Ali Pazokitoroudi

Functionally informed cis and trans proteome-wide association studies prioritize disease-critical genes

The paper develops PolyPWAS, a framework combining cis- and trans-pQTLs to prioritize disease-critical genes by improving protein prediction with functional annotations and showing better disease heritability explanation.

Fast variance component analysis using large-scale ancestral recombination graphs

The paper introduces ARG-RHE, a method to estimate heritability and perform association testing using ancestral recombination graphs, showing improved results over imputation alone.

Characterizing the genetic architecture of drug response using gene-context interaction methods

This study quantifies the heritability of drug response to statins, metformin, warfarin, and methotrexate in UK Biobank participants and identifies genetic modifiers of drug effects and side effects.

Scalable summary statistics-based heritability estimation method with individual genotype level accuracy

SUM-RHE estimates SNP heritability using summary statistics with accuracy comparable to individual-level methods.

A scalable and robust variance components method reveals insights into the architecture of gene-environment interactions underlying complex traits

The paper introduces a variance components method to estimate gene-environment interaction heritability in complex traits using UK Biobank data, finding significant GxE effects for several trait-environment pairs.

Deep Learning-based Phenotype Imputation on Population-scale Biobank Data Increases Genetic Discoveries

AutoComplete improves phenotype imputation in biobank data, enhancing GWAS power and genetic discovery.

A biobank-scale test of marginal epistasis reveals genome-wide signals of polygenic epistasis

The paper tests for polygenic epistasis in biobank-scale data and finds 16 trait-loci pairs with strong evidence of interaction effects.

Fast Kernel-based Association Testing of non-linear genetic effects for Biobank-scale data

FastKAST detects non-linear genetic effects on traits in large datasets by providing efficient kernel-based tests with calibrated hypothesis testing.

The lingering effects of Neanderthal introgression on human complex traits

This study assesses the contribution of Neanderthal introgression to human complex traits using UK Biobank data, finding significant but depleted effects compared to modern human variants.

Functional dynamic genetic effects on gene regulation are specific to particular cell types and environmental conditions

The paper identifies gene-environment interactions in gene regulation across cell types and treatments, revealing many genes missed by GTEx.

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

The paper estimates the contribution of dominance effects to complex trait variation using biobank-scale data and finds that dominance heritability is small compared to additive heritability.

Efficient variance components analysis across millions of genomes

The paper introduces an efficient algorithm for variance components analysis, enabling rapid estimation of hundreds of variance components across large genomic datasets and demonstrating its utility in heritability estimation and functional annotation partitioning.