Direct Inference of Base-Pairing Probabilities with Neural Networks Improves Prediction of RNA Secondary Structures with Pseudoknots
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Title
Direct Inference of Base-Pairing Probabilities with Neural Networks Improves Prediction of RNA Secondary Structures with Pseudoknots
Authors
Keywords
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Journal
Genes
Volume 13, Issue 11, Pages 2155
Publisher
MDPI AG
Online
2022-11-21
DOI
10.3390/genes13112155
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Note: Only part of the references are listed.- RNA secondary structure prediction using deep learning with thermodynamic integration
- (2021) Kengo Sato et al. Nature Communications
- Prediction of RNA secondary structure including pseudoknots for long sequences
- (2021) Kengo Sato et al. BRIEFINGS IN BIOINFORMATICS
- UFold: fast and accurate RNA secondary structure prediction with deep learning
- (2021) Laiyi Fu et al. NUCLEIC ACIDS RESEARCH
- RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning
- (2019) Jaswinder Singh et al. Nature Communications
- Knotty: efficient and accurate prediction of complex RNA pseudoknot structures
- (2018) Hosna Jabbari et al. BIOINFORMATICS
- A max-margin training of RNA secondary structure prediction integrated with the thermodynamic model
- (2018) Manato Akiyama et al. Journal of Bioinformatics and Computational Biology
- Elements and machinery of non-coding RNAs: toward their taxonomy
- (2014) T. Hirose et al. EMBO REPORTS
- The four ingredients of single-sequence RNA secondary structure prediction. A unifying perspective
- (2013) Elena Rivas RNA Biology
- DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition
- (2012) Kengo Sato et al. BIOINFORMATICS
- ViennaRNA Package 2.0
- (2011) Ronny Lorenz et al. Algorithms for Molecular Biology
- IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming
- (2011) Kengo Sato et al. BIOINFORMATICS
- Rich Parameterization Improves RNA Structure Prediction
- (2011) Shay Zakov et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more
- (2011) E. Rivas et al. RNA
- RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming
- (2010) Yuki Kato et al. BIOINFORMATICS
- RNAstructure: software for RNA secondary structure prediction and analysis
- (2010) Jessica S Reuter et al. BMC BIOINFORMATICS
- Rfam: Wikipedia, clans and the "decimal" release
- (2010) P. P. Gardner et al. NUCLEIC ACIDS RESEARCH
- Computational approaches for RNA energy parameter estimation
- (2010) M. Andronescu et al. RNA
- ProbKnot: Fast prediction of RNA secondary structure including pseudoknots
- (2010) S. Bellaousov et al. RNA
- Genome-wide searching with base-pairing kernel functions for noncoding RNAs: computational and expression analysis of snoRNA families in Caenorhabditis elegans
- (2009) K. Morita et al. NUCLEIC ACIDS RESEARCH
- CENTROIDFOLD: a web server for RNA secondary structure prediction
- (2009) K. Sato et al. NUCLEIC ACIDS RESEARCH
- NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure
- (2009) Douglas H. Turner et al. NUCLEIC ACIDS RESEARCH
- Improved free energy parameters for RNA pseudoknotted secondary structure prediction
- (2009) M. S. Andronescu et al. RNA
- Improved RNA secondary structure prediction by maximizing expected pair accuracy
- (2009) Z. J. Lu et al. RNA
- FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space
- (2008) Xiang Chen et al. BIOINFORMATICS
- Prediction of RNA secondary structure using generalized centroid estimators
- (2008) Michiaki Hamada et al. BIOINFORMATICS
- Directed acyclic graph kernels for structural RNA analysis
- (2008) Kengo Sato et al. BMC BIOINFORMATICS
- RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database
- (2008) Mirela Andronescu et al. BMC BIOINFORMATICS
- Centroid estimation in discrete high-dimensional spaces with applications in biology
- (2008) L. E. Carvalho et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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