Published in Nucleic Acids Res on January 01, 2004
Discovering sequence motifs with arbitrary insertions and deletions. PLoS Comput Biol (2008) 4.10
DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res (2007) 3.80
Prediction of transcriptional terminators in Bacillus subtilis and related species. PLoS Comput Biol (2005) 2.54
DBD: a transcription factor prediction database. Nucleic Acids Res (2006) 2.46
Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chem Rev (2007) 2.40
SwissRegulon: a database of genome-wide annotations of regulatory sites. Nucleic Acids Res (2006) 2.30
Bacterial regulatory networks are extremely flexible in evolution. Nucleic Acids Res (2006) 2.04
MiST: a microbial signal transduction database. Nucleic Acids Res (2006) 1.96
RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. Nucleic Acids Res (2006) 1.95
Computational identification of transcriptional regulatory elements in DNA sequence. Nucleic Acids Res (2006) 1.88
High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs. PLoS One (2008) 1.80
Operon formation is driven by co-regulation and not by horizontal gene transfer. Genome Res (2005) 1.64
ODB: a database of operons accumulating known operons across multiple genomes. Nucleic Acids Res (2006) 1.58
Orthologous transcription factors in bacteria have different functions and regulate different genes. PLoS Comput Biol (2007) 1.58
The genome of Bacillus subtilis bacteriophage SPO1. J Mol Biol (2009) 1.53
Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis. BMC Syst Biol (2008) 1.40
Bacterial transcriptomics: what is beyond the RNA horiz-ome? Nat Rev Microbiol (2011) 1.39
Critical dynamics in genetic regulatory networks: examples from four kingdoms. PLoS One (2008) 1.35
Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes. Nucleic Acids Res (2005) 1.30
A novel method for prokaryotic promoter prediction based on DNA stability. BMC Bioinformatics (2005) 1.28
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
Promoter prediction and annotation of microbial genomes based on DNA sequence and structural responses to superhelical stress. BMC Bioinformatics (2006) 1.20
Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups. Nucleic Acids Res (2006) 1.12
Identification and analysis of DNA-binding transcription factors in Bacillus subtilis and other Firmicutes--a genomic approach. BMC Genomics (2006) 1.11
The role of DNA-binding specificity in the evolution of bacterial regulatory networks. J Mol Biol (2008) 1.11
Transcriptional organization and regulation of magnetosome operons in Magnetospirillum gryphiswaldense. Appl Environ Microbiol (2006) 1.10
Transcriptional regulation shapes the organization of genes on bacterial chromosomes. Nucleic Acids Res (2009) 1.09
Molecular characterization of the eis promoter of Mycobacterium tuberculosis. J Bacteriol (2004) 1.01
Identification of the sigmaB regulon of Bacillus cereus and conservation of sigmaB-regulated genes in low-GC-content gram-positive bacteria. J Bacteriol (2007) 1.00
Reconstruction and regulation of the central catabolic pathway in the thermophilic propionate-oxidizing syntroph Pelotomaculum thermopropionicum. J Bacteriol (2006) 0.97
Assessment of CcpA-mediated catabolite control of gene expression in Bacillus cereus ATCC 14579. BMC Microbiol (2008) 0.97
Bipartite pattern discovery by entropy minimization-based multiple local alignment. Nucleic Acids Res (2004) 0.96
Transcriptome analysis of sorbic acid-stressed Bacillus subtilis reveals a nutrient limitation response and indicates plasma membrane remodeling. J Bacteriol (2007) 0.96
Reconstruction of the regulatory network of Lactobacillus plantarum WCFS1 on basis of correlated gene expression and conserved regulatory motifs. Microb Biotechnol (2010) 0.93
High- and low-affinity cre boxes for CcpA binding in Bacillus subtilis revealed by genome-wide analysis. BMC Genomics (2012) 0.93
Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions. Nucleic Acids Res (2007) 0.92
SpotXplore: a Cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks. Bioinformatics (2010) 0.92
Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium. Genome Biol (2011) 0.91
Network inference and network response identification: moving genome-scale data to the next level of biological discovery. Mol Biosyst (2009) 0.91
DISCLOSE : DISsection of CLusters Obtained by SEries of transcriptome data using functional annotations and putative transcription factor binding sites. BMC Bioinformatics (2008) 0.91
Detection of prokaryotic promoters from the genomic distribution of hexanucleotide pairs. BMC Bioinformatics (2006) 0.90
Transcriptional activity around bacterial cell death reveals molecular biomarkers for cell viability. BMC Genomics (2008) 0.89
Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet. Nat Protoc (2009) 0.89
Impact of Transcription Units rearrangement on the evolution of the regulatory network of gamma-proteobacteria. BMC Genomics (2008) 0.88
Unravelling the transcriptome profile of the Swine respiratory tract mycoplasmas. PLoS One (2014) 0.88
PromBase: a web resource for various genomic features and predicted promoters in prokaryotic genomes. BMC Res Notes (2011) 0.87
Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks. Brief Bioinform (2008) 0.83
Adaptation of cells to new environments. Wiley Interdiscip Rev Syst Biol Med (2010) 0.82
Network component analysis provides quantitative insights on an Arabidopsis transcription factor-gene regulatory network. BMC Syst Biol (2013) 0.81
Predicted transcription factor binding sites as predictors of operons in Escherichia coli and Streptomyces coelicolor. BMC Genomics (2008) 0.78
Bacillus thermoamylovorans Spores with Very-High-Level Heat Resistance Germinate Poorly in Rich Medium despite the Presence of ger Clusters but Efficiently upon Exposure to Calcium-Dipicolinic Acid. Appl Environ Microbiol (2015) 0.77
Enterococcus faecalis reconfigures its transcriptional regulatory network activation at different copper levels. Metallomics (2014) 0.76
Different evolutionary modifications as a guide to rewire two-component systems. Bioinform Biol Insights (2012) 0.76
Parametric bootstrapping for biological sequence motifs. BMC Bioinformatics (2016) 0.75
SEARCHPATTOOL: a new method for mining the most specific frequent patterns for binding sites with application to prokaryotic DNA sequences. BMC Bioinformatics (2007) 0.75
Contributions of 5'-UTR and 3'-UTR cis elements to Cyt1Aa synthesis in Bacillus thuringiensis subsp. israelensis. J Invertebr Pathol (2017) 0.75
The COG database: an updated version includes eukaryotes. BMC Bioinformatics (2003) 60.98
The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature (1997) 33.47
Essential Bacillus subtilis genes. Proc Natl Acad Sci U S A (2003) 14.01
SubtiList: the reference database for the Bacillus subtilis genome. Nucleic Acids Res (2002) 2.99
Systematic function analysis of Bacillus subtilis genes. Res Microbiol (2000) 2.82
DBTBS: a database of Bacillus subtilis promoters and transcription factors. Nucleic Acids Res (2001) 2.35
Prediction of co-regulated genes in Bacillus subtilis on the basis of upstream elements conserved across three closely related species. Genome Biol (2001) 1.39
WoLF PSORT: protein localization predictor. Nucleic Acids Res (2007) 10.14
Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat Genet (2003) 7.98
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res (2011) 6.88
Genome sequencing and analysis of Aspergillus oryzae. Nature (2005) 5.47
Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater. Proc Natl Acad Sci U S A (2002) 5.40
Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome Res (2005) 5.22
Extensive feature detection of N-terminal protein sorting signals. Bioinformatics (2002) 5.16
Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature (2004) 5.08
Genome structure of the legume, Lotus japonicus. DNA Res (2008) 4.93
The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection. Nat Immunol (2010) 4.66
DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs. Nucleic Acids Res (2002) 4.29
PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria. Nucleic Acids Res (2003) 4.25
BioRuby: bioinformatics software for the Ruby programming language. Bioinformatics (2010) 3.85
DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res (2007) 3.80
ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Res (2006) 3.74
DBTSS, DataBase of Transcriptional Start Sites: progress report 2004. Nucleic Acids Res (2004) 3.73
DBTSS: database of transcription start sites, progress report 2008. Nucleic Acids Res (2007) 3.11
T cell receptor stimulation-induced epigenetic changes and Foxp3 expression are independent and complementary events required for Treg cell development. Immunity (2012) 2.78
Prediction of transcriptional terminators in Bacillus subtilis and related species. PLoS Comput Biol (2005) 2.54
DBTSS: DataBase of Human Transcription Start Sites, progress report 2006. Nucleic Acids Res (2006) 2.52
A widespread family of bacterial cell wall assembly proteins. EMBO J (2011) 2.33
Escherichia coli histone-like protein H-NS preferentially binds to horizontally acquired DNA in association with RNA polymerase. DNA Res (2006) 2.11
