Deep learning models for RNA secondary structure prediction (probably) do not generalize across families

RNA secondary structure prediction using deep learning with thermodynamic integration

(2021) Kengo Sato et al.   Nature Communications

A novel end-to-end method to predict RNA secondary structure profile based on bidirectional LSTM and residual neural network

(2021) Linyu Wang et al.   BMC BIOINFORMATICS

RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers

(2020) Zhichao Miao et al.   RNA

Rfam 14: expanded coverage of metagenomic, viral and microRNA families

(2020) Ioanna Kalvari et al.   NUCLEIC ACIDS RESEARCH

DMfold: A Novel Method to Predict RNA Secondary Structure With Pseudoknots Based on Deep Learning and Improved Base Pair Maximization Principle

(2019) Linyu Wang et al.   Frontiers in Genetics

Determining Parameters for Non-Linear Models of Multi-Loop Free Energy Change

(2019) Max Ward et al.   BIOINFORMATICS

How to benchmark RNA secondary structure prediction accuracy

(2019) David H. Mathews   METHODS

RNA sequencing: the teenage years

(2019) Rory Stark et al.   NATURE REVIEWS GENETICS

RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning

(2019) Jaswinder Singh et al.   Nature Communications

bpRNA: large-scale automated annotation and analysis of RNA secondary structure

(2018) Padideh Danaee et al.   NUCLEIC ACIDS RESEARCH

Advanced multi-loop algorithms for RNA secondary structure prediction reveal that the simplest model is best

(2017) Max Ward et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Zhen Tan et al.   NUCLEIC ACIDS RESEARCH

A high-throughput approach to profile RNA structure

(2016) Riccardo Delli Ponti et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Michael F. Sloma et al.   RNA

RNA design rules from a massive open laboratory

(2014) Jeehyung Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions

(2013) Zsuzsanna Sükösd et al.   NUCLEIC ACIDS RESEARCH

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots

(2013) C. E. Hajdin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The four ingredients of single-sequence RNA secondary structure prediction. A unifying perspective

(2013) Elena Rivas   RNA Biology

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular 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

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

Computational approaches for RNA energy parameter estimation

(2010) M. Andronescu et al.   RNA

RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database

(2008) Mirela Andronescu et al.   BMC BIOINFORMATICS

tRNAdb 2009: compilation of tRNA sequences and tRNA genes

(2008) F. Juhling et al.   NUCLEIC ACIDS RESEARCH

Accurate SHAPE-directed RNA structure determination

(2008) K. E. Deigan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA