ViennaRNA Package 2.0.

RNA-guided human genome engineering via Cas9. Science (2013) 48.29

Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System. Cell (2015) 5.97

The favorable IFNL3 genotype escapes mRNA decay mediated by AU-rich elements and hepatitis C virus-induced microRNAs. Nat Immunol (2013) 2.60

A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets. Nat Methods (2013) 2.16

Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome. Science (2017) 2.09

CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nat Methods (2015) 1.88

The dynamic N(1)-methyladenosine methylome in eukaryotic messenger RNA. Nature (2016) 1.88

High-throughput determination of RNA structure by proximity ligation. Nat Biotechnol (2015) 1.66

Reversible methylation of m(6)Am in the 5' cap controls mRNA stability. Nature (2016) 1.63

Rapid identification of cell-specific, internalizing RNA aptamers with bioinformatics analyses of a cell-based aptamer selection. PLoS One (2012) 1.60

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nat Genet (2016) 1.54

Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. PLoS Genet (2016) 1.49

Genetic Codes with No Dedicated Stop Codon: Context-Dependent Translation Termination. Cell (2016) 1.45

Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis. PLoS Comput Biol (2015) 1.44

A novel translational control mechanism involving RNA structures within coding sequences. Genome Res (2016) 1.43

hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1. Nature (2015) 1.42

Insights into the design and interpretation of iCLIP experiments. Genome Biol (2017) 1.40

Translation of 5' leaders is pervasive in genes resistant to eIF2 repression. Elife (2015) 1.40

General rules for functional microRNA targeting. Nat Genet (2016) 1.39

Mirnacle: machine learning with SMOTE and random forest for improving selectivity in pre-miRNA ab initio prediction. BMC Bioinformatics (2016) 1.38

Retrozymes are a unique family of non-autonomous retrotransposons with hammerhead ribozymes that propagate in plants through circular RNAs. Genome Biol (2016) 1.38

CRISPR/Cas9: a molecular Swiss army knife for simultaneous introduction of multiple genetic modifications in Saccharomyces cerevisiae. FEMS Yeast Res (2015) 1.25

CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains. Nucleic Acids Res (2014) 1.23

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. Nucleic Acids Res (2016) 1.18

The fitness landscape of a tRNA gene. Science (2016) 1.18

repRNA: a web server for generating various feature vectors of RNA sequences. Mol Genet Genomics (2015) 1.16

EF-P dependent pauses integrate proximal and distal signals during translation. PLoS Genet (2014) 1.14

The coding and noncoding architecture of the Caulobacter crescentus genome. PLoS Genet (2014) 1.11

Are viral small RNA regulating Dengue virus replication beyond serotype 2? Proc Natl Acad Sci U S A (2014) 1.09

Genome-wide discovery of human splicing branchpoints. Genome Res (2015) 1.08

De novo design of a synthetic riboswitch that regulates transcription termination. Nucleic Acids Res (2012) 1.07

Clarifying the Translational Pausing Landscape in Bacteria by Ribosome Profiling. Cell Rep (2016) 1.06

Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams. Bioinformatics (2015) 1.06

Dynamic landscape and regulation of RNA editing in mammals. Nature (2017) 1.06

RNA secondary structure analysis using RNAstructure. Curr Protoc Bioinformatics (2006) 1.04

TargetRNA2: identifying targets of small regulatory RNAs in bacteria. Nucleic Acids Res (2014) 1.04

RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs. Hum Mutat (2013) 1.03

Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation. Elife (2016) 1.02

Differential expression of tomato spotted wilt virus-derived viral small RNAs in infected commercial and experimental host plants. PLoS One (2013) 1.02

GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes. Nucleic Acids Res (2015) 1.01

Transcription signatures encoded by ultraconserved genomic regions in human prostate cancer. Mol Cancer (2013) 1.01

The RNAsnp web server: predicting SNP effects on local RNA secondary structure. Nucleic Acids Res (2013) 1.00

Finding the target sites of RNA-binding proteins. Wiley Interdiscip Rev RNA (2013) 0.99

Evidence for the widespread distribution of CRISPR-Cas system in the Phylum Cyanobacteria. RNA Biol (2013) 0.99

Mapping overlapping functional elements embedded within the protein-coding regions of RNA viruses. Nucleic Acids Res (2014) 0.99

Probing Xist RNA Structure in Cells Using Targeted Structure-Seq. PLoS Genet (2015) 0.98

Catalysts from synthetic genetic polymers. Nature (2014) 0.98

Predicting sRNAs and their targets in bacteria. Genomics Proteomics Bioinformatics (2012) 0.98

Intron retention in the 5'UTR of the novel ZIF2 transporter enhances translation to promote zinc tolerance in arabidopsis. PLoS Genet (2014) 0.97

In vivo ligands of MDA5 and RIG-I in measles virus-infected cells. PLoS Pathog (2014) 0.97

Novel modes of RNA editing in mitochondria. Nucleic Acids Res (2016) 0.97

Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design. Genome Biol (2016) 0.96

Dynamical features of the Plasmodium falciparum ribosome during translation. Nucleic Acids Res (2015) 0.95

Dengue virus RNA structure specialization facilitates host adaptation. PLoS Pathog (2015) 0.95

Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function. PLoS Genet (2015) 0.95

Genome sequence and genetic diversity of European ash trees. Nature (2016) 0.95

MIR137 variants identified in psychiatric patients affect synaptogenesis and neuronal transmission gene sets. Mol Psychiatry (2014) 0.94

Diverse roles of assembly factors revealed by structures of late nuclear pre-60S ribosomes. Nature (2016) 0.94

The origin of biased sequence depth in sequence-independent nucleic acid amplification and optimization for efficient massive parallel sequencing. PLoS One (2013) 0.94

RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments. Nucleic Acids Res (2013) 0.93

DNA secondary structures are associated with recombination in major Plasmodium falciparum variable surface antigen gene families. Nucleic Acids Res (2013) 0.92

A pRNA-induced structural rearrangement triggers 6S-1 RNA release from RNA polymerase in Bacillus subtilis. EMBO J (2012) 0.92

DSSR: an integrated software tool for dissecting the spatial structure of RNA. Nucleic Acids Res (2015) 0.92

Profiling the RNA editomes of wild-type C. elegans and ADAR mutants. Genome Res (2014) 0.91

Bellman's GAP--a language and compiler for dynamic programming in sequence analysis. Bioinformatics (2013) 0.91

Inferring fitness landscapes by regression produces biased estimates of epistasis. Proc Natl Acad Sci U S A (2014) 0.91

The RNA shapes studio. Bioinformatics (2014) 0.91

Hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data. Methods (2013) 0.91

A comparison of performance of plant miRNA target prediction tools and the characterization of features for genome-wide target prediction. BMC Genomics (2014) 0.91

Primary transcriptome map of the hyperthermophilic archaeon Thermococcus kodakarensis. BMC Genomics (2014) 0.90

Next generation sequencing reveals regulation of distinct Aedes microRNAs during chikungunya virus development. PLoS Negl Trop Dis (2014) 0.90

Direct evaluation of tRNA aminoacylation status by the T-box riboswitch using tRNA-mRNA stacking and steric readout. Mol Cell (2014) 0.90

Diverse human extracellular RNAs are widely detected in human plasma. Nat Commun (2016) 0.90

Evaluating the fitness cost of protein expression in Saccharomyces cerevisiae. Genome Biol Evol (2013) 0.90

APOBEC3A cytidine deaminase induces RNA editing in monocytes and macrophages. Nat Commun (2015) 0.89

microRNAs miR-27a and miR-27b directly regulate liver dihydropyrimidine dehydrogenase expression through two conserved binding sites. Mol Cancer Ther (2014) 0.89

mRNA secondary structure optimization using a correlated stem-loop prediction. Nucleic Acids Res (2013) 0.89

The discriminant power of RNA features for pre-miRNA recognition. BMC Bioinformatics (2014) 0.89

COFOLD: an RNA secondary structure prediction method that takes co-transcriptional folding into account. Nucleic Acids Res (2013) 0.89

MREdictor: a two-step dynamic interaction model that accounts for mRNA accessibility and Pumilio binding accurately predicts microRNA targets. Nucleic Acids Res (2013) 0.89

RNA Structure Duplications and Flavivirus Host Adaptation. Trends Microbiol (2016) 0.89

PARP13 regulates cellular mRNA post-transcriptionally and functions as a pro-apoptotic factor by destabilizing TRAILR4 transcript. Nat Commun (2014) 0.89

Design and bioinformatics analysis of genome-wide CLIP experiments. Nucleic Acids Res (2015) 0.88

Aptamer Selection Technology and Recent Advances. Mol Ther Nucleic Acids (2016) 0.88

Tunable protein synthesis by transcript isoforms in human cells. Elife (2016) 0.88

The role of RNA structure at 5' untranslated region in microRNA-mediated gene regulation. RNA (2014) 0.88

CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data. Genome Biol (2014) 0.88

mirMark: a site-level and UTR-level classifier for miRNA target prediction. Genome Biol (2014) 0.88

The paradox of dual roles in the RNA world: resolving the conflict between stable folding and templating ability. J Mol Evol (2013) 0.87

ARGONAUTE2 cooperates with SWI/SNF complex to determine nucleosome occupancy at human Transcription Start Sites. Nucleic Acids Res (2015) 0.87

Blood feeding and Plasmodium infection alters the miRNome of Anopheles stephensi. PLoS One (2014) 0.87

SHAPE directed RNA folding. Bioinformatics (2015) 0.87

Analysis of the RNA Binding Specificity Landscape of C5 Protein Reveals Structure and Sequence Preferences that Direct RNase P Specificity. Cell Chem Biol (2016) 0.87

Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA. PLoS Comput Biol (2015) 0.86

Finding microRNA targets in plants: current status and perspectives. Genomics Proteomics Bioinformatics (2012) 0.86

RNA Enrichment Method for Quantitative Transcriptional Analysis of Pathogens In Vivo Applied to the Fungus Candida albicans. MBio (2015) 0.86

Genomic analyses reveal broad impact of miR-137 on genes associated with malignant transformation and neuronal differentiation in glioblastoma cells. PLoS One (2014) 0.86

Rationally designed, heterologous S. cerevisiae transcripts expose novel expression determinants. RNA Biol (2015) 0.86

Computational Characterization of Exogenous MicroRNAs that Can Be Transferred into Human Circulation. PLoS One (2015) 0.86

Hyper conserved elements in vertebrate mRNA 3'-UTRs reveal a translational network of RNA-binding proteins controlled by HuR. Nucleic Acids Res (2013) 0.86

Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A (1988) 193.60

Clustal W and Clustal X version 2.0. Bioinformatics (2007) 126.47

Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res (1981) 61.59

Improved estimation of secondary structure in ribonucleic acids. Nat New Biol (1973) 46.33

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol (1999) 41.48

MicroRNA targets in Drosophila. Genome Biol (2003) 23.59

Estimation of secondary structure in ribonucleic acids. Nature (1971) 20.52

On finding all suboptimal foldings of an RNA molecule. Science (1989) 20.36

Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci U S A (1986) 19.52

Fast and effective prediction of microRNA/target duplexes. RNA (2004) 18.10

Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim Biophys Acta (1975) 17.03

GenBank. Nucleic Acids Res (2008) 13.29

Infernal 1.0: inference of RNA alignments. Bioinformatics (2009) 12.98

Rfam: updates to the RNA families database. Nucleic Acids Res (2008) 11.61

Improved predictions of secondary structures for RNA. Proc Natl Acad Sci U S A (1989) 11.52

The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers (1990) 10.92

A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure. BMC Bioinformatics (2002) 10.84

Fast algorithm for predicting the secondary structure of single-stranded RNA. Proc Natl Acad Sci U S A (1980) 10.48

Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci U S A (2004) 10.35

Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry (1998) 9.75

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

Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers (1999) 7.80

The thermodynamics of DNA structural motifs. Annu Rev Biophys Biomol Struct (2004) 6.96

UNAFold: software for nucleic acid folding and hybridization. Methods Mol Biol (2008) 6.83

From sequences to shapes and back: a case study in RNA secondary structures. Proc Biol Sci (1994) 6.01

An improved algorithm for nucleic acid secondary structure display. Comput Appl Biosci (1988) 5.91

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

VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics (2009) 5.66

RNAML: a standard syntax for exchanging RNA information. RNA (2002) 5.34

Prediction of hybridization and melting for double-stranded nucleic acids. Biophys J (2004) 5.11

A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res (2003) 4.62

Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res (2003) 4.41

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

Dynalign: an algorithm for finding the secondary structure common to two RNA sequences. J Mol Biol (2002) 3.88

RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA (2005) 3.80

Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinformatics (2004) 3.60

NUPACK: Analysis and design of nucleic acid systems. J Comput Chem (2011) 3.33

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

Automatic detection of conserved RNA structure elements in complete RNA virus genomes. Nucleic Acids Res (1998) 3.18

