Published in J Bioinform Comput Biol on April 01, 2009
Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biol (2010) 3.19
An allosteric self-splicing ribozyme triggered by a bacterial second messenger. Science (2010) 2.33
Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis. Nature (2009) 1.43
New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes. Genome Res (2011) 1.32
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Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science (2008) 4.89
Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comput Biol (2007) 4.28
The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biol (2007) 3.80
Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Res (2007) 3.59
CMfinder--a covariance model based RNA motif finding algorithm. Bioinformatics (2005) 2.96
Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria. RNA (2008) 1.67
Riboswitches and the role of noncoding RNAs in bacterial metabolic control. Curr Opin Chem Biol (2005) 1.61
Guanine riboswitch variants from Mesoplasma florum selectively recognize 2'-deoxyguanosine. Proc Natl Acad Sci U S A (2007) 1.54
A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes. PLoS Comput Biol (2007) 1.53
The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches. RNA (2008) 1.39
Riboswitches that sense S-adenosylhomocysteine and activate genes involved in coenzyme recycling. Mol Cell (2008) 1.38
Prediction of structured non-coding RNAs in the genomes of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae. J Exp Zool B Mol Dev Evol (2006) 1.34
A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism. Mol Microbiol (2008) 1.33
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
Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature (2002) 8.14
Gene regulation by riboswitches. Nat Rev Mol Cell Biol (2004) 7.00
Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell (2003) 6.21
Control of gene expression by a natural metabolite-responsive ribozyme. Nature (2004) 6.04
Sequence-based heuristics for faster annotation of non-coding RNA families. Bioinformatics (2005) 6.00
Regulation of bacterial gene expression by riboswitches. Annu Rev Microbiol (2005) 5.66
Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol (2006) 5.44
Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. Chem Biol (2004) 5.44
An mRNA structure that controls gene expression by binding FMN. Proc Natl Acad Sci U S A (2002) 5.02
A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science (2004) 4.91
Genetic control by a metabolite binding mRNA. Chem Biol (2002) 4.85
The RNA WikiProject: community annotation of RNA families. RNA (2008) 4.83
Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming. Dev Cell (2010) 4.50
New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc Natl Acad Sci U S A (2004) 4.35
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Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch. Nature (2006) 3.90
Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature (2007) 3.87
Adenine riboswitches and gene activation by disruption of a transcription terminator. Nat Struct Mol Biol (2003) 3.84
Riboswitches as versatile gene control elements. Curr Opin Struct Biol (2005) 3.83
The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biol (2007) 3.80
An mRNA structure that controls gene expression by binding S-adenosylmethionine. Nat Struct Biol (2003) 3.75
The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Mol Cell (2005) 3.62
Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Res (2007) 3.59
Metabolite-binding RNA domains are present in the genes of eukaryotes. RNA (2003) 3.42
An mRNA structure in bacteria that controls gene expression by binding lysine. Genes Dev (2003) 3.37
Structural basis of ligand binding by a c-di-GMP riboswitch. Nat Struct Mol Biol (2009) 3.28
Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biol (2010) 3.19
Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy. Bioinformatics (2004) 3.14
MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries. Stem Cells (2008) 3.14
Riboswitches as antibacterial drug targets. Nat Biotechnol (2006) 3.01
The kinetics of ligand binding by an adenine-sensing riboswitch. Biochemistry (2005) 2.98
CMfinder--a covariance model based RNA motif finding algorithm. Bioinformatics (2005) 2.96
Antibacterial lysine analogs that target lysine riboswitches. Nat Chem Biol (2006) 2.94
In-line probing analysis of riboswitches. Methods Mol Biol (2008) 2.76
Tandem riboswitch architectures exhibit complex gene control functions. Science (2006) 2.63
