Published in Mol Microbiol on December 01, 2003
High- and low-threshold genes in the Spo0A regulon of Bacillus subtilis. J Bacteriol (2005) 3.87
Bistability and biofilm formation in Bacillus subtilis. Mol Microbiol (2007) 3.83
The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis. PLoS Biol (2004) 3.33
Follow the leader: the use of leader peptides to guide natural product biosynthesis. Nat Chem Biol (2010) 3.16
Evidence that entry into sporulation in Bacillus subtilis is governed by a gradual increase in the level and activity of the master regulator Spo0A. Genes Dev (2005) 3.01
Compartmentalization of gene expression during Bacillus subtilis spore formation. Microbiol Mol Biol Rev (2004) 2.96
Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome. Proc Natl Acad Sci U S A (2005) 2.95
The origins of 168, W23, and other Bacillus subtilis legacy strains. J Bacteriol (2008) 2.86
Sticking together: building a biofilm the Bacillus subtilis way. Nat Rev Microbiol (2013) 2.68
Temporal competition between differentiation programs determines cell fate choice. Mol Syst Biol (2011) 2.61
Routine markerless gene replacement in Bacillus anthracis. Infect Immun (2006) 2.42
Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chem Rev (2007) 2.40
The Bacillus subtilis endospore: assembly and functions of the multilayered coat. Nat Rev Microbiol (2012) 2.30
Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901. PLoS Genet (2005) 2.21
Pulsed feedback defers cellular differentiation. PLoS Biol (2012) 2.13
Recent progress in Bacillus subtilis sporulation. FEMS Microbiol Rev (2011) 2.12
Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites. Genes Dev (2005) 2.06
The Clostridium difficile spo0A gene is a persistence and transmission factor. Infect Immun (2012) 2.02
Imaging mass spectrometry of intraspecies metabolic exchange revealed the cannibalistic factors of Bacillus subtilis. Proc Natl Acad Sci U S A (2010) 1.90
Multiple orphan histidine kinases interact directly with Spo0A to control the initiation of endospore formation in Clostridium acetobutylicum. Mol Microbiol (2011) 1.81
Transcriptional program of early sporulation and stationary-phase events in Clostridium acetobutylicum. J Bacteriol (2005) 1.66
Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes. Environ Microbiol (2012) 1.59
Effects of phosphorelay perturbations on architecture, sporulation, and spore resistance in biofilms of Bacillus subtilis. J Bacteriol (2006) 1.56
Global position analysis of the Pseudomonas aeruginosa quorum-sensing transcription factor LasR. Mol Microbiol (2009) 1.55
A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA. Proc Natl Acad Sci U S A (2005) 1.54
Hierarchical evolution of the bacterial sporulation network. Curr Biol (2010) 1.50
A mechanism for cell cycle regulation of sporulation initiation in Bacillus subtilis. Genes Dev (2009) 1.49
The transcriptional program underlying the physiology of clostridial sporulation. Genome Biol (2008) 1.48
Multiple factors modulate biofilm formation by the anaerobic pathogen Clostridium difficile. J Bacteriol (2012) 1.47
Genes for small, noncoding RNAs under sporulation control in Bacillus subtilis. J Bacteriol (2006) 1.41
Genome-wide analysis of the role of GlnR in Streptomyces venezuelae provides new insights into global nitrogen regulation in actinomycetes. BMC Genomics (2011) 1.38
Structural basis of response regulator dephosphorylation by Rap phosphatases. PLoS Biol (2011) 1.35
Transcriptional analysis of spo0A overexpression in Clostridium acetobutylicum and its effect on the cell's response to butanol stress. J Bacteriol (2004) 1.34
Parallel pathways of repression and antirepression governing the transition to stationary phase in Bacillus subtilis. Proc Natl Acad Sci U S A (2008) 1.32
The key sigma factor of transition phase, SigH, controls sporulation, metabolism, and virulence factor expression in Clostridium difficile. J Bacteriol (2011) 1.30
Paralogous antirepressors acting on the master regulator for biofilm formation in Bacillus subtilis. Mol Microbiol (2009) 1.29
Characterization of sporulation histidine kinases of Bacillus anthracis. J Bacteriol (2005) 1.28
Mechanisms and evolution of control logic in prokaryotic transcriptional regulation. Microbiol Mol Biol Rev (2009) 1.25
In vivo dissection of the Helicobacter pylori Fur regulatory circuit by genome-wide location analysis. J Bacteriol (2006) 1.24
KinD is a checkpoint protein linking spore formation to extracellular-matrix production in Bacillus subtilis biofilms. MBio (2010) 1.23
Rap phosphatase of virulence plasmid pXO1 inhibits Bacillus anthracis sporulation. J Bacteriol (2006) 1.23
Optimizing information flow in small genetic networks. Phys Rev E Stat Nonlin Soft Matter Phys (2009) 1.23
Heterochronic phosphorelay gene expression as a source of heterogeneity in Bacillus subtilis spore formation. J Bacteriol (2010) 1.23
Modulation of the ComA-dependent quorum response in Bacillus subtilis by multiple Rap proteins and Phr peptides. J Bacteriol (2006) 1.22
Visualization of differential gene expression by improved cyan fluorescent protein and yellow fluorescent protein production in Bacillus subtilis. Appl Environ Microbiol (2004) 1.21
Intracellular butyryl phosphate and acetyl phosphate concentrations in Clostridium acetobutylicum and their implications for solvent formation. Appl Environ Microbiol (2005) 1.21
Spore formation in Bacillus subtilis. Environ Microbiol Rep (2013) 1.19
SporeWeb: an interactive journey through the complete sporulation cycle of Bacillus subtilis. Nucleic Acids Res (2013) 1.19
Characterization of the global transcriptional responses to different types of DNA damage and disruption of replication in Bacillus subtilis. J Bacteriol (2006) 1.19
Transcriptional organization of the Clostridium acetobutylicum genome. Nucleic Acids Res (2004) 1.16
SirA enforces diploidy by inhibiting the replication initiator DnaA during spore formation in Bacillus subtilis. Mol Microbiol (2009) 1.16
Evidence that metabolism and chromosome copy number control mutually exclusive cell fates in Bacillus subtilis. EMBO J (2011) 1.16
Spo0A, the key transcriptional regulator for entrance into sporulation, is an inhibitor of DNA replication. EMBO J (2006) 1.15
Interspecies interactions that result in Bacillus subtilis forming biofilms are mediated mainly by members of its own genus. Proc Natl Acad Sci U S A (2011) 1.14
The conserved sporulation protein YneE inhibits DNA replication in Bacillus subtilis. J Bacteriol (2009) 1.14
DegU and Spo0A jointly control transcription of two loci required for complex colony development by Bacillus subtilis. J Bacteriol (2008) 1.14
A genomic signature and the identification of new sporulation genes. J Bacteriol (2013) 1.12
The Mycobacterium bovis BCG cyclic AMP receptor-like protein is a functional DNA binding protein in vitro and in vivo, but its activity differs from that of its M. tuberculosis ortholog, Rv3676. Infect Immun (2007) 1.12
Genome-wide analysis of cell type-specific gene transcription during spore formation in Clostridium difficile. PLoS Genet (2013) 1.12
Delineation of the Salmonella enterica serovar Typhimurium HilA regulon through genome-wide location and transcript analysis. J Bacteriol (2007) 1.11
Phenotypic and transcriptomic characterization of Bacillus subtilis mutants with grossly altered membrane composition. J Bacteriol (2008) 1.08
Genome-wide dynamic transcriptional profiling in Clostridium beijerinckii NCIMB 8052 using single-nucleotide resolution RNA-Seq. BMC Genomics (2012) 1.08
Comparative analyses imply that the enigmatic Sigma factor 54 is a central controller of the bacterial exterior. BMC Genomics (2011) 1.07
The threshold level of the sensor histidine kinase KinA governs entry into sporulation in Bacillus subtilis. J Bacteriol (2010) 1.07
Reversible and noisy progression towards a commitment point enables adaptable and reliable cellular decision-making. PLoS Comput Biol (2011) 1.06
Evidence for cyclic Di-GMP-mediated signaling in Bacillus subtilis. J Bacteriol (2012) 1.06
DNA repair and genome maintenance in Bacillus subtilis. Microbiol Mol Biol Rev (2012) 1.03
Ultrasensitivity of the Bacillus subtilis sporulation decision. Proc Natl Acad Sci U S A (2012) 1.02
A novel family of toxin/antitoxin proteins in Bacillus species. FEBS Lett (2011) 1.01
Indirect repression by Bacillus subtilis CodY via displacement of the activator of the proline utilization operon. J Mol Biol (2011) 1.01
An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network. Mol Syst Biol (2015) 1.00
Negative regulation of Bacillus anthracis sporulation by the Spo0E family of phosphatases. J Bacteriol (2007) 1.00
