Allele-specific expression changes dynamically during T cell activation in HLA and other autoimmune loci

Expression estimation and eQTL mapping for HLA genes with a personalized pipeline

(2019) Vitor R. C. Aguiar et al.   PLoS Genetics

Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks

(2018) Richard C. Pelikan et al.   Nature Communications

Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk

(2018) Stephane E. Castel et al.   NATURE GENETICS

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

Mixed-effects association of single cells identifies an expanded effector CD4+ T cell subset in rheumatoid arthritis

(2018) Chamith Y. Fonseka et al.   Science Translational Medicine

Pathologically expanded peripheral T helper cell subset drives B cells in rheumatoid arthritis

(2017) Deepak A. Rao et al.   NATURE

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

Allele-specific expression reveals interactions between genetic variation and environment

(2017) David A Knowles et al.   NATURE METHODS

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

CHiCP: a web-based tool for the integrative and interactive visualization of promoter capture Hi-C datasets

(2016) E. C. Schofield et al.   BIOINFORMATICS

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

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

(2016) Yohann Nédélec et al.   CELL

High-throughput allele-specific expression across 250 environmental conditions

(2016) Gregory A. Moyerbrailean et al.   GENOME RESEARCH

Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA

(2016) Christopher D Richardson et al.   NATURE BIOTECHNOLOGY

Autoimmune diseases — connecting risk alleles with molecular traits of the immune system

(2016) Maria Gutierrez-Arcelus et al.   NATURE REVIEWS GENETICS

Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mechanisms

(2016) Michael H. Guo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MHC class II super-enhancer increases surface expression of HLA-DR and HLA-DQ and affects cytokine production in autoimmune vitiligo

(2016) Giulio Cavalli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulatory polymorphisms modulate the expression of HLA class II molecules and promote autoimmunity

(2016) Prithvi Raj et al.   eLife

Fitting Linear Mixed-Effects Models Usinglme4

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

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

Additive and interaction effects at three amino acid positions in HLA-DQ and HLA-DR molecules drive type 1 diabetes risk

(2015) Xinli Hu et al.   NATURE GENETICS

Improved genome inference in the MHC using a population reference graph

(2015) Alexander Dilthey et al.   NATURE GENETICS

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

(2015) Bryce van de Geijn et al.   NATURE METHODS

Generation of knock-in primary human T cells using Cas9 ribonucleoproteins

(2015) Kathrin Schumann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SNPsea: an algorithm to identify cell types, tissues and pathways affected by risk loci

(2014) Kamil Slowikowski et al.   BIOINFORMATICS

Genetic and epigenetic fine mapping of causal autoimmune disease variants

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

Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins

(2014) Alfonso Buil et al.   NATURE GENETICS

The IPD and IMGT/HLA database: allele variant databases

(2014) James Robinson et al.   NUCLEIC ACIDS RESEARCH

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

Regulation of Gene Expression in Autoimmune Disease Loci and the Genetic Basis of Proliferation in CD4+ Effector Memory T Cells

(2014) Xinli Hu et al.   PLoS Genetics

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Imputing Amino Acid Polymorphisms in Human Leukocyte Antigens

(2013) Xiaoming Jia et al.   PLoS One

Passive and active DNA methylation and the interplay with genetic variation in gene regulation

(2013) Maria Gutierrez-Arcelus et al.   eLife

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Five amino acids in three HLA proteins explain most of the association between MHC and seropositive rheumatoid arthritis

(2012) Soumya Raychaudhuri et al.   NATURE GENETICS

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

(2012) Gosia Trynka et al.   NATURE GENETICS

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Pervasive haplotypic variation in the spliceo-transcriptome of the human major histocompatibility complex

(2011) C. Vandiedonck et al.   GENOME RESEARCH

A linear complexity phasing method for thousands of genomes

(2011) Olivier Delaneau et al.   NATURE METHODS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Permutation P-values Should Never Be Zero: Calculating Exact P-values When Permutations Are Randomly Drawn

(2010) Belinda Phipson et al.   Statistical Applications in Genetics and Molecular Biology

Common Regulatory Variation Impacts Gene Expression in a Cell Type-Dependent Manner

(2009) A. S. Dimas et al.   SCIENCE

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

(2009) Bryan N. Howie et al.   PLoS Genetics