Integrated Enrichment Analysis of Variants and Pathways in Genome-Wide Association Studies Indicates Central Role for IL-2 Signaling Genes in Type 1 Diabetes, and Cytokine Signaling Genes in Crohn's Disease

Polygenic Modeling with Bayesian Sparse Linear Mixed Models

(2013) Xiang Zhou et al.   PLoS Genetics

INRICH: interval-based enrichment analysis for genome-wide association studies

(2012) Phil H. Lee et al.   BIOINFORMATICS

1000 Genomes-based imputation identifies novel and refined associations for the Wellcome Trust Case Control Consortium phase 1 Data

(2012) Jie Huang et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

A Bayesian Integrative Genomic Model for Pathway Analysis of Complex Traits

(2012) Brooke L. Fridley et al.   GENETIC EPIDEMIOLOGY

Linking disease associations with regulatory information in the human genome

(2012) M. A. Schaub et al.   GENOME RESEARCH

Annotation of functional variation in personal genomes using RegulomeDB

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

Type 1 Diabetes-Associated IL2RA Variation Lowers IL-2 Signaling and Contributes to Diminished CD4+CD25+ Regulatory T Cell Function

(2012) G. Garg et al.   JOURNAL OF IMMUNOLOGY

DNase I sensitivity QTLs are a major determinant of human expression variation

(2012) Jacob F. Degner et al.   NATURE

Dysfunction of lipid sensor GPR120 leads to obesity in both mouse and human

(2012) Atsuhiko Ichimura et al.   NATURE

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

(2012) Luke Jostins et al.   NATURE

Interpreting noncoding genetic variation in complex traits and human disease

(2012) Lucas D Ward et al.   NATURE BIOTECHNOLOGY

High-density genetic mapping identifies new susceptibility loci for rheumatoid arthritis

(2012) Steve Eyre et al.   NATURE GENETICS

Including known covariates can reduce power to detect genetic effects in case-control studies

(2012) Matti Pirinen et al.   NATURE GENETICS

An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations

(2012) Vincent Segura et al.   NATURE GENETICS

A pathway analysis method for genome-wide association studies

(2012) Babak Shahbaba et al.   STATISTICS IN MEDICINE

Pathway analysis of genomic data: concepts, methods, and prospects for future development

(2012) Vijay K. Ramanan et al.   TRENDS IN GENETICS

Dissecting the regulatory architecture of gene expression QTLs

(2012) Daniel J Gaffney et al.   GENOME BIOLOGY

Bayesian variable selection regression for genome-wide association studies and other large-scale problems

(2011) Yongtao Guan et al.   Annals of Applied Statistics

Crohn disease: A current perspective on genetics, autophagy and immunity

(2011) Thaddeus S. Stappenbeck et al.   Autophagy

An efficient hierarchical generalized linear mixed model for pathway analysis of genome-wide association studies

(2011) Lily Wang et al.   BIOINFORMATICS

Critical assessment of human metabolic pathway databases: a stepping stone for future integration

(2011) Miranda D Stobbe et al.   BMC Systems Biology

Central Role for Interleukin-2 in Type 1 Diabetes

(2011) M. A. Hulme et al.   DIABETES

Assessment of rare BRCA1 and BRCA2 variants of unknown significance using hierarchical modeling

(2011) Marinela Capanu et al.   GENETIC EPIDEMIOLOGY

Gene set analysis of genome-wide association studies: Methodological issues and perspectives

(2011) Lily Wang et al.   GENOMICS

Pathway-driven gene stability selection of two rheumatoid arthritis GWAS identifies and validates new susceptibility genes in receptor mediated signalling pathways

(2011) Hariklia Eleftherohorinou et al.   HUMAN MOLECULAR GENETICS

A bias-reducing pathway enrichment analysis of genome-wide association data confirmed association of the MHC region with schizophrenia

(2011) Peilin Jia et al.   JOURNAL OF MEDICAL GENETICS

Genetics and pathogenesis of inflammatory bowel disease

(2011) Bernard Khor et al.   NATURE

Understanding type 1 diabetes through genetics: advances and prospects

(2011) Constantin Polychronakos et al.   NATURE REVIEWS GENETICS

Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data

(2011) Gregory M. Cooper et al.   NATURE REVIEWS GENETICS

The Pathogenesis of Rheumatoid Arthritis

(2011) Iain B. McInnes et al.   NEW ENGLAND JOURNAL OF MEDICINE

WikiPathways: building research communities on biological pathways

(2011) T. Kelder et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: extensions and updates 2011

(2011) T. R. Dreszer et al.   NUCLEIC ACIDS RESEARCH

Type 1 Diabetes: Etiology, Immunology, and Therapeutic Strategies

(2011) Tom L. Van Belle et al.   PHYSIOLOGICAL REVIEWS

Tumor suppressor protein (p)53, is a regulator of NF- B repression by the glucocorticoid receptor

(2011) S. H. Murphy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Incorporating Biological Pathways via a Markov Random Field Model in Genome-Wide Association Studies

(2011) Min Chen et al.   PLoS Genetics

Pathways of Distinction Analysis: A New Technique for Multi–SNP Analysis of GWAS Data

(2011) Rosemary Braun et al.   PLoS Genetics

Pervasive Sharing of Genetic Effects in Autoimmune Disease

(2011) Chris Cotsapas et al.   PLoS Genetics

Insights into Colon Cancer Etiology via a Regularized Approach to Gene Set Analysis of GWAS Data

(2010) Lin S. Chen et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Functional Gene Group Analysis Reveals a Role of Synaptic Heterotrimeric G Proteins in Cognitive Ability

(2010) Dina Ruano et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Prioritizing GWAS Results: A Review of Statistical Methods and Recommendations for Their Application

(2010) Rita M. Cantor et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Integrating Pathway Analysis and Genetics of Gene Expression for Genome-wide Association Studies

(2010) Hua Zhong et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

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

A variable selection method for genome-wide association studies

(2010) Qianchuan He et al.   BIOINFORMATICS

Consistency, comprehensiveness, and compatibility of pathway databases

(2010) Donny Soh et al.   BMC BIOINFORMATICS

A variational Bayes algorithm for fast and accurate multiple locus genome-wide association analysis

(2010) Benjamin A Logsdon et al.   BMC BIOINFORMATICS

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

(2010) David Ballard et al.   BMC Medical Genomics

A guide to web tools to prioritize candidate genes

(2010) L.-C. Tranchevent et al.   BRIEFINGS IN BIOINFORMATICS

Acute Insulin Signaling in Pancreatic Beta-Cells Is Mediated by Multiple Raf-1 Dependent Pathways

(2010) Emilyn U. Alejandro et al.   ENDOCRINOLOGY

Genome-wide gene and pathway analysis

(2010) Li Luo et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

ATG16L1 and NOD2 Interact in an Autophagy-Dependent Antibacterial Pathway Implicated in Crohn's Disease Pathogenesis

(2010) Craig R. Homer et al.   GASTROENTEROLOGY

Pathway-based analysis for genome-wide association studies using supervised principal components

(2010) Xi Chen et al.   GENETIC EPIDEMIOLOGY

Bayesian mixture models for the incorporation of prior knowledge to inform genetic association studies

(2010) Brooke L. Fridley et al.   GENETIC EPIDEMIOLOGY

Locus category based analysis of a large genome-wide association study of rheumatoid arthritis

(2010) Jan Freudenberg et al.   HUMAN MOLECULAR GENETICS

Etiology of Type 1 Diabetes

(2010) John A. Todd   IMMUNITY

Molecular pathways involved in neuronal cell adhesion and membrane scaffolding contribute to schizophrenia and bipolar disorder susceptibility

(2010) C O'Dushlaine et al.   MOLECULAR PSYCHIATRY

The BioPAX community standard for pathway data sharing

(2010) Emek Demir et al.   NATURE BIOTECHNOLOGY

Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci

(2010) Eli A Stahl 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

Analysing biological pathways in genome-wide association studies

(2010) Kai Wang et al.   NATURE REVIEWS GENETICS

Genotype imputation for genome-wide association studies

(2010) Jonathan Marchini et al.   NATURE REVIEWS GENETICS

Missing heritability and strategies for finding the underlying causes of complex disease

