Factorizing polygenic epistasis improves prediction and uncovers biological pathways in complex traits

Evidence of epistasis in regions of long-range linkage disequilibrium across five complex diseases in the UK Biobank and eMERGE datasets

(2023) Pankhuri Singhal et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Causal effects on complex traits are similar for common variants across segments of different continental ancestries within admixed individuals

(2023) Kangcheng Hou et al.   NATURE GENETICS

Shared components of heritability across genetically correlated traits

(2022) Jenna Lee Ballard et al.   AMERICAN JOURNAL OF HUMAN GENETICS

An integrated framework for local genetic correlation analysis

(2022) Josefin Werme et al.   NATURE GENETICS

Idiosyncratic epistasis leads to global fitness–correlated trends

(2022) Christopher W. Bakerlee et al.   SCIENCE

On the cross‐validation bias due to unsupervised preprocessing

(2022) Amit Moscovich et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Nested epistasis enhancer networks for robust genome regulation

(2022) Xueqiu Lin et al.   SCIENCE

ExPRSweb: An online repository with polygenic risk scores for common health-related exposures

(2022) Ying Ma et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Ubiquitous bias and false discovery due to model misspecification in analysis of statistical interactions: The role of the outcome’s distribution and metric properties.

(2022) Benjamin W. Domingue et al.   PSYCHOLOGICAL METHODS

Cross-trait assortative mating is widespread and inflates genetic correlation estimates

(2022) Richard Border et al.   SCIENCE

GWAS of three molecular traits highlights core genes and pathways alongside a highly polygenic background

(2021) Nasa Sinnott-Armstrong et al.   eLife

Estimation of non-additive genetic variance in human complex traits from a large sample of unrelated individuals

(2021) Valentin Hivert et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Quantifying the contribution of dominance deviation effects to complex trait variation in biobank-scale data

(2021) Ali Pazokitoroudi et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A model and test for coordinated polygenic epistasis in complex traits

(2021) Brooke Sheppard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phantom epistasis between unlinked loci

(2021) Gibran Hemani et al.   NATURE

Protein-coding repeat polymorphisms strongly shape diverse human phenotypes

(2021) Ronen E. Mukamel et al.   SCIENCE

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

(2021) Pinar Demetci et al.   PLoS Genetics

Modeling Interaction and Dispersion Effects in the Analysis of Gene-by-Environment Interaction

(2021) Benjamin W. Domingue et al.   BEHAVIOR GENETICS

Incorporating functional priors improves polygenic prediction accuracy in UK Biobank and 23andMe data sets

(2021) Carla Márquez-Luna et al.   Nature Communications

GIGYF2 and 4EHP Inhibit Translation Initiation of Defective Messenger RNAs to Assist Ribosome-Associated Quality Control

(2020) Kelsey L. Hickey et al.   MOLECULAR CELL

Phantom Epistasis in Genomic Selection: On the Predictive Ability of Epistatic Models

(2020) Matías F. Schrauf et al.   G3-Genes Genomes Genetics

Genetic Influences on Disease Subtypes

(2020) Andy Dahl et al.   Annual Review of Genomics and Human Genetics

The impact of sex on gene expression across human tissues

(2020) Meritxell Oliva et al.   SCIENCE

Modeling epistasis in mice and yeast using the proportion of two or more distinct genetic backgrounds: Evidence for “polygenic epistasis”

(2020) Christoph D. Rau et al.   PLoS Genetics

Imperfect Linkage Disequilibrium Generates Phantom Epistasis (& Perils of Big Data)

(2019) Gustavo de los Campos et al.   G3-Genes Genomes Genetics

Trans Effects on Gene Expression Can Drive Omnigenic Inheritance

(2019) Xuanyao Liu et al.   CELL

Synergistic effects of common schizophrenia risk variants

(2019) Nadine Schrode et al.   NATURE GENETICS

Exploring genetic interaction manifolds constructed from rich single-cell phenotypes

(2019) Thomas M. Norman et al.   SCIENCE

Mapping the Genetic Landscape of Human Cells

(2018) Max A. Horlbeck et al.   CELL

Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types

(2018) Hilary K. Finucane et al.   NATURE GENETICS

Relatedness disequilibrium regression estimates heritability without environmental bias

(2018) Alexander I. Young et al.   NATURE GENETICS

Type 2 diabetes genetic loci informed by multi-trait associations point to disease mechanisms and subtypes: A soft clustering analysis

(2018) Miriam S. Udler et al.   PLOS MEDICINE

Joint Contributions of Rare Copy Number Variants and Common SNPs to Risk for Schizophrenia

(2018) Sarah E. Bergen et al.   AMERICAN JOURNAL OF PSYCHIATRY

Genome-wide association studies of brain imaging phenotypes in UK Biobank

(2018) Lloyd T. Elliott et al.   NATURE

The role of sex in the genomics of human complex traits

(2018) Ekaterina A. Khramtsova et al.   NATURE REVIEWS GENETICS

Accounting for genetic interactions improves modeling of individual quantitative trait phenotypes in yeast

(2017) Simon K G Forsberg et al.   NATURE GENETICS

Polygenic transmission disequilibrium confirms that common and rare variation act additively to create risk for autism spectrum disorders

(2017) Daniel J Weiner et al.   NATURE GENETICS

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

(2017) Lorin Crawford et al.   PLoS Genetics

Are Interactions between cis -Regulatory Variants Evidence for Biological Epistasis or Statistical Artifacts?

(2016) Alexandra E. Fish et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genotypic Context and Epistasis in Individuals and Populations

(2016) Timothy B. Sackton et al.   CELL

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

How does epistasis influence the response to selection?

(2016) N H Barton   HEREDITY

A method for identifying genetic heterogeneity within phenotypically defined disease subgroups

(2016) James Liley et al.   NATURE GENETICS

Genetic Background Limits Generalizability of Genotype-Phenotype Relationships

(2016) Laura J. Sittig et al.   NEURON

Epistasis in protein evolution

(2016) Tyler N. Starr et al.   PROTEIN SCIENCE

The Genetic Architecture of Quantitative Traits Cannot Be Inferred from Variance Component Analysis

(2016) Wen Huang et al.   PLoS Genetics

Two locus inheritance of non-syndromic midline craniosynostosis via rare SMAD6 and common BMP2 alleles

(2016) Andrew T Timberlake et al.   eLife

Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores

(2015) Bjarni J. Vilhjálmsson et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Locally Epistatic Genomic Relationship Matrices for Genomic Association and Prediction

(2015) D. Akdemir et al.   GENETICS

Modeling Epistasis in Genomic Selection

(2015) Yong Jiang et al.   GENETICS

Partitioning heritability by functional annotation using genome-wide association summary statistics

(2015) Hilary K Finucane et al.   NATURE GENETICS

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

(2015) Eric R Gamazon et al.   NATURE GENETICS

Genetic interactions contribute less than additive effects to quantitative trait variation in yeast

(2015) Joshua S. Bloom et al.   Nature Communications

Modeling Epistasis in Genomic Selection

(2015) Yong Jiang et al.   GENETICS

Detection and replication of epistasis influencing transcription in humans

(2014) Gibran Hemani et al.   NATURE

Cystic fibrosis genetics: from molecular understanding to clinical application

(2014) Garry R. Cutting   NATURE REVIEWS GENETICS

Genetic interactions affecting human gene expression identified by variance association mapping

(2014) Andrew Anand Brown et al.   eLife

Finding the sources of missing heritability in a yeast cross

(2013) Joshua S. Bloom et al.   NATURE

Genetic incompatibilities are widespread within species

(2013) Russell B. Corbett-Detig et al.   NATURE

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

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

Quantifying Missing Heritability at Known GWAS Loci

(2013) Alexander Gusev et al.   PLoS Genetics

Epistasis dominates the genetic architecture of Drosophila quantitative traits

(2012) W. Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The mystery of missing heritability: Genetic interactions create phantom heritability

(2012) O. Zuk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modifier genes in Mendelian disorders: the example of cystic fibrosis

(2010) Garry R. Cutting   Annals of the New York Academy of Sciences

Interpretation of interactions: guide for the perplexed

(2010) Kenneth S. Kendler et al.   BRITISH JOURNAL OF PSYCHIATRY

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

Genetic architecture of complex traits: Large phenotypic effects and pervasive epistasis

(2008) H. Shao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Data and Theory Point to Mainly Additive Genetic Variance for Complex Traits

(2008) William G. Hill et al.   PLoS Genetics