Inactivation of σF in Clostridium acetobutylicum ATCC 824 blocks sporulation prior to asymmetric division and abolishes σE and σG protein expression but does not block solvent formation. J Bacteriol (2011) 1.00
Transcriptional analysis of Clostridium beijerinckii NCIMB 8052 and the hyper-butanol-producing mutant BA101 during the shift from acidogenesis to solventogenesis. Appl Environ Microbiol (2008) 0.99
Genome-wide identification of in vivo binding sites of GlxR, a cyclic AMP receptor protein-type regulator in Corynebacterium glutamicum. J Bacteriol (2011) 0.98
C. difficile 630Δerm Spo0A regulates sporulation, but does not contribute to toxin production, by direct high-affinity binding to target DNA. PLoS One (2012) 0.98
A plasmid-encoded phosphatase regulates Bacillus subtilis biofilm architecture, sporulation, and genetic competence. J Bacteriol (2013) 0.97
Gene conservation among endospore-forming bacteria reveals additional sporulation genes in Bacillus subtilis. J Bacteriol (2012) 0.97
A serine sensor for multicellularity in a bacterium. Elife (2013) 0.97
The Clostridium sporulation programs: diversity and preservation of endospore differentiation. Microbiol Mol Biol Rev (2015) 0.96
oriC-encoded instructions for the initiation of bacterial chromosome replication. Front Microbiol (2015) 0.96
Draft Genome Sequence of Alicyclobacillus acidoterrestris Strain ATCC 49025. Genome Announc (2013) 0.94
Expression of abrB310 and SinR, and effects of decreased abrB310 expression on the transition from acidogenesis to solventogenesis, in Clostridium acetobutylicum ATCC 824. Appl Environ Microbiol (2005) 0.94
Further characterization of Clostridium perfringens small acid soluble protein-4 (Ssp4) properties and expression. PLoS One (2009) 0.93
A disulfide bond-containing alkaline phosphatase triggers a BdbC-dependent secretion stress response in Bacillus subtilis. Appl Environ Microbiol (2006) 0.92
Just-in-time control of Spo0A synthesis in Bacillus subtilis by multiple regulatory mechanisms. J Bacteriol (2011) 0.91
Spo0A~P imposes a temporal gate for the bimodal expression of competence in Bacillus subtilis. PLoS Genet (2012) 0.90
The RapP-PhrP quorum-sensing system of Bacillus subtilis strain NCIB3610 affects biofilm formation through multiple targets, due to an atypical signal-insensitive allele of RapP. J Bacteriol (2014) 0.90
Accidental selection and intentional restoration of sporulation-deficient Bacillus anthracis mutants. Appl Environ Microbiol (2010) 0.87
Non-canonical protein-DNA interactions identified by ChIP are not artifacts. BMC Genomics (2013) 0.87
Cytological characterization of YpsB, a novel component of the Bacillus subtilis divisome. J Bacteriol (2008) 0.87
Functional characterization of the YmcB and YqeV tRNA methylthiotransferases of Bacillus subtilis. Nucleic Acids Res (2010) 0.86
The flagellin FliC of Clostridium difficile is responsible for pleiotropic gene regulation during in vivo infection. PLoS One (2014) 0.86
ExsA recruits RNA polymerase to an extended -10 promoter by contacting region 4.2 of sigma-70. J Bacteriol (2010) 0.86
Systematic domain deletion analysis of the major sporulation kinase in Bacillus subtilis. J Bacteriol (2010) 0.85
Promoter activation by repositioning of RNA polymerase. J Bacteriol (2008) 0.85
A complex of YlbF, YmcA and YaaT regulates sporulation, competence and biofilm formation by accelerating the phosphorylation of Spo0A. Mol Microbiol (2013) 0.84
Defense against cannibalism: the SdpI family of bacterial immunity/signal transduction proteins. J Membr Biol (2010) 0.84
Unique regulatory mechanism of sporulation and enterotoxin production in Clostridium perfringens. J Bacteriol (2013) 0.84
Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature (2012) 18.23
Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. Am J Hum Genet (2001) 10.48
An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat Biotechnol (2002) 10.23
Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms. Am J Hum Genet (2002) 10.12
Methylation of histone H3 Lys 4 in coding regions of active genes. Proc Natl Acad Sci U S A (2002) 7.67
Model-based analysis of two-color arrays (MA2C). Genome Biol (2007) 7.28
Bistability in bacteria. Mol Microbiol (2006) 6.47