(2010) Evan E. Eichler et al.   NATURE REVIEWS GENETICS

Genomics, Type 2 Diabetes, and Obesity

(2010) Mark I. McCarthy   NEW ENGLAND JOURNAL OF MEDICINE

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami et al.   NUCLEIC ACIDS RESEARCH

Reactome: a database of reactions, pathways and biological processes

(2010) D. Croft et al.   NUCLEIC ACIDS RESEARCH

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

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

NetPath: a public resource of curated signal transduction pathways

(2010) Kumaran Kandasamy et al.   GENOME BIOLOGY

Gene Ontology Analysis of GWA Study Data Sets Provides Insights into the Biology of Bipolar Disorder

(2009) Peter Holmans et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Diverse Genome-wide Association Studies Associate the IL12/IL23 Pathway with Crohn Disease

(2009) Kai Wang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Genetics of Crohn's Disease

(2009) Johan Van Limbergen et al.   Annual Review of Genomics and Human Genetics

Genotype Imputation

(2009) Yun Li et al.   Annual Review of Genomics and Human Genetics

Genome-wide association analysis by lasso penalized logistic regression

(2009) Tong Tong Wu et al.   BIOINFORMATICS

Regulation of PKD by the MAPK p38δ in Insulin Secretion and Glucose Homeostasis

(2009) Grzegorz Sumara et al.   CELL

Interrogating Type 2 Diabetes Genome-Wide Association Data Using a Biological Pathway-Based Approach

(2009) J. R.B. Perry et al.   DIABETES

Gene and pathway-based second-wave analysis of genome-wide association studies

(2009) Gang Peng et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Analysis of 55 autoimmune disease and type II diabetes loci: further confirmation of chromosomes 4q27, 12q13.2 and 12q24.13 as type I diabetes loci and support for a new locus, 12q13.3–q14.1

(2009) J D Cooper et al.   GENES AND IMMUNITY

Follow-up of 1715 SNPs from the Wellcome Trust Case Control Consortium genome-wide association study in type I diabetes families

(2009) J D Cooper et al.   GENES AND IMMUNITY

Pathway analysis by adaptive combination ofP-values

(2009) Kai Yu et al.   GENETIC EPIDEMIOLOGY

Identification of AF4/FMR2 family, member 3 (AFF3) as a novel rheumatoid arthritis susceptibility locus and confirmation of two further pan-autoimmune susceptibility genes

(2009) Anne Barton et al.   HUMAN MOLECULAR GENETICS

Pathway and network-based analysis of genome-wide association studies in multiple sclerosis

(2009) S. E. Baranzini et al.   HUMAN MOLECULAR GENETICS

Fibroblast-like synoviocytes: key effector cells in rheumatoid arthritis

(2009) Beatrix Bartok et al.   IMMUNOLOGICAL REVIEWS

Association of Measles Virus with Rheumatoid Arthritis

(2009) B. J. ROSENAU et al.   JOURNAL OF RHEUMATOLOGY

Pathway databases and tools for their exploitation: benefits, current limitations and challenges

(2009) Anna Bauer-Mehren et al.   Molecular Systems Biology

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

Molecular networks as sensors and drivers of common human diseases

(2009) Eric E. Schadt   NATURE

Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes

(2009) Jeffrey C Barrett et al.   NATURE GENETICS

Human genetic variation and its contribution to complex traits

(2009) Kelly A. Frazer et al.   NATURE REVIEWS GENETICS

Bayesian statistical methods for genetic association studies

(2009) Matthew Stephens et al.   NATURE REVIEWS GENETICS

Mapping complex disease traits with global gene expression

(2009) William Cookson et al.   NATURE REVIEWS GENETICS

Inflammatory Bowel Disease

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

Genomewide Association Studies — Illuminating Biologic Pathways

(2009) Joel N. Hirschhorn   NEW ENGLAND JOURNAL OF MEDICINE

KEGG for representation and analysis of molecular networks involving diseases and drugs

(2009) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The NCBI BioSystems database

(2009) Lewis Y. Geer et al.   NUCLEIC ACIDS RESEARCH

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium

(2009) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2009) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Pathway Analysis of GWAS Provides New Insights into Genetic Susceptibility to 3 Inflammatory Diseases

(2009) Hariklia Eleftherohorinou et al.   PLoS One

Mapping of multiple susceptibility variants within the MHC region for 7 immune-mediated diseases

(2009) et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) Soumya Raychaudhuri et al.   PLoS Genetics

Learning a Prior on Regulatory Potential from eQTL Data

(2009) Su-In Lee et al.   PLoS Genetics

The Immunopathogenesis of Rheumatoid Arthritis

(2008) John B. Imboden   Annual Review of Pathology-Mechanisms of Disease

Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence

(2008) Scott F. Saccone et al.   BIOINFORMATICS

GSEA-SNP: applying gene set enrichment analysis to SNP data from genome-wide association studies

(2008) Marit Holden et al.   BIOINFORMATICS

Regulatory T Cells and Immune Tolerance

(2008) Shimon Sakaguchi et al.   CELL

Bayesian variable and model selection methods for genetic association studies

(2008) Brooke L. Fridley   GENETIC EPIDEMIOLOGY

Bayesian LASSO for Quantitative Trait Loci Mapping

(2008) Nengjun Yi et al.   GENETICS

Pathway analysis of seven common diseases assessed by genome-wide association

(2008) Ali Torkamani et al.   GENOMICS

Pathways-based analyses of whole-genome association study data in bipolar disorder reveal genes mediating ion channel activity and synaptic neurotransmission

(2008) Kathleen Askland et al.   HUMAN GENETICS

The crucial role of IL-2/IL-2RA-mediated immune regulation in the pathogenesis of type 1 diabetes, an evidence coming from genetic and animal model studies

(2008) Dimitry A. Chistiakov et al.   IMMUNOLOGY LETTERS

How to Interpret a Genome-wide Association Study

(2008) Thomas A. Pearson   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

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

(2008) Jason D Cooper et al.   NATURE GENETICS

Rheumatoid arthritis susceptibility loci at chromosomes 10p15, 12q13 and 22q13

(2008) Anne Barton et al.   NATURE GENETICS

Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn's disease

(2008) Sheila A Fisher et al.   NATURE GENETICS

Common variants at CD40 and other loci confer risk of rheumatoid arthritis

(2008) Soumya Raychaudhuri et al.   NATURE GENETICS

Common and rare variants in multifactorial susceptibility to common diseases

(2008) Walter Bodmer et al.   NATURE GENETICS

Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes

(2008) Eleftheria Zeggini 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

Genome-wide association studies for complex traits: consensus, uncertainty and challenges

(2008) Mark I. McCarthy et al.   NATURE REVIEWS GENETICS

Detecting shared pathogenesis from the shared genetics of immune-related diseases

(2008) Alexandra Zhernakova et al.   NATURE REVIEWS GENETICS

PID: the Pathway Interaction Database

(2008) Carl F. Schaefer et al.   NUCLEIC ACIDS RESEARCH

Genetic Mapping in Human Disease

(2008) D. Altshuler et al.   SCIENCE

The use of hierarchical models for estimating relative risks of individual genetic variants: An application to a study of melanoma

(2008) Marinela Capanu et al.   STATISTICS IN MEDICINE

WikiPathways: Pathway Editing for the People

(2008) Alexander R Pico et al.   PLOS BIOLOGY

Defining the Role of the MHC in Autoimmunity: A Review and Pooled Analysis

(2008) Michelle M. A. Fernando et al.   PLoS Genetics

Simultaneous Analysis of All SNPs in Genome-Wide and Re-Sequencing Association Studies

(2008) Clive J. Hoggart et al.   PLoS Genetics

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

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

Practical Issues in Imputation-Based Association Mapping

(2008) Yongtao Guan et al.   PLoS Genetics