Yang Luo

This paper introduces scTAPAS, a method to reconstruct donor genotypes from scRNA-seq data, enabling eQTL and HLA-TCR analysis without conventional genotyping.

ORBIT integrates omics data across studies and layers to identify convergent disease mechanisms by prioritizing concordant signals using rank-based methods.

This study maps MHC-pQTL across ancestries, identifying genetic associations with plasma proteins and linking HLA genes to immune-related traits.

This paper integrates multi-omic data from 46,081 individuals to identify latent factors associated with diseases, showing improved prediction performance compared to single biomarkers.

The paper identifies genetic determinants of CD8+ T cell receptor (TCR) repertoire in cancer patients before and after immune checkpoint blockade (ICB) treatment, finding associations with HLA alleles and treatment response.

The paper identifies disease-specific genetic regulation of gene expression in immune cells during COVID-19 infection using single-cell eQTL mapping.

This paper introduces HLA-colocalization, a method for genetic colocalization at the HLA locus using HLA alleles, showing it identifies novel causal associations between viruses and autoimmune diseases.

PlantCADB compiles and annotates chromatin accessibility data from 37 plant species, providing tools to study regulatory networks and genetic mechanisms in development, stress responses, and evolution.

This paper provides a statistical genetics guide for imputing HLA alleles from genotype data and offers best practices for association testing to identify HLA variants driving complex diseases.

This study finds that higher Native Peruvian ancestry is associated with increased tuberculosis progression risk, independent of socio-demographic and environmental factors.

The paper investigates how HLA alleles influence TCR CDR3 composition and finds strong associations between HLA risk alleles and specific CDR3 amino acid features linked to autoimmune diseases.

This study conducts a trans-ancestry GWAS of rheumatoid arthritis, identifying 124 loci, 34 novel, and shows improved polygenic risk score performance across populations.

The paper identifies a sex-specific evolutionary interaction between ADCY9 and CETP variants associated with dalcetrapib response and cardiovascular traits.

The paper identifies state-dependent eQTLs in memory T cells by analyzing single-cell RNA and protein data from Peruvians, showing that gene regulation varies with cell states and disease-associated variants are enriched in these contexts.

The paper develops a method to identify population-specific causal effect sizes in functionally important regions using trans-ethnic genetic correlations.

This paper introduces cov-LDSC, a method to estimate heritability and its enrichment in tissue-specific gene sets in admixed populations, showing high concordance across populations but population-specific differences for some traits.

The paper identifies HLA-B*55:01 as a genetic risk factor for penicillin allergy through genome-wide analysis of electronic health records and imputed HLA data.

The paper identifies dynamic allele-specific expression changes in T cell activation, particularly in HLA genes, showing regulatory effects linked to autoimmune risk.

The paper identifies a genetic variant on 3q23 associated with early progression from Mycobacterium tuberculosis exposure to active tuberculosis in Peruvians, showing higher heritability than general TB susceptibility.

IMPACT improves regulatory element annotation by integrating TF binding profiles with epigenomic data, showing better performance in predicting eQTLs and capturing RA heritability.

A common missense variant in FBN1 reduces height by 2.2 cm in Peruvians, showing strong positive selection and higher frequency in coastal Native American populations.

The paper identifies in vivo eQTL interactions with cytokine levels in a lupus trial, finding novel regulatory mechanisms and potential therapeutic targets.

This study fine-maps RA and T1D loci outside the MHC, identifying causal variants and confirming their functional impact through allele-specific binding and enhancer activity.

This paper estimates narrow-sense heritability using identity-by-descent information in unrelated individuals and finds that IBD-based methods can capture rare variant contributions but are affected by stratification.

This study uses whole genome sequencing to explore the genetic architecture of inflammatory bowel diseases, identifying a risk variant in ADCY7 for ulcerative colitis but finding limited contribution of low-frequency variants to heritability.

The paper identifies a protein truncating variant in RNF186 that protects against ulcerative colitis by reducing disease risk.