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

Gene expression inference with deep learning

(2016) Yifei Chen et al.   BIOINFORMATICS

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

A method to predict the impact of regulatory variants from DNA sequence

(2015) Dongwon Lee et al.   NATURE GENETICS

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

RSAT 2015: Regulatory Sequence Analysis Tools

(2015) Alejandra Medina-Rivera et al.   NUCLEIC ACIDS RESEARCH

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

Motif signatures in stretch enhancers are enriched for disease-associated genetic variants

(2015) Daniel X Quang et al.   Epigenetics & Chromatin

EXTREME: an online EM algorithm for motif discovery

(2014) Daniel Quang et al.   BIOINFORMATICS

GRASP: analysis of genotype-phenotype results from 1390 genome-wide association studies and corresponding open access database

(2014) R. Leslie et al.   BIOINFORMATICS

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

(2014) Daniel Quang et al.   BIOINFORMATICS

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

(2014) Mahmoud Ghandi et al.   PLoS Computational Biology

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA