Xuanyao Liu

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.

CACTI improves cQTL mapping by using correlations between regulatory elements, identifying more signals and colocalizing with GWAS loci better than traditional methods.

The paper identifies disease-specific risk variants and shared effector genes in allergic diseases using functional fine-mapping and expression quantitative trait loci.

LeafCutter2 identifies and quantifies unproductive splicing events from RNA-seq data, revealing their role in gene regulation and disease, including Alzheimer's.

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.

The paper links trans-pQTLs to protein-protein interactions and GWAS loci, identifying therapeutic targets in autoimmune diseases.

The paper introduces trans-PCO, a method for trans-eQTL mapping that improves detection of genetic variants affecting gene regulatory networks, identifying 14,985 high-quality trans-eSNP-module pairs.

The paper investigates how allele frequency differences of causal variants impact PRS portability between European and African populations, finding they significantly reduce accuracy.

GBAT improves detection of trans-gene regulation by addressing multiple testing, read-mapping biases, and confounders in eQTL analysis.

The paper constructs cell-type-specific TF binding annotations by combining sequence-based predictions with chromatin data, showing increased heritability enrichment for 49 diseases.

The paper proposes a model where trans-acting variation drives most genetic variance in complex traits through co-regulated networks of core genes.

The paper introduces ADGLM to model population variance structure, showing it biases genetic association studies and identifies novel genotype-variance associations.

The paper quantifies genetic components of population differentiation in UK Biobank traits to detect polygenic selection signals across geographic gradients.

The paper uses molecular QTL annotations to identify genetic variants associated with disease heritability, finding stronger enrichments using causal posterior probabilities than standard annotations.

The paper quantifies linkage disequilibrium (LD) dependent architecture of complex traits, finding that low LD SNPs have higher heritability, likely due to negative selection.

The paper develops GECS regression to estimate how much disease heritability is mediated by gene expression levels, finding that 21% of heritability is mediated across 30 traits.

This study partitions the heritability of local and distal gene expression regulation across 15 human tissues, identifying enriched functional categories and tissue-specific patterns.