MicroInspector: a web tool for detection of miRNA binding sites in an RNA sequence. Nucleic Acids Res (2005) 2.87

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

The impact of target site accessibility on the design of effective siRNAs. Nat Biotechnol (2008) 2.51

RNA folding at elementary step resolution. RNA (2000) 2.50

NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure. Nucleic Acids Res (2009) 2.49

Prediction of RNA secondary structure using generalized centroid estimators. Bioinformatics (2008) 2.48

Alignment of RNA base pairing probability matrices. Bioinformatics (2004) 2.42

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

Local similarity in RNA secondary structures. Proc IEEE Comput Soc Bioinform Conf (2003) 2.33

Early events in RNA folding. Annu Rev Phys Chem (2001) 2.29

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

Statistics of RNA secondary structures. Biopolymers (1993) 2.06

Prediction of locally stable RNA secondary structures for genome-wide surveys. Bioinformatics (2004) 1.93

RNAz 2.0: improved noncoding RNA detection. Pac Symp Biocomput (2010) 1.87

RNAplex: a fast tool for RNA-RNA interaction search. Bioinformatics (2008) 1.80

INFO-RNA--a fast approach to inverse RNA folding. Bioinformatics (2006) 1.73

Nearest-neighbor parameters for G.U mismatches: [formula; see text] is destabilizing in the contexts [formula; see text] and [formula; see text] but stabilizing in [formula; see text]. Biochemistry (1991) 1.70

Design of multistable RNA molecules. RNA (2001) 1.65

RNAsoft: A suite of RNA secondary structure prediction and design software tools. Nucleic Acids Res (2003) 1.61

Nucleic acid sequence design via efficient ensemble defect optimization. J Comput Chem (2010) 1.60

Automatic detection of conserved base pairing patterns in RNA virus genomes. Comput Chem (1999) 1.53

RNA multi-structure landscapes. A study based on temperature dependent partition functions. Eur Biophys J (1993) 1.51

SnoReport: computational identification of snoRNAs with unknown targets. Bioinformatics (2007) 1.51

The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search. Nucleic Acids Res (2005) 1.47

A computer model of evolutionary optimization. Biophys Chem (1987) 1.47

Robust prediction of consensus secondary structures using averaged base pairing probability matrices. Bioinformatics (2006) 1.39

MicroTar: predicting microRNA targets from RNA duplexes. BMC Bioinformatics (2006) 1.26

Improved free energy parameters for RNA pseudoknotted secondary structure prediction. RNA (2009) 1.24

Physical aspects of evolutionary optimization and adaptation. Phys Rev A Gen Phys (1989) 1.21

Accurate and efficient reconstruction of deep phylogenies from structured RNAs. Nucleic Acids Res (2009) 1.19

BioXSD: the common data-exchange format for everyday bioinformatics web services. Bioinformatics (2010) 1.18

Structural profiles of human miRNA families from pairwise clustering. Bioinformatics (2008) 1.16

Fast accessibility-based prediction of RNA-RNA interactions. Bioinformatics (2011) 1.09

Lightweight comparison of RNAs based on exact sequence-structure matches. Bioinformatics (2009) 1.07

Prediction of RNA base pairing probabilities on massively parallel computers. J Comput Biol (2000) 1.07

Rich parameterization improves RNA structure prediction. J Comput Biol (2011) 1.05

RNAstrand: reading direction of structured RNAs in multiple sequence alignments. Algorithms Mol Biol (2007) 1.03

A folding algorithm for extended RNA secondary structures. Bioinformatics (2011) 1.03

RNAsnoop: efficient target prediction for H/ACA snoRNAs. Bioinformatics (2009) 1.01

RNA-related tools on the Bielefeld Bioinformatics Server. Nucleic Acids Res (2003) 1.00

taveRNA: a web suite for RNA algorithms and applications. Nucleic Acids Res (2007) 0.98

The unsuccessful self-treatment of a case of "writer's block". J Appl Behav Anal (1974) 0.86

RNA secondary structure analysis using the RNAshapes package. Curr Protoc Bioinformatics (2009) 0.86

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

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

Analyses of pig genomes provide insight into porcine demography and evolution. Nature (2012) 5.58

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

The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks. Bioinformatics (2006) 1.61

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

A generalized model of the repressilator. J Math Biol (2006) 1.29

RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction. Nucleic Acids Res (2012) 1.27