Bacterially speaking. Cell (2006) 6.01
Cannibalism by sporulating bacteria. Science (2003) 5.62
A major protein component of the Bacillus subtilis biofilm matrix. Mol Microbiol (2006) 5.09
Integrating regulatory motif discovery and genome-wide expression analysis. Proc Natl Acad Sci U S A (2003) 4.74
A master regulator for biofilm formation by Bacillus subtilis. Mol Microbiol (2005) 4.44
Bayesian inference of epistatic interactions in case-control studies. Nat Genet (2007) 4.31
Control of cell fate by the formation of an architecturally complex bacterial community. Genes Dev (2008) 3.92
High- and low-threshold genes in the Spo0A regulon of Bacillus subtilis. J Bacteriol (2005) 3.87
Bistability and biofilm formation in Bacillus subtilis. Mol Microbiol (2007) 3.83
Amyloid fibers provide structural integrity to Bacillus subtilis biofilms. Proc Natl Acad Sci U S A (2010) 3.78
D-amino acids trigger biofilm disassembly. Science (2010) 3.60
RacA, a bacterial protein that anchors chromosomes to the cell poles. Science (2002) 3.44
Swarming motility in undomesticated Bacillus subtilis. Mol Microbiol (2003) 3.39
The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis. PLoS Biol (2004) 3.33
Genome-wide analysis of the stationary-phase sigma factor (sigma-H) regulon of Bacillus subtilis. J Bacteriol (2002) 3.25
Genomic sequence is highly predictive of local nucleosome depletion. PLoS Comput Biol (2007) 3.24
Targets of the master regulator of biofilm formation in Bacillus subtilis. Mol Microbiol (2006) 3.21
Asymmetric cell division in B. subtilis involves a spiral-like intermediate of the cytokinetic protein FtsZ. Cell (2002) 3.12
Generating and exploiting polarity in bacteria. Science (2002) 3.06
A widely conserved bacterial cell division protein that promotes assembly of the tubulin-like protein FtsZ. Genes Dev (2002) 3.03
Evidence that entry into sporulation in Bacillus subtilis is governed by a gradual increase in the level and activity of the master regulator Spo0A. Genes Dev (2005) 3.01
Genes involved in formation of structured multicellular communities by Bacillus subtilis. J Bacteriol (2004) 2.86
Cell population heterogeneity during growth of Bacillus subtilis. Genes Dev (2005) 2.81
A three-protein signaling pathway governing immunity to a bacterial cannibalism toxin. Cell (2006) 2.78
Sticking together: building a biofilm the Bacillus subtilis way. Nat Rev Microbiol (2013) 2.68
Additional targets of the Bacillus subtilis global regulator CodY identified by chromatin immunoprecipitation and genome-wide transcript analysis. J Bacteriol (2003) 2.65
The sigmaE regulon and the identification of additional sporulation genes in Bacillus subtilis. J Mol Biol (2003) 2.59
Structurally diverse natural products that cause potassium leakage trigger multicellularity in Bacillus subtilis. Proc Natl Acad Sci U S A (2008) 2.54
Recursive SVM feature selection and sample classification for mass-spectrometry and microarray data. BMC Bioinformatics (2006) 2.53
The forespore line of gene expression in Bacillus subtilis. J Mol Biol (2006) 2.52
Thinking about Bacillus subtilis as a multicellular organism. Curr Opin Microbiol (2007) 2.48
Genes governing swarming in Bacillus subtilis and evidence for a phase variation mechanism controlling surface motility. Mol Microbiol (2004) 2.48
The Bacillus subtilis endospore: assembly and functions of the multilayered coat. Nat Rev Microbiol (2012) 2.30
Modeling within-motif dependence for transcription factor binding site predictions. Bioinformatics (2004) 2.29
Geometric cue for protein localization in a bacterium. Science (2009) 2.27
Ecology and genomics of Bacillus subtilis. Trends Microbiol (2008) 2.22
GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data. Bioinformatics (2012) 2.21
De novo cis-regulatory module elicitation for eukaryotic genomes. Proc Natl Acad Sci U S A (2005) 2.20
A data-driven clustering method for time course gene expression data. Nucleic Acids Res (2006) 2.20
An open letter to Elias Zerhouni. Science (2005) 2.19
An accessory protein required for anchoring and assembly of amyloid fibres in B. subtilis biofilms. Mol Microbiol (2011) 2.17
Negative membrane curvature as a cue for subcellular localization of a bacterial protein. Proc Natl Acad Sci U S A (2009) 2.12
Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome. Proc Natl Acad Sci U S A (2007) 2.09
