ProbFold: a probabilistic method for integration of probing data in RNA secondary structure prediction

SHAPE directed RNA folding

(2015) Ronny Lorenz et al.   BIOINFORMATICS

Computational Analysis of Conserved RNA Secondary Structure in Transcriptomes and Genomes

(2014) Sean R. Eddy   Annual Review of Biophysics

RNA secondary structure modeling at consistent high accuracy using differential SHAPE

(2014) G. M. Rice et al.   RNA

Infernal 1.1: 100-fold faster RNA homology searches

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

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

An RNA Mapping DataBase for curating RNA structure mapping experiments

(2012) Pablo Cordero et al.   BIOINFORMATICS

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

(2012) Z. Ouyang et al.   GENOME RESEARCH

Correction to The Mechanisms of RNA SHAPE Chemistry

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

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

Speeding up the Consensus Clustering methodology for microarray data analysis

(2011) Raffaele Giancarlo et al.   Algorithms for Molecular Biology

Understanding the transcriptome through RNA structure

(2011) Yue Wan et al.   NATURE REVIEWS GENETICS

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

Advances in RNA structure analysis by chemical probing

(2010) Kevin M Weeks   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

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

(2010) S. Quarrier et al.   RNA

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