypical characterization of rpoN, ptsN, and ptsA mutants. J Bacteriol (1998) 1.36
High-resolution transcriptional analysis of the symbiotic plasmid of Rhizobium sp. NGR234. Mol Microbiol (1999) 1.35
Bradyrhizobium japonicum glnB, a putative nitrogen-regulatory gene, is regulated by NtrC at tandem promoters. J Bacteriol (1989) 1.33
Rhizobium type III secretion systems: legume charmers or alarmers? Curr Opin Plant Biol (2001) 1.30
Processing and export of peptide pheromones and bacteriocins in Gram-negative bacteria. Trends Microbiol (2001) 1.30
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Roles of DctA and DctB in signal detection by the dicarboxylic acid transport system of Rhizobium leguminosarum. J Bacteriol (1998) 1.26
sigma54, a vital protein for Myxococcus xanthus. Proc Natl Acad Sci U S A (1997) 1.22
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Evaluation of thresholds for the detection of binding sites for regulatory proteins in Escherichia coli K12 DNA. Genome Biol (2002) 1.18
Expression of the fixR-nifA operon in Bradyrhizobium japonicum depends on a new response regulator, RegR. J Bacteriol (1998) 1.17
Regulation of the fixA gene and fixBC operon in Bradyrhizobium japonicum. J Bacteriol (1988) 1.17
Transcription of a Rhizobium leguminosarum biovar phaseoli gene needed for melanin synthesis is activated by nifA of Rhizobium and Klebsiella pneumoniae. Mol Microbiol (1988) 1.10
Identification of a gene linked to Rhizobium meliloti ntrA whose product is homologous to a family to ATP-binding proteins. J Bacteriol (1989) 1.10
Azorhizobium caulinodans nitrogen fixation (nif/fix) gene regulation: mutagenesis of the nifA -24/-12 promoter element, characterization of a ntrA(rpoN) gene, and derivation of a model. Mol Plant Microbe Interact (1993) 1.09
Sequence and analysis of the rpoN sigma factor gene of rhizobium sp. strain NGR234, a primary coregulator of symbiosis. J Bacteriol (1990) 1.08
Differential regulation of Rhizobium etli rpoN2 gene expression during symbiosis and free-living growth. J Bacteriol (1998) 1.07
Rhizobium meliloti nifN (fixF) gene is part of an operon regulated by a nifA-dependent promoter and codes for a polypeptide homologous to the nifK gene product. J Bacteriol (1987) 1.04
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The Rhizobium etli amtB gene coding for an NH4+ transporter is down-regulated early during bacteroid differentiation. Mol Plant Microbe Interact (1998) 1.01
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HoxA is a transcriptional regulator for expression of the hup structural genes in free-living Bradyrhizobium japonicum. Mol Microbiol (1997) 0.98
Sinorhizobium meliloti nfe (nodulation formation efficiency) genes exhibit temporal and spatial expression patterns similar to those of genes involved in symbiotic nitrogen fixation. Mol Plant Microbe Interact (2000) 0.98
Characterization of the Rhizobium leguminosarum biovar phaseoli nifA gene, a positive regulator of nif gene expression. Arch Microbiol (1994) 0.95
The Rhizobium etli gene iscN is highly expressed in bacteroids and required for nitrogen fixation. Mol Genet Genomics (2002) 0.94
Three new NifA-regulated genes in the Bradyrhizobium japonicum symbiotic gene region discovered by competitive DNA-RNA hybridization. J Bacteriol (2000) 0.94
RpoN of Rhizobium leguminosarum bv. viciae strain VF39SM plays a central role in FnrN-dependent microaerobic regulation of genes involved in nitrogen fixation. Mol Gen Genet (2001) 0.92
Rhizobium tropici teu genes involved in specific uptake of Phaseolus vulgaris bean-exudate compounds. Mol Gen Genet (1998) 0.92
RpoN (sigma 54) is required for conversion of phenol to catechol in Acinetobacter calcoaceticus. J Bacteriol (1994) 0.92