Does RNA polymerase help drive chromosome segregation in bacteria? Proc Natl Acad Sci U S A (2002) 2.01
Macromolecule biosynthesis: a key function of sleep. Physiol Genomics (2007) 1.93
The Bacillus subtilis spore coat protein interaction network. Mol Microbiol (2006) 1.88
An investigation into the compartmentalization of the sporulation transcription factor sigmaE in Bacillus subtilis. Mol Microbiol (2002) 1.86
HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms. Bioinformatics (2004) 1.86
Tracing the domestication of a biofilm-forming bacterium. J Bacteriol (2011) 1.85
An epigenetic switch governing daughter cell separation in Bacillus subtilis. Genes Dev (2010) 1.85
Paracrine signaling in a bacterium. Genes Dev (2009) 1.83
Dynamics of spore coat morphogenesis in Bacillus subtilis. Mol Microbiol (2011) 1.81
HiCNorm: removing biases in Hi-C data via Poisson regression. Bioinformatics (2012) 1.77
A novel regulatory protein governing biofilm formation in Bacillus subtilis. Mol Microbiol (2008) 1.74
Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies. Genome Res (2004) 1.74
Paradoxical DNA repair and peroxide resistance gene conservation in Bacillus pumilus SAFR-032. PLoS One (2007) 1.71
Decoding human regulatory circuits. Genome Res (2004) 1.70
Information flow analysis of interactome networks. PLoS Comput Biol (2009) 1.68
Cannibalism enhances biofilm development in Bacillus subtilis. Mol Microbiol (2009) 1.68
A sporulation membrane protein tethers the pro-sigmaK processing enzyme to its inhibitor and dictates its subcellular localization. Genes Dev (2002) 1.68
Bayesian inference of spatial organizations of chromosomes. PLoS Comput Biol (2013) 1.66
A Bayesian partition method for detecting pleiotropic and epistatic eQTL modules. PLoS Comput Biol (2010) 1.66
Incorporating genotyping uncertainty in haplotype inference for single-nucleotide polymorphisms. Am J Hum Genet (2004) 1.66
Statistical resynchronization and Bayesian detection of periodically expressed genes. Nucleic Acids Res (2004) 1.64
Protein subcellular localization in bacteria. Cold Spring Harb Perspect Biol (2010) 1.62
Bacillus subtilis genome diversity. J Bacteriol (2006) 1.60
Peptide anchoring spore coat assembly to the outer forespore membrane in Bacillus subtilis. Mol Microbiol (2006) 1.58
Clustering analysis of SAGE data using a Poisson approach. Genome Biol (2004) 1.58
A novel pathway of intercellular signalling in Bacillus subtilis involves a protein with similarity to a component of type III secretion channels. Mol Microbiol (2008) 1.58
A feeding tube model for activation of a cell-specific transcription factor during sporulation in Bacillus subtilis. Genes Dev (2009) 1.56
Broadly heterogeneous activation of the master regulator for sporulation in Bacillus subtilis. Proc Natl Acad Sci U S A (2010) 1.56
BioOptimizer: a Bayesian scoring function approach to motif discovery. Bioinformatics (2004) 1.55
Identification of a new gene essential for germination of Bacillus subtilis spores with Ca2+-dipicolinate. J Bacteriol (2003) 1.55
LEAFY target genes reveal floral regulatory logic, cis motifs, and a link to biotic stimulus response. Dev Cell (2011) 1.53
A boosting approach for motif modeling using ChIP-chip data. Bioinformatics (2005) 1.53
Hierarchical evolution of the bacterial sporulation network. Curr Biol (2010) 1.50
MicroRNA promoter element discovery in Arabidopsis. RNA (2006) 1.49
Small untranslated RNA antitoxin in Bacillus subtilis. J Bacteriol (2005) 1.49
Clustering of genes into regulons using integrated modeling-COGRIM. Genome Biol (2007) 1.48
Subcellular localization of a small sporulation protein in Bacillus subtilis. J Bacteriol (2003) 1.48
Cooperation between Polycomb and androgen receptor during oncogenic transformation. Genome Res (2011) 1.47
Competencies: a cure for pre-med curriculum. Science (2011) 1.47
Evidence for a novel protease governing regulated intramembrane proteolysis and resistance to antimicrobial peptides in Bacillus subtilis. Genes Dev (2006) 1.47
Cis-regulatory modules in the mammalian liver: composition depends on strength of Foxa2 consensus site. Nucleic Acids Res (2008) 1.46
A Bacillus subtilis sensor kinase involved in triggering biofilm formation on the roots of tomato plants. Mol Microbiol (2012) 1.45