Improved integrative framework combining association data with gene expression features to prioritize Crohn's disease genes

XIAP variants in male Crohn's disease

(2014) Yvonne Zeissig et al.   GUT

A Crohn’s disease variant in Atg16l1 enhances its degradation by caspase 3

(2014) Aditya Murthy et al.   NATURE

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

Sherlock: Detecting Gene-Disease Associations by Matching Patterns of Expression QTL and GWAS

(2013) Xin He et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Peripheral Blood Based Discrimination of Ulcerative Colitis and Crohn’s Disease from Non-IBD Colitis by Genome-Wide Gene Expression Profiling

(2013) Ferenc Sipos et al.   DISEASE MARKERS

Expression Quantitative Trait Loci Analysis Identifies Associations Between Genotype and Gene Expression in Human Intestine

(2013) Boyko Kabakchiev et al.   GASTROENTEROLOGY

Monogenic diseases associated with intestinal inflammation: implications for the understanding of inflammatory bowel disease

(2013) Holm H Uhlig   GUT

Phenotypic Characterization of Very Early-onset IBD Due to Mutations in the IL10, IL10 Receptor Alpha or Beta Gene

(2013) Bénédicte Pigneur et al.   INFLAMMATORY BOWEL DISEASES

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

(2012) Luke Jostins et al.   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

ENCODE Data in the UCSC Genome Browser: year 5 update

(2012) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Effector CD4+ T Cell Expression Signatures and Immune-Mediated Disease Associated Genes

(2012) Wei Zhang et al.   PLoS One

Unraveling the Regulatory Mechanisms Underlying Tissue-Dependent Genetic Variation of Gene Expression

(2012) Jingyuan Fu et al.   PLoS Genetics

Dissecting the regulatory architecture of gene expression QTLs

(2012) Daniel J Gaffney et al.   GENOME BIOLOGY

pROC: an open-source package for R and S+ to analyze and compare ROC curves

(2011) Xavier Robin et al.   BMC BIOINFORMATICS

A survey of the genetics of stomach, liver, and adipose gene expression from a morbidly obese cohort

(2011) D. M. Greenawalt et al.   GENOME RESEARCH

Endotoxin Tolerance Represents a Distinctive State of Alternative Polarization (M2) in Human Mononuclear Cells

(2011) O. M. Pena et al.   JOURNAL OF IMMUNOLOGY

Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease

(2011) Manuel A Rivas et al.   NATURE GENETICS

Pervasive Sharing of Genetic Effects in Autoimmune Disease

(2011) Chris Cotsapas et al.   PLoS Genetics

The Architecture of Gene Regulatory Variation across Multiple Human Tissues: The MuTHER Study

(2011) Alexandra C. Nica et al.   PLoS Genetics

Proteins Encoded in Genomic Regions Associated with Immune-Mediated Disease Physically Interact and Suggest Underlying Biology

(2011) Elizabeth J. Rossin et al.   PLoS Genetics

A Versatile Gene-Based Test for Genome-wide Association Studies

(2010) Jimmy Z. Liu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Infant colitis—it's in the genes

(2010) Erik-Oliver Glocker et al.   LANCET

Genome-wide association study of ankylosing spondylitis identifies non-MHC susceptibility loci

(2010) John D Reveille et al.   NATURE GENETICS

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

(2010) Andre Franke et al.   NATURE GENETICS

Trait-Associated SNPs Are More Likely to Be eQTLs: Annotation to Enhance Discovery from GWAS

(2010) Dan L. Nicolae et al.   PLoS Genetics

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Inflammatory Bowel Disease

(2009) Clara Abraham et al.   NEW ENGLAND JOURNAL OF MEDICINE

Inflammatory Bowel Disease and Mutations Affecting the Interleukin-10 Receptor

(2009) Erik-Oliver Glocker et al.   NEW ENGLAND JOURNAL OF MEDICINE

Identifying Relationships among Genomic Disease Regions: Predicting Genes at Pathogenic SNP Associations and Rare Deletions

(2009) Soumya Raychaudhuri et al.   PLoS Genetics

lumi: a pipeline for processing Illumina microarray

(2008) P. Du et al.   BIOINFORMATICS