Published in RNA on March 26, 2012
High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome. Nature (2013) 1.66
Argonaute-associated short introns are a novel class of gene regulators. Nat Commun (2016) 1.40
CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems. Nucleic Acids Res (2013) 1.16
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GraphClust: alignment-free structural clustering of local RNA secondary structures. Bioinformatics (2012) 0.88
Structure of the complete bacterial SRP Alu domain. Nucleic Acids Res (2014) 0.86
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ITS2 Secondary Structure Improves Discrimination between Medicinal "Mu Tong" Species when Using DNA Barcoding. PLoS One (2015) 0.84
Conserved RNA secondary structures and long-range interactions in hepatitis C viruses. RNA (2015) 0.83
CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci. Bioinformatics (2014) 0.83
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Characterization of the two intra-individual sequence variants in the 18S rRNA gene in the plant parasitic nematode, Rotylenchulus reniformis. PLoS One (2013) 0.81
Identification of non-coding RNAs with a new composite feature in the Hybrid Random Forest Ensemble algorithm. Nucleic Acids Res (2014) 0.80
The incidence and pattern of copollinator diversification in dioecious and monoecious figs. Evolution (2015) 0.80
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LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search. Algorithms Mol Biol (2013) 0.79
ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs. BMC Bioinformatics (2014) 0.78
IF-combined smRNA FISH reveals interaction of MCPIP1 protein with IER3 mRNA. Biol Open (2016) 0.77
Small regulatory RNA-induced growth rate heterogeneity of Bacillus subtilis. PLoS Genet (2015) 0.77
Survey of Natural Language Processing Techniques in Bioinformatics. Comput Math Methods Med (2015) 0.77
An internal ribosome entry site in the 5' untranslated region of epidermal growth factor receptor allows hypoxic expression. Oncogenesis (2015) 0.77
Bioinformatics of prokaryotic RNAs. RNA Biol (2014) 0.77
Effective alignment of RNA pseudoknot structures using partition function posterior log-odds scores. BMC Bioinformatics (2015) 0.77
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Human immunodeficiency virus Tat associates with a specific set of cellular RNAs. Retrovirology (2014) 0.76
Loss of Conserved Noncoding RNAs in Genomes of Bacterial Endosymbionts. Genome Biol Evol (2016) 0.76
Insights into the Evolutionary History of an Extinct South American Freshwater Snail Based on Historical DNA. PLoS One (2016) 0.75
Elaborate uORF/IRES features control expression and localization of human glycyl-tRNA synthetase. RNA Biol (2015) 0.75
The Conserved Dcw Gene Cluster of R. sphaeroides Is Preceded by an Uncommonly Extended 5' Leader Featuring the sRNA UpsM. PLoS One (2016) 0.75
Optimizing RNA structures by sequence extensions using RNAcop. Nucleic Acids Res (2015) 0.75
Identification of Conserved and Potentially Regulatory Small RNAs in Heterocystous Cyanobacteria. Front Microbiol (2016) 0.75
ITS1, 5.8S and ITS2 secondary structure modelling for intra-specific differentiation among species of the Colletotrichum gloeosporioides sensu lato species complex. Springerplus (2014) 0.75
High diversity of picornaviruses in rats from different continents revealed by deep sequencing. Emerg Microbes Infect (2016) 0.75
In silico discovery and modeling of non-coding RNA structure in viruses. Methods (2015) 0.75
The sRNAome mining revealed existence of unique signature small RNAs derived from 5.8SrRNA from Piper nigrum and other plant lineages. Sci Rep (2017) 0.75
Small non-coding RNAs in plant-pathogenic Xanthomonas spp. RNA Biol (2014) 0.75
Phylogenetic distribution of plant snoRNA families. BMC Genomics (2016) 0.75
Mycoplasma non-coding RNA: identification of small RNAs and targets. BMC Genomics (2016) 0.75
Genome-wide identification of Wig-1 mRNA targets by RIP-Seq analysis. Oncotarget (2016) 0.75
Dengue virus genomic variation associated with mosquito adaptation defines the pattern of viral non-coding RNAs and fitness in human cells. PLoS Pathog (2017) 0.75
PARTICLE triplexes cluster in the tumor suppressor WWOX and may extend throughout the human genome. Sci Rep (2017) 0.75
Complete Genome Sequences of Three phi29-Like Bacillus cereus Group Podoviridae. Genome Announc (2017) 0.75
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An extensive class of small RNAs in Caenorhabditis elegans. Science (2001) 34.17
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
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Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science (2005) 16.82
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A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes Dev (2009) 5.04
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Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comput Biol (2007) 4.28
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CMfinder--a covariance model based RNA motif finding algorithm. Bioinformatics (2005) 2.96
A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Res (2005) 2.89
Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure. Genome Res (2006) 2.68
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Local similarity in RNA secondary structures. Proc IEEE Comput Soc Bioinform Conf (2003) 2.33
Probalign: multiple sequence alignment using partition function posterior probabilities. Bioinformatics (2006) 2.13
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Multiple structural alignment and clustering of RNA sequences. Bioinformatics (2007) 1.98
MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons. Bioinformatics (2005) 1.98
Prediction of locally stable RNA secondary structures for genome-wide surveys. Bioinformatics (2004) 1.93
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
MSARI: multiple sequence alignments for statistical detection of RNA secondary structure. Proc Natl Acad Sci U S A (2004) 1.85
A global view of genomic information--moving beyond the gene and the master regulator. Trends Genet (2009) 1.72
The final cut. The importance of tRNA 3'-processing. EMBO Rep (2001) 1.59
Evidence for human microRNA-offset RNAs in small RNA sequencing data. Bioinformatics (2009) 1.55
Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization. BMC Bioinformatics (2007) 1.51
Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions. Genome Res (2007) 1.37
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
Processing of precursor tRNAs in Drosophila. Processing of the 3' end involves an endonucleolytic cleavage and occurs after 5' end maturation. J Biol Chem (1985) 1.29
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
Non-coding RNAs in Ciona intestinalis. Bioinformatics (2005) 1.21
Strategies for measuring evolutionary conservation of RNA secondary structures. BMC Bioinformatics (2008) 1.21
Specific alignment of structured RNA: stochastic grammars and sequence annealing. Bioinformatics (2008) 1.16
Computational RNomics of drosophilids. BMC Genomics (2007) 1.15
The 5'-flanking sequences of Drosophila melanogaster tRNA5Asn genes differentially arrest RNA polymerase III. J Biol Chem (1986) 1.14
Lightweight comparison of RNAs based on exact sequence-structure matches. Bioinformatics (2009) 1.07
Arthropod 7SK RNA. Mol Biol Evol (2008) 1.04
Evolution of 7SK RNA and its protein partners in metazoa. Mol Biol Evol (2009) 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
The Vienna RNA websuite. Nucleic Acids Res (2008) 9.02
Secondary structure prediction for aligned RNA sequences. J Mol Biol (2002) 8.80
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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
IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics (2008) 2.88
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
Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity. Nat Genet (2004) 2.41
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
The small RNA PhrS stimulates synthesis of the Pseudomonas aeruginosa quinolone signal. Mol Microbiol (2011) 2.00
Tandem stem-loops in roX RNAs act together to mediate X chromosome dosage compensation in Drosophila. Mol Cell (2013) 1.99
MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons. Bioinformatics (2005) 1.98
Pre-mRNA secondary structures influence exon recognition. PLoS Genet (2007) 1.92
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
Freiburg RNA Tools: a web server integrating INTARNA, EXPARNA and LOCARNA. Nucleic Acids Res (2010) 1.84
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
INFO-RNA--a fast approach to inverse RNA folding. Bioinformatics (2006) 1.73
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
Using RNA secondary structures to guide sequence motif finding towards single-stranded regions. Nucleic Acids Res (2006) 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
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
Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments. Nucleic Acids Res (2008) 1.47
Visualization of barrier tree sequences. IEEE Trans Vis Comput Graph (2006) 1.45
Parallel evolution of tumour subclones mimics diversity between tumours. J Pathol (2013) 1.42
RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data. RNA (2011) 1.42
Characterization of CRISPR RNA processing in Clostridium thermocellum and Methanococcus maripaludis. Nucleic Acids Res (2012) 1.41
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
Global or local? Predicting secondary structure and accessibility in mRNAs. Nucleic Acids Res (2012) 1.36
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
Single-nucleotide polymorphisms in NAGNAG acceptors are highly predictive for variations of alternative splicing. Am J Hum Genet (2005) 1.29
Comparative genomics boosts target prediction for bacterial small RNAs. Proc Natl Acad Sci U S A (2013) 1.29
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