Identifying and exploiting trait-relevant tissues with multiple functional annotations in genome-wide association studies

PTPN2-deficiency exacerbates T follicular helper cell and B cell responses and promotes the development of autoimmunity

(2017) Florian Wiede et al.   JOURNAL OF AUTOIMMUNITY

Linkage disequilibrium–dependent architecture of human complex traits shows action of negative selection

(2017) Steven Gazal et al.   NATURE GENETICS

Leveraging functional annotations in genetic risk prediction for human complex diseases

(2017) Yiming Hu et al.   PLoS Computational Biology

Systematic tissue-specific functional annotation of the human genome highlights immune-related DNA elements for late-onset Alzheimer’s disease

(2017) Qiongshi Lu et al.   PLoS Genetics

Associations between NOD2, IRGM and ORMDL3 polymorphisms and pediatric-onset inflammatory bowel disease in the Lithuanian population

(2016) Gitana Pranculienė et al.   Medicina-Lithuania

A spectral approach integrating functional genomic annotations for coding and noncoding variants

(2016) Iuliana Ionita-Laza et al.   NATURE GENETICS

Type 2 diabetes: genetic data sharing to advance complex disease research

(2016) Jason Flannick et al.   NATURE REVIEWS GENETICS

Joint Bayesian inference of risk variants and tissue-specific epigenomic enrichments across multiple complex human diseases

(2016) Yue Li et al.   NUCLEIC ACIDS RESEARCH

RNA splicing is a primary link between genetic variation and disease

(2016) Yang I. Li et al.   SCIENCE

Systematic Analysis of Drug Targets Confirms Expression in Disease-Relevant Tissues

(2016) Vinod Kumar et al.   Scientific Reports

Integrative Tissue-Specific Functional Annotations in the Human Genome Provide Novel Insights on Many Complex Traits and Improve Signal Prioritization in Genome Wide Association Studies

(2016) Qiongshi Lu et al.   PLoS Genetics

Associations between NOD2, IRGM and ORMDL3 polymorphisms and pediatric-onset inflammatory bowel disease in the Lithuanian population

(2016) Gitana Pranculienė et al.   Medicina-Lithuania

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

Genotyping Informatics and Quality Control for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort

(2015) Mark N. Kvale et al.   GENETICS

Characterizing Race/Ethnicity and Genetic Ancestry for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort

(2015) Yambazi Banda et al.   GENETICS

Genome wide identification of new genes and pathways in patients with both autoimmune thyroiditis and type 1 diabetes

(2015) Yaron Tomer et al.   JOURNAL OF AUTOIMMUNITY

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease

(2015) Elizabeta Gjoneska et al.   NATURE

Understanding multicellular function and disease with human tissue-specific networks

(2015) Casey S Greene et al.   NATURE GENETICS

Partitioning heritability by functional annotation using genome-wide association summary statistics

(2015) Hilary K Finucane et al.   NATURE GENETICS

The connectomics of brain disorders

(2015) Alex Fornito et al.   NATURE REVIEWS NEUROSCIENCE

A Statistical Framework to Predict Functional Non-Coding Regions in the Human Genome Through Integrated Analysis of Annotation Data

(2015) Qiongshi Lu et al.   Scientific Reports

Genetic Variations of PTPN2 and PTPN22: Role in the Pathogenesis of Type 1 Diabetes and Crohn's Disease

(2015) Robert C. Sharp et al.   Frontiers in Cellular and Infection Microbiology

Genotyping Informatics and Quality Control for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort

(2015) Mark N. Kvale et al.   GENETICS

Characterizing Race/Ethnicity and Genetic Ancestry for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort

(2015) Yambazi Banda et al.   GENETICS

The Association of Type 2 Diabetes Loci Identified in Genome-Wide Association Studies with Metabolic Syndrome and Its Components in a Chinese Population with Type 2 Diabetes

(2015) Xiaomu Kong et al.   PLoS One

Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases

(2014) Alexander Gusev et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Joint Analysis of Functional Genomic Data and Genome-wide Association Studies of 18 Human Traits

(2014) Joseph K. Pickrell   AMERICAN JOURNAL OF HUMAN GENETICS

Genetic studies of Crohn's disease: Past, present and future

(2014) Jimmy Z. Liu et al.   BEST PRACTICE & RESEARCH IN CLINICAL GASTROENTEROLOGY

Identifying Causal Variants at Loci with Multiple Signals of Association

(2014) F. Hormozdiari et al.   GENETICS

Genetic and epigenetic fine mapping of causal autoimmune disease variants

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

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

Defining functional DNA elements in the human genome

(2014) M. Kellis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GPA: A Statistical Approach to Prioritizing GWAS Results by Integrating Pleiotropy and Annotation

(2014) Dongjun Chung et al.   PLoS Genetics

Integrating Functional Data to Prioritize Causal Variants in Statistical Fine-Mapping Studies

(2014) Gleb Kichaev et al.   PLoS Genetics

Improving the Accuracy and Efficiency of Partitioning Heritability into the Contributions of Genomic Regions

(2013) Emrah Kostem et al.   AMERICAN JOURNAL OF HUMAN GENETICS

General Framework for Meta-analysis of Rare Variants in Sequencing Association Studies

(2013) Seunggeun Lee et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Sequence Kernel Association Tests for the Combined Effect of Rare and Common Variants

(2013) Iuliana Ionita-Laza et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

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

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

Polygenic Modeling with Bayesian Sparse Linear Mixed Models

(2013) Xiang Zhou et al.   PLoS Genetics

Improved Heritability Estimation from Genome-wide SNPs

(2012) Doug Speed et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Microglia and Inflammation in Alzheimers Disease

(2012) Shweta Mandrekar-Colucci et al.   CNS & Neurological Disorders-Drug Targets

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

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

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

(2012) Gosia Trynka et al.   NATURE GENETICS

Genome-wide efficient mixed-model analysis for association studies

(2012) Xiang Zhou et al.   NATURE GENETICS

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Improved whole-chromosome phasing for disease and population genetic studies

(2012) Olivier Delaneau et al.   NATURE METHODS

Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes

(2012) J. A. Tennessen et al.   SCIENCE

Regulation of chromatin by histone modifications

(2011) Andrew J Bannister et al.   CELL RESEARCH

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

(2011) Jason Ernst et al.   NATURE

A linear complexity phasing method for thousands of genomes

(2011) Olivier Delaneau et al.   NATURE METHODS

Genetic Evidence Supporting the Association of Protease and Protease Inhibitor Genes with Inflammatory Bowel Disease: A Systematic Review

(2011) Isabelle Cleynen et al.   PLoS One

Powerful SNP-Set Analysis for Case-Control Genome-wide Association Studies

(2010) Michael C. Wu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

GCTA: A Tool for Genome-wide Complex Trait Analysis

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

Allelic variants in the PHTF1-PTPN22, C12orf30 and CD226 regions as candidate susceptibility factors for the type 1 diabetes in the Estonian population

(2010) Konstantinos Douroudis et al.   BMC Medical Genetics

Pathway analysis comparison using Crohn's disease genome wide association studies

(2010) David Ballard et al.   BMC Medical Genomics

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

Common SNPs explain a large proportion of the heritability for human height

(2010) Jian Yang 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

Abnormal neural oscillations and synchrony in schizophrenia

(2010) Peter J. Uhlhaas et al.   NATURE REVIEWS NEUROSCIENCE

Variants inTNFAIP3,STAT4, andC12orf30loci associated with multiple autoimmune diseases are also associated with juvenile idiopathic arthritis

(2009) Sampath Prahalad et al.   ARTHRITIS AND RHEUMATISM

Genome-wide association analysis by lasso penalized logistic regression

(2009) Tong Tong Wu et al.   BIOINFORMATICS

Effect of BSN-MST1 locus on inflammatory bowel disease and multiple sclerosis susceptibility

(2009) A Márquez et al.   GENES AND IMMUNITY

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

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

A Novel Susceptibility Locus for Type 1 Diabetes on Chr12q13 Identified by a Genome-Wide Association Study

(2008) H. Hakonarson et al.   DIABETES

A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes

(2008) K. Lage et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA