Sequential regulatory activity prediction across chromosomes with convolutional neural networks

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Regulatory feedback from nascent RNA to chromatin and transcription

(2017) Lenka Skalska et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters

(2016) Biola M. Javierre et al.   CELL

The 3D Genome as Moderator of Chromosomal Communication

(2016) Job Dekker et al.   CELL

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long et al.   CELL

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

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

Open Targets: a platform for therapeutic target identification and validation

(2016) Gautier Koscielny et al.   NUCLEIC ACIDS RESEARCH

The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)

(2016) Jacqueline MacArthur et al.   NUCLEIC ACIDS RESEARCH

RNA splicing is a primary link between genetic variation and disease

(2016) Yang I. Li et al.   SCIENCE

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions

(2015) Fabian Grubert et al.   CELL

Population Variation and Genetic Control of Modular Chromatin Architecture in Humans

(2015) Sebastian M. Waszak 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

Early enhancer establishment and regulatory locus complexity shape transcriptional programs in hematopoietic differentiation

(2015) Alvaro J González et al.   NATURE GENETICS

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

(2015) Borbala Mifsud et al.   NATURE GENETICS

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

(2015) Dongwon Lee et al.   NATURE GENETICS

Partitioning heritability by functional annotation using genome-wide association summary statistics

(2015) Hilary K Finucane et al.   NATURE GENETICS

LD Score regression distinguishes confounding from polygenicity in genome-wide association studies

(2015) Brendan K Bulik-Sullivan et al.   NATURE GENETICS

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

(2015) Jian Zhou et al.   NATURE METHODS

The role of regulatory variation in complex traits and disease

(2015) Frank W. Albert et al.   NATURE REVIEWS GENETICS

FTO Obesity Variant Circuitry and Adipocyte Browning in Humans

(2015) Melina Claussnitzer et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

On Pixel-Wise Explanations for Non-Linear Classifier Decisions by Layer-Wise Relevance Propagation

(2015) Sebastian Bach et al.   PLoS One

CNV-guided multi-read allocation for ChIP-seq

(2014) Qi Zhang et al.   BIOINFORMATICS

A promoter-level mammalian expression atlas

(2014)   NATURE

Genetic and epigenetic fine mapping of causal autoimmune disease variants

(2014) Kyle Kai-How Farh et al.   NATURE

Predicting the human epigenome from DNA motifs

(2014) John W Whitaker et al.   NATURE METHODS

Identifying and mitigating bias in next-generation sequencing methods for chromatin biology

(2014) Clifford A. Meyer et al.   NATURE REVIEWS GENETICS

Impact of regulatory variation from RNA to protein

(2014) A. Battle et al.   SCIENCE

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

(2014) Mahmoud Ghandi et al.   PLoS Computational Biology

The Functional Consequences of Variation in Transcription Factor Binding

(2014) Darren A. Cusanovich et al.   PLoS Genetics

Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis

(2013) Ashley H Beecham et al.   NATURE GENETICS

Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease

(2013) Jean-Charles Lambert et al.   NATURE GENETICS

Dynamics and Memory of Heterochromatin in Living Cells

(2012) Nathaniel A. Hathaway et al.   CELL

Understanding transcriptional regulation by integrative analysis of transcription factor binding data

(2012) C. Cheng et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Metazoan promoters: emerging characteristics and insights into transcriptional regulation

(2012) Boris Lenhard et al.   NATURE REVIEWS GENETICS

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Transcriptional Enhancers in Animal Development and Evolution

(2010) Mike Levine   CURRENT BIOLOGY

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

Fingolimod (FTY720): discovery and development of an oral drug to treat multiple sclerosis

(2010) Volker Brinkmann et al.   NATURE REVIEWS DRUG DISCOVERY

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY