Transcription factors operate across disease loci, with EBNA2 implicated in autoimmunity

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

(2016) Biola M. Javierre et al.   CELL

The role of GATA3 in breast carcinomas: a review

(2016) Rebecca Asch-Kendrick et al.   HUMAN PATHOLOGY

High-density genotyping of immune-related loci identifies new SLE risk variants in individuals with Asian ancestry

(2016) Celi Sun et al.   NATURE GENETICS

XGR software for enhanced interpretation of genomic summary data, illustrated by application to immunological traits

(2016) Hai Fang et al.   Genome Medicine

BS69/ZMYND11 C-Terminal Domains Bind and Inhibit EBNA2

(2016) Matthew R. Harter et al.   PLoS Pathogens

Genome-Wide Association Study in an Amerindian Ancestry Population Reveals Novel Systemic Lupus Erythematosus Risk Loci and the Role of European Admixture

(2016) Marta E. Alarcón-Riquelme et al.   Arthritis & Rheumatology

Disentangling the Effects of Colocalizing Genomic Annotations to Functionally Prioritize Non-coding Variants within Complex-Trait Loci

(2015) Gosia Trynka et al.   AMERICAN JOURNAL OF HUMAN GENETICS

PKC theta and p38 MAPK activate the EBV lytic cycle through autophagy induction

(2015) Roberta Gonnella et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

ABC: a tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments: Fig. 1.

(2015) Swneke D. Bailey et al.   BIOINFORMATICS

Removing reference mapping biases using limited or no genotype data identifies allelic differences in protein binding at disease-associated loci

(2015) Martin L. Buchkovich et al.   BMC Medical Genomics

Epstein-Barr Virus Oncoprotein Super-enhancers Control B Cell Growth

(2015) Hufeng Zhou et al.   Cell Host & Microbe

Persistent androgen receptor addiction in castration-resistant prostate cancer

(2015) Michael T. Schweizer et al.   Journal of Hematology & Oncology

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

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

Fine-mapping cellular QTLs with RASQUAL and ATAC-seq

(2015) Natsuhiko Kumasaka et al.   NATURE GENETICS

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

(2015) Borbala Mifsud et al.   NATURE GENETICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

The Role of Latently Infected B Cells in CNS Autoimmunity

(2015) Ana Citlali Márquez et al.   Frontiers in Immunology

EBNA2 Binds to Genomic Intervals Associated with Multiple Sclerosis and Overlaps with Vitamin D Receptor Occupancy

(2015) Vito A. G. Ricigliano et al.   PLoS One

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Genetic and epigenetic fine mapping of causal autoimmune disease variants

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

Genome-wide association analysis of eosinophilic esophagitis provides insight into the tissue specificity of this allergic disease

(2014) Leah C Kottyan et al.   NATURE GENETICS

Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape

(2014) Aurélien Griffon et al.   NUCLEIC ACIDS RESEARCH

Systematic review and meta-analysis of the sero-epidemiological association between Epstein-Barr virus and systemic lupus erythematosus

(2014) Peter Hanlon et al.   ARTHRITIS RESEARCH & THERAPY

RTeQTL: Real-Time Online Engine for Expression Quantitative Trait Loci Analyses

(2014) B. Ma et al.   Database-The Journal of Biological Databases and Curation

Imputation and quality control steps for combining multiple genome-wide datasets

(2014) Shefali S. Verma et al.   Frontiers in Genetics

Epstein-Barr Virus in Systemic Autoimmune Diseases

(2013) Anette Holck Draborg et al.   Clinical & Developmental Immunology

A cross-platform analysis of 14,177 expression quantitative trait loci derived from lymphoblastoid cell lines

(2013) L. Liang et al.   GENOME RESEARCH

Genetics of rheumatoid arthritis contributes to biology and drug discovery

(2013) Yukinori Okada et al.   NATURE

A statin-dependent QTL for GATM expression is associated with statin-induced myopathy

(2013) Lara M. Mangravite et al.   NATURE

A genome-wide association study in Han Chinese identifies a susceptibility locus for primary Sjögren's syndrome at 7q11.23

(2013) Yongzhe Li et al.   NATURE GENETICS

DGIdb: mining the druggable genome

(2013) Malachi Griffith et al.   NATURE METHODS

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

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

NF-κB-mediated transcriptional upregulation of TNFAIP2 by the Epstein–Barr virus oncoprotein, LMP1, promotes cell motility in nasopharyngeal carcinoma

(2013) C-C Chen et al.   ONCOGENE

Systematic Review and Meta-Analysis of the Sero-Epidemiological Association between Epstein Barr Virus and Multiple Sclerosis

(2013) Yahya H. Almohmeed et al.   PLoS One

NF-κB and IRF7 Pathway Activation by Epstein-Barr Virus Latent Membrane Protein 1

(2013) Ina Ersing et al.   Viruses-Basel

Genetic susceptibility to lupus: the biological basis of genetic risk found in B cell signaling pathways

(2012) Samuel E. Vaughn et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Analysis of Epstein-Barr Virus-Regulated Host Gene Expression Changes through Primary B-Cell Outgrowth Reveals Delayed Kinetics of Latent Membrane Protein 1-Mediated NF- B Activation

(2012) A. M. Price et al.   JOURNAL OF VIROLOGY

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Infection and autoimmune disease

(2012) Asli Gamze Sener et al.   RHEUMATOLOGY INTERNATIONAL

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Dissecting the regulatory architecture of gene expression QTLs

(2012) Daniel J Gaffney et al.   GENOME BIOLOGY

Integrating Autoimmune Risk Loci with Gene-Expression Data Identifies Specific Pathogenic Immune Cell Subsets

(2011) Xinli Hu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Canonical NF- B Activation Is Essential for Epstein-Barr Virus Latent Membrane Protein 1 TES2/CTAR2 Gene Regulation

(2011) B. E. Gewurz et al.   JOURNAL OF VIROLOGY

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

(2011) Jason Ernst et al.   NATURE

Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease

(2011) Gosia Trynka et al.   NATURE GENETICS

Transcriptome genetics using second generation sequencing in a Caucasian population

(2010) Stephen B. Montgomery et al.   NATURE

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

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

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

(2009) A. S. Dimas et al.   SCIENCE

The role of infections in autoimmune disease

(2008) A. M. Ercolini et al.   CLINICAL AND EXPERIMENTAL IMMUNOLOGY

The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences

(2008) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

High-Resolution Mapping of Expression-QTLs Yields Insight into Human Gene Regulation

(2008) Jean-Baptiste Veyrieras et al.   PLoS Genetics