Zepeng Mu

Identifying the causal allele in the CD40 autoimmune locus enables discovery of context-specific trans-effects in B cells

The paper identifies a causal allele in the CD40 locus and demonstrates context-specific trans-effects in B cells using CITE-seq and CRAFT-seq.

Widespread gene-environment interactions shape the immune response to SARS-CoV-2 infection in hospitalized COVID-19 patients

This study identifies gene-environment interactions influencing immune response to SARS-CoV-2 in hospitalized patients using single-cell RNA-sequencing and eQTL analysis.

Impact of disease-associated chromatin accessibility QTLs across immune cell types and contexts

The paper identifies chromatin accessibility QTLs (caQTLs) in immune cells and finds they colocalize more with GWAS loci than eQTLs, but often lack downstream gene expression effects.

Cell-type-resolved chromatin accessibility in the human intestine identifies complex regulatory programs and clarifies genetic associations in Crohn's disease

The paper constructs a cell-type-resolved chromatin accessibility atlas in the human intestine and identifies regulatory programs and genetic variants associated with Crohn's disease.

A splicing-based multi-tissue joint transcriptome-wide association study identifies susceptibility genes for breast cancer

This study performs a multi-tissue splicing-TWAS to identify breast cancer susceptibility genes, finding 240 significant genes and highlighting the importance of splicing over expression.

Epigenetic variation impacts ancestry-associated differences in the transcriptional response to influenza infection

The paper shows ancestry-related differences in transcriptional response to influenza are driven by epigenetic variation and genetic control of enhancer activity.

Impact of cell-type and context-dependent regulatory variants on human immune traits

The paper examines how regulatory variants in immune cells affect genetic risk for immune traits by analyzing QTLs and GWAS loci overlap.

Alignment of single-cell RNA-seq samples without over-correction using kernel density matching

Dmatch aligns scRNA-seq datasets to reduce batch effects without over-correction, enabling cell-type-specific comparisons and eQTL mapping.

De novo assembly of 64 haplotype-resolved human genomes of diverse ancestry and integrated analysis of structural variation

The paper presents 64 haplotype-resolved human genomes using long-read sequencing and identifies structural variants, SV-eQTLs, and adaptive selection candidates.

Single-cell RNA-sequencing reveals pervasive but highly cell type-specific genetic ancestry effects on the response to viral infection

The paper uses single-cell RNA-sequencing to show genetic ancestry affects gene expression during viral infection, with effects varying by cell type.

Alternative polyadenylation mediates genetic regulation of gene expression

The paper identifies genetic variants affecting alternative polyadenylation (APA) and shows their impact on gene expression, protein levels, and disease risk.