Computational analysis of noncoding RNAs

TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots

(2012) Matthew G. Seetin et al.   BIOINFORMATICS

RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction

(2012) Stefan Washietl et al.   NUCLEIC ACIDS RESEARCH

LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs

(2012) S. Will et al.   RNA

Sparsification of RNA structure prediction including pseudoknots

(2011) Mathias Möhl et al.   Algorithms for Molecular Biology

Protein-coding structured RNAs: A computational survey of conserved RNA secondary structures overlapping coding regions in drosophilids

(2011) Sven Findeiß et al.   BIOCHIMIE

A folding algorithm for extended RNA secondary structures

(2011) C. H. zu Siederdissen et al.   BIOINFORMATICS

IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming

(2011) Kengo Sato et al.   BIOINFORMATICS

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

(2011) M. F. Lin et al.   BIOINFORMATICS

TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences

(2011) Arif O Harmanci et al.   BMC BIOINFORMATICS

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Unusually effective microRNA targeting within repeat-rich coding regions of mammalian mRNAs

(2011) M. Schnall-Levin et al.   GENOME RESEARCH

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

TT2NE: a novel algorithm to predict RNA secondary structures with pseudoknots

(2011) Michaël Bon et al.   NUCLEIC ACIDS RESEARCH

Computing the Partition Function for Kinetically Trapped RNA Secondary Structures

(2011) William A. Lorenz et al.   PLoS One

Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)

(2011) J. B. Lucks et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNAcentral: A vision for an international database of RNA sequences

(2011) A. Bateman et al.   RNA

RNAcode: Robust discrimination of coding and noncoding regions in comparative sequence data

(2011) S. Washietl et al.   RNA

The Reality of Pervasive Transcription

(2011) Michael B. Clark et al.   PLOS BIOLOGY

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

RNA–RNA interaction prediction based on multiple sequence alignments

(2010) Andrew X. Li et al.   BIOINFORMATICS

PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences

(2010) Stefan E. Seemann et al.   BIOINFORMATICS

MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data

(2010) Anthony Mathelier et al.   BIOINFORMATICS

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

Advances in RNA structure analysis by chemical probing

(2010) Kevin M Weeks   CURRENT OPINION IN STRUCTURAL BIOLOGY

Computational approaches to 3D modeling of RNA

(2010) Christian Laing et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

Alternative expression analysis by RNA sequencing

(2010) Malachi Griffith et al.   NATURE METHODS

FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing

(2010) Jason G Underwood et al.   NATURE METHODS

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

Detection of splice junctions from paired-end RNA-seq data by SpliceMap

(2010) K. F. Au et al.   NUCLEIC ACIDS RESEARCH

Rfam: Wikipedia, clans and the "decimal" release

(2010) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

miRBase: integrating microRNA annotation and deep-sequencing data

(2010) A. Kozomara et al.   NUCLEIC ACIDS RESEARCH

lncRNAdb: a reference database for long noncoding RNAs

(2010) Paulo P. Amaral et al.   NUCLEIC ACIDS RESEARCH

The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection

(2010) M. Y. Galperin et al.   NUCLEIC ACIDS RESEARCH

Conserved microRNA targeting in Drosophila is as widespread in coding regions as in 3'UTRs

(2010) M. Schnall-Levin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational approaches for RNA energy parameter estimation

(2010) M. Andronescu et al.   RNA

BarMap: RNA folding on dynamic energy landscapes

(2010) I. L. Hofacker et al.   RNA

Riboswitches and the RNA World

(2010) R. R. Breaker   Cold Spring Harbor Perspectives in Biology

Most “Dark Matter” Transcripts Are Associated With Known Genes

(2010) Harm van Bakel et al.   PLOS BIOLOGY

miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data

(2010) David Hendrix et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

ISOFORM ABUNDANCE INFERENCE PROVIDES A MORE ACCURATE ESTIMATION OF GENE EXPRESSION LEVELS IN RNA-SEQ

(2010) XI WANG et al.   Journal of Bioinformatics and Computational Biology

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

Activation of gene expression by small RNA

(2009) Kathrin S. Fröhlich et al.   CURRENT OPINION IN MICROBIOLOGY

An O(n5) Algorithm for MFE Prediction of Kissing Hairpins and 4-Chains in Nucleic Acids

(2009) Ho-Lin Chen et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis

(2009) Zasha Weinberg et al.   NATURE

A distinct class of small RNAs arises from pre-miRNA–proximal regions in a simple chordate

(2009) Weiyang Shi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The tedious task of finding homologous noncoding RNA genes

(2009) P. Menzel et al.   RNA

Improved free energy parameters for RNA pseudoknotted secondary structure prediction

(2009) M. S. Andronescu et al.   RNA

Improved RNA secondary structure prediction by maximizing expected pair accuracy

(2009) Z. J. Lu et al.   RNA

RNA Folding: Conformational Statistics, Folding Kinetics, and Ion Electrostatics

(2008) Shi-Jie Chen   Annual Review of Biophysics

A max-margin model for efficient simultaneous alignment and folding of RNA sequences

(2008) C. B. Do et al.   BIOINFORMATICS

IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions

(2008) Anke Busch et al.   BIOINFORMATICS

RNAalifold: improved consensus structure prediction for RNA alignments

(2008) Stephan H Bernhart et al.   BMC BIOINFORMATICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Topological Classification of RNA Structures

(2008) Michael Bon et al.   JOURNAL OF MOLECULAR BIOLOGY

Simulating RNA Folding Kinetics on Approximated Energy Landscapes

(2008) Xinyu Tang et al.   JOURNAL OF MOLECULAR BIOLOGY

Beyond energy minimization: approaches to the kinetic folding of RNA

(2008) Christoph Flamm et al.   MONATSHEFTE FUR CHEMIE

The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data

(2008) Marc Parisien et al.   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

(2008) Stefan E. Seemann et al.   NUCLEIC ACIDS RESEARCH

The Vienna RNA Websuite

(2008) A. R. Gruber et al.   NUCLEIC ACIDS RESEARCH

The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs

(2008) T. Mituyama et al.   NUCLEIC ACIDS RESEARCH

miR2Disease: a manually curated database for microRNA deregulation in human disease

(2008) Q. Jiang et al.   NUCLEIC ACIDS RESEARCH

Accurate SHAPE-directed RNA structure determination

(2008) K. E. Deigan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

KnotSeeker: Heuristic pseudoknot detection in long RNA sequences

(2008) J. Sperschneider et al.   RNA

The Eukaryotic Genome as an RNA Machine

(2008) P. P. Amaral et al.   SCIENCE

Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities

(2008) Marcel E. Dinger et al.   PLoS Computational Biology

Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum

(2007) T. Mourier et al.   GENOME RESEARCH