Halit Ongen

VIDRA models genetic dose-response relationships to predict drug mechanisms, therapeutic potential, and adverse events using phenotypically associated variants.

The paper identifies USP18 as a negative regulator of interferon response at a lupus risk locus through trans-eQTL analysis in lymphoblastoid cell lines.

The paper identifies TE-eQTLs in colorectal cancer and shows that tumor-specific TEs mediate genetic effects on gene expression, including cancer driver genes.

The paper integrates regulatory activity variability with gene expression and genotype data to identify genetic regulation changes in schizophrenia.

The paper combines regulatory element activity, gene expression, and genetic variation data across cell types to show how chromatin structure influences regulatory networks and genetic effects.

This study identifies non-coding cis-regulatory domains in CLL and skin cancer by analyzing somatic mutations in histone modification patterns, revealing functional regulatory regions and their associated genes.

The paper develops S-PrediXcan to compute gene expression associations from GWAS summary data and applies it to 44 GTEx tissues and 100+ phenotypes, finding tissue-specific effects and colocalized associations.

This study identifies distinct susceptibility and activity/severity signatures in SLE using transcriptomics and genetics, enabling improved diagnosis and personalized therapy.

This paper estimates the causal tissues for complex traits and diseases by analyzing eQTLs from the GTEx consortium and adapting the RTC score to calculate tissue sharing probabilities.

QTLtools is a modular framework for molecular QTL discovery and analysis, integrating data preparation, molQTL detection, and GWAS variant integration.

FastQTL efficiently maps QTLs by correlating molecular phenotypes with genetic variants using permutation-based p-value estimation, improving speed over previous methods.

This paper introduces Altrans, a method for discovering alternative splicing QTLs, and compares its performance to Cufflinks in European and African populations, finding more asQTLs with Altrans.