Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA

Computational Analysis of Conserved RNA Secondary Structure in Transcriptomes and Genomes

(2014) Sean R. Eddy   Annual Review of Biophysics

RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)

(2014) Nathan A Siegfried et al.   NATURE METHODS

Insights into RNA structure and function from genome-wide studies

(2014) Stefanie A. Mortimer et al.   NATURE REVIEWS GENETICS

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

Comparison of SIV and HIV-1 Genomic RNA Structures Reveals Impact of Sequence Evolution on Conserved and Non-Conserved Structural Motifs

(2013) Elizabeth Pollom et al.   PLoS Pathogens

Cyclic Diguanylate Inversely Regulates Motility and Aggregation in Clostridium difficile

(2012) E. B. Purcell et al.   JOURNAL OF BACTERIOLOGY

Structural Constraints Identified with Covariation Analysis in Ribosomal RNA

(2012) Lei Shang et al.   PLoS One

Exploring RNA Structural Codes with SHAPE Chemistry

(2011) Kevin M. Weeks et al.   ACCOUNTS OF CHEMICAL RESEARCH

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Differential assembly of 16S rRNA domains during 30S subunit formation

(2010) Z. Xu et al.   RNA

Infernal 1.0: inference of RNA alignments

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

Influence of nucleotide identity on ribose 2'-hydroxyl reactivity in RNA

(2009) K. A. Wilkinson et al.   RNA

RNAalifold: improved consensus structure prediction for RNA alignments

(2008) Stephan H Bernhart et al.   BMC BIOINFORMATICS

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