Computational Analysis of Conserved RNA Secondary Structure in Transcriptomes and Genomes

LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search

(2013) Sebastian Will et al.   Algorithms for Molecular Biology

GeneScissors: a comprehensive approach to detecting and correcting spurious transcriptome inference owing to RNA-seq reads misalignment

(2013) Zhaojun Zhang et al.   BIOINFORMATICS

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

A Decade of Riboswitches

(2013) Alexander Serganov et al.   CELL

The ENCODE project: Missteps overshadowing a success

(2013) Sean R. Eddy   CURRENT BIOLOGY

Structure-based whole-genome realignment reveals many novel noncoding RNAs

(2013) S. Will et al.   GENOME RESEARCH

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

Circular RNAs are a large class of animal RNAs with regulatory potency

(2013) Sebastian Memczak et al.   NATURE

Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing

(2013) Yue Wan et al.   Nature Protocols

Eukaryotic TPP riboswitch regulation of alternative splicing involving long-distance base pairing

(2013) Sanshu Li et al.   NUCLEIC ACIDS RESEARCH

Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions

(2013) Zsuzsanna Sükösd et al.   NUCLEIC ACIDS RESEARCH

Widespread purifying selection on RNA structure in mammals

(2013) Martin A. Smith et al.   NUCLEIC ACIDS RESEARCH

Genomic era analyses of RNA secondary structure and RNA-binding proteins reveal their significance to post-transcriptional regulation in plants

(2013) Ian M. Silverman et al.   PLANT SCIENCE

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots

(2013) C. E. Hajdin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs

(2013) Matthew J. Hangauer et al.   PLoS Genetics

Genome Regulation by Long Noncoding RNAs

(2012) John L. Rinn et al.   Annual Review of Biochemistry

Quantitative Dimethyl Sulfate Mapping for Automated RNA Secondary Structure Inference

(2012) Pablo Cordero et al.   BIOCHEMISTRY

PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data

(2012) Z. Sukosd et al.   BIOINFORMATICS

Transcripts with in silico predicted RNA structure are enriched everywhere in the mouse brain

(2012) Stefan E Seemann et al.   BMC GENOMICS

SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data

(2012) Z. Ouyang et al.   GENOME RESEARCH

The Mechanisms of RNA SHAPE Chemistry

(2012) Jennifer L. McGinnis et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Modular regulatory principles of large non-coding RNAs

(2012) Mitchell Guttman et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

RNA SHAPE analysis in living cells

(2012) Robert C Spitale et al.   Nature Chemical Biology

Structural architecture of the human long non-coding RNA, steroid receptor RNA activator

(2012) Irina V. Novikova et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Stefan Washietl et al.   NUCLEIC ACIDS RESEARCH

Integrating Chemical Footprinting Data into RNA Secondary Structure Prediction

(2012) Kourosh Zarringhalam et al.   PLoS One

Global Analysis of RNA Secondary Structure in Two Metazoans

(2012) Fan Li et al.   Cell Reports

Coding vs non-coding: Translatability of short ORFs found in putative non-coding transcripts

(2011) Yuji Kageyama et al.   BIOCHIMIE

Mirtrons: microRNA biogenesis via splicing

(2011) Jakub O. Westholm et al.   BIOCHIMIE

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

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

An expanding universe of small proteins

(2011) Errett C Hobbs et al.   CURRENT OPINION IN MICROBIOLOGY

New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes

(2011) B. J. Parker et al.   GENOME RESEARCH

Regulation by Small RNAs in Bacteria: Expanding Frontiers

(2011) Gisela Storz et al.   MOLECULAR CELL

A two-dimensional mutate-and-map strategy for non-coding RNA structure

(2011) Wipapat Kladwang et al.   Nature Chemistry

BlastR—fast and accurate database searches for non-coding RNAs

(2011) Giovanni Bussotti et al.   NUCLEIC ACIDS RESEARCH

Simplified RNA secondary structure mapping by automation of SHAPE data analysis

(2011) Phillip S. Pang et al.   NUCLEIC ACIDS RESEARCH

Modeling and automation of sequencing-based characterization of RNA structure

(2011) S. Aviran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more

(2011) E. Rivas et al.   RNA

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

(2011) S. Washietl et al.   RNA

Response to “The Reality of Pervasive Transcription”

(2011) Harm van Bakel et al.   PLOS BIOLOGY

The Reality of Pervasive Transcription

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

Identification of Hammerhead Ribozymes in All Domains of Life Reveals Novel Structural Variations

(2011) Jonathan Perreault et al.   PLoS Computational Biology

Transcribed dark matter: meaning or myth?

(2010) C. P. Ponting et al.   HUMAN MOLECULAR GENETICS

SHAPE-directed RNA secondary structure prediction

(2010) Justin T. Low et al.   METHODS

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

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

(2010) Jason G Underwood et al.   NATURE METHODS

Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome

(2010) Daniel P. Riordan et al.   NUCLEIC ACIDS RESEARCH

Evaluation of the information content of RNA structure mapping data for secondary structure prediction

(2010) S. Quarrier et al.   RNA

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

Bacterial Small RNA Regulators: Versatile Roles and Rapidly Evolving Variations

(2010) S. Gottesman et al.   Cold Spring Harbor Perspectives in Biology

2-D Structure of the A Region of Xist RNA and Its Implication for PRC2 Association

(2010) Sylvain Maenner et al.   PLOS BIOLOGY

Most “Dark Matter” Transcripts Are Associated With Known Genes

(2010) Harm van Bakel et al.   PLOS BIOLOGY

Noisy Splicing Drives mRNA Isoform Diversity in Human Cells

(2010) Joseph K. Pickrell et al.   PLoS Genetics

Genome-Wide Double-Stranded RNA Sequencing Reveals the Functional Significance of Base-Paired RNAs in Arabidopsis

(2010) Qi Zheng et al.   PLoS Genetics

Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies

(2009) Parvez Anandam et al.   BIOINFORMATICS

Critical evaluation of the FANTOM3 non-coding RNA transcripts

(2009) Karl J.V. Nordström et al.   GENOMICS

Architecture and secondary structure of an entire HIV-1 RNA genome

(2009) Joseph M. Watts et al.   NATURE

Evolutionary Modeling and Prediction of Non-Coding RNAs in Drosophila

(2009) Robert K. Bradley et al.   PLoS One

An unexpected ending: Noncanonical 3' end processing mechanisms

(2009) J. E. Wilusz et al.   RNA

Dinucleotide controlled null models for comparative RNA gene prediction

(2008) Tanja Gesell et al.   BMC BIOINFORMATICS

Strategies for measuring evolutionary conservation of RNA secondary structures

(2008) Andreas R Gruber et al.   BMC BIOINFORMATICS

3′ End Processing of a Long Nuclear-Retained Noncoding RNA Yields a tRNA-like Cytoplasmic RNA

(2008) Jeremy E. Wilusz et al.   CELL

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis

(2008) Somdeb Mitra et al.   NUCLEIC ACIDS RESEARCH

R-Coffee: a method for multiple alignment of non-coding RNA

(2008) A. Wilm et al.   NUCLEIC ACIDS RESEARCH

Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes

(2008) M. Rabani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

ShapeFinder: A software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis

(2008) S. M. Vasa et al.   RNA

Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System

(2008) Daniel J Hogan et al.   PLOS BIOLOGY