Predicting RNA structures and functions by artificial intelligence

ETGPDA: identification of piRNA-disease associations based on embedding transformation graph convolutional network

(2023) Xianghan Meng et al.   BMC GENOMICS

Machine learning for RNA 2D structure prediction benchmarked on experimental data

(2023) Marek Justyna et al.   BRIEFINGS IN BIOINFORMATICS

Algorithm for Optimized mRNA Design Improves Stability and Immunogenicity

(2023) He Zhang et al.   NATURE

RNA independent fragment partition method based on deep learning for RNA secondary structure prediction

(2023) Qi Zhao et al.   Scientific Reports

GCNfold: A novel lightweight model with valid extractors for RNA secondary structure prediction

(2023) Enbin Yang et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Prediction of on-target and off-target activity of CRISPR–Cas13d guide RNAs using deep learning

(2023) Hans-Hermann Wessels et al.   NATURE BIOTECHNOLOGY

RNA tertiary structure modeling with BRiQ potential in CASP15

(2023) Ke Chen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

PST-PRNA: prediction of RNA-binding sites using protein surface topography and deep learning

(2022) Pengpai Li et al.   BIOINFORMATICS

PDMDA: predicting deep-level miRNA–disease associations with graph neural networks and sequence features

(2022) Cheng Yan et al.   BIOINFORMATICS

RNA secondary structure prediction with convolutional neural networks

(2022) Mehdi Saman Booy et al.   BMC BIOINFORMATICS

Multi-channel graph attention autoencoders for disease-related lncRNAs prediction

(2022) Nan Sheng et al.   BRIEFINGS IN BIOINFORMATICS

Hierarchical graph attention network for miRNA-disease association prediction

(2022) Zhengwei Li et al.   MOLECULAR THERAPY

Length-Dependent Deep Learning Model for RNA Secondary Structure Prediction

(2022) Kangkun Mao et al.   MOLECULES

Nucleic Acid Architectonics for pH-Responsive DNA Systems and Devices

(2022) Mohamed Nabeel Mattath et al.   ACS Omega

Identification of miRNA–disease associations via deep forest ensemble learning based on autoencoder

(2022) Wei Liu et al.   BRIEFINGS IN BIOINFORMATICS

Predicting RNA distance-based contact maps by integrated deep learning on physics-inferred secondary structure and evolutionary-derived mutational coupling

(2022) Jaswinder Singh et al.   BIOINFORMATICS

Aptamers targeting SARS-COV-2: a promising tool to fight against COVID-19

(2022) Yang Zhang et al.   TRENDS IN BIOTECHNOLOGY

iPiDA-LTR: Identifying piwi-interacting RNA-disease associations based on Learning to Rank

(2022) Wenxiang Zhang et al.   PLoS Computational Biology

Self-supervised contrastive learning for integrative single cell RNA-seq data analysis

(2022) Wenkai Han et al.   BRIEFINGS IN BIOINFORMATICS

Advances and opportunities in RNA structure experimental determination and computational modeling

(2022) Jinsong Zhang et al.   NATURE METHODS

iPiDA-GCN: Identification of piRNA-disease associations based on Graph Convolutional Network

(2022) Jialu Hou et al.   PLoS Computational Biology

BAT-Net: An enhanced RNA Secondary Structure prediction via bidirectional GRU-based network with attention mechanism

(2022) Cong Shen et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Direct Inference of Base-Pairing Probabilities with Neural Networks Improves Prediction of RNA Secondary Structures with Pseudoknots

(2022) Manato Akiyama et al.   Genes

Improved RNA Secondary Structure and Tertiary Base-pairing Prediction Using Evolutionary Profile, Mutational Coupling and Two-dimensional Transfer Learning

(2021) Jaswinder Singh et al.   BIOINFORMATICS

Predicting dynamic cellular protein–RNA interactions by deep learning using in vivo RNA structures

(2021) Lei Sun et al.   CELL RESEARCH

RNA secondary structure prediction using deep learning with thermodynamic integration

(2021) Kengo Sato et al.   Nature Communications

Proteomic and Transcriptome Profiling of G-Quadruplex Aptamers Developed for Cell Internalization

(2021) Yang Zhang et al.   ANALYTICAL CHEMISTRY

iCircDA-LTR: identification of circRNA-disease associations based on Learning to Rank

(2021) Hang Wei et al.   BIOINFORMATICS

Multi-view Multichannel Attention Graph Convolutional Network for miRNA–disease association prediction

(2021) Xinru Tang et al.   BRIEFINGS IN BIOINFORMATICS

Pairing a high-resolution statistical potential with a nucleobase-centric sampling algorithm for improving RNA model refinement

(2021) Peng Xiong et al.   Nature Communications

AptaNet as a deep learning approach for aptamer–protein interaction prediction

(2021) Neda Emami et al.   Scientific Reports

RNAcmap: a fully automatic pipeline for predicting contact maps of RNAs by evolutionary coupling analysis

(2021) Tongchuan Zhang et al.   BIOINFORMATICS

Highly accurate protein structure prediction for the human proteome

(2021) Kathryn Tunyasuvunakool et al.   NATURE

RNA structure probing uncovers RNA structure-dependent biological functions

(2021) Xi-Wen Wang et al.   Nature Chemical Biology

mRNA vaccines for infectious diseases: principles, delivery and clinical translation

(2021) Namit Chaudhary et al.   NATURE REVIEWS DRUG DISCOVERY

catRAPID omics v2.0: going deeper and wider in the prediction of protein–RNA interactions

(2021) Alexandros Armaos et al.   NUCLEIC ACIDS RESEARCH

Temperature effects on RNA polymerase initiation kinetics reveal which open complex initiates and that bubble collapse is stepwise

(2021) Dylan M. Plaskon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Geometric deep learning of RNA structure

(2021) Raphael J. L. Townshend et al.   SCIENCE

Accurate prediction of protein structures and interactions using a three-track neural network

(2021) Minkyung Baek et al.   SCIENCE

A deep learning approach to identify gene targets of a therapeutic for human splicing disorders

(2021) Dadi Gao et al.   Nature Communications

MGRCDA: Metagraph Recommendation Method for Predicting CircRNA–Disease Association

(2021) Lei Wang et al.   IEEE Transactions on Cybernetics

PmliPred: a method based on hybrid model and fuzzy decision for plant miRNA–lncRNA interaction prediction

(2020) Qiang Kang et al.   BIOINFORMATICS

Alternate RNA Structures

(2020) Marie Teng-Pei Wu et al.   Cold Spring Harbor Perspectives in Biology

Realistic in silico generation and augmentation of single-cell RNA-seq data using generative adversarial networks

(2020) Mohamed Marouf et al.   Nature Communications

PASSION: an ensemble neural network approach for identifying the binding sites of RBPs on circRNAs

(2020) Cangzhi Jia et al.   BIOINFORMATICS

GCNCDA: A new method for predicting circRNA-disease associations based on Graph Convolutional Network Algorithm

(2020) Lei Wang et al.   PLoS Computational Biology

PPAI: a web server for predicting protein-aptamer interactions

(2020) Jianwei Li et al.   BMC BIOINFORMATICS

Discovery of G-quadruplex-forming sequences in SARS-CoV-2

(2020) Danyang Ji et al.   BRIEFINGS IN BIOINFORMATICS

GAERF: predicting lncRNA-disease associations by graph auto-encoder and random forest

(2020) Qing-Wen Wu et al.   BRIEFINGS IN BIOINFORMATICS

DMFLDA: A Deep Learning Framework for Predicting lncRNA–Disease Associations

(2020) Min Zeng et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Predicting Splicing from Primary Sequence with Deep Learning

(2019) Kishore Jaganathan et al.   CELL

Recent Advances in Aptamer Discovery and Applications

(2019) Yang Zhang et al.   MOLECULES

RNA structure drives interaction with proteins

(2019) Natalia Sanchez de Groot et al.   Nature Communications

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

(2019) Jaswinder Singh et al.   Nature Communications

An Efficient Approach based on Multi-sources Information to Predict CircRNA-disease Associations Using Deep Convoltional Neural Network

(2019) Lei Wang et al.   BIOINFORMATICS

DeepMirTar: a deep-learning approach for predicting human miRNA targets

(2018) Ming Wen et al.   BIOINFORMATICS

Predicting RNA–protein binding sites and motifs through combining local and global deep convolutional neural networks

(2018) Xiaoyong Pan et al.   BIOINFORMATICS

Solving the RNA design problem with reinforcement learning

(2018) Peter Eastman et al.   PLoS Computational Biology

miRAW: A deep learning-based approach to predict microRNA targets by analyzing whole microRNA transcripts

(2018) Albert Pla et al.   PLoS Computational Biology

Emerging Roles for Intermolecular RNA-RNA Interactions in RNP Assemblies

(2018) Briana Van Treeck et al.   CELL

RNA3DCNN: Local and global quality assessments of RNA 3D structures using 3D deep convolutional neural networks

(2018) Jun Li et al.   PLoS Computational Biology

Structural imprints in vivo decode RNA regulatory mechanisms

(2015) Robert C. Spitale et al.   NATURE

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Infernal 1.1: 100-fold faster RNA homology searches

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