Representation learning of genomic sequence motifs with convolutional neural networks

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

(2019) Ameni Trabelsi et al.   BIOINFORMATICS

COSSMO: predicting competitive alternative splice site selection using deep learning

(2018) Hannes Bretschneider et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Sequential regulatory activity prediction across chromosomes with convolutional neural networks

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

DeFine: deep convolutional neural networks accurately quantify intensities of transcription factor-DNA binding and facilitate evaluation of functional non-coding variants

(2018) Meng Wang et al.   NUCLEIC ACIDS RESEARCH

DeepPolyA: A Convolutional Neural Network Approach for Polyadenylation Site Prediction

(2018) Xin Gao et al.   IEEE Access

Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties

(2018) Ling Chen et al.   PLoS Computational Biology

Deep learning of the regulatory grammar of yeast 5′ untranslated regions from 500,000 random sequences

(2017) Josh T. Cuperus et al.   GENOME RESEARCH

gkmSVM: an R package for gapped-kmer SVM

(2016) Mahmoud Ghandi et al.   BIOINFORMATICS

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

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

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Protein-DNA binding: complexities and multi-protein codes

(2013) T. Siggers et al.   NUCLEIC ACIDS RESEARCH