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

Nature protocols, 2015-11, Vol.10 (11), p.1643-1669

2015

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Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing

Cell, 2018-03, Vol.173 (1), p.181-195.e18

2018

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

Nature methods, 2014-09, Vol.11 (9), p.959-965

2014

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Genomic RNA Elements Drive Phase Separation of the SARS-CoV-2 Nucleocapsid

Molecular cell, 2020-12, Vol.80 (6), p.1078-1091.e6

2020

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Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution

Nature protocols, 2006-11, Vol.1 (3), p.1610-1616

2006

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SHAPE-directed RNA secondary structure prediction

Methods (San Diego, Calif.), 2010-10, Vol.52 (2), p.150-158

2010

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Single-molecule correlated chemical probing reveals large-scale structural communication in the ribosome and the mechanism of the antibiotic spectinomycin in living cells

PLoS biology, 2019-09, Vol.17 (9), p.e3000393-e3000393

2019

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Visualization of RNA structure models within the Integrative Genomics Viewer

RNA (Cambridge), 2017-07, Vol.23 (7), p.1012-1018

2017

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High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states

PLoS biology, 2008-04, Vol.6 (4), p.e96-e96

2008

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ShapeFinder: a software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis

RNA (Cambridge), 2008-10, Vol.14 (10), p.1979-1990

2008

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Challenge of Mimicking the Influences of the Cellular Environment on RNA Structure by PEG-Induced Macromolecular Crowding

Biochemistry (Easton), 2015-10, Vol.54 (42), p.6447-6453

2015

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The Cellular Environment Stabilizes Adenine Riboswitch RNA Structure

Biochemistry (Easton), 2013-12, Vol.52 (48), p.8777-8785

2013

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Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures

Nucleic acids research, 2022-08, Vol.50 (14), p.8168-8192

2022

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Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2

RNA (Cambridge), 2018-02, Vol.24 (2), p.143-148

2018

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Identifying proximal RNA interactions from cDNA-encoded crosslinks with ShapeJumper

PLoS computational biology, 2021-12, Vol.17 (12), p.e1009632-e1009632

2021

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

FEBS letters, 2013-04, Vol.587 (8), p.1180-1188

2013

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Advances in RNA structure analysis by chemical probing

Current opinion in structural biology, 2010-06, Vol.20 (3), p.295-304

Weeks, Kevin M

2010

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Three-dimensional RNA structure refinement by hydroxyl radical probing

Nature methods, 2012-06, Vol.9 (6), p.603-608

2012

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

PLoS computational biology, 2015-05, Vol.11 (5), p.e1004230

2015

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Guidelines for SHAPE Reagent Choice and Detection Strategy for RNA Structure Probing Studies

Biochemistry (Easton), 2019-06, Vol.58 (23), p.2655-2664

2019

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

PLoS computational biology, 2015-05, Vol.11 (5), p.e1004126-e1004126

2015

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In-cell RNA structure probing with SHAPE-MaP

Nature protocols, 2018-06, Vol.13 (6), p.1181-1195

2018

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

RNA (Cambridge), 2009-07, Vol.15 (7), p.1314-1321

2009

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Detection of RNA–Protein Interactions in Living Cells with SHAPE

Biochemistry (Easton), 2015-11, Vol.54 (46), p.6867-6875

2015

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Messenger RNA Structure Regulates Translation Initiation: A Mechanism Exploited from Bacteria to Humans

Biochemistry (Easton), 2018-07, Vol.57 (26), p.3537-3539

2018

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

Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing

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

Genomic RNA Elements Drive Phase Separation of the SARS-CoV-2 Nucleocapsid

Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution

SHAPE-directed RNA secondary structure prediction

Single-molecule correlated chemical probing reveals large-scale structural communication in the ribosome and the mechanism of the antibiotic spectinomycin in living cells

Visualization of RNA structure models within the Integrative Genomics Viewer

High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states

ShapeFinder: a software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis

Challenge of Mimicking the Influences of the Cellular Environment on RNA Structure by PEG-Induced Macromolecular Crowding

The Cellular Environment Stabilizes Adenine Riboswitch RNA Structure

Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures

Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2

Identifying proximal RNA interactions from cDNA-encoded crosslinks with ShapeJumper

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

Advances in RNA structure analysis by chemical probing

Three-dimensional RNA structure refinement by hydroxyl radical probing

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

Guidelines for SHAPE Reagent Choice and Detection Strategy for RNA Structure Probing Studies

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

In-cell RNA structure probing with SHAPE-MaP

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

Detection of RNA–Protein Interactions in Living Cells with SHAPE

Messenger RNA Structure Regulates Translation Initiation: A Mechanism Exploited from Bacteria to Humans

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