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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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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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Accurate SHAPE-directed RNA structure determination

Proceedings of the National Academy of Sciences - PNAS, 2009-01, Vol.106 (1), p.97-102

2009

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Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots

Proceedings of the National Academy of Sciences - PNAS, 2013-04, Vol.110 (14), p.5498-5503

2013

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

Nature (London), 2009-08, Vol.460 (7256), p.711-716

2009

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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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Single-molecule correlated chemical probing of RNA

Proceedings of the National Academy of Sciences - PNAS, 2014-09, Vol.111 (38), p.13858-13863

2014

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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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Direct detection of RNA modifications and structure using single-molecule nanopore sequencing

Cell genomics, 2022-02, Vol.2 (2), p.100097, Article 100097

2022

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RNA Structure Analysis at Single Nucleotide Resolution by Selective 2‘-Hydroxyl Acylation and Primer Extension (SHAPE)

Journal of the American Chemical Society, 2005-03, Vol.127 (12), p.4223-4231

2005

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SHAPE Directed Discovery of New Functions in Large RNAs

Accounts of chemical research, 2021-05, Vol.54 (10), p.2502-2517

Weeks, Kevin M

2021

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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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Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing

eLife, 2022-06, Vol.11

2022

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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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Principles for targeting RNA with drug-like small molecules

Nature reviews. Drug discovery, 2018-08, Vol.17 (8), p.547-558

2018

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

Proceedings of the National Academy of Sciences - PNAS, 2015-02, Vol.112 (8), p.2425-2430

2015

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Piercing the fog of the RNA structure-ome

Science (American Association for the Advancement of Science), 2021-08, Vol.373 (6558), p.964-965

Weeks, Kevin M

2021

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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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RNA Structures Facilitate Recombination-Mediated Gene Swapping in HIV-1

Journal of Virology, 2010-12, Vol.84 (24), p.12675-12682

2010

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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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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

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

Accurate SHAPE-directed RNA structure determination

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots

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

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

Visualization of RNA structure models within the Integrative Genomics Viewer

Single-molecule correlated chemical probing of RNA

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

Direct detection of RNA modifications and structure using single-molecule nanopore sequencing

RNA Structure Analysis at Single Nucleotide Resolution by Selective 2‘-Hydroxyl Acylation and Primer Extension (SHAPE)

SHAPE Directed Discovery of New Functions in Large RNAs

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

Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing

Identifying proximal RNA interactions from cDNA-encoded crosslinks with ShapeJumper

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

Principles for targeting RNA with drug-like small molecules

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

Piercing the fog of the RNA structure-ome

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

RNA Structures Facilitate Recombination-Mediated Gene Swapping in HIV-1

In-cell RNA structure probing with SHAPE-MaP

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