Selene: a PyTorch-based deep learning library for sequence data

pysster: classification of biological sequences by learning sequence and structure motifs with convolutional neural networks

(2018) Stefan Budach et al.   BIOINFORMATICS

Sequential regulatory activity prediction across chromosomes with convolutional neural networks

(2018) David R. Kelley et al.   GENOME RESEARCH

Opportunities and obstacles for deep learning in biology and medicine

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

Predicting the clinical impact of human mutation with deep neural networks

(2018) Laksshman Sundaram et al.   NATURE GENETICS

Planning chemical syntheses with deep neural networks and symbolic AI

(2018) Marwin H. S. Segler et al.   NATURE

A common haplotype lowers PU.1 expression in myeloid cells and delays onset of Alzheimer's disease

(2017) Kuan-lin Huang et al.   NATURE NEUROSCIENCE

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

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

Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse

(2016) Shenglin Mei et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Daniel Quang et al.   NUCLEIC ACIDS RESEARCH

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

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

Follow-up of loci from the International Genomics of Alzheimer’s Disease Project identifies TRIP4 as a novel susceptibility gene

(2014) A Ruiz et al.   Translational Psychiatry

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Tabix: fast retrieval of sequence features from generic TAB-delimited files

(2011) H. Li   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS