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

Review toward all RNA structures, concisely

(2015) Kevin M. Weeks   BIOPOLYMERS

In-cell SHAPE reveals that free 30S ribosome subunits are in the inactive state

(2015) Jennifer L. McGinnis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes

(2015) Christopher A. Lavender et al.   PLoS Computational Biology

Ribosome RNA Assembly Intermediates Visualized in Living Cells

(2014) Jennifer L. McGinnis et al.   BIOCHEMISTRY

Catalysts from synthetic genetic polymers

(2014) Alexander I. Taylor 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

Functional long-range RNA–RNA interactions in positive-strand RNA viruses

(2014) Beth L. Nicholson et al.   NATURE REVIEWS MICROBIOLOGY

Structural basis for activity of highly efficient RNA mimics of green fluorescent protein

(2014) Katherine Deigan Warner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

RNA secondary structure modeling at consistent high accuracy using differential SHAPE

(2014) G. M. Rice et al.   RNA

Mod-seq: high-throughput sequencing for chemical probing of RNA structure

(2014) J. Talkish et al.   RNA

RNA-guided assembly of Rev-RRE nuclear export complexes

(2014) Yun Bai et al.   eLife

The Cellular Environment Stabilizes Adenine Riboswitch RNA Structure

(2013) Jillian Tyrrell et al.   BIOCHEMISTRY

Long-Range Architecture in a Viral RNA Genome

(2013) Eva J. Archer et al.   BIOCHEMISTRY

The genetic code as expressed through relationships between mRNA structure and protein function

(2013) David M. Mauger et al.   FEBS LETTERS

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

Biases in small RNA deep sequencing data

(2013) Carsten A. Raabe et al.   NUCLEIC ACIDS RESEARCH

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

Safer one-pot synthesis of the 'SHAPE' reagent 1-methyl-7-nitroisatoic anhydride (1m7)

(2013) R. Turner et al.   RNA

A Guanosine-Centric Mechanism for RNA Chaperone Function

(2013) J. K. Grohman et al.   SCIENCE

Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction

(2012) Jian Ye et al.   BMC BIOINFORMATICS

Fingerprinting Noncanonical and Tertiary RNA Structures by Differential SHAPE Reactivity

(2012) Kady-Ann Steen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Mechanisms of RNA SHAPE Chemistry

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

Functional complexity and regulation through RNA dynamics

(2012) Elizabeth A. Dethoff et al.   NATURE

RNA SHAPE analysis in living cells

(2012) Robert C Spitale et al.   Nature Chemical Biology

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

Nonhierarchical Ribonucleoprotein Assembly Suggests a Strain-Propagation Model for Protein-Facilitated RNA Folding

(2010) Caia D. S. Duncan et al.   BIOCHEMISTRY

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

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

Definition of a high-affinity Gag recognition structure mediating packaging of a retroviral RNA genome

(2010) C. Gherghe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Centrality of RNA

(2009) Phillip A. Sharp   CELL

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

(2009) Joseph M. Watts et al.   NATURE

C2'-endo nucleotides as molecular timers suggested by the folding of an RNA domain

(2009) S. A. Mortimer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) K. A. Wilkinson et al.   RNA

Complex Ligand-Induced Conformational Changes in tRNAAspRevealed by Single-Nucleotide Resolution SHAPE Chemistry†

(2008) Bin Wang et al.   BIOCHEMISTRY

SHAPE Analysis of Long-Range Interactions Reveals Extensive and Thermodynamically Preferred Misfolding in a Fragile Group I Intron RNA†

(2008) Caia D. S. Duncan et al.   BIOCHEMISTRY

Strong Correlation between SHAPE Chemistry and the Generalized NMR Order Parameter (S2) in RNA

(2008) Costin M. Gherghe et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Time-Resolved RNA SHAPE Chemistry

(2008) Stefanie A. Mortimer et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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