A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain. Nat Struct Mol Biol (2007) 2.52
Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes. Nucleic Acids Res (2004) 2.47
Genetic control by metabolite-binding riboswitches. Chembiochem (2003) 2.32
Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria. Genome Biol (2005) 2.32
6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter. RNA (2005) 2.28
Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes. Nat Biotechnol (2005) 2.22
Riboswitch control of gene expression in plants by splicing and alternative 3' end processing of mRNAs. Plant Cell (2007) 2.18
DUX4 activates germline genes, retroelements, and immune mediators: implications for facioscapulohumeral dystrophy. Dev Cell (2011) 2.17
Thiamine pyrophosphate riboswitches are targets for the antimicrobial compound pyrithiamine. Chem Biol (2005) 2.00
Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis. RNA (2007) 1.96
Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions. RNA (2006) 1.81
Compression of next-generation sequencing reads aided by highly efficient de novo assembly. Nucleic Acids Res (2012) 1.76
Ribozyme speed limits. RNA (2003) 1.68
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
R2R--software to speed the depiction of aesthetic consensus RNA secondary structures. BMC Bioinformatics (2011) 1.60
Guanine riboswitch variants from Mesoplasma florum selectively recognize 2'-deoxyguanosine. Proc Natl Acad Sci U S A (2007) 1.54
A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes. PLoS Comput Biol (2007) 1.53
Roseoflavin is a natural antibacterial compound that binds to FMN riboswitches and regulates gene expression. RNA Biol (2009) 1.50
Genetic and epigenetic determinants of neurogenesis and myogenesis. Dev Cell (2012) 1.47
Riboswitches in eubacteria sense the second messenger c-di-AMP. Nat Chem Biol (2013) 1.47
Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis. Nature (2009) 1.43
Fluoride resistance and transport by riboswitch-controlled CLC antiporters. Proc Natl Acad Sci U S A (2012) 1.41
The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches. RNA (2008) 1.39
Riboswitches that sense S-adenosylhomocysteine and activate genes involved in coenzyme recycling. Mol Cell (2008) 1.38
Characteristics of ligand recognition by a glmS self-cleaving ribozyme. Angew Chem Int Ed Engl (2006) 1.38
Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions. Genome Res (2007) 1.37
Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteine. Biochem Cell Biol (2008) 1.35
A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism. Mol Microbiol (2008) 1.33
A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria. RNA (2009) 1.32
De novo prediction of structured RNAs from genomic sequences. Trends Biotechnol (2009) 1.31
Identification of hammerhead ribozymes in all domains of life reveals novel structural variations. PLoS Comput Biol (2011) 1.29
Design and antimicrobial action of purine analogues that bind Guanine riboswitches. ACS Chem Biol (2009) 1.29
Purine sensing by riboswitches. Biol Cell (2008) 1.24
Eukaryotic resistance to fluoride toxicity mediated by a widespread family of fluoride export proteins. Proc Natl Acad Sci U S A (2013) 1.22
Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'. BMC Genomics (2009) 1.21
Riboswitches: from ancient gene-control systems to modern drug targets. Future Microbiol (2009) 1.16
Challenges of ligand identification for riboswitch candidates. RNA Biol (2011) 1.16
A regression-based K nearest neighbor algorithm for gene function prediction from heterogeneous data. BMC Bioinformatics (2006) 1.15
A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate. Chem Biol (2010) 1.14
Integron attI1 sites, not riboswitches, associate with antibiotic resistance genes. Cell (2013) 1.10
RNIE: genome-wide prediction of bacterial intrinsic terminators. Nucleic Acids Res (2011) 1.09
An integrative genomic approach identifies p73 and p63 as activators of miR-200 microRNA family transcription. 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
Molecular-recognition characteristics of SAM-binding riboswitches. Angew Chem Int Ed Engl (2006) 1.06
Evidence for widespread gene control function by the ydaO riboswitch candidate. J Bacteriol (2010) 1.05
Transcriptional analyses of Barrett's metaplasia and normal upper GI mucosae. Neoplasia (2002) 1.03
Ligating DNA with DNA. J Am Chem Soc (2004) 1.01
Engineered allosteric ribozymes that respond to specific divalent metal ions. Nucleic Acids Res (2005) 1.01