Cardiometabolic risk loci share downstream cis- and trans-gene regulation across tissues and diseases

Circulating Proprotein Convertase Subtilisin/Kexin Type 9 (PCSK9) Predicts Future Risk of Cardiovascular Events Independently of Established Risk FactorsCLINICAL PERSPECTIVE

(2016) Karin Leander et al.   CIRCULATION

Cross-Tissue Regulatory Gene Networks in Coronary Artery Disease

(2016) Husain A. Talukdar et al.   Cell Systems

Expression Quantitative Trait Loci Acting Across Multiple Tissues Are Enriched in Inherited Risk for Coronary Artery DiseaseCLINICAL PERSPECTIVE

(2015) Hassan Foroughi Asl et al.   Circulation-Cardiovascular Genetics

New genetic loci link adipose and insulin biology to body fat distribution

(2015) Dmitry Shungin et al.   NATURE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

A comprehensive 1000 Genomes–based genome-wide association meta-analysis of coronary artery disease

(2015) Majid Nikpay et al.   NATURE GENETICS

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

Expression Quantitative Trait Loci Acting Across Multiple Tissues Are Enriched in Inherited Risk for Coronary Artery DiseaseCLINICAL PERSPECTIVE

(2015) Hassan Foroughi Asl et al.   Circulation-Cardiovascular Genetics

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Detecting epistasis in human complex traits

(2014) Wen-Hua Wei et al.   NATURE REVIEWS GENETICS

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

Polarization of the Effects of Autoimmune and Neurodegenerative Risk Alleles in Leukocytes

(2014) T. Raj et al.   SCIENCE

A Role for Noncoding Variation in Schizophrenia

(2014) Panos Roussos et al.   Cell Reports

Plasma Cholesterol–Induced Lesion Networks Activated before Regression of Early, Mature, and Advanced Atherosclerosis

(2014) Johan L. M. Björkegren et al.   PLoS Genetics

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

(2013) A. Battle et al.   GENOME RESEARCH

Genetic susceptibility to SLE: Recent progress from GWAS

(2013) Yong Cui et al.   JOURNAL OF AUTOIMMUNITY

Genome-wide association study identifies common loci influencing circulating glycated hemoglobin (HbA1c) levels in non-diabetic subjects: The Long Life Family Study (LLFS)

(2013) Ping An et al.   METABOLISM-CLINICAL AND EXPERIMENTAL

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories

(2013) Peter A C 't Hoen et al.   NATURE BIOTECHNOLOGY

Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease

(2013) Jean-Charles Lambert et al.   NATURE GENETICS

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

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

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

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

A Statistical Framework for Joint eQTL Analysis in Multiple Tissues

(2013) Timothée Flutre et al.   PLoS Genetics

All SNPs Are Not Created Equal: Genome-Wide Association Studies Reveal a Consistent Pattern of Enrichment among Functionally Annotated SNPs

(2013) Andrew J. Schork et al.   PLoS Genetics

Five Years of GWAS Discovery

(2012) Peter M. Visscher et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

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

(2012)   NATURE

Fast and accurate genotype imputation in genome-wide association studies through pre-phasing

(2012) Bryan Howie et al.   NATURE GENETICS

A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance

(2012) Alisa K Manning et al.   NATURE GENETICS

Patterns of Cis Regulatory Variation in Diverse Human Populations

(2012) Barbara E. Stranger et al.   PLoS Genetics

Assessment of Genetic Determinants of the Association of γ′ Fibrinogen in Relation to Cardiovascular Disease

(2011) Rehana S. Lovely et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

GC-Content Normalization for RNA-Seq Data

(2011) Davide Risso et al.   BMC BIOINFORMATICS

Genome-Wide Association Identifies Nine Common Variants Associated With Fasting Proinsulin Levels and Provides New Insights Into the Pathophysiology of Type 2 Diabetes

(2011) R. J. Strawbridge et al.   DIABETES

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

Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk

(2011) Georg B. Ehret et al.   NATURE

A genome-wide association study in Europeans and South Asians identifies five new loci for coronary artery disease

(2011) John F Peden et al.   NATURE GENETICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47

(2011) Carl A Anderson et al.   NATURE GENETICS

A linear complexity phasing method for thousands of genomes

(2011) Olivier Delaneau et al.   NATURE METHODS

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

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

Common Variants at 10 Genomic Loci Influence Hemoglobin A1C Levels via Glycemic and Nonglycemic Pathways

(2010) N. Soranzo et al.   DIABETES

From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus

(2010) Kiran Musunuru et al.   NATURE

Biological, clinical and population relevance of 95 loci for blood lipids

(2010) Tanya M. Teslovich et al.   NATURE

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein 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

New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk

(2010) Josée Dupuis et al.   NATURE GENETICS

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

Assessment of the SYNTAX score in the Syntax study

(2010) Patrick Serruys et al.   EuroIntervention

Candidate Causal Regulatory Effects by Integration of Expression QTLs with Complex Trait Genetic Associations

(2010) Alexandra C. Nica et al.   PLoS Genetics

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Genotype Imputation

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

QuickGO: a web-based tool for Gene Ontology searching

(2009) D. Binns et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Disentangling molecular relationships with a causal inference test

(2009) Joshua Millstein et al.   BMC GENETICS

Improved estimators for a general class of beta regression models

(2009) Alexandre B. Simas et al.   COMPUTATIONAL STATISTICS & DATA ANALYSIS

Multi-Organ Expression Profiling Uncovers a Gene Module in Coronary Artery Disease Involving Transendothelial Migration of Leukocytes and LIM Domain Binding 2: The Stockholm Atherosclerosis Gene Expression (STAGE) Study

(2009) Sara Hägg et al.   PLoS 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

Epistasis — the essential role of gene interactions in the structure and evolution of genetic systems

(2008) Patrick C. Phillips   NATURE REVIEWS GENETICS

Transcriptional Profiling Uncovers a Network of Cholesterol-Responsive Atherosclerosis Target Genes

(2008) Josefin Skogsberg et al.   PLoS Genetics