Regulatory genomic circuitry of human disease loci by integrative epigenomics

Index and biological spectrum of human DNase I hypersensitive sites

(2020) Wouter Meuleman et al.   NATURE

Global reference mapping of human transcription factor footprints

(2020) Jeff Vierstra et al.   NATURE

Expanded encyclopaedias of DNA elements in the human and mouse genomes

(2020) Jill E. Moore et al.   NATURE

Beyond the neuron–cellular interactions early in Alzheimer disease pathogenesis

(2019) Christopher M. Henstridge et al.   NATURE REVIEWS NEUROSCIENCE

WashU Epigenome Browser update 2019

(2019) Daofeng Li et al.   NUCLEIC ACIDS RESEARCH

Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

(2019) Charles P. Fulco et al.   NATURE GENETICS

The Post-GWAS Era: From Association to Function

(2018) Michael D. Gallagher et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

(2018) Annalisa Buniello et al.   NUCLEIC ACIDS RESEARCH

Association analysis identifies 65 new breast cancer risk loci

(2017) Kyriaki Michailidou et al.   NATURE

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

(2017) Ivan V Kulakovskiy et al.   NUCLEIC ACIDS RESEARCH

The SIN3A histone deacetylase complex is required for a complete transcriptional response to hypoxia

(2017) Maria Tiana et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Liver-specific deletion of the Plpp3 gene alters plasma lipid composition and worsens atherosclerosis in apoE−/− mice

(2017) Marco Busnelli et al.   Scientific Reports

Identification of 64 Novel Genetic Loci Provides an Expanded View on the Genetic Architecture of Coronary Artery Disease

(2017) Pim van der Harst et al.   CIRCULATION RESEARCH

The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery

(2016) Hendrik G. Stunnenberg et al.   CELL

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

(2016) Jacqueline MacArthur et al.   NUCLEIC ACIDS RESEARCH

H3K9me3-Dependent Heterochromatin: Barrier to Cell Fate Changes

(2016) Justin S. Becker et al.   TRENDS IN GENETICS

Which Genetics Variants in DNase-Seq Footprints Are More Likely to Alter Binding?

(2016) Gregory A. Moyerbrailean et al.   PLoS Genetics

Genome-wide association study of schizophrenia in Ashkenazi Jews

(2015) Fernando S. Goes et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART B-NEUROPSYCHIATRIC GENETICS

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues

(2015) Jason Ernst et al.   NATURE BIOTECHNOLOGY

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

The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study

(2015) Thomas W. Winkler et al.   PLoS Genetics

Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases

(2014) Alexander Gusev et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Joint Analysis of Functional Genomic Data and Genome-wide Association Studies of 18 Human Traits

(2014) Joseph K. Pickrell   AMERICAN JOURNAL OF HUMAN GENETICS

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

A vital role for complement in heart disease

(2014) Knut T. Lappegård et al.   MOLECULAR IMMUNOLOGY

Genetic and epigenetic fine mapping of causal autoimmune disease variants

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

The UCSC Genome Browser database: 2015 update

(2014) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits

(2013) O. Corradin et al.   GENOME RESEARCH

Modification of Enhancer Chromatin: What, How, and Why?

(2013) Eliezer Calo et al.   MOLECULAR CELL

Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments

(2013) P. Kheradpour et al.   NUCLEIC ACIDS RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Interpreting noncoding genetic variation in complex traits and human disease

(2012) Lucas D Ward et al.   NATURE BIOTECHNOLOGY

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

(2012) Michael M Hoffman et al.   NATURE METHODS

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants

(2011) L. D. Ward et al.   NUCLEIC ACIDS RESEARCH

Prioritizing GWAS Results: A Review of Statistical Methods and Recommendations for Their Application

(2010) Rita M. Cantor et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Common Regulatory Variation Impacts Gene Expression in a Cell Type-Dependent Manner

(2009) A. S. Dimas et al.   SCIENCE

Design and analysis of ChIP-seq experiments for DNA-binding proteins

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY