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

Genome-wide Measurement of RNA Folding Energies

(2012) Yue Wan et al.   MOLECULAR CELL

Global Analysis of RNA Secondary Structure in Two Metazoans

(2012) Fan Li et al.   Cell Reports

Prospects for Riboswitch Discovery and Analysis

(2011) Ronald R. Breaker   MOLECULAR CELL

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

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

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

(2010) Qi Zheng et al.   PLoS Genetics

VARNA: Interactive drawing and editing of the RNA secondary structure

(2009) Kévin Darty et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The Centrality of RNA

(2009) Phillip A. Sharp   CELL

Bidirectional promoters generate pervasive transcription in yeast

(2009) Zhenyu Xu et al.   NATURE

Widespread bidirectional promoters are the major source of cryptic transcripts in yeast

(2009) Helen Neil et al.   NATURE

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

(2009) Joseph M. Watts et al.   NATURE

SHRiMP: Accurate Mapping of Short Color-space Reads

(2009) Stephen M. Rumble et al.   PLoS Computational Biology

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

A large genome center's improvements to the Illumina sequencing system

(2008) Michael A Quail et al.   NATURE METHODS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

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

High-Throughput SHAPE Analysis Reveals Structures in HIV-1 Genomic RNA Strongly Conserved across Distinct Biological States

(2008) Kevin A Wilkinson et al.   PLOS BIOLOGY

Novel Low Abundance and Transient RNAs in Yeast Revealed by Tiling Microarrays and Ultra High–Throughput Sequencing Are Not Conserved Across Closely Related Yeast Species

(2008) Albert Lee et al.   PLoS Genetics