Maximum entropy methods for extracting the learned features of deep neural networks

Convolutional neural network architectures for predicting DNA–protein binding

(2016) Haoyang Zeng et al.   BIOINFORMATICS

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

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

Categorical spectral analysis of periodicity in nucleosomal DNA

(2016) Hu Jin 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

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Mechanisms Underlying Nucleosome Positioning In Vivo

(2014) Amanda L. Hughes et al.   Annual Review of Biophysics

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

CCCTC-Binding Factor Confines the Distal Action of Estrogen Receptor

(2008) Chang S. Chan et al.   CANCER RESEARCH