Cross-species regulatory sequence activity prediction

The mutational constraint spectrum quantified from variation in 141,456 humans

(2020) Konrad J. Karczewski et al.   NATURE

Predicting mRNA Abundance Directly from Genomic Sequence Using Deep Convolutional Neural Networks

(2020) Vikram Agarwal et al.   Cell Reports

Predicting Splicing from Primary Sequence with Deep Learning

(2019) Kishore Jaganathan et al.   CELL

Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk

(2019) Jian Zhou et al.   NATURE GENETICS

Cross-Cell-Type Prediction of TF-Binding Site by Integrating Convolutional Neural Network and Adversarial Network

(2019) Gongqiang Lan et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

OUP accepted manuscript

(2018)   BIOINFORMATICS

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

Sequential regulatory activity prediction across chromosomes with convolutional neural networks

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

The human noncoding genome defined by genetic diversity

(2018) Julia di Iulio et al.   NATURE GENETICS

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk

(2018) Yakir A. Reshef et al.   NATURE GENETICS

A database of tissue-specific rhythmically expressed human genes has potential applications in circadian medicine

(2018) Marc D. Ruben et al.   Science Translational Medicine

Found In Translation: a machine learning model for mouse-to-human inference

(2018) Rachelly Normand et al.   NATURE METHODS

Nuclear receptor HNF4A transrepresses CLOCK:BMAL1 and modulates tissue-specific circadian networks

(2018) Meng Qu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder

(2018) Joon-Yong An et al.   SCIENCE

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

(2018) Ling Chen et al.   PLoS Computational Biology

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

ClinVar: improving access to variant interpretations and supporting evidence

(2017) Melissa J Landrum et al.   NUCLEIC ACIDS RESEARCH

Transcriptional regulatory logic of the diurnal cycle in the mouse liver

(2017) Jonathan Aryeh Sobel et al.   PLOS BIOLOGY

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

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

Learning the Sequence Determinants of Alternative Splicing from Millions of Random Sequences

(2015) Alexander B. Rosenberg et al.   CELL

A Century of Cholesterol and Coronaries: From Plaques to Genes to Statins

(2015) Joseph L. Goldstein et al.   CELL

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs 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

Conservation of transcription factor binding specificities across 600 million years of bilateria evolution

(2015) Kazuhiro R Nitta et al.   eLife

Alignathon: a competitive assessment of whole-genome alignment methods

(2014) Dent Earl et al.   GENOME RESEARCH

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

Evolution of transcription factor binding in metazoans — mechanisms and functional implications

(2014) Diego Villar et al.   NATURE REVIEWS GENETICS

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

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

(2012) Eilon Sharon et al.   NATURE BIOTECHNOLOGY

Massively parallel functional dissection of mammalian enhancers in vivo

(2012) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Complex effects of nucleotide variants in a mammalian cis-regulatory element

(2012) J. C. Kwasnieski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions

(2011) Joseph K. Pickrell et al.   BIOINFORMATICS

Organogenesis and Development of the Liver

(2010) Karim Si-Tayeb et al.   DEVELOPMENTAL CELL

From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus

(2010) Kiran Musunuru et al.   NATURE

The Simons Simplex Collection: A Resource for Identification of Autism Genetic Risk Factors

(2010) Gerald D. Fischbach et al.   NEURON

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Species-Specific Transcription in Mice Carrying Human Chromosome 21

(2008) M. D. Wilson et al.   SCIENCE