Genetic effects on liver chromatin accessibility identify disease regulatory variants

Functional effects of variation in transcription factor binding highlight long-range gene regulation by epromoters

(2020) Joanna Mitchelmore et al.   NUCLEIC ACIDS RESEARCH

Quantification, Dynamic Visualization, and Validation of Bias in ATAC-Seq Data with ataqv

(2020) Peter Orchard et al.   Cell Systems

Chromatin accessibility and the regulatory epigenome

(2019) Sandy L. Klemm et al.   NATURE REVIEWS GENETICS

GARFIELD classifies disease-relevant genomic features through integration of functional annotations with association signals

(2019) Valentina Iotchkova et al.   NATURE GENETICS

Genetic and Epigenetic Fine Mapping of Complex Trait Associated Loci in the Human Liver

(2019) Minal Çalışkan et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A compendium of promoter-centered long-range chromatin interactions in the human genome

(2019) Inkyung Jung et al.   NATURE GENETICS

Adipose Tissue Gene Expression Associations Reveal Hundreds of Candidate Genes for Cardiometabolic Traits

(2019) Chelsea K. Raulerson et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A New Liver Expression Quantitative Trait Locus Map From 1,183 Individuals Provides Evidence for Novel Expression Quantitative Trait Loci of Drug Response, Metabolic, and Sex‐Biased Phenotypes

(2019) Amy S. Etheridge et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Single-cell ATAC-Seq in human pancreatic islets and deep learning upscaling of rare cells reveals cell-specific type 2 diabetes regulatory signatures

(2019) Vivek Rai et al.   Molecular Metabolism

Landscape of Conditional eQTL in Dorsolateral Prefrontal Cortex and Co-localization with Schizophrenia GWAS

(2018) Amanda Dobbyn et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis

(2018) Luis de la Torre-Ubieta et al.   CELL

Pioneer transcription factors shape the epigenetic landscape

(2018) Alexandre Mayran et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response

(2018) Kaur Alasoo et al.   NATURE GENETICS

Genetic analysis of quantitative traits in the Japanese population links cell types to complex human diseases

(2018) Masahiro Kanai et al.   NATURE GENETICS

Genetic determinants of co-accessible chromatin regions in activated T cells across humans

(2018) Rachel E. Gate et al.   NATURE GENETICS

A mega-analysis of expression quantitative trait loci (eQTL) provides insight into the regulatory architecture of gene expression variation in liver

(2018) Tobias Strunz et al.   Scientific Reports

Type 2 Diabetes Associated Genetic Variants Regulate Chromatin Accessibility in Human Islets

(2018) Shubham Khetan et al.   DIABETES

Meta-analysis of genome-wide association studies for height and body mass index in ∼700000 individuals of European ancestry

(2018) Loic Yengo et al.   HUMAN MOLECULAR GENETICS

Meta-analysis of genome-wide association studies for body fat distribution in 694,649 individuals of European ancestry

(2018) Sara L Pulit et al.   HUMAN MOLECULAR GENETICS

Power, false discovery rate and Winner’s Curse in eQTL studies

(2018) Qin Qin Huang et al.   NUCLEIC ACIDS RESEARCH

Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia

(2018) Julien Bryois et al.   Nature Communications

Leveraging Polygenic Functional Enrichment to Improve GWAS Power

(2018) Gleb Kichaev et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Fine-mapping type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps

(2018) Anubha Mahajan et al.   NATURE GENETICS

Genetics of blood lipids among ~300,000 multi-ethnic participants of the Million Veteran Program

(2018) Derek Klarin et al.   NATURE GENETICS

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

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

A genome-wide interactome of DNA-associated proteins in the human liver

(2017) Ryne C. Ramaker et al.   GENOME RESEARCH

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections

(2017) Jaime Abraham Castro-Mondragon et al.   NUCLEIC ACIDS RESEARCH

Genetic regulatory signatures underlying islet gene expression and type 2 diabetes

(2017) Arushi Varshney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

An Efficient Multiple-Testing Adjustment for eQTL Studies that Accounts for Linkage Disequilibrium between Variants

(2016) Joe R. Davis et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Fast and accurate long-range phasing in a UK Biobank cohort

(2016) Po-Ru Loh et al.   NATURE GENETICS

A reference panel of 64,976 haplotypes for genotype imputation

(2016)   NATURE GENETICS

Next-generation genotype imputation service and methods

(2016) Sayantan Das et al.   NATURE GENETICS

The genetic regulatory signature of type 2 diabetes in human skeletal muscle

(2016) Laura J. Scott et al.   Nature Communications

QoRTs: a comprehensive toolset for quality control and data processing of RNA-Seq experiments

(2015) Stephen W. Hartley et al.   BMC BIOINFORMATICS

Evaluation of the lipopolysaccharide-induced transcription of the human TREM-1 gene in vitamin D3-matured THP-1 macrophage-like cells

(2015) HIROSHI HOSODA et al.   INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Fine-mapping cellular QTLs with RASQUAL and ATAC-seq

(2015) Natsuhiko Kumasaka et al.   NATURE GENETICS

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

(2015) Hilary K Finucane et al.   NATURE GENETICS

WASP: allele-specific software for robust molecular quantitative trait locus discovery

(2015) Bryce van de Geijn et al.   NATURE METHODS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Arginine Methylation of CRTC2 Is Critical in the Transcriptional Control of Hepatic Glucose Metabolism

(2014) H.-S. Han et al.   Science Signaling

Identification of a Regulatory Variant That Binds FOXA1 and FOXA2 at the CDC123/CAMK1D Type 2 Diabetes GWAS Locus

(2014) Marie P. Fogarty et al.   PLoS Genetics

Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics

(2014) Claudia Giambartolomei et al.   PLoS Genetics

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions

(2013) N. C. Sheffield et al.   GENOME RESEARCH

Genetics of rheumatoid arthritis contributes to biology and drug discovery

(2013) Yukinori Okada et al.   NATURE

Discovery and refinement of loci associated with lipid levels

(2013) Cristen J Willer et al.   NATURE GENETICS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data

(2012) Goo Jun et al.   AMERICAN JOURNAL OF HUMAN GENETICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

DNase I sensitivity QTLs are a major determinant of human expression variation

(2012) Jacob F. Degner et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Fraternal twins: Swiprosin-1/EFhd2 and Swiprosin-2/EFhd1, two homologous EF-hand containing calcium binding adaptor proteins with distinct functions

(2011) Sebastian Dütting et al.   Cell Communication and Signaling

Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma

(2011) John C Chambers et al.   NATURE GENETICS

LocusZoom: regional visualization of genome-wide association scan results

(2010) R. J. Pruim et al.   BIOINFORMATICS

Robust relationship inference in genome-wide association studies

(2010) Ani Manichaikul et al.   BIOINFORMATICS

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

(2010) Robert C McLeay et al.   BMC BIOINFORMATICS

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

(2010) Kiran Musunuru et al.   NATURE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Transcription factor HNF and hepatocyte differentiation

(2008) Masahito Nagaki et al.   HEPATOLOGY RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY