DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo

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

Detection of RNA–Protein Interactions in Living Cells with SHAPE

(2015) Matthew J. Smola et al.   BIOCHEMISTRY

A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation

(2015) Alexander P. Fields et al.   MOLECULAR CELL

Structural imprints in vivo decode RNA regulatory mechanisms

(2015) Robert C. Spitale et al.   NATURE

Selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis

(2015) Matthew J Smola et al.   Nature Protocols

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

Systematic imaging reveals features and changing localization of mRNAs in Drosophila development

(2015) Helena Jambor et al.   eLife

Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA

(2014) Schraga Schwartz et al.   CELL

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

(2014) Thomas M. Carlile et al.   NATURE

Landscape and variation of RNA secondary structure across the human transcriptome

(2014) Yue Wan et al.   NATURE

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

Broad and adaptable RNA structure recognition by the human interferon-induced tetratricopeptide repeat protein IFIT5

(2014) G. E. Katibah et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-molecule correlated chemical probing of RNA

(2014) P. J. Homan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rational experiment design for sequencing-based RNA structure mapping

(2014) Sharon Aviran et al.   RNA

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

(2013) Yiliang Ding et al.   NATURE

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

(2013) Silvi Rouskin et al.   NATURE

Comparative analysis of RNA sequencing methods for degraded or low-input samples

(2013) Xian Adiconis et al.   NATURE METHODS

Thermostable group II intron reverse transcriptase fusion proteins and their use in cDNA synthesis and next-generation RNA sequencing

(2013) S. Mohr et al.   RNA

Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons

(2012) Kate D. Meyer et al.   CELL

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

(2012) Z. Ouyang et al.   GENOME RESEARCH

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

(2012) Dan Dominissini et al.   NATURE

ViennaRNA Package 2.0

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

Deciphering 3′ss Selection in the Yeast Genome Reveals an RNA Thermosensor that Mediates Alternative Splicing

(2011) Markus Meyer et al.   MOLECULAR CELL

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

Conserved RNA structures in the non-canonical Hac1/Xbp1 intron

(2011) Katarzyna B. Hooks et al.   RNA Biology

Dimerization of oskar 3' UTRs promotes hitchhiking for RNA localization in the Drosophila oocyte

(2011) H. Jambor et al.   RNA

The Structure of the Eukaryotic Ribosome at 3.0 A Resolution

(2011) A. Ben-Shem et al.   SCIENCE

A′-form RNA helices are required for cytoplasmic mRNA transport in Drosophila

(2010) Simon L Bullock et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

VARNA: Interactive drawing and editing of the RNA secondary structure

(2009) Kévin Darty et al.   BIOINFORMATICS

Novel structural determinants in human SECIS elements modulate the translational recoding of UGA as selenocysteine

(2009) Lynda Latrèche et al.   NUCLEIC ACIDS RESEARCH

Coding-Sequence Determinants of Gene Expression in Escherichia coli

(2009) G. Kudla et al.   SCIENCE

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Messenger RNA targeting to endoplasmic reticulum stress signalling sites

(2008) Tomás Aragón et al.   NATURE

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