Published in Bioinformatics on July 01, 2011
ViennaRNA Package 2.0. Algorithms Mol Biol (2011) 9.43
Computational analysis of noncoding RNAs. Wiley Interdiscip Rev RNA (2012) 1.01
CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction. Nucleic Acids Res (2013) 0.97
Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure. Bioinformatics (2012) 0.90
Automated identification of RNA 3D modules with discriminative power in RNA structural alignments. Nucleic Acids Res (2013) 0.85
The four ingredients of single-sequence RNA secondary structure prediction. A unifying perspective. RNA Biol (2013) 0.81
JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs. Nucleic Acids Res (2016) 0.78
Predicting RNA 3D structure using a coarse-grain helix-centered model. RNA (2015) 0.78
Algebraic Dynamic Programming over general data structures. BMC Bioinformatics (2015) 0.75
New in silico approach to assessing RNA secondary structures with non-canonical base pairs. BMC Bioinformatics (2015) 0.75
Geometric nomenclature and classification of RNA base pairs. RNA (2001) 9.08
The kink-turn: a new RNA secondary structure motif. EMBO J (2001) 8.58
Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers (1999) 7.80
UNAFold: software for nucleic acid folding and hybridization. Methods Mol Biol (2008) 6.83
RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics (2010) 5.71
The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature (2008) 5.67
The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res (2002) 5.35
Prediction of hybridization and melting for double-stranded nucleic acids. Biophys J (2004) 5.11
CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics (2006) 4.31
Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comput Biol (2007) 4.28
RSEARCH: finding homologs of single structured RNA sequences. BMC Bioinformatics (2003) 4.14
Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinformatics (2004) 3.60
RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics (2008) 3.29
The building blocks and motifs of RNA architecture. Curr Opin Struct Biol (2006) 2.94
Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments. Nucleic Acids Res (2005) 2.88
NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure. Nucleic Acids Res (2009) 2.49
RNA STRAND: the RNA secondary structure and statistical analysis database. BMC Bioinformatics (2008) 2.39
Efficient parameter estimation for RNA secondary structure prediction. Bioinformatics (2007) 2.36
A new algorithm for RNA secondary structure design. J Mol Biol (2004) 1.96
Frequency and isostericity of RNA base pairs. Nucleic Acids Res (2009) 1.88
INFO-RNA--a fast approach to inverse RNA folding. Bioinformatics (2006) 1.73
Predicting helical coaxial stacking in RNA multibranch loops. RNA (2007) 1.40
Computational approaches for RNA energy parameter estimation. RNA (2010) 1.33
Effective ambiguity checking in biosequence analysis. BMC Bioinformatics (2005) 1.06
RNAMotifScan: automatic identification of RNA structural motifs using secondary structural alignment. Nucleic Acids Res (2010) 1.01
Consensus folding of unaligned RNA sequences revisited. J Comput Biol (2006) 0.97
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
The Vienna RNA websuite. Nucleic Acids Res (2008) 9.02
Secondary structure prediction for aligned RNA sequences. J Mol Biol (2002) 8.80
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
The reality of pervasive transcription. PLoS Biol (2011) 3.41
MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol (2012) 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
The impact of target site accessibility on the design of effective siRNAs. Nat Biotechnol (2008) 2.51
Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics. J Mol Biol (2004) 2.49
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
The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures. Nucleic Acids Res (2007) 1.88
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
RNAplex: a fast tool for RNA-RNA interaction search. Bioinformatics (2008) 1.80
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
AREsite: a database for the comprehensive investigation of AU-rich elements. Nucleic Acids Res (2010) 1.58
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
RNAs everywhere: genome-wide annotation of structured RNAs. J Exp Zool B Mol Dev Evol (2007) 1.38
Structure and function of the smallest vertebrate telomerase RNA from teleost fish. J Biol Chem (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
De novo prediction of structured RNAs from genomic sequences. Trends Biotechnol (2009) 1.31
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
Non-coding RNAs in Ciona intestinalis. Bioinformatics (2005) 1.21
Detection of small RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatic tools. Microbiology (2008) 1.21
Strategies for measuring evolutionary conservation of RNA secondary structures. BMC Bioinformatics (2008) 1.21