The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res (2007) 2.07
PrognoScan: a new database for meta-analysis of the prognostic value of genes. BMC Med Genomics (2009) 2.07
Discovery of two novel families of proteins that are proposed to interact with prokaryotic SMC proteins, and characterization of the Bacillus subtilis family members ScpA and ScpB. Mol Microbiol (2002) 2.06
A functional link between RuBisCO-like protein of Bacillus and photosynthetic RuBisCO. Science (2003) 2.03
Whole-genome analysis of genes regulated by the Bacillus subtilis competence transcription factor ComK. J Bacteriol (2002) 2.01
An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA. Mol Cell (2003) 1.90
Six GTP-binding proteins of the Era/Obg family are essential for cell growth in Bacillus subtilis. Microbiology (2002) 1.76
Zinc is a key factor in controlling alternation of two types of L31 protein in the Bacillus subtilis ribosome. Mol Microbiol (2004) 1.65
Proteomics characterization of novel spore proteins of Bacillus subtilis. Microbiology (2002) 1.61
Massive transcriptional start site analysis of human genes in hypoxia cells. Nucleic Acids Res (2009) 1.60
The BceRS two-component regulatory system induces expression of the bacitracin transporter, BceAB, in Bacillus subtilis. Mol Microbiol (2003) 1.58
Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity. Gene (2005) 1.57
Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis. Genome Res (2011) 1.57
Noc protein binds to specific DNA sequences to coordinate cell division with chromosome segregation. EMBO J (2009) 1.56
HitPredict: a database of quality assessed protein-protein interactions in nine species. Nucleic Acids Res (2010) 1.50
A new FtsZ-interacting protein, YlmF, complements the activity of FtsA during progression of cell division in Bacillus subtilis. Mol Microbiol (2006) 1.49
Binding of response regulator DegU to the aprE promoter is inhibited by RapG, which is counteracted by extracellular PhrG in Bacillus subtilis. Mol Microbiol (2003) 1.47
Identification of a protein, YneA, responsible for cell division suppression during the SOS response in Bacillus subtilis. Mol Microbiol (2003) 1.47
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. J Biomed Semantics (2013) 1.44
TogoWS: integrated SOAP and REST APIs for interoperable bioinformatics Web services. Nucleic Acids Res (2010) 1.37
Distinct class of putative "non-conserved" promoters in humans: comparative studies of alternative promoters of human and mouse genes. Genome Res (2007) 1.37
Distribution of stable DnaA-binding sites on the Bacillus subtilis genome detected using a modified ChIP-chip method. DNA Res (2007) 1.37
DBTSS provides a tissue specific dynamic view of Transcription Start Sites. Nucleic Acids Res (2009) 1.36
Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues. Nucleic Acids Res (2005) 1.35
Inferring gene regulatory networks from time-ordered gene expression data of Bacillus subtilis using differential equations. Pac Symp Biocomput (2003) 1.34
Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs. Nucleic Acids Res (2006) 1.34
DBTSS: DataBase of Transcriptional Start Sites progress report in 2012. Nucleic Acids Res (2011) 1.33
Enhanced recombinant protein productivity by genome reduction in Bacillus subtilis. DNA Res (2008) 1.32
The GTP-binding protein YlqF participates in the late step of 50 S ribosomal subunit assembly in Bacillus subtilis. J Biol Chem (2006) 1.32
Genome-wide binding profiles of the Bacillus subtilis transition state regulator AbrB and its homolog Abh reveals their interactive role in transcriptional regulation. Nucleic Acids Res (2010) 1.30
Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content. BMC Genomics (2009) 1.29
Global regulation by horizontally transferred regulators establishes the pathogenicity of Escherichia coli. DNA Res (2008) 1.27
Synergistic regulation of competence development in Bacillus subtilis by two Rap-Phr systems. J Bacteriol (2005) 1.27
A complete set of Escherichia coli open reading frames in mobile plasmids facilitating genetic studies. DNA Res (2005) 1.26
Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions. Genome Res (2004) 1.25
Bacillus minimum genome factory: effective utilization of microbial genome information. Biotechnol Appl Biochem (2007) 1.25
Systematic analysis of SigD-regulated genes in Bacillus subtilis by DNA microarray and Northern blotting analyses. Gene (2004) 1.22
Prediction of subcellular locations of proteins: where to proceed? Proteomics (2010) 1.22
