Single-cell eQTL mapping identifies cell type–specific genetic control of autoimmune disease

Identification of 38 novel loci for systemic lupus erythematosus and genetic heterogeneity between ancestral groups

(2021) Yong-Fei Wang et al.   Nature Communications

Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression

(2021) Urmo Võsa et al.   NATURE GENETICS

LDlinkR: An R Package for Rapidly Calculating Linkage Disequilibrium Statistics in Diverse Populations

(2020) Timothy A. Myers et al.   Frontiers in Genetics

Single-cell transcriptomics identifies an effectorness gradient shaping the response of CD4+ T cells to cytokines

(2020) Eddie Cano-Gamez et al.   Nature Communications

A simple new approach to variable selection in regression, with application to genetic fine mapping

(2020) Gao Wang et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Trans-ethnic and Ancestry-Specific Blood-Cell Genetics in 746,667 Individuals from 5 Global Populations

(2020) Ming-Huei Chen et al.   CELL

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

Where Are the Disease-Associated eQTLs?

(2020) Benjamin D. Umans et al.   TRENDS IN GENETICS

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Dynamic genetic regulation of gene expression during cellular differentiation

(2019) B. J. Strober et al.   SCIENCE

Shared genetic and experimental links between obesity-related traits and asthma subtypes in UK Biobank

(2019) Zhaozhong Zhu et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Visualizing structure and transitions in high-dimensional biological data

(2019) Kevin R. Moon et al.   NATURE BIOTECHNOLOGY

Homeobox protein Hhex negatively regulates Treg cells by inhibiting Foxp3 expression and function

(2019) Sung Woong Jang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

NK Cells Stimulate Recruitment of cDC1 into the Tumor Microenvironment Promoting Cancer Immune Control

(2018) Jan P. Böttcher et al.   CELL

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

(2018) Farhad Hormozdiari et al.   NATURE GENETICS

Characterization of the enhancer and promoter landscape of inflammatory bowel disease from human colon biopsies

(2018) Mette Boyd et al.   Nature Communications

Human Sox4 facilitates the development of CXCL13-producing helper T cells in inflammatory environments

(2018) Hiroyuki Yoshitomi et al.   Nature Communications

Genetics of rheumatoid arthritis: 2018 status

(2018) Yukinori Okada et al.   ANNALS OF THE RHEUMATIC DISEASES

Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression

(2018) Benjamin J. Schmiedel et al.   CELL

High-Dimensional Single-Cell Analysis Identifies Organ-Specific Signatures and Conserved NK Cell Subsets in Humans and Mice

(2018) Adeline Crinier et al.   IMMUNITY

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

Meta-analysis of Immunochip data of four autoimmune diseases reveals novel single-disease and cross-phenotype associations

(2018) Ana Márquez et al.   Genome Medicine

ORMDL3 Facilitates the Survival of Splenic B Cells via an ATF6α–Endoplasmic Reticulum Stress–Beclin1 Autophagy Regulatory Pathway

(2017) Jie Dang et al.   JOURNAL OF IMMUNOLOGY

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

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

(2017) Hyun Min Kang et al.   NATURE BIOTECHNOLOGY

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

(2017) Kazuyoshi Ishigaki 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

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

(2017) Alexandra-Chloé Villani et al.   SCIENCE

Transancestral mapping and genetic load in systemic lupus erythematosus

(2017) Carl D. Langefeld et al.   Nature Communications

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

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

Reference-based phasing using the Haplotype Reference Consortium panel

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

A reference panel of 64,976 haplotypes for genotype imputation

(2016)   NATURE GENETICS

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

(2016) Zhihong Zhu et al.   NATURE GENETICS

RNA splicing is a primary link between genetic variation and disease

(2016) Yang I. Li et al.   SCIENCE

Variation in the Human Immune System Is Largely Driven by Non-Heritable Influences

(2015) Petter Brodin et al.   CELL

CD160 is essential for NK-mediated IFN-γ production

(2015) Tony C. Tu et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

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

Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus

(2015) James Bentham et al.   NATURE GENETICS

A Genome-Wide Association Study of Myasthenia Gravis

(2015) Alan E. Renton et al.   JAMA Neurology

Autoimmune Disease-Associated Haplotypes ofBLKExhibit Lowered Thresholds for B Cell Activation and Expansion of Ig Class-Switched B Cells

(2015) Kim R. Simpfendorfer et al.   Arthritis & Rheumatology

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

High-density genotyping of immune loci in Koreans and Europeans identifies eight new rheumatoid arthritis risk loci

(2014) Kwangwoo Kim et al.   ANNALS OF THE RHEUMATIC DISEASES

Citrullination regulates pluripotency and histone H1 binding to chromatin

(2014) Maria A. Christophorou et al.   NATURE

Autosomal dominant immune dysregulation syndrome in humans with CTLA4 mutations

(2014) Desirée Schubert et al.   NATURE MEDICINE

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

(2014) C. J. Ye et al.   SCIENCE

Immune dysregulation in human subjects with heterozygous germline mutations in CTLA4

(2014) H. S. Kuehn et al.   SCIENCE

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

(2014) B. P. Fairfax et al.   SCIENCE

Identification of Novel Genetic Loci Associated with Thyroid Peroxidase Antibodies and Clinical Thyroid Disease

(2014) Marco Medici et al.   PLoS Genetics

Genetic Variants Regulating Immune Cell Levels in Health and Disease

(2013) Valeria Orrù et al.   CELL

Variants at multiple loci implicated in both innate and adaptive immune responses are associated with Sjögren's syndrome

(2013) Christopher J Lessard et al.   NATURE GENETICS

Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis

(2013) Ashley H Beecham et al.   NATURE GENETICS

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

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

BACH2 represses effector programmes to stabilize Treg-mediated immune homeostasis - a new target in tumor immunotherapy?

(2013) Rahul Roychoudhuri et al.   Journal for ImmunoTherapy of Cancer

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

Human CD8+ T cells and NK cells express and secrete S100B upon stimulation

(2011) Johann Steiner et al.   BRAIN BEHAVIOR AND IMMUNITY

Genetic control of gene expression in whole blood and lymphoblastoid cell lines is largely independent

(2011) J. E. Powell et al.   GENOME RESEARCH

IFN-  Acts on the Airway Epithelium To Inhibit Local and Systemic Pathology in Allergic Airway Disease

(2011) C. Mitchell et al.   JOURNAL OF IMMUNOLOGY

GCTA: A Tool for Genome-wide Complex Trait Analysis

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

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

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

REL, encoding a member of the NF-κB family of transcription factors, is a newly defined risk locus for rheumatoid arthritis

(2009) Peter K Gregersen et al.   NATURE GENETICS

Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes

(2009) Jeffrey C Barrett et al.   NATURE GENETICS

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of Monomeric Yeast and Mammalian Sec61 Complexes Interacting with the Translating Ribosome

(2009) T. Becker et al.   SCIENCE

Structure of the Dual Enzyme Ire1 Reveals the Basis for Catalysis and Regulation in Nonconventional RNA Splicing

(2008) Kenneth P.K. Lee et al.   CELL

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

The unfolded protein response signals through high-order assembly of Ire1

(2008) Alexei V. Korennykh et al.   NATURE

Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci

(2008) Jason D Cooper et al.   NATURE GENETICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY