Published in Trends Genet on July 01, 2005
A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol Direct (2006) 11.31
Regulatory RNAs in bacteria. Cell (2009) 9.57
Ecological genomics of marine picocyanobacteria. Microbiol Mol Biol Rev (2009) 3.62
Quantitative characteristics of gene regulation by small RNA. PLoS Biol (2007) 3.35
The rise of regulatory RNA. Nat Rev Genet (2014) 3.02
IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics (2008) 2.88
Staphylococcus aureus RNAIII coordinately represses the synthesis of virulence factors and the transcription regulator Rot by an antisense mechanism. Genes Dev (2007) 2.86
Prospects for riboswitch discovery and analysis. Mol Cell (2011) 2.84
Comparative transcriptomics of pathogenic and non-pathogenic Listeria species. Mol Syst Biol (2012) 2.64
Identification of a novel regulatory protein (CsrD) that targets the global regulatory RNAs CsrB and CsrC for degradation by RNase E. Genes Dev (2006) 2.59
Characterization of the Staphylococcus aureus heat shock, cold shock, stringent, and SOS responses and their effects on log-phase mRNA turnover. J Bacteriol (2006) 2.50
The genome of Aeromonas salmonicida subsp. salmonicida A449: insights into the evolution of a fish pathogen. BMC Genomics (2008) 2.40
Small RNA regulators and the bacterial response to stress. Cold Spring Harb Symp Quant Biol (2006) 2.31
Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing. Nucleic Acids Res (2009) 2.25
Regulation of gene expression by small non-coding RNAs: a quantitative view. Mol Syst Biol (2007) 2.19
Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool sRNAPredict2. Nucleic Acids Res (2006) 2.11
Translational repression is sufficient for gene silencing by bacterial small noncoding RNAs in the absence of mRNA destruction. Proc Natl Acad Sci U S A (2006) 2.08
Identification of regulatory RNAs in Bacillus subtilis. Nucleic Acids Res (2010) 1.99
Ten years of bacterial genome sequencing: comparative-genomics-based discoveries. Funct Integr Genomics (2006) 1.86
High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs. PLoS One (2008) 1.80
Identification of small RNAs in Mycobacterium tuberculosis. Mol Microbiol (2009) 1.75
Impact of the RNA chaperone Hfq on the fitness and virulence potential of uropathogenic Escherichia coli. Infect Immun (2008) 1.65
Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements. Biol Direct (2009) 1.58
The intracellular sRNA transcriptome of Listeria monocytogenes during growth in macrophages. Nucleic Acids Res (2011) 1.47
S-box and T-box riboswitches and antisense RNA control a sulfur metabolic operon of Clostridium acetobutylicum. Nucleic Acids Res (2008) 1.47
To be or not to be: regulation of restriction-modification systems and other toxin-antitoxin systems. Nucleic Acids Res (2013) 1.42
Bacterial transcriptomics: what is beyond the RNA horiz-ome? Nat Rev Microbiol (2011) 1.39
Global discovery of small RNAs in Yersinia pseudotuberculosis identifies Yersinia-specific small, noncoding RNAs required for virulence. Proc Natl Acad Sci U S A (2011) 1.38
The group A Streptococcus small regulatory RNA FasX enhances streptokinase activity by increasing the stability of the ska mRNA transcript. Mol Microbiol (2010) 1.37
A genome-wide analysis of small regulatory RNAs in the human pathogen group A Streptococcus. PLoS One (2009) 1.36
Controlling RNA self-assembly to form filaments. Nucleic Acids Res (2006) 1.33
A structural basis for the recognition of 2'-deoxyguanosine by the purine riboswitch. J Mol Biol (2008) 1.31
Structural insights into the dynamics and function of the C-terminus of the E. coli RNA chaperone Hfq. Nucleic Acids Res (2011) 1.30
Genome reannotation of Escherichia coli CFT073 with new insights into virulence. BMC Genomics (2009) 1.30
RNA, but not protein partners, is directly responsible for translational silencing by a bacterial Hfq-binding small RNA. Proc Natl Acad Sci U S A (2008) 1.28
The RNA chaperone Hfq is involved in stress response and virulence in Neisseria meningitidis and is a pleiotropic regulator of protein expression. Infect Immun (2009) 1.27
RNase E-dependent processing stabilizes MicX, a Vibrio cholerae sRNA. Mol Microbiol (2007) 1.26
sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes. Nucleic Acids Res (2008) 1.26
Multiple small RNAs identified in Mycobacterium bovis BCG are also expressed in Mycobacterium tuberculosis and Mycobacterium smegmatis. Nucleic Acids Res (2010) 1.26
Mechanisms and evolution of control logic in prokaryotic transcriptional regulation. Microbiol Mol Biol Rev (2009) 1.25
Biocomputational prediction of non-coding RNAs in model cyanobacteria. BMC Genomics (2009) 1.25
Small RNAs establish delays and temporal thresholds in gene expression. Biophys J (2008) 1.24
Extensive and genome-wide changes in the transcription profile of Staphylococcus aureus induced by modulating the transcription of the cell wall synthesis gene murF. J Bacteriol (2006) 1.23
A conserved RpoS-dependent small RNA controls the synthesis of major porin OmpD. Nucleic Acids Res (2011) 1.23
Dynamic features of gene expression control by small regulatory RNAs. Proc Natl Acad Sci U S A (2009) 1.23
Translation on demand by a simple RNA-based thermosensor. Nucleic Acids Res (2010) 1.20
Identification and characterization of noncoding small RNAs in Streptococcus pneumoniae serotype 2 strain D39. J Bacteriol (2010) 1.19
Translational regulation of gene expression by an anaerobically induced small non-coding RNA in Escherichia coli. J Biol Chem (2010) 1.19
A partition function algorithm for interacting nucleic acid strands. Bioinformatics (2009) 1.18
MglA regulates Francisella tularensis subsp. novicida (Francisella novicida) response to starvation and oxidative stress. J Bacteriol (2007) 1.17
Seed-based INTARNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1. Bioinformatics (2009) 1.17
A broadening world of bacterial small RNAs. Curr Opin Microbiol (2009) 1.15
Messenger RNA Turnover Processes in Escherichia coli, Bacillus subtilis, and Emerging Studies in Staphylococcus aureus. Int J Microbiol (2009) 1.15
Rapid cleavage of RNA by RNase E in the absence of 5' monophosphate stimulation. Mol Microbiol (2009) 1.14
Identification of novel non-coding small RNAs from Streptococcus pneumoniae TIGR4 using high-resolution genome tiling arrays. BMC Genomics (2010) 1.12
Engineering ligand-responsive gene-control elements: lessons learned from natural riboswitches. Gene Ther (2009) 1.11
An integrated approach to functional genomics: construction of a novel reporter gene fusion library for Sinorhizobium meliloti. Appl Environ Microbiol (2006) 1.10
Construction of an rsmX co-variance model and identification of five rsmX non-coding RNAs in Pseudomonas syringae pv. tomato DC3000. RNA Biol (2010) 1.09
Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011. BMC Genomics (2008) 1.09
A highly conserved protein of unknown function in Sinorhizobium meliloti affects sRNA regulation similar to Hfq. Nucleic Acids Res (2011) 1.08
Identification of a large noncoding RNA in extremophilic eubacteria. Proc Natl Acad Sci U S A (2006) 1.08
Growth-induced instability in metabolic networks. Phys Rev Lett (2007) 1.08
Metabolic Regulation of a Bacterial Cell System with Emphasis on Escherichia coli Metabolism. ISRN Biochem (2013) 1.07
RNase E action at a distance: degradation of target mRNAs mediated by an Hfq-binding small RNA in bacteria. Genes Dev (2011) 1.06
Oligoribonuclease is a common downstream target of lithium-induced pAp accumulation in Escherichia coli and human cells. Nucleic Acids Res (2006) 1.05
Translational activation by the noncoding RNA DsrA involves alternative RNase III processing in the rpoS 5'-leader. RNA (2008) 1.05
Translational activation of rpoS mRNA by the non-coding RNA DsrA and Hfq does not require ribosome binding. Nucleic Acids Res (2009) 1.04
De novo computational prediction of non-coding RNA genes in prokaryotic genomes. Bioinformatics (2009) 1.04
Identification of small noncoding RNAs in Helicobacter pylori by a bioinformatics-based approach. Curr Microbiol (2009) 1.04
Analysis of the genetic variation in Mycobacterium tuberculosis strains by multiple genome alignments. BMC Res Notes (2008) 1.02
Identification of two small regulatory RNAs linked to virulence in Brucella abortus 2308. Mol Microbiol (2012) 1.01
Functional heterogeneity of RpoS in stress tolerance of enterohemorrhagic Escherichia coli strains. Appl Environ Microbiol (2006) 1.01
Structural analysis of the Anti-Q-Qs interaction: RNA-mediated regulation of E. faecalis plasmid pCF10 conjugation. Plasmid (2010) 1.01
Regulation Systems of Bacteria such as Escherichia coli in Response to Nutrient Limitation and Environmental Stresses. Metabolites (2013) 0.99
The small regulatory RNA FasX controls pilus expression and adherence in the human bacterial pathogen group A Streptococcus. Mol Microbiol (2012) 0.99
Translational regulation by an intramolecular stem-loop is required for intermolecular RNA regulation of the par addiction module. J Bacteriol (2008) 0.98
Regulating the many to benefit the few: role of weak small RNA targets. Biophys J (2013) 0.98
A motif-based search in bacterial genomes identifies the ortholog of the small RNA Yfr1 in all lineages of cyanobacteria. BMC Genomics (2007) 0.98
Quality control of bacterial mRNA decoding and decay. Biochim Biophys Acta (2008) 0.98
The Yersinia pestis gcvB gene encodes two small regulatory RNA molecules. BMC Microbiol (2006) 0.97
The Hfq-dependent small noncoding RNA NrrF directly mediates Fur-dependent positive regulation of succinate dehydrogenase in Neisseria meningitidis. J Bacteriol (2008) 0.97
Influences of diet and the gut microbiome on epigenetic modulation in cancer and other diseases. Clin Epigenetics (2015) 0.96
Developmental expression of non-coding RNAs in Chlamydia trachomatis during normal and persistent growth. Nucleic Acids Res (2010) 0.96
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
Association of OLE RNA with bacterial membranes via an RNA-protein interaction. Mol Microbiol (2010) 0.94
Moraxella catarrhalis expresses an unusual Hfq protein. Infect Immun (2008) 0.94
How do base-pairing small RNAs evolve? FEMS Microbiol Rev (2015) 0.93
Impact of Hfq on global gene expression and virulence in Klebsiella pneumoniae. PLoS One (2011) 0.92
Adaptive evolution of an sRNA that controls Myxococcus development. Science (2010) 0.92
Characterization of the small RNA transcriptome of the diatom, Thalassiosira pseudonana. PLoS One (2011) 0.92
Genome-wide analysis of small RNAs expressed by Yersinia pestis identifies a regulator of the Yop-Ysc type III secretion system. J Bacteriol (2014) 0.91
Transcription by the numbers redux: experiments and calculations that surprise. Trends Cell Biol (2010) 0.91
A screen for non-coding RNA in Mycobacterium tuberculosis reveals a cAMP-responsive RNA that is expressed during infection. Gene (2012) 0.91
Requirement of the CsdA DEAD-box helicase for low temperature riboregulation of rpoS mRNA. RNA Biol (2010) 0.91
Comparative genomics reveals adaptation by Alteromonas sp. SN2 to marine tidal-flat conditions: cold tolerance and aromatic hydrocarbon metabolism. PLoS One (2012) 0.91
Computational identification of functional RNA homologs in metagenomic data. RNA Biol (2013) 0.91
Characterization of a Streptococcus mutans intergenic region containing a small toxic peptide and its cis-encoded antisense small RNA antitoxin. PLoS One (2013) 0.90
The Sinorhizobium meliloti RNA chaperone Hfq mediates symbiosis of S. meliloti and alfalfa. J Bacteriol (2010) 0.89
Proteome-wide alterations in Escherichia coli translation rates upon anaerobiosis. Mol Cell Proteomics (2010) 0.89
Post-transcriptional regulation of gene expression in Yersinia species. Front Cell Infect Microbiol (2012) 0.88