CyanoBase and RhizoBase: databases of manually curated annotations for cyanobacterial and rhizobial genomes. Nucleic Acids Res (2013) 1.20
H-DBAS: alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational. Nucleic Acids Res (2006) 1.20
Complete genome sequence of Bradyrhizobium sp. S23321: insights into symbiosis evolution in soil oligotrophs. Microbes Environ (2012) 1.19
Sequence- and species-dependence of proteasomal processivity. ACS Chem Biol (2012) 1.18
Escherichia coli with a linear genome. EMBO Rep (2007) 1.16
Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals. Nucleic Acids Res (2005) 1.15
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. J Biomed Semantics (2014) 1.12
Inferring the choreography of parental genomes during fertilization from ultralarge-scale whole-transcriptome analysis. Genes Dev (2013) 1.11
Genomic cis-regulatory networks in the early Ciona intestinalis embryo. Development (2010) 1.10
Bacillus subtilis RghR (YvaN) represses rapG and rapH, which encode inhibitors of expression of the srfA operon. Mol Microbiol (2006) 1.09
Increasing the ratio of Soj to Spo0J promotes replication initiation in Bacillus subtilis. J Bacteriol (2003) 1.09
Bacillus subtilis YabA is involved in determining the timing and synchrony of replication initiation. FEMS Microbiol Lett (2005) 1.08
Cloning and characterization of mevalonate pathway genes in a natural rubber producing plant, Hevea brasiliensis. Biosci Biotechnol Biochem (2008) 1.08
The Bacillus subtilis YufLM two-component system regulates the expression of the malate transporters MaeN (YufR) and YflS, and is essential for utilization of malate in minimal medium. Microbiology (2003) 1.06
Pseudocounts for transcription factor binding sites. Nucleic Acids Res (2008) 1.06
spoIVH (ykvV), a requisite cortex formation gene, is expressed in both sporulating compartments of Bacillus subtilis. J Bacteriol (2004) 1.06
Transcriptional, functional and cytochemical analyses of the veg gene in Bacillus subtilis. J Biochem (2003) 1.05
Bacillus subtilis EzrA and FtsL synergistically regulate FtsZ ring dynamics during cell division. Microbiology (2006) 1.05
Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli. BMC Genomics (2007) 1.05
Metabolomics approach for determining growth-specific metabolites based on Fourier transform ion cyclotron resonance mass spectrometry. Anal Bioanal Chem (2008) 1.04
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*. J Biomed Semantics (2010) 1.04
The functional analysis of YabA, which interacts with DnaA and regulates initiation of chromosome replication in Bacillus subtils. Genes Genet Syst (2008) 1.04
The GTP-binding protein YqeH participates in biogenesis of the 30S ribosome subunit in Bacillus subtilis. Genes Genet Syst (2007) 1.03
Large ring polymers align FtsZ polymers for normal septum formation. EMBO J (2011) 1.03
The phylogenetic position of red algae revealed by multiple nuclear genes from mitochondria-containing eukaryotes and an alternative hypothesis on the origin of plastids. J Mol Evol (2003) 1.03
Two separate DNA sequences within oriC participate in accurate chromosome segregation in Bacillus subtilis. Mol Microbiol (2002) 1.02
Functional analysis of the YvrGHb two-component system of Bacillus subtilis: identification of the regulated genes by DNA microarray and northern blot analyses. Biosci Biotechnol Biochem (2005) 1.02
Retrotransposition as a source of new promoters. Mol Biol Evol (2008) 1.00
Structural and genetic analyses reveal the protein SepF as a new membrane anchor for the Z ring. Proc Natl Acad Sci U S A (2013) 1.00
Small open reading frames in 5' untranslated regions of mRnas. C R Biol (2004) 1.00
Comprehensive detection of human terminal oligo-pyrimidine (TOP) genes and analysis of their characteristics. Nucleic Acids Res (2008) 0.99
The H2O2 stress-responsive regulator PerR positively regulates srfA expression in Bacillus subtilis. J Bacteriol (2005) 0.99
The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. J Biomed Semantics (2011) 0.99
Challenges of the next decade for the Asia Pacific region: 2010 International Conference in Bioinformatics (InCoB 2010). BMC Genomics (2010) 0.98
Differential binding profiles of StpA in wild-type and h-ns mutant cells: a comparative analysis of cooperative partners by chromatin immunoprecipitation-microarray analysis. J Bacteriol (2009) 0.98
Large-scale collection and characterization of promoters of human and mouse genes. In Silico Biol (2004) 0.97
Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs. Nucleic Acids Res (2008) 0.97