Published in Trends Biochem Sci on January 01, 2004
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Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. Chem Biol (2004) 5.44
Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch. Nature (2006) 3.90
Initiation of protein synthesis in bacteria. Microbiol Mol Biol Rev (2005) 3.78
Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125. Genome Res (2005) 2.89
TonB-dependent transporters: regulation, structure, and function. Annu Rev Microbiol (2010) 2.72
Two seemingly homologous noncoding RNAs act hierarchically to activate glmS mRNA translation. PLoS Biol (2008) 2.61
Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation. Nat Struct Mol Biol (2005) 2.50
Structural insights into amino acid binding and gene control by a lysine riboswitch. Nature (2008) 2.41
Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria. Genome Biol (2005) 2.32
Linking metabolic QTLs with network and cis-eQTLs controlling biosynthetic pathways. PLoS Genet (2007) 2.15
RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements. Nucleic Acids Res (2005) 2.12
An intermolecular base triple as the basis of ligand specificity and affinity in the guanine- and adenine-sensing riboswitch RNAs. Proc Natl Acad Sci U S A (2005) 2.07
Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch. Nature (2009) 1.90
Unique folding of precursor microRNAs: quantitative evidence and implications for de novo identification. RNA (2006) 1.85
Ligand-induced folding of the thiM TPP riboswitch investigated by a structure-based fluorescence spectroscopic approach. Nucleic Acids Res (2007) 1.79
Ligand-dependent folding of the three-way junction in the purine riboswitch. RNA (2008) 1.77
The expanding transcriptome: the genome as the 'Book of Sand'. EMBO J (2006) 1.73
A loop loop interaction and a K-turn motif located in the lysine aptamer domain are important for the riboswitch gene regulation control. RNA (2007) 1.73
Natural variability in S-adenosylmethionine (SAM)-dependent riboswitches: S-box elements in bacillus subtilis exhibit differential sensitivity to SAM In vivo and in vitro. J Bacteriol (2007) 1.73
Ligand-induced folding of the guanine-sensing riboswitch is controlled by a combined predetermined induced fit mechanism. RNA (2007) 1.70
Control of mammalian translation by mRNA structure near caps. RNA (2006) 1.66
A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo. Nucleic Acids Res (2004) 1.66
Structural insights into ligand recognition by a sensing domain of the cooperative glycine riboswitch. Mol Cell (2010) 1.66
RNAs: regulators of bacterial virulence. Nat Rev Microbiol (2010) 1.63
The long and the short of riboswitches. Curr Opin Struct Biol (2009) 1.59
A high-throughput screen for synthetic riboswitches reveals mechanistic insights into their function. Chem Biol (2007) 1.56
Metabolite recognition principles and molecular mechanisms underlying riboswitch function. Annu Rev Biophys (2012) 1.47
Riboswitch-dependent gene regulation and its evolution in the plant kingdom. Genes Dev (2007) 1.47
Mutational analysis of the purine riboswitch aptamer domain. Biochemistry (2007) 1.44
Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis. PLoS Comput Biol (2015) 1.44
Structural basis of cooperative ligand binding by the glycine riboswitch. Chem Biol (2011) 1.43
Time-resolved NMR methods resolving ligand-induced RNA folding at atomic resolution. Proc Natl Acad Sci U S A (2007) 1.39
The ligand-free state of the TPP riboswitch: a partially folded RNA structure. J Mol Biol (2009) 1.39
Screening for engineered neomycin riboswitches that control translation initiation. RNA (2007) 1.38
Genetic control of biosynthesis and transport of riboflavin and flavin nucleotides and construction of robust biotechnological producers. Microbiol Mol Biol Rev (2011) 1.38
Folding of a transcriptionally acting preQ1 riboswitch. Proc Natl Acad Sci U S A (2010) 1.34
Biology by design: reduction and synthesis of cellular components and behaviour. J R Soc Interface (2007) 1.33
Core requirements of the adenine riboswitch aptamer for ligand binding. RNA (2007) 1.33
A structural basis for the recognition of 2'-deoxyguanosine by the purine riboswitch. J Mol Biol (2008) 1.31
A pseudoknot in the 3' non-core region of the glmS ribozyme enhances self-cleavage activity. RNA (2005) 1.29
Evolution of the iron-responsive element. RNA (2007) 1.27
sinI- and expR-dependent quorum sensing in Sinorhizobium meliloti. J Bacteriol (2005) 1.27
Fluoride ion encapsulation by Mg2+ ions and phosphates in a fluoride riboswitch. Nature (2012) 1.26
Structural features of metabolite-sensing riboswitches. Trends Biochem Sci (2007) 1.26
S-adenosylmethionine directly inhibits binding of 30S ribosomal subunits to the SMK box translational riboswitch RNA. Proc Natl Acad Sci U S A (2007) 1.24
Genome-wide identification of regulatory RNAs in the human pathogen Clostridium difficile. PLoS Genet (2013) 1.23
Molecular analysis of a synthetic tetracycline-binding riboswitch. RNA (2005) 1.20
An RNA Mapping DataBase for curating RNA structure mapping experiments. Bioinformatics (2012) 1.19
An artificial riboswitch for controlling pre-mRNA splicing. RNA (2005) 1.17
Coenzyme B12 controls transcription of the Streptomyces class Ia ribonucleotide reductase nrdABS operon via a riboswitch mechanism. J Bacteriol (2006) 1.15
Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding. RNA (2010) 1.13
Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch. Nucleic Acids Res (2009) 1.13
Applications of isothermal titration calorimetry in RNA biochemistry and biophysics. Biopolymers (2007) 1.12
Tuning a riboswitch response through structural extension of a pseudoknot. Proc Natl Acad Sci U S A (2013) 1.09
Bacteriophage-mediated toxin gene regulation in Clostridium difficile. J Virol (2009) 1.09
Folding and ligand recognition of the TPP riboswitch aptamer at single-molecule resolution. Proc Natl Acad Sci U S A (2013) 1.08
c-di-AMP binds the ydaO riboswitch in two pseudo-symmetry-related pockets. Nat Chem Biol (2014) 1.07
Comprehensive analysis of the Corynebacterium glutamicum transcriptome using an improved RNAseq technique. BMC Genomics (2013) 1.07
Conformational changes involved in initiation of minus-strand synthesis of a virus-associated RNA. RNA (2005) 1.07
Core requirements for glmS ribozyme self-cleavage reveal a putative pseudoknot structure. Nucleic Acids Res (2006) 1.06
Raman crystallography of RNA. Methods (2009) 1.06
Emerging applications of riboswitches in chemical biology. ACS Chem Biol (2010) 1.05
Cooperative and directional folding of the preQ1 riboswitch aptamer domain. J Am Chem Soc (2011) 1.05
Cell wall hydrolases affect germination, vegetative growth, and sporulation in Streptomyces coelicolor. J Bacteriol (2009) 1.04
Encoding folding paths of RNA switches. Nucleic Acids Res (2006) 1.03
Thiamin (vitamin B1) biosynthesis and regulation: a rich source of antimicrobial drug targets? Int J Biol Sci (2011) 1.03
Ribosome heterogeneity: another level of complexity in bacterial translation regulation. Curr Opin Microbiol (2013) 1.03
Folding of the cocaine aptamer studied by EPR and fluorescence spectroscopies using the bifunctional spectroscopic probe Ç. Nucleic Acids Res (2009) 1.01
Role of the adenine ligand on the stabilization of the secondary and tertiary interactions in the adenine riboswitch. J Mol Biol (2009) 1.01
Long-range pseudoknot interactions dictate the regulatory response in the tetrahydrofolate riboswitch. Proc Natl Acad Sci U S A (2011) 1.01
Elucidating the higher-order structure of biopolymers by structural probing and mass spectrometry: MS3D. J Mass Spectrom (2010) 1.00
