Multi-scale inference of genetic trait architecture using biologically annotated neural networks

T cell metabolism: new insights in systemic lupus erythematosus pathogenesis and therapy

(2020) Amir Sharabi et al.   Nature Reviews Rheumatology

The impact of adjusting for baseline in pharmacogenomic genome-wide association studies of quantitative change

(2020) Akinyemi Oni-Orisan et al.   npj Genomic Medicine

Accurate and Scalable Construction of Polygenic Scores in Large Biobank Data Sets

(2020) Sheng Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Evaluating the relationship between circulating lipoprotein lipids and apolipoproteins with risk of coronary heart disease: A multivariable Mendelian randomisation analysis

(2020) Tom G. Richardson et al.   PLOS MEDICINE

A simple new approach to variable selection in regression, with application to genetic fine mapping

(2020) Gao Wang et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Systemic lupus erythematosus favors the generation of IL-17 producing double negative T cells

(2020) Hao Li et al.   Nature Communications

Estimation of non-null SNP effect size distributions enables the detection of enriched genes underlying complex traits

(2020) Wei Cheng et al.   PLoS Genetics

Machine Learning SNP Based Prediction for Precision Medicine

(2019) Daniel Sik Wai Ho et al.   Frontiers in Genetics

Powerful gene set analysis in GWAS with the Generalized Berk-Jones statistic

(2019) Ryan Sun et al.   PLoS Genetics

Fast and flexible linear mixed models for genome-wide genetics

(2019) Daniel E. Runcie et al.   PLoS Genetics

A Candidate-Gene Approach Identifies Novel Associations Between Common Variants in/Near Syndromic Obesity Genes and BMI in Pediatric and Adult European Populations

(2019) Dominic X. Wang et al.   DIABETES

Human Gain-of-Function MC4R Variants Show Signaling Bias and Protect against Obesity

(2019) Luca A. Lotta et al.   CELL

Variable prioritization in nonlinear black box methods: A genetic association case study

(2019) Lorin Crawford et al.   Annals of Applied Statistics

A resource-efficient tool for mixed model association analysis of large-scale data

(2019) Longda Jiang et al.   NATURE GENETICS

Brain age prediction using deep learning uncovers associated sequence variants

(2019) B. A. Jonsson et al.   Nature Communications

Improved polygenic prediction by Bayesian multiple regression on summary statistics

(2019) Luke R. Lloyd-Jones et al.   Nature Communications

Heritability Estimation and Differential Analysis with Generalized Linear Mixed Models in Genomic Sequencing Studies

(2018) Shiquan Sun et al.   BIOINFORMATICS

Common Disease Is More Complex Than Implied by the Core Gene Omnigenic Model

(2018) Naomi R. Wray et al.   CELL

Bayesian Neural Networks for Selection of Drug Sensitive Genes

(2018) Faming Liang et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Mixed-model association for biobank-scale datasets

(2018) Po-Ru Loh et al.   NATURE GENETICS

Using deep learning to model the hierarchical structure and function of a cell

(2018) Jianzhu Ma et al.   NATURE METHODS

Prediction of inherited genomic susceptibility to 20 common cancer types by a supervised machine-learning method

(2018) Byung-Ju Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide association study identifies novel recessive genetic variants for high TGs in an Arab population

(2018) Prashantha Hebbar et al.   JOURNAL OF LIPID RESEARCH

Estimation of complex effect-size distributions using summary-level statistics from genome-wide association studies across 32 complex traits

(2018) Yan Zhang et al.   NATURE GENETICS

Genome-wide enrichment of m6A-associated single-nucleotide polymorphisms in the lipid loci

(2018) Xingbo Mo et al.   PHARMACOGENOMICS JOURNAL

Integrative effects of dystrophin loss on metabolic function of the mdx mouse

(2018) Jana Strakova et al.   Scientific Reports

Leveraging Polygenic Functional Enrichment to Improve GWAS Power

(2018) Gleb Kichaev et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The UK Biobank resource with deep phenotyping and genomic data

(2018) Clare Bycroft et al.   NATURE

Genetics of blood lipids among ~300,000 multi-ethnic participants of the Million Veteran Program

(2018) Derek Klarin et al.   NATURE GENETICS

Mouse Genome Database (MGD) 2019

(2018) Carol J Bult et al.   NUCLEIC ACIDS RESEARCH

CADD: predicting the deleteriousness of variants throughout the human genome

(2018) Philipp Rentzsch et al.   NUCLEIC ACIDS RESEARCH

Large-scale genome-wide enrichment analyses identify new trait-associated genes and pathways across 31 human phenotypes

(2018) Xiang Zhu et al.   Nature Communications

Overview of the BioBank Japan Project: Study design and profile

(2017) Akiko Nagai et al.   JOURNAL OF EPIDEMIOLOGY

Bayesian Approximate Kernel Regression With Variable Selection

(2017) Lorin Crawford et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Variational Inference: A Review for Statisticians

(2017) David M. Blei et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Exome-wide association study of plasma lipids in >300,000 individuals

(2017) Dajiang J Liu et al.   NATURE GENETICS

Non-parametric genetic prediction of complex traits with latent Dirichlet process regression models

(2017) Ping Zeng et al.   Nature Communications

Serum ApoB levels in depressive patients: associated with cognitive deficits

(2017) Li Hui et al.   Scientific Reports

Detecting epistasis with the marginal epistasis test in genetic mapping studies of quantitative traits

(2017) Lorin Crawford et al.   PLoS Genetics

A machine-learning heuristic to improve gene score prediction of polygenic traits

(2017) Guillaume Paré et al.   Scientific Reports

Colocalization of GWAS and eQTL Signals Detects Target Genes

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

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

(2016) Christian Benner et al.   BIOINFORMATICS

Gene and Network Analysis of Common Variants Reveals Novel Associations in Multiple Complex Diseases

(2016) P. Nakka et al.   GENETICS

Multikernel linear mixed models for complex phenotype prediction

(2016) Omer Weissbrod et al.   GENOME RESEARCH

Variation in the glucose transporter gene SLC2A2 is associated with glycemic response to metformin

(2016) Kaixin Zhou et al.   NATURE GENETICS

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

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(2016) David Heckerman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Myt3 suppression sensitizes islet cells to high glucose-induced cell death via Bim induction

(2016) B R Tennant et al.   Cell Death & Disease

Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics

(2016) David Lamparter et al.   PLoS Computational Biology

Weak Epistasis Generally Stabilizes Phenotypes in a Mouse Intercross

(2016) Anna L. Tyler et al.   PLoS Genetics

Mixed Model with Correction for Case-Control Ascertainment Increases Association Power

(2015) Tristan J. Hayeck et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

Modeling Epistasis in Genomic Selection

(2015) Yong Jiang et al.   GENETICS

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(2015) Yann LeCun et al.   NATURE

LD Score regression distinguishes confounding from polygenicity in genome-wide association studies

(2015) Brendan K Bulik-Sullivan et al.   NATURE GENETICS

Accurate liability estimation improves power in ascertained case-control studies

(2015) Omer Weissbrod et al.   NATURE METHODS

FTO Obesity Variant Circuitry and Adipocyte Browning in Humans

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

MAGMA: Generalized Gene-Set Analysis of GWAS Data

(2015) Christiaan A. de Leeuw et al.   PLoS Computational Biology

Simultaneous Discovery, Estimation and Prediction Analysis of Complex Traits Using a Bayesian Mixture Model

(2015) Gerhard Moser et al.   PLoS Genetics

Modeling Epistasis in Genomic Selection

(2015) Yong Jiang et al.   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

Advantages and pitfalls in the application of mixed-model association methods

(2014) Jian Yang et al.   NATURE GENETICS

Efficient multivariate linear mixed model algorithms for genome-wide association studies

(2014) Xiang Zhou et al.   NATURE METHODS

Familial risk for alcohol dependence and developmental changes in BMI: the moderating influence of addiction and obesity genes

(2014) Sarah D Lichenstein et al.   PHARMACOGENOMICS

Measuring missing heritability: Inferring the contribution of common variants

(2014) David Golan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Amerindian-specific regions under positive selection harbour new lipid variants in Latinos

(2014) Arthur Ko et al.   Nature Communications

Pharmacogenetic meta-analysis of genome-wide association studies of LDL cholesterol response to statins

(2014) Iris Postmus et al.   Nature Communications

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

Selective Search for Object Recognition

(2013) J. R. R. Uijlings et al.   INTERNATIONAL JOURNAL OF COMPUTER VISION

Epistasis and quantitative traits: using model organisms to study gene–gene interactions

(2013) Trudy F. C. Mackay   NATURE REVIEWS GENETICS

Neuropsychological Deficits in Mice Depleted of the Schizophrenia Susceptibility Gene CSMD1

(2013) Vidar M. Steen et al.   PLoS One

What are lipoproteins doing in the brain?

(2013) Hong Wang et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Wdpcp, a PCP Protein Required for Ciliogenesis, Regulates Directional Cell Migration and Cell Polarity by Direct Modulation of the Actin Cytoskeleton

(2013) Cheng Cui et al.   PLOS BIOLOGY

Pathways-Driven Sparse Regression Identifies Pathways and Genes Associated with High-Density Lipoprotein Cholesterol in Two Asian Cohorts

(2013) Matt Silver et al.   PLoS Genetics

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

(2013) Peter Carbonetto et al.   PLoS Genetics

Polygenic Modeling with Bayesian Sparse Linear Mixed Models

(2013) Xiang Zhou et al.   PLoS Genetics

Optimal Unified Approach for Rare-Variant Association Testing with Application to Small-Sample Case-Control Whole-Exome Sequencing Studies

(2012) Seunggeun Lee et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Five Years of GWAS Discovery

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

Leveraging models of cell regulation and GWAS data in integrative network-based association studies

(2012) Andrea Califano et al.   NATURE GENETICS

A mixed-model approach for genome-wide association studies of correlated traits in structured populations

(2012) Arthur Korte et al.   NATURE GENETICS

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(2012) Xiang Zhou et al.   NATURE GENETICS

The Number of X Chromosomes Causes Sex Differences in Adiposity in Mice

(2012) Xuqi Chen et al.   PLoS Genetics

Estimating Missing Heritability for Disease from Genome-wide Association Studies

(2011) Sang Hong Lee et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

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

A conditional knockout resource for the genome-wide study of mouse gene function

(2011) William C. Skarnes et al.   NATURE

FaST linear mixed models for genome-wide association studies

(2011) Christoph Lippert et al.   NATURE METHODS

A High-Resolution Anatomical Atlas of the Transcriptome in the Mouse Embryo

(2011) Graciana Diez-Roux et al.   PLOS BIOLOGY

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

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

A Versatile Gene-Based Test for Genome-wide Association Studies

(2010) Jimmy Z. Liu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Variance component model to account for sample structure in genome-wide association studies

(2010) Hyun Min Kang et al.   NATURE GENETICS

New approaches to population stratification in genome-wide association studies

(2010) Alkes L. Price et al.   NATURE REVIEWS GENETICS

Gene-centric Association Signals for Lipids and Apolipoproteins Identified via the HumanCVD BeadChip

(2009) Philippa J. Talmud et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

Multiple Genes Influence BMI on Chromosome 7q31–34: The NHLBI Family Heart Study

(2009) Jason M. Laramie et al.   Obesity

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

(2008) Marit Holden et al.   BIOINFORMATICS

Efficient Control of Population Structure in Model Organism Association Mapping

(2008) H. M. Kang et al.   GENETICS

Large-scale gene trapping in C57BL/6N mouse embryonic stem cells

(2008) G. M. Hansen et al.   GENOME RESEARCH

LDL-cholesterol concentrations: a genome-wide association study

(2008) Manjinder S Sandhu et al.   LANCET

Genome-wide association analysis of metabolic traits in a birth cohort from a founder population

(2008) Chiara Sabatti et al.   NATURE GENETICS

Newly identified loci that influence lipid concentrations and risk of coronary artery disease

(2008) Cristen J Willer et al.   NATURE GENETICS

Mapping the Genetic Architecture of Gene Expression in Human Liver

(2008) Eric E Schadt et al.   PLOS BIOLOGY

An Integrated Approach for the Analysis of Biological Pathways using Mixed Models

(2008) Lily Wang et al.   PLoS Genetics