Dynamic landscape of immune cell-specific gene regulation in immune-mediated diseases

Comparison of host immune responses to LPS in human using an immune profiling panel, in vivo endotoxemia versus ex vivo stimulation

(2020) Dina M. Tawfik et al.   Scientific Reports

Cell type–specific genetic regulation of gene expression across human tissues

(2020) Sarah Kim-Hellmuth et al.   SCIENCE

The GTEx Consortium atlas of genetic regulatory effects across human tissues

(2020)   SCIENCE

ANCA-associated vasculitis

(2020) A. Richard Kitching et al.   Nature Reviews Disease Primers

PLD4 is a genetic determinant to systemic lupus erythematosus and involved in murine autoimmune phenotypes

(2019) Shuji Akizuki et al.   ANNALS OF THE RHEUMATIC DISEASES

Cytokine Networks in the Pathophysiology of Inflammatory Bowel Disease

(2019) Matthias Friedrich et al.   IMMUNITY

High-throughput identification of human SNPs affecting regulatory element activity

(2019) Joris van Arensbergen et al.   NATURE GENETICS

Landscape of stimulation-responsive chromatin across diverse human immune cells

(2019) Diego Calderon et al.   NATURE GENETICS

Single-cell RNA sequencing identifies celltype-specific cis-eQTLs and co-expression QTLs

(2018) Monique G. P. van der Wijst et al.   NATURE GENETICS

Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation

(2018) Eric R. Gamazon et al.   NATURE GENETICS

Leveraging molecular quantitative trait loci to understand the genetic architecture of diseases and complex traits

(2018) Farhad Hormozdiari et al.   NATURE GENETICS

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

(2018) Kaur Alasoo et al.   NATURE GENETICS

A Positive Feedback Amplifier Circuit That Regulates Interferon (IFN)-Stimulated Gene Expression and Controls Type I and Type II IFN Responses

(2018) Agata Michalska et al.   Frontiers in Immunology

A One-Penny Imputed Genome from Next-Generation Reference Panels

(2018) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression

(2018) Benjamin J. Schmiedel et al.   CELL

Distinct Effector B Cells Induced by Unregulated Toll-like Receptor 7 Contribute to Pathogenic Responses in Systemic Lupus Erythematosus

(2018) Scott A. Jenks et al.   IMMUNITY

Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions

(2018) Sarah M. Urbut 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

Regulation of the Cell Cycle and Inflammatory Arthritis by the Transcription CofactorLBHGene

(2017) Shinji Matsuda et al.   JOURNAL OF IMMUNOLOGY

Discovery of stimulation-responsive immune enhancers with CRISPR activation

(2017) Dimitre R. Simeonov et al.   NATURE

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Polygenic burdens on cell-specific pathways underlie the risk of rheumatoid arthritis

(2017) Kazuyoshi Ishigaki et al.   NATURE GENETICS

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

jMorp: Japanese Multi Omics Reference Panel

(2017) Shu Tadaka et al.   NUCLEIC ACIDS RESEARCH

RNAi Screen and Proteomics Reveal NXF1 as a Novel Regulator of IRF5 Signaling

(2017) Bishi Fu et al.   Scientific Reports

Colocalization of GWAS and eQTL Signals Detects Target Genes

(2016) Farhad Hormozdiari et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

(2016) Lu Chen et al.   CELL

Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens

(2016) Yohann Nédélec et al.   CELL

Genetic Adaptation and Neandertal Admixture Shaped the Immune System of Human Populations

(2016) Hélène Quach et al.   CELL

Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation

(2016) Jernej Godec et al.   IMMUNITY

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

(2016) Daria V Zhernakova et al.   NATURE GENETICS

Fast and efficient QTL mapper for thousands of molecular phenotypes

(2015) Halit Ongen et al.   BIOINFORMATICS

The WNT-controlled transcriptional regulator LBH is required for mammary stem cell expansion and maintenance of the basal lineage

(2015) L. E. Lindley et al.   DEVELOPMENT

Anti-dsDNA antibodies induce inflammation via endoplasmic reticulum stress in human mesangial cells

(2015) Hui Zhang et al.   Journal of Translational Medicine

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations

(2015) Jimmy Z Liu et al.   NATURE GENETICS

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

(2015) Hilary K Finucane et al.   NATURE GENETICS

LD Score regression distinguishes confounding from polygenicity in genome-wide association studies

(2015) Brendan K Bulik-Sullivan et al.   NATURE GENETICS

Heterogeneity of autoimmune diseases: pathophysiologic insights from genetics and implications for new therapies

(2015) Judy H Cho et al.   NATURE MEDICINE

The selection and function of cell type-specific enhancers

(2015) Sven Heinz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Perception of self: distinguishing autoimmunity from autoinflammation

(2015) Tessa S. van Kempen et al.   Nature Reviews Rheumatology

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

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

Review: A20-Binding Inhibitor of NF-κB Activation 1 Is a Physiologic Inhibitor of NF-κB: A Molecular Switch for Inflammation and Autoimmunity

(2015) Rachel T. G'Sell et al.   Arthritis & Rheumatology

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Identifying Causal Variants at Loci with Multiple Signals of Association

(2014) F. Hormozdiari et al.   GENETICS

Genetic and epigenetic fine mapping of causal autoimmune disease variants

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

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

(2014) B. P. Fairfax et al.   SCIENCE

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

(2014) Claudia Giambartolomei et al.   PLoS Genetics

2013 Classification Criteria for Systemic Sclerosis: An American College of Rheumatology/European League Against Rheumatism Collaborative Initiative

(2013) Frank van den Hoogen et al.   ARTHRITIS AND RHEUMATISM

TCC: an R package for comparing tag count data with robust normalization strategies

(2013) Jianqiang Sun et al.   BMC BIOINFORMATICS

The Satb1 Protein Directs Hematopoietic Stem Cell Differentiation toward Lymphoid Lineages

(2013) Yusuke Satoh et al.   IMMUNITY

Immunopathogenic mechanisms of systemic autoimmune disease

(2013) Marie Wahren-Herlenius et al.   LANCET

Genetics of rheumatoid arthritis contributes to biology and drug discovery

(2013) Yukinori Okada et al.   NATURE

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

Effectively Identifying eQTLs from Multiple Tissues by Combining Mixed Model and Meta-analytic Approaches

(2013) Jae Hoon Sul et al.   PLoS Genetics

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Dendritic Cell-Specific Disruption of TGF-  Receptor II Leads to Altered Regulatory T Cell Phenotype and Spontaneous Multiorgan Autoimmunity

(2012) R. Ramalingam et al.   JOURNAL OF IMMUNOLOGY

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

(2012) Gosia Trynka et al.   NATURE GENETICS

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

(2012) Oliver Stegle et al.   Nature Protocols

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

The use of Systemic Lupus Erythematosus Disease Activity Index-2000 to define active disease and minimal clinically meaningful change based on data from a large cohort of systemic lupus erythematosus patients

(2011) C.-S. Yee et al.   RHEUMATOLOGY

The American College of Rheumatology 1990 criteria for the classification of takayasu arteritis

(2010) William P. Arend et al.   ARTHRITIS AND RHEUMATISM

2010 Rheumatoid arthritis classification criteria: An American College of Rheumatology/European League Against Rheumatism collaborative initiative

(2010) Daniel Aletaha et al.   ARTHRITIS AND RHEUMATISM

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay

(2009) Kazufumi Matsushita et al.   NATURE

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS