Global or local? Predicting secondary structure and accessibility in mRNAs (Q28727954)

6

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author name string

Sita J Lange

1

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Daniel Maticzka

2

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Mathias Möhl

3

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Joshua N Gagnon

4

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Chris M Brown

Creative Commons Attribution-NonCommercial 3.0 Unported

5

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language of work or name

English

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publication date

July 2012

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published in

Nucleic Acids Research

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volume

40

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issue

12

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page(s)

5215-26

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copyright license

start time

8 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

Two covariance models for iron-responsive elements

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

Rfam: Wikipedia, clans and the "decimal" release

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

Discriminatory power of RNA family models

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

RNAstructure: software for RNA secondary structure prediction and analysis

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

Seed-based INTARNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

Transterm: a database to aid the analysis of regulatory sequences in mRNAs

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

Using RNA secondary structures to guide sequence motif finding towards single-stranded regions

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

CONTRAfold: RNA secondary structure prediction without physics-based models

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

Rfam: annotating non-coding RNAs in complete genomes

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

A novel RNA structural motif in the selenocysteine insertion element of eukaryotic selenoprotein mRNAs

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

Basic local alignment search tool

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

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

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

The role of site accessibility in microRNA target recognition

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

From structure prediction to genomic screens for novel non-coding RNAs

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

A conserved stem loop motif in the 5'untranslated region regulates transforming growth factor-β(1) translation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

Genome-wide measurement of RNA secondary structure in yeast

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

Efficient use of accessibility in microRNA target prediction

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

Translation efficiency is determined by both codon bias and folding energy

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

IRESite--a tool for the examination of viral and cellular internal ribosome entry sites

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

Relative contribution of sequence and structure features to the mRNA binding of Argonaute/EIF2C-miRNA complexes and the degradation of miRNA targets

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

Immunopurification of Ago1 miRNPs selects for a distinct class of microRNA targets.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

Improved RNA secondary structure prediction by maximizing expected pair accuracy

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

Coding-sequence determinants of gene expression in Escherichia coli

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

A hierarchical model for evolution of 23S ribosomal RNA.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

UNAFold: software for nucleic acid folding and hybridization

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

RNA STRAND: the RNA secondary structure and statistical analysis database

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

Centroid estimation in discrete high-dimensional spaces with applications in biology

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

Pre-mRNA secondary structures influence exon recognition.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

Rational design and rapid screening of antisense oligonucleotides for prokaryotic gene modulation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

A comparison of thermodynamic foldings with comparatively derived structures of 16S and 16S-like rRNAs.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

Sequential folding of a messenger RNA molecule

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3384308

The impact of target site accessibility on the design of effective siRNAs

3 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS181

A detailed investigation of accessibilities around target sites of siRNAs and miRNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS181

Fast folding and comparison of RNA secondary structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS181

Prediction of locally stable RNA secondary structures for genome-wide surveys

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS181

Rfold: an exact algorithm for computing local base pairing probabilities

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS181

Local RNA base pairing probabilities in large sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS181

RNA Accessibility in cubic time

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS181

The language of RNA: a formal grammar that includes pseudoknots.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS181

Clustering of RNA secondary structures with application to messenger RNAs.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS181

An analysis of large rRNA sequences folded by a thermodynamic method.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS181

Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS181

Thermodynamics of three-way multibranch loops in RNA

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22373926

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKS181

1 reference

1 reference

1 reference

PubMed publication ID

22373926

1 reference