Structure-seq2: sensitive and accurate genome-wide profiling of RNA structure in vivo

Genome-Wide Analysis of RNA Secondary Structure

(2016) Philip C. Bevilacqua et al.   Annual Review of Genetics

RNA systems biology: uniting functional discoveries and structural tools to understand global roles of RNAs

(2016) Eric J Strobel et al.   CURRENT OPINION IN BIOTECHNOLOGY

The complete structure of the chloroplast 70S ribosome in complex with translation factor pY

(2016) Philipp Bieri et al.   EMBO JOURNAL

Bridging the gap between in vitro and in vivo RNA folding

(2016) Kathleen A. Leamy et al.   QUARTERLY REVIEWS OF BIOPHYSICS

StructureFold: genome-wide RNA secondary structure mapping and reconstructionin vivo

(2015) Yin Tang et al.   BIOINFORMATICS

Progress and challenges for chemical probing of RNA structure inside living cells

(2015) Miles Kubota et al.   Nature Chemical Biology

Genome-wide profiling of in vivo RNA structure at single-nucleotide resolution using structure-seq

(2015) Yiliang Ding et al.   Nature Protocols

The Conserved Endoribonuclease YbeY Is Required for Chloroplast Ribosomal RNA Processing in Arabidopsis

(2015) Jinwen Liu et al.   PLANT PHYSIOLOGY

SHAPE Selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data

(2015) Line Dahl Poulsen et al.   RNA

The RNA structurome: transcriptome-wide structure probing with next-generation sequencing

(2015) Chun Kit Kwok et al.   TRENDS IN BIOCHEMICAL SCIENCES

An efficient and sensitive method for preparing cDNA libraries from scarce biological samples

(2014) Catherine H. Sterling et al.   NUCLEIC ACIDS RESEARCH

Snapshots of pre-rRNA structural flexibility reveal eukaryotic 40S assembly dynamics at nucleotide resolution

(2014) Ralph D. Hector et al.   NUCLEIC ACIDS RESEARCH

Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility

(2014) Lukasz Jan Kielpinski et al.   NUCLEIC ACIDS RESEARCH

SHAPE-Seq 2.0: systematic optimization and extension of high-throughput chemical probing of RNA secondary structure with next generation sequencing

(2014) David Loughrey et al.   NUCLEIC ACIDS RESEARCH

PLAZA 3.0: an access point for plant comparative genomics

(2014) Sebastian Proost et al.   NUCLEIC ACIDS RESEARCH

A hybridization-based approach for quantitative and low-bias single-stranded DNA ligation

(2013) Chun Kit Kwok et al.   ANALYTICAL BIOCHEMISTRY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Large Scale Loss of Data in Low-Diversity Illumina Sequencing Libraries Can Be Recovered by Deferred Cluster Calling

(2011) Felix Krueger et al.   PLoS One

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS