(Q35795056)

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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

scientific article published on October 2015

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scholarly article

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Europe PubMed Central

10 August 2017

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

1 reference

Europe PubMed Central

10 August 2017

1 reference

based on heuristic

inferred from title

Matthew J Smola

1

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26426499%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

Greggory M Rice

2

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4 June 2020

author name string

Steven Busan

3

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4 June 2020

Nathan A Siegfried

4

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4 June 2020

Kevin M Weeks

5

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4 June 2020

publication date

1 October 2015

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Nature Protocols

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4 June 2020

10

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4 June 2020

1643-1669

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4 June 2020

11

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4 June 2020

https://scigraph.springernature.com/pub.10.1038/nprot.2015.103

0 references

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

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12 July 2018

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

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12 July 2018

Functionally conserved architecture of hepatitis C virus RNA genomes

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12 July 2018

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

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12 July 2018

Review toward all RNA structures, concisely

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12 July 2018

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12 July 2018

Genome-wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome

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12 July 2018

SHAPE-Seq 2.0: systematic optimization and extension of high-throughput chemical probing of RNA secondary structure with next generation sequencing

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12 July 2018

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12 July 2018

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12 July 2018

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

1 reference

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12 July 2018

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

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

1 reference

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12 July 2018

Insights into RNA structure and function from genome-wide studies

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12 July 2018

Ribosome RNA assembly intermediates visualized in living cells

1 reference

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12 July 2018

RNA secondary structure modeling at consistent high accuracy using differential SHAPE.

1 reference

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12 July 2018

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

1 reference

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12 July 2018

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

1 reference

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12 July 2018

The cellular environment stabilizes adenine riboswitch RNA structure

1 reference

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12 July 2018

Biases in small RNA deep sequencing data

1 reference

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12 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4900152

12 July 2018

Long-range architecture in a viral RNA genome

1 reference

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12 July 2018

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4900152

12 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4900152

12 July 2018

A guanosine-centric mechanism for RNA chaperone function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4900152

12 July 2018

Fingerprinting noncanonical and tertiary RNA structures by differential SHAPE reactivity.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4900152

12 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4900152

12 July 2018

The mechanisms of RNA SHAPE chemistry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4900152

12 July 2018

Fast gapped-read alignment with Bowtie 2

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4900152

12 July 2018

Functional complexity and regulation through RNA dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4900152

12 July 2018

Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4900152

12 July 2018

FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4900152

12 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4900152

12 July 2018

High-throughput SHAPE and hydroxyl radical analysis of RNA structure and ribonucleoprotein assembly

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4900152

12 July 2018

Genome-wide measurement of RNA secondary structure in yeast

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4900152

12 July 2018

Nonhierarchical ribonucleoprotein assembly suggests a strain-propagation model for protein-facilitated RNA folding

1 reference

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12 July 2018

Advances in RNA structure analysis by chemical probing

1 reference

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12 July 2018

RNAstructure: software for RNA secondary structure prediction and analysis

1 reference

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12 July 2018

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

1 reference

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12 July 2018

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

1 reference

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12 July 2018

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

1 reference

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4900152

12 July 2018

Accurate SHAPE-directed RNA structure determination

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4900152

12 July 2018

Strong correlation between SHAPE chemistry and the generalized NMR order parameter (S2) in RNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4900152

12 July 2018

SHAPE analysis of long-range interactions reveals extensive and thermodynamically preferred misfolding in a fragile group I intron RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4900152

12 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4900152

12 July 2018

A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4900152

12 July 2018

PseudoViewer: web application and web service for visualizing RNA pseudoknots and secondary structures

1 reference

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12 July 2018

Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch

1 reference

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12 July 2018

CLIP: a method for identifying protein-RNA interaction sites in living cells

1 reference

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12 July 2018

RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4900152

12 July 2018

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1 reference

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12 July 2018

Precise branch point mapping and quantification of splicing intermediates

1 reference

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12 July 2018

The equilibrium partition function and base pair binding probabilities for RNA secondary structure

1 reference

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12 July 2018

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4900152

25 September 2018

RNA SHAPE analysis in living cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4900152

25 September 2018

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1 reference

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25 September 2018

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1 reference

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25 September 2018

A Mathematical Theory of Communication

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2015.103

21 January 2018

Identifiers

10.1038/NPROT.2015.103

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26426499%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

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4 June 2020

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26426499%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

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