Published in J Mol Biol on June 21, 2002
Vienna RNA secondary structure server. Nucleic Acids Res (2003) 19.69
Rfam: updates to the RNA families database. Nucleic Acids Res (2008) 11.61
ViennaRNA Package 2.0. Algorithms Mol Biol (2011) 9.43
The Vienna RNA websuite. Nucleic Acids Res (2008) 9.02
Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci U S A (2005) 8.15
Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. Genome Res (2006) 6.59
Genome-wide measurement of RNA secondary structure in yeast. Nature (2010) 5.74
RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics (2010) 5.71
Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res (2003) 4.41
Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comput Biol (2007) 4.28
Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes. Genome Res (2007) 4.28
Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinformatics (2004) 3.60
Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework. BMC Bioinformatics (2008) 3.55
RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics (2008) 3.29
A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics (2004) 3.20
A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Res (2005) 2.89
The expansion of the metazoan microRNA repertoire. BMC Genomics (2006) 2.80
Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Nature (2009) 2.72
R-Coffee: a method for multiple alignment of non-coding RNA. Nucleic Acids Res (2008) 2.69
Structured RNAs in the ENCODE selected regions of the human genome. Genome Res (2007) 2.69
Genomic organization, differential expression, and interaction of SQUAMOSA promoter-binding-like transcription factors and microRNA156 in rice. Plant Physiol (2006) 2.56
Yeast telomerase RNA: a flexible scaffold for protein subunits. Proc Natl Acad Sci U S A (2004) 2.52
Understanding the transcriptome through RNA structure. Nat Rev Genet (2011) 2.46
The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems. RNA Biol (2013) 2.44
Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems. Nucleic Acids Res (2013) 2.35
An enhanced RNA alignment benchmark for sequence alignment programs. Algorithms Mol Biol (2006) 2.35
Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis. Nucleic Acids Res (2008) 2.10
Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. BMC Bioinformatics (2006) 2.08
A fast structural multiple alignment method for long RNA sequences. BMC Bioinformatics (2008) 2.07
HotKnots: heuristic prediction of RNA secondary structures including pseudoknots. RNA (2005) 1.97
Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures. RNA (2005) 1.94
Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix. PLoS Comput Biol (2007) 1.90
A comparative method for finding and folding RNA secondary structures within protein-coding regions. Nucleic Acids Res (2004) 1.89
The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures. Nucleic Acids Res (2007) 1.88
MSARI: multiple sequence alignments for statistical detection of RNA secondary structure. Proc Natl Acad Sci U S A (2004) 1.85
A universal telomerase RNA core structure includes structured motifs required for binding the telomerase reverse transcriptase protein. Proc Natl Acad Sci U S A (2004) 1.83
Systematic discovery of structural elements governing stability of mammalian messenger RNAs. Nature (2012) 1.80
Improved RNA secondary structure prediction by maximizing expected pair accuracy. RNA (2009) 1.78
Phylogenetic position of the acariform mites: sensitivity to homology assessment under total evidence. BMC Evol Biol (2010) 1.76
Bioinformatic and functional analysis of RNA secondary structure elements among different genera of human and animal caliciviruses. Nucleic Acids Res (2008) 1.63
miROrtho: computational survey of microRNA genes. Nucleic Acids Res (2008) 1.60
IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. Bioinformatics (2011) 1.59
Evolution of small nucleolar RNAs in nematodes. Nucleic Acids Res (2006) 1.58
Structural architecture of the human long non-coding RNA, steroid receptor RNA activator. Nucleic Acids Res (2012) 1.58
Identification and analysis of ribonuclease P and MRP RNA in a broad range of eukaryotes. Nucleic Acids Res (2005) 1.56
Two antisense RNAs target the transcriptional regulator CsgD to inhibit curli synthesis. EMBO J (2010) 1.53
Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes. Proc Natl Acad Sci U S A (2008) 1.51
Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization. BMC Bioinformatics (2007) 1.51
Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments. Nucleic Acids Res (2008) 1.47
PicXAA-R: efficient structural alignment of multiple RNA sequences using a greedy approach. BMC Bioinformatics (2011) 1.46
An emerging consensus for telomerase RNA structure. Proc Natl Acad Sci U S A (2004) 1.40
Predicting helical coaxial stacking in RNA multibranch loops. RNA (2007) 1.40
Identification and comparative analysis of telomerase RNAs from Candida species reveal conservation of functional elements. RNA (2009) 1.39
RNA secondary structure in the coding region of dengue virus type 2 directs translation start codon selection and is required for viral replication. J Virol (2006) 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
Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures. Proc Natl Acad Sci U S A (2007) 1.36
Large retrotransposon derivatives: abundant, conserved but nonautonomous retroelements of barley and related genomes. Genetics (2004) 1.36
XML schemas for common bioinformatic data types and their application in workflow systems. BMC Bioinformatics (2006) 1.33
Discovery of frameshifting in Alphavirus 6K resolves a 20-year enigma. Virol J (2008) 1.33
CRS1, a chloroplast group II intron splicing factor, promotes intron folding through specific interactions with two intron domains. Plant Cell (2004) 1.32
Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs. Nucleic Acids Res (2005) 1.30
Identification of novel Drosophila melanogaster microRNAs. PLoS One (2007) 1.28
Molecular analysis of virulent determinants of enterovirus 71. PLoS One (2011) 1.25
Evolution of spliceosomal snRNA genes in metazoan animals. J Mol Evol (2008) 1.25
Biocomputational prediction of non-coding RNAs in model cyanobacteria. BMC Genomics (2009) 1.25
A method for aligning RNA secondary structures and its application to RNA motif detection. BMC Bioinformatics (2005) 1.25
Structator: fast index-based search for RNA sequence-structure patterns. BMC Bioinformatics (2011) 1.24
A new sexannulate species of Orobdella (Hirudinida, Arhynchobdellida, Orobdellidae) from Yakushima Island, Japan. Zookeys (2012) 1.24
BayesFold: rational 2 degrees folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequences. RNA (2004) 1.24
Dinucleotide controlled null models for comparative RNA gene prediction. BMC Bioinformatics (2008) 1.23
A max-margin model for efficient simultaneous alignment and folding of RNA sequences. Bioinformatics (2008) 1.23
PARTS: probabilistic alignment for RNA joinT secondary structure prediction. Nucleic Acids Res (2008) 1.22
SimulFold: simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework. PLoS Comput Biol (2007) 1.21
Strategies for measuring evolutionary conservation of RNA secondary structures. BMC Bioinformatics (2008) 1.21
Predicting helical topologies in RNA junctions as tree graphs. PLoS One (2013) 1.20
Accurate and efficient reconstruction of deep phylogenies from structured RNAs. Nucleic Acids Res (2009) 1.19
RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers. RNA (2006) 1.19
Non-coding RNA annotation of the genome of Trichoplax adhaerens. Nucleic Acids Res (2009) 1.18
Folding and finding RNA secondary structure. Cold Spring Harb Perspect Biol (2010) 1.18
Widespread purifying selection on RNA structure in mammals. Nucleic Acids Res (2013) 1.18
Co-transcriptional folding is encoded within RNA genes. BMC Mol Biol (2004) 1.16
Specific alignment of structured RNA: stochastic grammars and sequence annealing. Bioinformatics (2008) 1.16
A critical three-way junction is conserved in budding yeast and vertebrate telomerase RNAs. Nucleic Acids Res (2007) 1.15
Glyceraldehyde-3-phosphate dehydrogenase regulates endothelin-1 expression by a novel, redox-sensitive mechanism involving mRNA stability. Mol Cell Biol (2008) 1.15
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
Molecular phylogeny restores the supra-generic subdivision of homoscleromorph sponges (Porifera, Homoscleromorpha). PLoS One (2010) 1.09
Computational methods in noncoding RNA research. J Math Biol (2007) 1.08
R-Coffee: a web server for accurately aligning noncoding RNA sequences. Nucleic Acids Res (2008) 1.07
Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch. Proc Natl Acad Sci U S A (2012) 1.07
Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum. BMC Genomics (2009) 1.06
Improving the accuracy of predicting secondary structure for aligned RNA sequences. Nucleic Acids Res (2010) 1.06
Chikungunya virus 3' untranslated region: adaptation to mosquitoes and a population bottleneck as major evolutionary forces. PLoS Pathog (2013) 1.04
Accessibility and conservation: general features of bacterial small RNA-mRNA interactions? RNA Biol (2012) 1.04
Site-specific mobilization of vinyl chloride respiration islands by a mechanism common in Dehalococcoides. BMC Genomics (2011) 1.03
RNAstrand: reading direction of structured RNAs in multiple sequence alignments. Algorithms Mol Biol (2007) 1.03
Predictions of RNA secondary structure by combining homologous sequence information. Bioinformatics (2009) 1.03
RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs. Hum Mutat (2013) 1.03
Conflicting selection pressures on synonymous codon use in yeast suggest selection on mRNA secondary structures. BMC Evol Biol (2008) 1.02
Semiautomated improvement of RNA alignments. RNA (2007) 1.02
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science (2007) 18.59
ViennaRNA Package 2.0. Algorithms Mol Biol (2011) 9.43
Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci U S A (2005) 8.15
The primary transcriptome of the major human pathogen Helicobacter pylori. Nature (2010) 7.70
Molecular evolution of a microRNA cluster. J Mol Biol (2004) 5.94
Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol (2010) 5.39
Interleukin-6 dependent survival of multiple myeloma cells involves the Stat3-mediated induction of microRNA-21 through a highly conserved enhancer. Blood (2007) 5.14
tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res (2008) 4.88
Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Nat Biotechnol (2005) 4.68
Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comput Biol (2007) 4.28
Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLoS Comput Biol (2009) 4.24
Proteinortho: detection of (co-)orthologs in large-scale analysis. BMC Bioinformatics (2011) 4.15
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes. Nucleic Acids Res (2006) 3.59
MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol (2012) 3.41
The reality of pervasive transcription. PLoS Biol (2011) 3.41
RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics (2008) 3.29
Thermodynamics of RNA-RNA binding. Bioinformatics (2006) 3.10
The expansion of the metazoan microRNA repertoire. BMC Genomics (2006) 2.80
The African coelacanth genome provides insights into tetrapod evolution. Nature (2013) 2.78
Memory efficient folding algorithms for circular RNA secondary structures. Bioinformatics (2006) 2.77
Partition function and base pairing probabilities of RNA heterodimers. Algorithms Mol Biol (2006) 2.74
Structured RNAs in the ENCODE selected regions of the human genome. Genome Res (2007) 2.69
Alignment of RNA base pairing probability matrices. Bioinformatics (2004) 2.42
Evolution. Transitions from nonliving to living matter. Science (2004) 2.26
Local RNA base pairing probabilities in large sequences. Bioinformatics (2005) 2.17
Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data. Bioinformatics (2006) 2.13
Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis. Nucleic Acids Res (2008) 2.10
Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing. Nat Genet (2012) 2.07
Variations on RNA folding and alignment: lessons from Benasque. J Math Biol (2007) 1.91
RNAz 2.0: improved noncoding RNA detection. Pac Symp Biocomput (2010) 1.87
A survey of nematode SmY RNAs. RNA Biol (2009) 1.85
Conserved RNA secondary structures in Flaviviridae genomes. J Gen Virol (2004) 1.81
Evolution of microRNAs located within Hox gene clusters. J Exp Zool B Mol Dev Evol (2005) 1.77
Centers of complex networks. J Theor Biol (2003) 1.74
RNAcentral: A vision for an international database of RNA sequences. RNA (2011) 1.73
A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection. Genome Biol (2014) 1.60
Evidence for human microRNA-offset RNAs in small RNA sequencing data. Bioinformatics (2009) 1.55
The "fish-specific" Hox cluster duplication is coincident with the origin of teleosts. Mol Biol Evol (2005) 1.54
SnoReport: computational identification of snoRNAs with unknown targets. Bioinformatics (2007) 1.51
LocARNA-P: accurate boundary prediction and improved detection of structural RNAs. RNA (2012) 1.51
Evolutionary patterns of non-coding RNAs. Theory Biosci (2005) 1.49
Alu elements in ANRIL non-coding RNA at chromosome 9p21 modulate atherogenic cell functions through trans-regulation of gene networks. PLoS Genet (2013) 1.48
Independent Hox-cluster duplications in lampreys. J Exp Zool B Mol Dev Evol (2003) 1.48
Visualization of barrier tree sequences. IEEE Trans Vis Comput Graph (2006) 1.45
RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data. RNA (2011) 1.42
Genomic and morphological evidence converge to resolve the enigma of Strepsiptera. Curr Biol (2012) 1.40
Structure and function of the smallest vertebrate telomerase RNA from teleost fish. J Biol Chem (2007) 1.38
RNAs everywhere: genome-wide annotation of structured RNAs. J Exp Zool B Mol Dev Evol (2007) 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
RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction. Nucleic Acids Res (2012) 1.27
Counterexamples in chemical ring perception. J Chem Inf Comput Sci (2004) 1.27
Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions. Nucleic Acids Res (2011) 1.25
Evolution of spliceosomal snRNA genes in metazoan animals. J Mol Evol (2008) 1.25
RNApredator: fast accessibility-based prediction of sRNA targets. Nucleic Acids Res (2011) 1.25
Solvent exposure imparts similar selective pressures across a range of yeast proteins. Mol Biol Evol (2009) 1.24
Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements. Nucleic Acids Res (2011) 1.22
Detection of small RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatic tools. Microbiology (2008) 1.21
Non-coding RNAs in Ciona intestinalis. Bioinformatics (2005) 1.21
Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome. Proc Natl Acad Sci U S A (2010) 1.20
Multiple sequence alignment with user-defined anchor points. Algorithms Mol Biol (2006) 1.20
CREx: inferring genomic rearrangements based on common intervals. Bioinformatics (2007) 1.19
Accurate and efficient reconstruction of deep phylogenies from structured RNAs. Nucleic Acids Res (2009) 1.19
The common ancestral core of vertebrate and fungal telomerase RNAs. Nucleic Acids Res (2012) 1.18
A novel family of plasmid-transferred anti-sense ncRNAs. RNA Biol (2010) 1.18
Non-coding RNA annotation of the genome of Trichoplax adhaerens. Nucleic Acids Res (2009) 1.18
Widespread purifying selection on RNA structure in mammals. Nucleic Acids Res (2013) 1.18
Genetic aspects of mitochondrial genome evolution. Mol Phylogenet Evol (2012) 1.18
A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny. Mol Phylogenet Evol (2013) 1.17
The tedious task of finding homologous noncoding RNA genes. RNA (2009) 1.17
The effect of RNA secondary structures on RNA-ligand binding and the modifier RNA mechanism: a quantitative model. Gene (2005) 1.17
DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res (2011) 1.16
Noisy: identification of problematic columns in multiple sequence alignments. Algorithms Mol Biol (2008) 1.16
Structural profiles of human miRNA families from pairwise clustering. Bioinformatics (2008) 1.16
Topology and prediction of RNA pseudoknots. Bioinformatics (2011) 1.15
Computational RNomics of drosophilids. BMC Genomics (2007) 1.15
Bichir HoxA cluster sequence reveals surprising trends in ray-finned fish genomic evolution. Genome Res (2004) 1.13
Surveying phylogenetic footprints in large gene clusters: applications to Hox cluster duplications. Mol Phylogenet Evol (2004) 1.12
Comparative analysis of structured RNAs in S. cerevisiae indicates a multitude of different functions. BMC Biol (2007) 1.12
Multiple sequence alignments of partially coding nucleic acid sequences. BMC Bioinformatics (2005) 1.11
Mitochondrial genome evolution in Ophiuroidea, Echinoidea, and Holothuroidea: insights in phylogenetic relationships of Echinodermata. Mol Phylogenet Evol (2010) 1.11
FRANz: reconstruction of wild multi-generation pedigrees. Bioinformatics (2009) 1.10
Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation. BMC Bioinformatics (2006) 1.10
Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels. Mol Syst Biol (2012) 1.10
Traces of post-transcriptional RNA modifications in deep sequencing data. Biol Chem (2011) 1.09
Fast accessibility-based prediction of RNA-RNA interactions. Bioinformatics (2011) 1.09
Orthology relations, symbolic ultrametrics, and cographs. J Math Biol (2012) 1.09
Quasi-independence, homology and the unity of type: a topological theory of characters. J Theor Biol (2003) 1.08
Partition function and base pairing probabilities for RNA-RNA interaction prediction. Bioinformatics (2009) 1.08
The mitochondrial DNA of Xenoturbella bocki: genomic architecture and phylogenetic analysis. Theory Biosci (2007) 1.08
De novo design of a synthetic riboswitch that regulates transcription termination. Nucleic Acids Res (2012) 1.07
Modeling amino acid substitution patterns in orthologous and paralogous genes. Mol Phylogenet Evol (2006) 1.07
Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum. BMC Genomics (2009) 1.06
Folding kinetics of large RNAs. J Mol Biol (2008) 1.05
Arthropod 7SK RNA. Mol Biol Evol (2008) 1.04
RNAstrand: reading direction of structured RNAs in multiple sequence alignments. Algorithms Mol Biol (2007) 1.03
RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs. Hum Mutat (2013) 1.03
A folding algorithm for extended RNA secondary structures. Bioinformatics (2011) 1.03
Evolution of the vertebrate Y RNA cluster. Theory Biosci (2007) 1.02
Evolution of 7SK RNA and its protein partners in metazoa. Mol Biol Evol (2009) 1.02