Disease Mechanisms in Rheumatology-Tools and Pathways: Defining Functional Genetic Variants in Autoimmune Diseases

plink: AnRPackage for Linking Mixed-Format Tests Using IRT-Based Methods

(2015) Jonathan P. Weeks   Journal of Statistical Software

Congruency in the prediction of pathogenic missense mutations: state-of-the-art web-based tools

(2013) S. Castellana et al.   BRIEFINGS IN BIOINFORMATICS

Contribution of IKBKE and IFIH1 gene variants to SLE susceptibility

(2013) C Wang et al.   GENES AND IMMUNITY

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

TALENs and ZFNs are associated with different mutation signatures

(2013) Yongsub Kim et al.   NATURE METHODS

Genetic insights into common pathways and complex relationships among immune-mediated diseases

(2013) Miles Parkes et al.   NATURE REVIEWS GENETICS

HIBAG—HLA genotype imputation with attribute bagging

(2013) X Zheng et al.   PHARMACOGENOMICS JOURNAL

Multi-Population Classical HLA Type Imputation

(2013) Alexander Dilthey et al.   PLoS Computational Biology

Unraveling Multiple MHC Gene Associations with Systemic Lupus Erythematosus: Model Choice Indicates a Role for HLA Alleles and Non-HLA Genes in Europeans

(2012) David L. Morris et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Identification of IRF8, TMEM39A, and IKZF3-ZPBP2 as Susceptibility Loci for Systemic Lupus Erythematosus in a Large-Scale Multiracial Replication Study

(2012) Christopher J. Lessard et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A functional haplotype of UBE2L3 confers risk for systemic lupus erythematosus

(2012) S Wang et al.   GENES AND IMMUNITY

ChIA-PET analysis of transcriptional chromatin interactions

(2012) Jingyao Zhang et al.   METHODS

Hi–C: A comprehensive technique to capture the conformation of genomes

(2012) Jon-Matthew Belton et al.   METHODS

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

(2012)   NATURE

Robust 4C-seq data analysis to screen for regulatory DNA interactions

(2012) Harmen J G van de Werken et al.   NATURE METHODS

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Fine-mapping and transethnic genotyping establish IL2/IL21 genetic association with lupus and localize this genetic effect to IL21

(2011) Travis Hughes et al.   ARTHRITIS AND RHEUMATISM

The genomics of autoimmune disease in the era of genome-wide association studies and beyond

(2011) Christopher J. Lessard et al.   AUTOIMMUNITY REVIEWS

seeQTL: a searchable database for human eQTLs

(2011) Kai Xia et al.   BIOINFORMATICS

dbNSFP: A lightweight database of human nonsynonymous SNPs and their functional predictions

(2011) Xiaoming Liu et al.   HUMAN MUTATION

Association of a functional variant downstream of TNFAIP3 with systemic lupus erythematosus

(2011) Indra Adrianto et al.   NATURE GENETICS

Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies

(2010) T.-P. Yang et al.   BIOINFORMATICS

MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes

(2010) Yun Li et al.   GENETIC EPIDEMIOLOGY

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

MutationTaster evaluates disease-causing potential of sequence alterations

(2010) Jana Marie Schwarz et al.   NATURE METHODS

Genotype imputation for genome-wide association studies

(2010) Jonathan Marchini et al.   NATURE REVIEWS GENETICS

ENCODE whole-genome data in the UCSC genome browser (2011 update)

(2010) Brian J. Raney et al.   NUCLEIC ACIDS RESEARCH

Accuracy of genome-wide imputation of untyped markers and impacts on statistical power for association studies

(2009) Ke Hao et al.   BMC GENETICS

Identification of deleterious mutations within three human genomes

(2009) S. Chun et al.   GENOME RESEARCH

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 nonsynonymous functional variant in integrin-αM (encoded by ITGAM) is associated with systemic lupus erythematosus

(2008) Swapan K Nath et al.   NATURE GENETICS