A primer on deep learning in genomics

Prediction of enhancer-promoter interactions via natural language processing

(2018) Wanwen Zeng et al.   BMC GENOMICS

Next-Generation Machine Learning for Biological Networks

(2018) Diogo M. Camacho et al.   CELL

Deep learning of genomic variation and regulatory network data

(2018) Amalio Telenti et al.   HUMAN MOLECULAR GENETICS

Opportunities and obstacles for deep learning in biology and medicine

(2018) Travers Ching et al.   Journal of the Royal Society Interface

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

(2018) Jian Zhou et al.   NATURE GENETICS

Predicting the clinical impact of human mutation with deep neural networks

(2018) Laksshman Sundaram et al.   NATURE GENETICS

A deep recurrent neural network discovers complex biological rules to decipher RNA protein-coding potential

(2018) Steven T Hill et al.   NUCLEIC ACIDS RESEARCH

Generalising better: Applying deep learning to integrate deleteriousness prediction scores for whole-exome SNV studies

(2018) Ilia Korvigo et al.   PLoS One

Deep learning for biology

(2018) Sarah Webb   NATURE

Enhancing GTEx by bridging the gaps between genotype, gene expression, and disease

(2017) Barbara E Stranger et al.   NATURE GENETICS

Using neural networks for reducing the dimensions of single-cell RNA-Seq data

(2017) Chieh Lin et al.   NUCLEIC ACIDS RESEARCH

Predicting clinical outcomes from large scale cancer genomic profiles with deep survival models

(2017) Safoora Yousefi et al.   Scientific Reports

DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads

(2017) Vladimír Boža et al.   PLoS One

Gene expression inference with deep learning

(2016) Yifei Chen et al.   BIOINFORMATICS

Convolutional neural network architectures for predicting DNA–protein binding

(2016) Haoyang Zeng et al.   BIOINFORMATICS

DeepGene: an advanced cancer type classifier based on deep learning and somatic point mutations

(2016) Yuchen Yuan et al.   BMC BIOINFORMATICS

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks

(2016) David R. Kelley et al.   GENOME RESEARCH

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

ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions

(2016) Jie Tan et al.   mSystems

Deep learning

(2015) Yann LeCun et al.   NATURE

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

Machine learning applications in genetics and genomics

(2015) Maxwell W. Libbrecht et al.   NATURE REVIEWS GENETICS

DANN: a deep learning approach for annotating the pathogenicity of genetic variants

(2014) Daniel Quang et al.   BIOINFORMATICS

DEEP: a general computational framework for predicting enhancers

(2014) Dimitrios Kleftogiannis et al.   NUCLEIC ACIDS RESEARCH