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

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation

(2017) Hyun Min Kang et al.   NATURE BIOTECHNOLOGY

Transcriptional risk scores link GWAS to eQTLs and predict complications in Crohn's disease

(2017) Urko M Marigorta et al.   NATURE GENETICS

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

(2016) Lu Chen et al.   CELL

The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease

(2016) William J. Astle et al.   CELL

ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing

(2016) Xingqi Chen et al.   NATURE METHODS

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

GREGOR: evaluating global enrichment of trait-associated variants in epigenomic features using a systematic, data-driven approach

(2015) Ellen M. Schmidt et al.   BIOINFORMATICS

Population Variation and Genetic Control of Modular Chromatin Architecture in Humans

(2015) Sebastian M. Waszak et al.   CELL

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Fine-mapping cellular QTLs with RASQUAL and ATAC-seq

(2015) Natsuhiko Kumasaka 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

Dynamic recruitment of Ets1 to both nucleosome-occupied and -depleted enhancer regions mediates a transcriptional program switch during early T-cell differentiation

(2015) Pierre Cauchy et al.   NUCLEIC ACIDS RESEARCH

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Genetic and epigenetic fine mapping of causal autoimmune disease variants

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

The transcription factor BATF operates as an essential differentiation checkpoint in early effector CD8+ T cells

(2014) Makoto Kurachi et al.   NATURE IMMUNOLOGY

Intersection of population variation and autoimmunity genetics in human T cell activation

(2014) C. J. Ye et al.   SCIENCE

Polarization of the Effects of Autoimmune and Neurodegenerative Risk Alleles in Leukocytes

(2014) T. Raj et al.   SCIENCE

Common Genetic Variants Modulate Pathogen-Sensing Responses in Human Dendritic Cells

(2014) M. N. Lee et al.   SCIENCE

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

(2014) Mahmoud Ghandi et al.   PLoS Computational Biology

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

The TGF-β-Smad3 pathway inhibits CD28-dependent cell growth and proliferation of CD4 T cells

(2013) J-S Delisle et al.   GENES AND IMMUNITY

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals

(2013) A. Battle et al.   GENOME RESEARCH

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

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

Extensive Variation in Chromatin States Across Humans

(2013) M. Kasowski et al.   SCIENCE

Coordinated Effects of Sequence Variation on DNA Binding, Chromatin Structure, and Transcription

(2013) H. Kilpinen et al.   SCIENCE

Identification of Genetic Variants That Affect Histone Modifications in Human Cells

(2013) G. McVicker et al.   SCIENCE

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

Five Years of GWAS Discovery

(2012) Peter M. Visscher et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

Foxp3 Exploits a Pre-Existent Enhancer Landscape for Regulatory T Cell Lineage Specification

(2012) Robert M. Samstein et al.   CELL

Characterization of an arachidonic acid-deficient (Fads1knockout) mouse model

(2012) Yang-Yi Fan et al.   JOURNAL OF LIPID RESEARCH

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

BATF–JUN is critical for IRF4-mediated transcription in T cells

(2012) Peng Li et al.   NATURE

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 accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Prostaglandin E2 and IL-23 plus IL-1β Differentially Regulate the Th1/Th17 Immune Response of Human CD161+CD4+ Memory T Cells

(2011) Arthur Barrie et al.   CTS-Clinical and Translational Science

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

CD39/ENTPD1 Expression by CD4+Foxp3+ Regulatory T Cells Promotes Hepatic Metastatic Tumor Growth in Mice

(2010) Xiaofeng Sun et al.   GASTROENTEROLOGY

Prostaglandin E2, an Immunoactivator

(2010) Daiji Sakata et al.   JOURNAL OF PHARMACOLOGICAL SCIENCES

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci

(2010) Andre Franke et al.   NATURE GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

Disruption of FADS2 gene in mice impairs male reproduction and causes dermal and intestinal ulceration

(2009) Chad K. Stroud et al.   JOURNAL OF LIPID RESEARCH

Foxp3+ regulatory T cells: differentiation, specification, subphenotypes

(2009) Markus Feuerer et al.   NATURE IMMUNOLOGY

DNA Specificity Determinants Associate with Distinct Transcription Factor Functions

(2009) Peter C. Hollenhorst et al.   PLoS Genetics

Genome-wide association studies for complex traits: consensus, uncertainty and challenges

(2008) Mark I. McCarthy et al.   NATURE REVIEWS GENETICS

CTCF-dependent enhancer-blocking by alternative chromatin loop formation

(2008) C. Hou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA