RNAdegformer: accurate prediction of mRNA degradation at nucleotide resolution with deep learning

Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics

(2022) Kathrin Leppek et al.   Nature Communications

mRNA-1273 vaccination protects against SARS-CoV-2 elicited lung inflammation in non-human primates

(2022) Adam T. Waickman et al.   JCI Insight

A transformer architecture based on BERT and 2D convolutional neural network to identify DNA enhancers from sequence information

(2021) Nguyen Quoc Khanh Le et al.   BRIEFINGS IN BIOINFORMATICS

mRNA vaccine: a potential therapeutic strategy

(2021) Yang Wang et al.   Molecular Cancer

mRNA-lipid nanoparticle COVID-19 vaccines: Structure and stability

(2021) Linde Schoenmaker et al.   INTERNATIONAL JOURNAL OF PHARMACEUTICS

A self-attention model for inferring cooperativity between regulatory features

(2021) Fahad Ullah et al.   NUCLEIC ACIDS RESEARCH

Machine learning for profile prediction in genomics

(2021) Jacob Schreiber et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Efficacy and Safety of the mRNA-1273 SARS-CoV-2 Vaccine

(2020) Lindsey R. Baden et al.   NEW ENGLAND JOURNAL OF MEDICINE

Identifying centromeric satellites with dna-brnn

(2019) Heng Li   BIOINFORMATICS

DeePromoter: Robust Promoter Predictor Using Deep Learning

(2019) Mhaned Oubounyt et al.   Frontiers in Genetics

Comprehensive evaluation of deep learning architectures for prediction of DNA/RNA sequence binding specificities

(2019) Ameni Trabelsi et al.   BIOINFORMATICS

DeepSite: bidirectional LSTM and CNN models for predicting DNA–protein binding

(2019) Yongqing Zhang et al.   International Journal of Machine Learning and Cybernetics

ViraMiner: Deep learning on raw DNA sequences for identifying viral genomes in human samples

(2019) Ardi Tampuu et al.   PLoS One

mRNA structure regulates protein expression through changes in functional half-life

(2019) David M. Mauger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Classifying Promoters by Interpreting the Hidden Information of DNA Sequences via Deep Learning and Combination of Continuous FastText N-Grams

(2019) Nguyen Quoc Khanh Le et al.   Frontiers in Bioengineering and Biotechnology

Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk

(2018) Jian Zhou et al.   NATURE GENETICS

mRNA vaccines — a new era in vaccinology

(2018) Norbert Pardi et al.   NATURE REVIEWS DRUG DISCOVERY

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

(2018) Padideh Danaee et al.   NUCLEIC ACIDS RESEARCH

Advances in the delivery of RNA therapeutics: from concept to clinical reality

(2017) James C. Kaczmarek et al.   Genome Medicine

Deep learning for computational biology

(2016) Christof Angermueller et al.   Molecular Systems Biology

DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences

(2016) Daniel Quang et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

A deep learning framework for modeling structural features of RNA-binding protein targets

(2015) Sai Zhang et al.   NUCLEIC ACIDS RESEARCH

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS