Effects of Type 1 Diabetes Risk Alleles on Immune Cell Gene Expression

Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data

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CHiCP: a web-based tool for the integrative and interactive visualization of promoter capture Hi-C datasets

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Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay

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Systematic Evaluation of Genes and Genetic Variants Associated with Type 1 Diabetes Susceptibility

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Detection and interpretation of shared genetic influences on 42 human traits

(2016) Joseph K Pickrell et al.   NATURE GENETICS

Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets

(2016) Zhihong Zhu et al.   NATURE GENETICS

PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions

(2016) Jaroslav Bendl et al.   PLoS Computational Biology

Insight into Genotype-Phenotype Associations through eQTL Mapping in Multiple Cell Types in Health and Immune-Mediated Disease

(2016) James E. Peters et al.   PLoS Genetics

An integrative approach to predicting the functional effects of non-coding and coding sequence variation

(2015) Hashem A. Shihab et al.   BIOINFORMATICS

GREGOR: evaluating global enrichment of trait-associated variants in epigenomic features using a systematic, data-driven approach

(2015) Ellen M. Schmidt et al.   BIOINFORMATICS

LDlink: a web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants: Fig. 1.

(2015) Mitchell J. Machiela et al.   BIOINFORMATICS

Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers

(2015) Suna Onengut-Gumuscu et al.   NATURE GENETICS

A gene-based association method for mapping traits using reference transcriptome data

(2015) Eric R Gamazon et al.   NATURE GENETICS

Re-Annotator: Annotation Pipeline for Microarray Probe Sequences

(2015) Janine Arloth et al.   PLoS One

DANN: a deep learning approach for annotating the pathogenicity of genetic variants

(2014) Daniel Quang et al.   BIOINFORMATICS

A promoter-level mammalian expression atlas

(2014)   NATURE

Genetic and epigenetic fine mapping of causal autoimmune disease variants

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

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

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

(2014) Martin Kircher et al.   NATURE GENETICS

Common Genetic Variants Modulate Pathogen-Sensing Responses in Human Dendritic Cells

(2014) M. N. Lee et al.   SCIENCE

Innate Immune Activity Conditions the Effect of Regulatory Variants upon Monocyte Gene Expression

(2014) B. P. Fairfax et al.   SCIENCE

PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations

(2014) Jaroslav Bendl et al.   PLoS Computational Biology

Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics

(2014) Claudia Giambartolomei et al.   PLoS Genetics

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

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

RNA-Seq optimization with eQTL gold standards

(2013) Shannon E Ellis et al.   BMC GENOMICS

Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits

(2013) O. Corradin et al.   GENOME RESEARCH

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals

(2013) A. Battle et al.   GENOME RESEARCH

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

Variants at multiple loci implicated in both innate and adaptive immune responses are associated with Sjögren's syndrome

(2013) Christopher J Lessard et al.   NATURE GENETICS

Systematic identification of trans eQTLs as putative drivers of known disease associations

(2013) Harm-Jan Westra et al.   NATURE GENETICS

A Statistical Framework for Joint eQTL Analysis in Multiple Tissues

(2013) Timothée Flutre et al.   PLoS Genetics

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

A decade of 3C technologies: insights into nuclear organization

(2012) E. de Wit et al.   GENES & DEVELOPMENT

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Genetics of gene expression in primary immune cells identifies cell type–specific master regulators and roles of HLA alleles

(2012) Benjamin P Fairfax et al.   NATURE GENETICS

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

(2012) Oliver Stegle et al.   Nature Protocols

MixupMapper: correcting sample mix-ups in genome-wide datasets increases power to detect small genetic effects

(2011) Harm-Jan Westra et al.   BIOINFORMATICS

Evidence of association with type 1 diabetes in the SLC11A1 gene region

(2011) Jennie HM Yang et al.   BMC Medical Genetics

An Allele ofIKZF1(Ikaros) Conferring Susceptibility to Childhood Acute Lymphoblastic Leukemia Protects Against Type 1 Diabetes

(2011) Austin D.-E. Swafford et al.   DIABETES

Tests for Genetic Interactions in Type 1 Diabetes

(2011) Grant Morahan et al.   DIABETES

Gut Microbiome Metagenomics Analysis Suggests a Functional Model for the Development of Autoimmunity for Type 1 Diabetes

(2011) Christopher T. Brown et al.   PLoS One

A Genome-Wide Meta-Analysis of Six Type 1 Diabetes Cohorts Identifies Multiple Associated Loci

(2011) Jonathan P. Bradfield et al.   PLoS Genetics

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis

(2010) Pan Du et al.   BMC BIOINFORMATICS

Subset Quantile Normalization Using Negative Control Features

(2010) Zhijin Wu et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

(2010) David Warde-Farley et al.   NUCLEIC ACIDS RESEARCH

New Insights into the Genetic Control of Gene Expression using a Bayesian Multi-tissue Approach

(2010) Enrico Petretto et al.   PLoS Computational Biology

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Technical note: An R package for fitting generalized linear mixed models in animal breeding1

(2009) A. I. Vazquez et al.   JOURNAL OF ANIMAL SCIENCE

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

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols

The UPS in diabetes and obesity

(2008) Simon S Wing   BMC BIOCHEMISTRY

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

(2008) H. Hakonarson et al.   DIABETES

Lipid and Lipoprotein Profiles in Youth With and Without Type 1 Diabetes: The SEARCH for Diabetes in Youth Case-Control Study

(2008) J. Guy et al.   DIABETES CARE

Efficient Control of Population Structure in Model Organism Association Mapping

(2008) H. M. Kang et al.   GENETICS

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

(2008) Jason D Cooper et al.   NATURE GENETICS

Shared and Distinct Genetic Variants in Type 1 Diabetes and Celiac Disease

(2008) Deborah J. Smyth et al.   NEW ENGLAND JOURNAL OF MEDICINE

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Influence of Morbid Obesity and Insulin Resistance on Gene Expression Levels of AQP7 in Visceral Adipose Tissue and AQP9 in Liver

(2008) Victoria Catalán et al.   OBESITY SURGERY