Xiaoyu Zhuo

This study develops pangenome-based frameworks to analyze DNA methylome variation across diverse human genomes, identifying genetic factors influencing methylation patterns and their associations with complex traits.

The paper analyzes polymorphic transposable elements in human pangenomes to reveal regulatory evolution mechanisms before fixation.

The paper presents a human panepigenome map of DNA methylation, revealing epigenomic diversity across populations and highlighting the role of genetic variation in CpG presence and absence.

460 haplotypes from 230 genomes, selected to maximize common-variant coverage, capture 99.43% of All of Us common small variants and halve structurally unreliable regions and base errors versus HPRC1.

The paper investigates methylation patterns of polymorphic transposable elements using long-read sequencing and the Human Pangenome Reference, revealing distinct methylation profiles and context-dependent interactions.

This study shows that using graph-based pangenomes and inferred donor-specific assemblies improves somatic variant detection compared to GRCh38.

The paper develops a pangenomic method to create a benchmark resource for somatic variant detection using HapMap mixtures, identifying millions of variants across different genomic regions.

The paper analyzes the contribution of transposable elements to regulatory elements in the human genome using ENCODE data, finding that ~25% of cCREs are TE-derived and show regulatory features similar to non-TE cCREs.

The paper introduces a comparative epigenome browser that enables visualization and comparison of genomic and epigenomic data across species and genome assemblies.

The paper analyzes gene regulatory programs in the neocortex of rodents and primates using single-cell multiomics, finding rapid evolution of cell type-specific gene expression and TE-driven cCREs.

The paper tests the regulatory activity of human LTR18A transposable elements and finds they have lost activity over time due to mutations in AP-1 and C/EBP motifs.

The paper introduces the WashU Virus Genome Browser, a web-based tool for viewing and comparing viral genomic data, including 16 complete 2019-nCoV sequences and related viruses.

Co-opted transposable elements maintain conserved 3D genome structures via CTCF binding site turnover in human and mouse.