Context-specific effects of genetic variants associated with autoimmune disease

An atlas of human long non-coding RNAs with accurate 5′ ends

(2017) Chung-Chau Hon 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

Reovirus infection triggers inflammatory responses to dietary antigens and development of celiac disease

(2017) Romain Bouziat et al.   SCIENCE

Genetic variants alter T-bet binding and gene expression in mucosal inflammatory disease

(2017) Katrina Soderquest et al.   PLoS Genetics

Pathogenic implications for autoimmune mechanisms derived by comparative eQTL analysis of CD4+ versus CD8+ T cells

(2017) Silva Kasela et al.   PLoS Genetics

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

(2016) Biola M. Javierre et al.   CELL

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

(2016) Lu Chen et al.   CELL

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity

(2016) Melanie Schirmer et al.   CELL

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

(2016) Hendrik G. Stunnenberg et al.   CELL

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay

(2016) Ryan Tewhey et al.   CELL

A Functional Genomics Approach to Understand Variation in Cytokine Production in Humans

(2016) Yang Li et al.   CELL

Refined mapping of autoimmune disease associated genetic variants with gene expression suggests an important role for non-coding RNAs

(2016) Isis Ricaño-Ponce et al.   JOURNAL OF AUTOIMMUNITY

Modeling disease risk through analysis of physical interactions between genetic variants within chromatin regulatory circuitry

(2016) Olivia Corradin et al.   NATURE GENETICS

Identification of context-dependent expression quantitative trait loci in whole blood

(2016) Daria V Zhernakova et al.   NATURE GENETICS

Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets

(2016) Zhihong Zhu et al.   NATURE GENETICS

Inter-individual variability and genetic influences on cytokine responses to bacteria and fungi

(2016) Yang Li et al.   NATURE MEDICINE

Genome-wide profiling of RNA polymerase transcription at nucleotide resolution in human cells with native elongating transcript sequencing

(2016) Andreas Mayer et al.   Nature Protocols

Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq)

(2016) Dig Bijay Mahat et al.   Nature Protocols

Enhanced Identification of Transcriptional Enhancers Provides Mechanistic Insights into Diseases

(2016) Yasuhiro Murakawa et al.   TRENDS IN GENETICS

Understanding Celiac Disease by Genomics

(2016) Sebo Withoff et al.   TRENDS IN GENETICS

Local Communication Among Mucosal Immune Cells in Patients With Celiac Disease

(2015) Jeroen van Bergen et al.   GASTROENTEROLOGY

Integration of disease association and eQTL data using a Bayesian colocalisation approach highlights six candidate causal genes in immune-mediated diseases

(2015) H. Guo et al.   HUMAN MOLECULAR GENETICS

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

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state

(2015) Assaf Rotem et al.   NATURE BIOTECHNOLOGY

Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo

(2015) Matthew T Maurano et al.   NATURE GENETICS

FTO Obesity Variant Circuitry and Adipocyte Browning in Humans

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

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

Genome-wide analysis of the genetic regulation of gene expression in human neutrophils

(2015) Anand Kumar Andiappan et al.   Nature Communications

Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs

(2015) Viren Amin et al.   Nature Communications

Genomic modulators of gene expression in human neutrophils

(2015) Vivek Naranbhai et al.   Nature Communications

Capture Hi-C reveals novel candidate genes and complex long-range interactions with related autoimmune risk loci

(2015) Paul Martin et al.   Nature Communications

Intestinal Microbiota and Celiac Disease: Cause, Consequence or Co-Evolution?

(2015) María Cenit et al.   Nutrients

Calling genotypes from public RNA-sequencing data enables identification of genetic variants that affect gene-expression levels

(2015) Patrick Deelen et al.   Genome Medicine

Cell Specific eQTL Analysis without Sorting Cells

(2015) Harm-Jan Westra et al.   PLoS Genetics

Expression analysis in intestinal mucosa reveals complex relations among genes under the association peaks in celiac disease

(2014) Leticia Plaza-Izurieta et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Coeliac disease-associated polymorphisms influence thymic gene expression

(2014) S S Amundsen et al.   GENES AND IMMUNITY

Principles of regulatory information conservation between mouse and human

(2014) Yong Cheng et al.   NATURE

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

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

(2014) Leighton J Core et al.   NATURE GENETICS

Heritability and genomics of gene expression in peripheral blood

(2014) Fred A Wright et al.   NATURE GENETICS

Mapping the Genetic Architecture of Gene Regulation in Whole Blood

(2014) Katharina Schramm et al.   PLoS One

Interindividual variation in human T regulatory cells

(2014) A. Ferraro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

(2014) B. P. Fairfax et al.   SCIENCE

Characterizing the genetic basis of innate immune response in TLR4-activated human monocytes

(2014) Sarah Kim et al.   Nature Communications

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

(2014) Claudia Giambartolomei et al.   PLoS Genetics

Computational deconvolution: extracting cell type-specific information from heterogeneous samples

(2013) Shai S Shen-Orr et al.   CURRENT OPINION IN IMMUNOLOGY

NF-κB: roles and regulation in different CD4+T-cell subsets

(2013) Hyunju Oh et al.   IMMUNOLOGICAL REVIEWS

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

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

(2013) Harm-Jan Westra et al.   NATURE GENETICS

Activation of Protein Tyrosine Phosphatase Non-Receptor Type 2 by Spermidine Exerts Anti-Inflammatory Effects in Human THP-1 Monocytes and in a Mouse Model of Acute Colitis

(2013) Belén Morón et al.   PLoS One

Functional genomics identifies type I interferon pathway as central for host defense against Candida albicans

(2013) Sanne P. Smeekens et al.   Nature Communications

DeepSAGE Reveals Genetic Variants Associated with Alternative Polyadenylation and Expression of Coding and Non-coding Transcripts

(2013) Daria V. Zhernakova et al.   PLoS Genetics

Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression

(2013) Vinod Kumar et al.   PLoS Genetics

Impact of common regulatory single-nucleotide variants on gene expression profiles in whole blood

(2012) Divya Mehta et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Genetics of gene expression in primary immune cells identifies cell type–specific master regulators and roles of HLA alleles

(2012) Benjamin P Fairfax et al.   NATURE GENETICS

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

(2012) Gosia Trynka et al.   NATURE GENETICS

Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection

(2012) L. B. Barreiro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Crohnʼs disease-associated polymorphism within the PTPN2 gene affects muramyl-dipeptide-induced cytokine secretion and autophagy

(2011) Michael Scharl et al.   INFLAMMATORY BOWEL DISEASES

Protein Tyrosine Phosphatase non-Receptor Type 2 regulates IFN-γ-induced cytokine signaling in THP-1 monocytes

(2010) Michael Scharl et al.   INFLAMMATORY BOWEL DISEASES

Multiple common variants for celiac disease influencing immune gene expression

(2010) Patrick C A Dubois et al.   NATURE GENETICS

Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan

(2010) Charles Plessy et al.   NATURE METHODS

Cell type–specific gene expression differences in complex tissues

(2010) Shai S Shen-Orr et al.   NATURE METHODS

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE