Identifying causal variants and genes using functional genomics in specialized cell types and contexts

Abundant associations with gene expression complicate GWAS follow-up

(2019) Boxiang Liu et al.   NATURE GENETICS

The Post-GWAS Era: From Association to Function

(2018) Michael D. Gallagher et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2018) Ryan Tewhey et al.   CELL

Regulatory variants at KLF14 influence type 2 diabetes risk via a female-specific effect on adipocyte size and body composition

(2018) Kerrin S. Small et al.   NATURE GENETICS

Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response

(2018) Kaur Alasoo et al.   NATURE GENETICS

From genome-wide associations to candidate causal variants by statistical fine-mapping

(2018) Daniel J. Schaid et al.   NATURE REVIEWS GENETICS

Genetic Regulatory Mechanisms of Smooth Muscle Cells Map to Coronary Artery Disease Risk Loci

(2018) Boxiang Liu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Single-cell analysis of early progenitor cells that build coronary arteries

(2018) Tianying Su et al.   NATURE

A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte

(2018) Lindsey W. Plasschaert et al.   NATURE

Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions

(2018) Sarah M. Urbut et al.   NATURE GENETICS

Fine-mapping type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps

(2018) Anubha Mahajan et al.   NATURE GENETICS

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Genetics of coronary artery disease: discovery, biology and clinical translation

(2017) Amit V. Khera et al.   NATURE REVIEWS GENETICS

Integrating molecular QTL data into genome-wide genetic association analysis: Probabilistic assessment of enrichment and colocalization

(2017) Xiaoquan Wen et al.   PLoS Genetics

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Colocalization of GWAS and eQTL Signals Detects Target Genes

(2016) Farhad Hormozdiari et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Molecular QTL discovery incorporating genomic annotations using Bayesian false discovery rate control

(2016) Xiaoquan Wen   Annals of Applied Statistics

FINEMAP: efficient variable selection using summary data from genome-wide association studies

(2016) Christian Benner et al.   BIOINFORMATICS

Incorporating Functional Annotations for Fine-Mapping Causal Variants in a Bayesian Framework Using Summary Statistics

(2016) W. Chen et al.   GENETICS

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

(2016) Zhihong Zhu et al.   NATURE GENETICS

Integrative approaches for large-scale transcriptome-wide association studies

(2016) Alexander Gusev et al.   NATURE GENETICS

Genome-Editing Technologies: Principles and Applications

(2016) Thomas Gaj et al.   Cold Spring Harbor Perspectives in Biology

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

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

(2015) Eric R Gamazon et al.   NATURE GENETICS

FTO Obesity Variant Circuitry and Adipocyte Browning in Humans

(2015) Melina Claussnitzer et al.   NEW ENGLAND JOURNAL OF MEDICINE

HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease

(2015) Lucas D. Ward et al.   NUCLEIC ACIDS RESEARCH

Type 2 diabetes mellitus

(2015) Ralph A. DeFronzo et al.   Nature Reviews Disease Primers

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

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

Identifying Causal Variants at Loci with Multiple Signals of Association

(2014) F. Hormozdiari et al.   GENETICS

Obesity-associated variants within FTO form long-range functional connections with IRX3

(2014) Scott Smemo et al.   NATURE

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

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

Common variants near ABCA1 and in PMM2 are associated with primary open-angle glaucoma

(2014) Yuhong Chen et al.   NATURE GENETICS

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

(2014) Claudia Giambartolomei et al.   PLoS Genetics

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

(2014) Gleb Kichaev et al.   PLoS Genetics

Beyond GWASs: Illuminating the Dark Road from Association to Function

(2013) Stacey L. Edwards et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Cell-type, allelic, and genetic signatures in the human pancreatic beta cell transcriptome

(2013) A. C. Nica et al.   GENOME RESEARCH

The bigger picture of FTO—the first GWAS-identified obesity gene

(2013) Ruth J. F. Loos et al.   Nature Reviews Endocrinology

A Statistical Framework for Joint eQTL Analysis in Multiple Tissues

(2013) Timothée Flutre et al.   PLoS Genetics

Effectively Identifying eQTLs from Multiple Tissues by Combining Mixed Model and Meta-analytic Approaches

(2013) Jae Hoon Sul et al.   PLoS Genetics

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

(2012) Oliver Stegle et al.   Nature Protocols

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

The UK Adult Twin Registry (TwinsUK Resource)

(2012) Alireza Moayyeri et al.   Twin Research and Human Genetics

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

(2010) Kiran Musunuru et al.   NATURE

Integrating common and rare genetic variation in diverse human populations

(2010)   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Long-range gene regulation links genomic type 2 diabetes and obesity risk regions to HHEX, SOX4, and IRX3

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