Convolutional neural network architectures for predicting DNA–protein binding

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

Learning Deep Generative Models

(2015) Ruslan Salakhutdinov   Annual Review of Statistics and Its Application

Predicting the human epigenome from DNA motifs

(2014) John W Whitaker et al.   NATURE METHODS

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

(2014) Mahmoud Ghandi et al.   PLoS Computational Biology

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH