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

hichipper: a preprocessing pipeline for calling DNA loops from HiChIP data

(2018) Caleb A Lareau et al.   NATURE METHODS

3D Chromosome Regulatory Landscape of Human Pluripotent Cells

(2016) Xiong Ji et al.   Cell Stem Cell

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

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

(2016) Olivia Corradin et al.   NATURE GENETICS

Genome-wide association meta-analysis in Chinese and European individuals identifies ten new loci associated with systemic lupus erythematosus

(2016) David L Morris et al.   NATURE GENETICS

Detection and interpretation of shared genetic influences on 42 human traits

(2016) Joseph K Pickrell et al.   NATURE GENETICS

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

(2016) Maxwell R Mumbach et al.   NATURE METHODS

Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse

(2016) Shenglin Mei et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Prithvi Raj et al.   eLife

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

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

WASP: allele-specific software for robust molecular quantitative trait locus discovery

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

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

(2015) Christopher C Chang et al.   GigaScience

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes

(2014) Jill M. Dowen et al.   CELL

Value of HLA-DR genotype in systemic lupus erythematosus and lupus nephritis: a meta-analysis

(2014) Zhili Niu et al.   International Journal of Rheumatic Diseases

Genetic and epigenetic fine mapping of causal autoimmune disease variants

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

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

(2014) Olivier Delaneau et al.   Nature Communications

LEVERAGING BIOLOGICAL REPLICATES TO IMPROVE ANALYSIS IN CHIP-SEQ EXPERIMENTS

(2014) Yajie Yang et al.   Computational and Structural Biotechnology Journal

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

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

(2013) Ashley H Beecham et al.   NATURE GENETICS

Epstein–Barr virus-mediated transformation of B cells induces global chromatin changes independent to the acquisition of proliferation

(2013) Henar Hernando et al.   NUCLEIC ACIDS RESEARCH

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

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

(2013) G. McVicker et al.   SCIENCE

The B cell transcription program mediates hypomethylation and overexpression of key genes in Epstein-Barr virus-associated proliferative conversion

(2013) Henar Hernando et al.   GENOME BIOLOGY

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

Annotation of functional variation in personal genomes using RegulomeDB

(2012) A. P. Boyle et al.   GENOME RESEARCH

Epigenetic Nucleosomes: Alu Sequences and CG as Nucleosome Positioning Element

(2012) F. Salih et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease

(2012) Luke Jostins et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Dense fine-mapping study identifies new susceptibility loci for primary biliary cirrhosis

(2012) Jimmy Z Liu et al.   NATURE GENETICS

Two new susceptibility loci for Kawasaki disease identified through genome-wide association analysis

(2012) Yi-Ching Lee et al.   NATURE GENETICS

A genome-wide association study identifies three new risk loci for Kawasaki disease

(2012) Yoshihiro Onouchi et al.   NATURE GENETICS

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

Fast and accurate genotype imputation in genome-wide association studies through pre-phasing

(2012) Bryan Howie et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

Genome-wide association study of rheumatoid arthritis in Koreans: Population-specific loci as well as overlap with European susceptibility loci

(2011) Jan Freudenberg et al.   ARTHRITIS AND RHEUMATISM

The effects of EBV transformation on gene expression levels and methylation profiles

(2011) Minal Çalışkan et al.   HUMAN MOLECULAR GENETICS

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47

(2011) Carl A Anderson et al.   NATURE GENETICS

Genome-Wide Scan Identifies TNIP1, PSORS1C1, and RHOB as Novel Risk Loci for Systemic Sclerosis

(2011) Yannick Allanore et al.   PLoS Genetics

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Integrating common and rare genetic variation in diverse human populations

(2010)   NATURE

Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci

(2010) Andre Franke et al.   NATURE GENETICS

The Lupus Family Registry and Repository

(2010) A. Rasmussen et al.   RHEUMATOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

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 in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus

(2009) Jian-Wen Han et al.   NATURE GENETICS

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

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

Variation analysis and gene annotation of eight MHC haplotypes: The MHC Haplotype Project

(2008) Roger Horton et al.   IMMUNOGENETICS

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

(2008) Jason D Cooper et al.   NATURE GENETICS

Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci

(2008) John B Harley et al.   NATURE GENETICS

Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease

(2008) Jeffrey C Barrett et al.   NATURE GENETICS

Association of Systemic Lupus Erythematosus withC8orf13–BLKandITGAM–ITGAX

(2008) Geoffrey Hom et al.   NEW ENGLAND JOURNAL OF MEDICINE