Published in Nucleic Acids Res on July 01, 2005
The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biol (2007) 3.80
Subtle genetic changes enhance virulence of methicillin resistant and sensitive Staphylococcus aureus. BMC Microbiol (2007) 3.25
Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biol (2010) 3.19
Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Nature (2009) 2.72
Riboswitch RNAs: using RNA to sense cellular metabolism. Genes Dev (2008) 2.47
RegRNA: an integrated web server for identifying regulatory RNA motifs and elements. Nucleic Acids Res (2006) 2.43
Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chem Rev (2007) 2.40
Riboswitch control of gene expression in plants by splicing and alternative 3' end processing of mRNAs. Plant Cell (2007) 2.18
Regulatory small RNAs circumvent the conventional quorum sensing pathway in pandemic Vibrio cholerae. Proc Natl Acad Sci U S A (2007) 2.13
Biochemical features and functional implications of the RNA-based T-box regulatory mechanism. Microbiol Mol Biol Rev (2009) 1.91
Genome-wide detection of novel regulatory RNAs in E. coli. Genome Res (2011) 1.82
Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria. RNA (2008) 1.67
Unique glycine-activated riboswitch linked to glycine-serine auxotrophy in SAR11. Environ Microbiol (2009) 1.61
Complete genomic sequence of bacteriophage felix o1. Viruses (2010) 1.50
Multiple posttranscriptional regulatory mechanisms partner to control ethanolamine utilization in Enterococcus faecalis. Proc Natl Acad Sci U S A (2009) 1.38
Single-nucleotide resolution analysis of the transcriptome structure of Clostridium beijerinckii NCIMB 8052 using RNA-Seq. BMC Genomics (2011) 1.29
The genome of the obligately intracellular bacterium Ehrlichia canis reveals themes of complex membrane structure and immune evasion strategies. J Bacteriol (2006) 1.28
Ethanolamine activates a sensor histidine kinase regulating its utilization in Enterococcus faecalis. J Bacteriol (2008) 1.21
Computational identification of riboswitches based on RNA conserved functional sequences and conformations. RNA (2009) 1.02
Ligands of thermophilic ABC transporters encoded in a newly sequenced genomic region of Thermotoga maritima MSB8 screened by differential scanning fluorimetry. Appl Environ Microbiol (2011) 1.02
Small RNAs in the genus Clostridium. MBio (2011) 1.00
Mining regulatory 5'UTRs from cDNA deep sequencing datasets. Nucleic Acids Res (2009) 0.99
Functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe. J Bacteriol (2014) 0.97
Thiamine is synthesized by a salvage pathway in Rhizobium leguminosarum bv. viciae strain 3841. J Bacteriol (2006) 0.97
Genome-wide detection of predicted non-coding RNAs in Rhizobium etli expressed during free-living and host-associated growth using a high-resolution tiling array. BMC Genomics (2010) 0.95
Transcription antitermination by a phosphorylated response regulator and cobalamin-dependent termination at a B₁₂ riboswitch contribute to ethanolamine utilization in Enterococcus faecalis. J Bacteriol (2011) 0.94
An atypical riboflavin pathway is essential for Brucella abortus virulence. PLoS One (2010) 0.91
Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria. BMC Genomics (2013) 0.91
Using the fast fourier transform to accelerate the computational search for RNA conformational switches. PLoS One (2012) 0.91
Riboswitch detection using profile hidden Markov models. BMC Bioinformatics (2009) 0.88
vttRA and vttRB Encode ToxR family proteins that mediate bile-induced expression of type three secretion system genes in a non-O1/non-O139 Vibrio cholerae strain. Infect Immun (2010) 0.87
Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions. Database (Oxford) (2010) 0.85
Analysing RNA-kinetics based on folding space abstraction. BMC Bioinformatics (2014) 0.84
The Myxococcus xanthus spore cuticula protein C is a fragment of FibA, an extracellular metalloprotease produced exclusively in aggregated cells. PLoS One (2011) 0.84
Maximum expected accuracy structural neighbors of an RNA secondary structure. BMC Bioinformatics (2012) 0.84
Transcriptomic profiling of Yersinia pseudotuberculosis reveals reprogramming of the Crp regulon by temperature and uncovers Crp as a master regulator of small RNAs. PLoS Genet (2015) 0.84
DNA-damaging agents induce the RecA-independent homologous recombination functions of integrating conjugative elements of the SXT/R391 family. J Bacteriol (2013) 0.82
Identification and characterization of RibN, a novel family of riboflavin transporters from Rhizobium leguminosarum and other proteobacteria. J Bacteriol (2013) 0.81
The multidrug ABC transporter BmrC/BmrD of Bacillus subtilis is regulated via a ribosome-mediated transcriptional attenuation mechanism. Nucleic Acids Res (2014) 0.80
Informatic resources for identifying and annotating structural RNA motifs. Mol Biotechnol (2008) 0.80
YlxM is a newly identified accessory protein that influences the function of signal recognition particle pathway components in Streptococcus mutans. J Bacteriol (2014) 0.79
Metabolite sensing in eukaryotic mRNA biology. Wiley Interdiscip Rev RNA (2013) 0.79
Cloning, expression and characterization of a pectate lyase from Paenibacillus sp. 0602 in recombinant Escherichia coli. BMC Biotechnol (2014) 0.79
A new approach for detecting riboswitches in DNA sequences. Bioinformatics (2014) 0.78
Hypoosmotic expression of Dunaliella bardawil ζ-carotene desaturase is attributed to a hypoosmolarity-responsive element different from other key carotenogenic genes. Plant Physiol (2014) 0.78
Complementation of Cobalamin Auxotrophy in Synechococcus sp. Strain PCC 7002 and Validation of a Putative Cobalamin Riboswitch In Vivo. J Bacteriol (2016) 0.77
Multiple mutations and increased RNA expression in tetracycline-resistant Streptococcus pneumoniae as determined by genome-wide DNA and mRNA sequencing. J Antimicrob Chemother (2015) 0.77
RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps. Nucleic Acids Res (2015) 0.77
Shewregdb: database and visualization environment for experimental and predicted regulatory information in Shewanella oneidensis mr-1. Bioinformation (2009) 0.77
Finding consensus stable local optimal structures for aligned RNA sequences and its application to discovering riboswitch elements. Int J Bioinform Res Appl (2014) 0.76
The MarR-Type Regulator Rdh2R Regulates rdh Gene Transcription in Dehalococcoides mccartyi Strain CBDB1. J Bacteriol (2016) 0.75
An Efficient Minimum Free Energy Structure-Based Search Method for Riboswitch Identification Based on Inverse RNA Folding. PLoS One (2015) 0.75
Expression, purification and preliminary X-ray diffraction studies of the transcriptional factor PyrR from Bacillus halodurans. Acta Crystallogr Sect F Struct Biol Cryst Commun (2008) 0.75
Differential regulation of riboflavin supply genes in Vibrio cholerae. Gut Pathog (2017) 0.75
Identification and Regulation of Genes for Cobalamin Transport in the Cyanobacterium Synechococcus sp. Strain PCC 7002. J Bacteriol (2016) 0.75
Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression. Microbiol Mol Biol Rev (2016) 0.75
Functional mining of transporters using synthetic selections. Nat Chem Biol (2016) 0.75
Identifying copy number variation of the dominant virulence factors msa and p22 within genomes of the fish pathogen Renibacterium salmoninarum. Microb Genom (2016) 0.75
Yersinia pestis and Yersinia pseudotuberculosis infection: a regulatory RNA perspective. Front Microbiol (2015) 0.75
Comparative genomics and phylogenomic analyses of lysine riboswitch distributions in bacteria. PLoS One (2017) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res (2000) 117.00
A genomic perspective on protein families. Science (1997) 50.51
Rfam: an RNA family database. Nucleic Acids Res (2003) 22.93
Combining evidence using p-values: application to sequence homology searches. Bioinformatics (1998) 16.51
Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature (2002) 8.14
The riboswitch control of bacterial metabolism. Trends Biochem Sci (2004) 4.95
New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc Natl Acad Sci U S A (2004) 4.35
Metabolite-binding RNA domains are present in the genes of eukaryotes. RNA (2003) 3.42
Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach. J Mol Evol (2004) 2.78
Transcription attenuation: a highly conserved regulatory strategy used by bacteria. Trends Genet (2005) 2.52
GeConT: gene context analysis. Bioinformatics (2004) 1.68
Riboswitch finder--a tool for identification of riboswitch RNAs. Nucleic Acids Res (2004) 1.47
Conserved regulatory motifs in bacteria: riboswitches and beyond. Trends Genet (2004) 1.22
RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res (2007) 7.64
Novel interactions between K+ channels and scorpion toxins. Trends Pharmacol Sci (2003) 1.91
Biochemical features and functional implications of the RNA-based T-box regulatory mechanism. Microbiol Mol Biol Rev (2009) 1.91
ProOpDB: Prokaryotic Operon DataBase. Nucleic Acids Res (2011) 1.40
Conserved regulatory motifs in bacteria: riboswitches and beyond. Trends Genet (2004) 1.22
Metabolic engineering of Bacillus subtilis for ethanol production: lactate dehydrogenase plays a key role in fermentative metabolism. Appl Environ Microbiol (2007) 1.19
Comparison of tryptophan biosynthetic operon regulation in different Gram-positive bacterial species. Trends Genet (2007) 1.07
Conservation of DNA curvature signals in regulatory regions of prokaryotic genes. Nucleic Acids Res (2003) 1.06
High accuracy operon prediction method based on STRING database scores. Nucleic Acids Res (2010) 0.99
New insights into the role of sigma factor RpoS as revealed in escherichia coli strains lacking the phosphoenolpyruvate:carbohydrate phosphotransferase system. J Mol Microbiol Biotechnol (2007) 0.91
A large number of novel Ergtoxin-like genes and ERG K+-channels blocking peptides from scorpions of the genus Centruroides. FEBS Lett (2002) 0.90
New insights into the regulatory networks of paralogous genes in bacteria. Microbiology (2009) 0.90
Homolactic fermentation from glucose and cellobiose using Bacillus subtilis. Microb Cell Fact (2009) 0.87
Down-regulation of PvTRE1 enhances nodule biomass and bacteroid number in the common bean. New Phytol (2012) 0.85
Lessons from the modular organization of the transcriptional regulatory network of Bacillus subtilis. BMC Syst Biol (2013) 0.80
Spatial and temporal expression of Zimp7 and Zimp10 PIAS-like proteins in the developing mouse embryo. Gene Expr Patterns (2007) 0.79
The DNA static curvature has a role in the regulation of the ompS1 porin gene in Salmonella enterica serovar Typhi. Microbiology (2009) 0.78
A novel class of peptide found in scorpion venom with neurodepressant effects in peripheral and central nervous system of the rat. Biochim Biophys Acta (2003) 0.77
GSEL version 2, an online genome-wide query system of operon organization and regulatory sequence elements of Geobacter sulfurreducens. OMICS (2009) 0.75
A Codon Deletion at the Beginning of Green Fluorescent Protein Genes Enhances Protein Expression. J Mol Microbiol Biotechnol (2016) 0.75