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

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

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Impact of regulatory variation across human iPSCs and differentiated cells

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Fine-mapping inflammatory bowel disease loci to single-variant resolution

(2017) Hailiang Huang et al.   NATURE

Discovery of stimulation-responsive immune enhancers with CRISPR activation

(2017) Dimitre R. Simeonov et al.   NATURE

Limited statistical evidence for shared genetic effects of eQTLs and autoimmune-disease-associated loci in three major immune-cell types

(2017) Sung Chun et al.   NATURE GENETICS

Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease

(2017) Katrina M de Lange et al.   NATURE GENETICS

Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations

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Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

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Memory of Inflammation in Regulatory T Cells

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CD8 + T Cells Utilize Highly Dynamic Enhancer Repertoires and Regulatory Circuitry in Response to Infections

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Near-optimal probabilistic RNA-seq quantification

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Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

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Next-generation genotype imputation service and methods

(2016) Sayantan Das et al.   NATURE GENETICS

Comparative In Vitro Immune Stimulation Analysis of Primary Human B Cells and B Cell Lines

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Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions

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Single-cell chromatin accessibility reveals principles of regulatory variation

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Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers

(2015) Suna Onengut-Gumuscu 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

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The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

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Genetic variants associated with autoimmunity drive NFκB signaling and responses to inflammatory stimuli

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

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

GRASP: analysis of genotype-phenotype results from 1390 genome-wide association studies and corresponding open access database

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UpSet: Visualization of Intersecting Sets

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Genetic and epigenetic fine mapping of causal autoimmune disease variants

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

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Associations between functional polymorphisms in the NFκB signaling pathway and response to anti-TNF treatment in Danish patients with inflammatory bowel disease

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

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

(2014) M. N. Lee et al.   SCIENCE

Innate Immune Activity Conditions the Effect of Regulatory Variants upon Monocyte Gene Expression

(2014) B. P. Fairfax et al.   SCIENCE

Latent Enhancers Activated by Stimulation in Differentiated Cells

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Systematic identification of trans eQTLs as putative drivers of known disease associations

(2013) Harm-Jan Westra 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

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

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GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph 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

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Chromatin marks identify critical cell types for fine mapping complex trait variants

(2012) Gosia Trynka et al.   NATURE GENETICS

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

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Integrating Autoimmune Risk Loci with Gene-Expression Data Identifies Specific Pathogenic Immune Cell Subsets

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The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

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