Synthesizing biomolecule-based Boolean logic gates. ACS Synth Biol (2013) 1.00
TRANSAT-- method for detecting the conserved helices of functional RNA structures, including transient, pseudo-knotted and alternative structures. PLoS Comput Biol (2010) 0.99
Structural principles of nucleoside selectivity in a 2'-deoxyguanosine riboswitch. Nat Chem Biol (2011) 0.99
Identification of 88 regulatory small RNAs in the TIGR4 strain of the human pathogen Streptococcus pneumoniae. RNA (2012) 0.99
From structure prediction to genomic screens for novel non-coding RNAs. PLoS Comput Biol (2011) 0.99
Identification of consensus RNA secondary structures using suffix arrays. BMC Bioinformatics (2006) 0.99
Identification of a mutation in the Bacillus subtilis S-adenosylmethionine synthetase gene that results in derepression of S-box gene expression. J Bacteriol (2006) 0.99
Genome-wide bioinformatic prediction and experimental evaluation of potential RNA thermometers. Mol Genet Genomics (2007) 0.98
Modulation of quaternary structure and enhancement of ligand binding by the K-turn of tandem glycine riboswitches. RNA (2012) 0.98
Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure. Nucleic Acids Res (2013) 0.98
Structure, composition and metagenomic profile of soil microbiomes associated to agricultural land use and tillage systems in Argentine Pampas. PLoS One (2014) 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
The riboswitch regulates a thiamine pyrophosphate ABC transporter of the oral spirochete Treponema denticola. J Bacteriol (2011) 0.95
Enhanced synthesis of internalin A in aro mutants of Listeria monocytogenes indicates posttranscriptional control of the inlAB mRNA. J Bacteriol (2005) 0.95
Cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways. Microbiol Mol Biol Rev (2009) 0.94
Analysis of metal ion dependence in glmS ribozyme self-cleavage and coenzyme binding. Chembiochem (2010) 0.94
Insights into metalloregulation by M-box riboswitch RNAs via structural analysis of manganese-bound complexes. J Mol Biol (2011) 0.93
Analysis of riboswitch structure and function by an energy landscape framework. J Mol Biol (2009) 0.93
Dynamic energy landscapes of riboswitches help interpret conformational rearrangements and function. PLoS Comput Biol (2012) 0.92
Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria. BMC Genomics (2013) 0.91
Riboswitches in unexpected places--a synthetic riboswitch in a protein coding region. RNA (2008) 0.91
Thermodynamics and folding pathway of tetraloop receptor-mediated RNA helical packing. J Mol Biol (2008) 0.91
Loop-loop interaction in an adenine-sensing riboswitch: a molecular dynamics study. RNA (2013) 0.91
Rapid steps in the glmS ribozyme catalytic pathway: cation and ligand requirements. Biochemistry (2011) 0.89
High-throughput mutate-map-rescue evaluates SHAPE-directed RNA structure and uncovers excited states. RNA (2014) 0.89
The riboswitch-mediated control of sulfur metabolism in bacteria. Proc Natl Acad Sci U S A (2003) 2.83
Comparison of the structure and regulation of the udp gene of Vibrio cholerae, Yersinia pseudotuberculosis, Salmonella typhimurium, and Escherichia coli. Res Microbiol (2003) 1.00
Proteasome inhibition enhances resistance to DNA damage via upregulation of Rpn4-dependent DNA repair genes. FEBS Lett (2013) 0.79
X-ray structure of Salmonella typhimurium uridine phosphorylase complexed with 5-fluorouracil and molecular modelling of the complex of 5-fluorouracil with uridine phosphorylase from Vibrio cholerae. Acta Crystallogr D Biol Crystallogr (2012) 0.78
Expression, purification, crystallization and preliminary X-ray structure analysis of Vibrio cholerae uridine phosphorylase in complex with thymidine. Acta Crystallogr Sect F Struct Biol Cryst Commun (2012) 0.77