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RNAstructure: software for RNA secondary structure prediction and analysis

BMC bioinformatics, 2010-03, Vol.11 (1), p.129-129, Article 129

2010

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How to benchmark RNA secondary structure prediction accuracy

Methods (San Diego, Calif.), 2019-06, Vol.162-163, p.60-67

Mathews, David H.

2019

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

Nucleic acids research, 2010-01, Vol.38 (Database issue), p.D280

2010

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LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search

Bioinformatics, 2019-07, Vol.35 (14), p.i295-i304

2019

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TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs

Nucleic acids research, 2017-11, Vol.45 (20), p.11570

2017

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RNAstructure: Web servers for RNA secondary structure prediction and analysis

Nucleic acids research, 2013-07, Vol.41 (Web Server issue), p.W471

2013

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LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities

Bioinformatics (Oxford, England), 2020-07, Vol.36 (Supplement_1), p.i258-i267

2020

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ProbKnot: fast prediction of RNA secondary structure including pseudoknots

RNA (Cambridge), 2010-10, Vol.16 (10), p.1870-1880

2010

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LazySampling and LinearSampling: fast stochastic sampling of RNA secondary structure with applications to SARS-CoV-2

Nucleic acids research, 2023-01, Vol.51 (2), p.e7

2023

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CRISPR-Cas9-based mutagenesis frequently provokes on-target mRNA misregulation

Nature communications, 2019-09, Vol.10 (1), p.4056-10, Article 4056

2019

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Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects

Nucleic acids research, 2022-05, Vol.50 (9), p.5251

2022

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Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures

RNA (Cambridge), 2016-12, Vol.22 (12), p.1808-1818

2016

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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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Prediction of RNA secondary structure by free energy minimization

Current opinion in structural biology, 2006-06, Vol.16 (3), p.270-278

2006

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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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Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization

RNA (Cambridge), 2004-08, Vol.10 (8), p.1178-1190

Mathews, David H

2004

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RNA Secondary Structure Analysis Using RNAstructure

Current Protocols in Bioinformatics, 2014-06, Vol.46 (1), p.12.6.1-12.6.25

Mathews, David H.

2014

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Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs

PLoS computational biology, 2017-11, Vol.13 (11), p.e1005827-e1005827

2017

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mRNAs and lncRNAs intrinsically form secondary structures with short end-to-end distances

Nature communications, 2018-10, Vol.9 (1), p.4328-11, Article 4328

2018

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Revolutions in RNA Secondary Structure Prediction

Journal of molecular biology, 2006-06, Vol.359 (3), p.526-532

Mathews, David H.

2006

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Improved RNA secondary structure prediction by maximizing expected pair accuracy

RNA (Cambridge), 2009-10, Vol.15 (10), p.1805-1813

2009

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Making ends meet: New functions of mRNA secondary structure

Wiley interdisciplinary reviews. RNA, 2021-03, Vol.12 (2), p.e1611-n/a

2021

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TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequences

BMC bioinformatics, 2011-04, Vol.12 (1), p.108-108, Article 108

2011

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

Nature methods, 2010-12, Vol.7 (12), p.995

2010

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A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control

Nature communications, 2022-01, Vol.13 (1), p.199-199, Article 199

2022

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RNAstructure: software for RNA secondary structure prediction and analysis

How to benchmark RNA secondary structure prediction accuracy

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

LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search

TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs

RNAstructure: Web servers for RNA secondary structure prediction and analysis

LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities

ProbKnot: fast prediction of RNA secondary structure including pseudoknots

LazySampling and LinearSampling: fast stochastic sampling of RNA secondary structure with applications to SARS-CoV-2

CRISPR-Cas9-based mutagenesis frequently provokes on-target mRNA misregulation

Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects

Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures

Accurate SHAPE-directed RNA structure determination

Prediction of RNA secondary structure by free energy minimization

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots

Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization

RNA Secondary Structure Analysis Using RNAstructure

Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs

mRNAs and lncRNAs intrinsically form secondary structures with short end-to-end distances

Revolutions in RNA Secondary Structure Prediction

Improved RNA secondary structure prediction by maximizing expected pair accuracy

Making ends meet: New functions of mRNA secondary structure

TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequences

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

A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control

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