Characterisation of the glnK-amtB operon and the involvement of AmtB in methylammonium uptake in Azorhizobium caulinodans. Mol Gen Genet (1998) 0.91
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The FixK2 protein is involved in regulation of symbiotic hydrogenase expression in Bradyrhizobium japonicum. J Bacteriol (1998) 0.88
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The upstream region of the nodD3 gene of Sinorhizobium meliloti carries enhancer sequences for the transcriptional activator NtrC. FEMS Microbiol Lett (1999) 0.80
Cloning and sequence of the Rhizobium leguminosarum biovar phaseoli fixA gene. Biochim Biophys Acta (1993) 0.80
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Dual control of the nodA operon of Azorhizobium caulinodans ORS571 by a nod box and a NifA-sigma54-type promoter. Mol Genet Genomics (2001) 0.77
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PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res (2002) 6.43
Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human- mucus binding protein. Proc Natl Acad Sci U S A (2009) 4.61
A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes. J Comput Biol (2002) 4.05
Host interactions of probiotic bacterial surface molecules: comparison with commensals and pathogens. Nat Rev Microbiol (2010) 3.45
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Genes and molecules of lactobacilli supporting probiotic action. Microbiol Mol Biol Rev (2008) 3.12
Advantages and limitations of current network inference methods. Nat Rev Microbiol (2010) 2.97
SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms. BMC Bioinformatics (2006) 2.82
Flagella-driven chemotaxis towards exudate components is an important trait for tomato root colonization by Pseudomonas fluorescens. Mol Plant Microbe Interact (2002) 2.42
Quorum sensing and swarming migration in bacteria. FEMS Microbiol Rev (2004) 2.38
Living on a surface: swarming and biofilm formation. Trends Microbiol (2008) 2.37
INCLUSive: integrated clustering, upstream sequence retrieval and motif sampling. Bioinformatics (2002) 2.13
Using ribosomal protein genes as reference: a tale of caution. PLoS One (2008) 2.06
New horizons for (p)ppGpp in bacterial and plant physiology. Trends Microbiol (2005) 2.00
Role of persister cells in chronic infections: clinical relevance and perspectives on anti-persister therapies. J Med Microbiol (2011) 1.90
O-antigen structural variation: mechanisms and possible roles in animal/plant-microbe interactions. FEMS Microbiol Rev (2002) 1.79
Identification of a Gene Cluster for the Biosynthesis of a Long, Galactose-Rich Exopolysaccharide in Lactobacillus rhamnosus GG and Functional Analysis of the Priming Glycosyltransferase. Appl Environ Microbiol (2009) 1.73
PKA and Sch9 control a molecular switch important for the proper adaptation to nutrient availability. Mol Microbiol (2005) 1.69
Adaptive quality-based clustering of gene expression profiles. Bioinformatics (2002) 1.68
Inferring transcriptional modules from ChIP-chip, motif and microarray data. Genome Biol (2006) 1.64
Rational design of photoconvertible and biphotochromic fluorescent proteins for advanced microscopy applications. Chem Biol (2011) 1.64
Auxin and plant-microbe interactions. Cold Spring Harb Perspect Biol (2011) 1.55
INCLUSive: A web portal and service registry for microarray and regulatory sequence analysis. Nucleic Acids Res (2003) 1.55
Computational approaches to identify promoters and cis-regulatory elements in plant genomes. Plant Physiol (2003) 1.50
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. BMC Syst Biol (2011) 1.50
The E2F-regulated gene Chk1 is highly expressed in triple-negative estrogen receptor /progesterone receptor /HER-2 breast carcinomas. Cancer Res (2007) 1.48
The universally conserved prokaryotic GTPases. Microbiol Mol Biol Rev (2011) 1.47
Pseudomonas aeruginosa fosfomycin resistance mechanisms affect non-inherited fluoroquinolone tolerance. J Med Microbiol (2011) 1.46
The functions of Ca(2+) in bacteria: a role for EF-hand proteins? Trends Microbiol (2002) 1.45
Unraveling the secret lives of bacteria: use of in vivo expression technology and differential fluorescence induction promoter traps as tools for exploring niche-specific gene expression. Microbiol Mol Biol Rev (2005) 1.45
Evidence for the isomerization and decarboxylation in the photoconversion of the red fluorescent protein DsRed. J Am Chem Soc (2005) 1.44
Comparison of the PhoPQ regulon in Escherichia coli and Salmonella typhimurium. J Mol Evol (2005) 1.41
Impact of environmental and genetic factors on biofilm formation by the probiotic strain Lactobacillus rhamnosus GG. Appl Environ Microbiol (2007) 1.41
Chemical synthesis of (S)-4,5-dihydroxy-2,3-pentanedione, a bacterial signal molecule precursor, and validation of its activity in Salmonella typhimurium. J Biol Chem (2005) 1.41
Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks. BMC Syst Biol (2009) 1.40
Functional analysis of luxS in the probiotic strain Lactobacillus rhamnosus GG reveals a central metabolic role important for growth and biofilm formation. J Bacteriol (2006) 1.39
Module networks revisited: computational assessment and prioritization of model predictions. Bioinformatics (2009) 1.38
DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli. Genome Biol (2009) 1.36
Detection, localization, and conformational analysis of single polysaccharide molecules on live bacteria. ACS Nano (2008) 1.35
Differential regulation of the insulin-like growth factor II mRNA-binding protein genes by architectural transcription factor HMGA2. FEBS Lett (2004) 1.35
The effect of a sertoli cell-selective knockout of the androgen receptor on testicular gene expression in prepubertal mice. Mol Endocrinol (2005) 1.34
The cin quorum sensing locus of Rhizobium etli CNPAF512 affects growth and symbiotic nitrogen fixation. J Biol Chem (2001) 1.34
Functional analysis of Lactobacillus rhamnosus GG pili in relation to adhesion and immunomodulatory interactions with intestinal epithelial cells. Appl Environ Microbiol (2011) 1.31
Exopolysaccharides of Lactobacillus rhamnosus GG form a protective shield against innate immune factors in the intestine. Microb Biotechnol (2010) 1.30
Let LuxS speak up in AI-2 signaling. Trends Microbiol (2006) 1.29
Evaluation of time profile reconstruction from complex two-color microarray designs. BMC Bioinformatics (2008) 1.27
Quorum signal molecules as biosurfactants affecting swarming in Rhizobium etli. Proc Natl Acad Sci U S A (2006) 1.26
Genome-specific higher-order background models to improve motif detection. Trends Microbiol (2003) 1.23
New-found fundamentals of bacterial persistence. Trends Microbiol (2012) 1.22
Brominated furanones inhibit biofilm formation by Salmonella enterica serovar Typhimurium. Appl Environ Microbiol (2008) 1.22
Adherence factors of Lactobacillus in the human gastrointestinal tract. FEMS Microbiol Lett (2007) 1.20
Novel persistence genes in Pseudomonas aeruginosa identified by high-throughput screening. FEMS Microbiol Lett (2009) 1.20
Rhizobial secreted proteins as determinants of host specificity in the rhizobium-legume symbiosis. FEMS Microbiol Lett (2008) 1.19
Functional analysis of D-alanylation of lipoteichoic acid in the probiotic strain Lactobacillus rhamnosus GG. Appl Environ Microbiol (2007) 1.17
In silico identification and experimental validation of PmrAB targets in Salmonella typhimurium by regulatory motif detection. Genome Biol (2004) 1.16
Synthesis of N-acyl homoserine lactone analogues reveals strong activators of SdiA, the Salmonella enterica serovar Typhimurium LuxR homologue. Appl Environ Microbiol (2006) 1.14
Genetic and biochemical characterization of the cell wall hydrolase activity of the major secreted protein of Lactobacillus rhamnosus GG. PLoS One (2012) 1.14
Resonance energy transfer in a calcium concentration-dependent cameleon protein. Biophys J (2002) 1.12
Adhesion and nanomechanics of pili from the probiotic Lactobacillus rhamnosus GG. ACS Nano (2013) 1.12
Flow cytometric testing of green fluorescent protein-tagged Lactobacillus rhamnosus GG for response to defensins. Appl Environ Microbiol (2006) 1.11
Microarray analysis and motif detection reveal new targets of the Salmonella enterica serovar Typhimurium HilA regulatory protein, including hilA itself. J Bacteriol (2005) 1.11
Delineation of the Salmonella enterica serovar Typhimurium HilA regulon through genome-wide location and transcript analysis. J Bacteriol (2007) 1.11
Strong antimicrobial activity of Lactobacillus rhamnosus GG against Salmonella typhimurium is due to accumulation of lactic acid. FEMS Microbiol Lett (2006) 1.09
Characterization of MabA, a modulator of Lactobacillus rhamnosus GG adhesion and biofilm formation. FEMS Immunol Med Microbiol (2010) 1.08
Constraints on detection of autoinducer-2 (AI-2) signalling molecules using Vibrio harveyi as a reporter. Microbiology (2003) 1.07
Functional characterization of a mucus-specific LPXTG surface adhesin from probiotic Lactobacillus rhamnosus GG. Appl Environ Microbiol (2011) 1.06
The major secreted protein Msp1/p75 is O-glycosylated in Lactobacillus rhamnosus GG. Microb Cell Fact (2012) 1.06
Vaginal microbiota and its role in HIV transmission and infection. FEMS Microbiol Rev (2013) 1.04
Phenotypic and genome-wide analysis of an antibiotic-resistant small colony variant (SCV) of Pseudomonas aeruginosa. PLoS One (2011) 1.03
Use of structural DNA properties for the prediction of transcription-factor binding sites in Escherichia coli. Nucleic Acids Res (2010) 1.03
Module network inference from a cancer gene expression data set identifies microRNA regulated modules. PLoS One (2010) 1.02
Structure-activity relationship of brominated 3-alkyl-5-methylene-2(5H)-furanones and alkylmaleic anhydrides as inhibitors of Salmonella biofilm formation and quorum sensing regulated bioluminescence in Vibrio harveyi. Bioorg Med Chem (2010) 1.02
COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia. Nucleic Acids Res (2013) 1.02
Identification of a complex genetic network underlying Saccharomyces cerevisiae colony morphology. Mol Microbiol (2012) 1.02
Stretching polysaccharides on live cells using single molecule force spectroscopy. Nat Protoc (2009) 1.01
Development and application of a dapB-based in vivo expression technology system to study colonization of rice by the endophytic nitrogen-fixing bacterium Pseudomonas stutzeri A15. Appl Environ Microbiol (2003) 1.01
Inferring the transcriptional network of Bacillus subtilis. Mol Biosyst (2009) 1.01
Defence of Rhizobium etli bacteroids against oxidative stress involves a complexly regulated atypical 2-Cys peroxiredoxin. Mol Microbiol (2005) 1.01
COLOMBOS: access port for cross-platform bacterial expression compendia. PLoS One (2011) 1.00
Analysis of the peptidoglycan hydrolase complement of Lactobacillus casei and characterization of the major γ-D-glutamyl-L-lysyl-endopeptidase. PLoS One (2012) 0.98
Stress response regulators identified through genome-wide transcriptome analysis of the (p)ppGpp-dependent response in Rhizobium etli. Genome Biol (2011) 0.97
M@CBETH: a microarray classification benchmarking tool. Bioinformatics (2005) 0.96