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mRNA structure determines specificity of a polyQ-driven phase separation

Science (American Association for the Advancement of Science), 2018-05, Vol.360 (6391), p.922-927

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

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

2015

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

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

2014

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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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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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Functional classification of long non-coding RNAs by k-mer content

Nature genetics, 2018-10, Vol.50 (10), p.1474-1482

2018

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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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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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Functionally conserved architecture of hepatitis C virus RNA genomes

Proceedings of the National Academy of Sciences - PNAS, 2015-03, Vol.112 (12), p.3692-3697

2015

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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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A Fast-Acting Reagent for Accurate Analysis of RNA Secondary and Tertiary Structure by SHAPE Chemistry

Journal of the American Chemical Society, 2007-04, Vol.129 (14), p.4144-4145

2007

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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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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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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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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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Targeting the Oncogenic Long Non-coding RNA SLNCR1 by Blocking Its Sequence-Specific Binding to the Androgen Receptor

Cell reports (Cambridge), 2020-01, Vol.30 (2), p.541-554.e5

2020

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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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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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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

2022

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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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Comparison of SIV and HIV-1 genomic RNA structures reveals impact of sequence evolution on conserved and non-conserved structural motifs

PLoS pathogens, 2013-04, Vol.9 (4), p.e1003294-e1003294

2013

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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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mRNA structure determines specificity of a polyQ-driven phase separation

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

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

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

SHAPE-directed RNA secondary structure prediction

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

Functional classification of long non-coding RNAs by k-mer content

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

Visualization of RNA structure models within the Integrative Genomics Viewer

Functionally conserved architecture of hepatitis C virus RNA genomes

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

A Fast-Acting Reagent for Accurate Analysis of RNA Secondary and Tertiary Structure by SHAPE Chemistry

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

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

Single-molecule correlated chemical probing of RNA

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

Targeting the Oncogenic Long Non-coding RNA SLNCR1 by Blocking Its Sequence-Specific Binding to the Androgen Receptor

The Cellular Environment Stabilizes Adenine Riboswitch RNA Structure

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

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

SHAPE Directed Discovery of New Functions in Large RNAs

Comparison of SIV and HIV-1 genomic RNA structures reveals impact of sequence evolution on conserved and non-conserved structural motifs

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

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