Zheng Dong

The genetic architecture of human DNA methylome variation

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.

GBZ-base and GAF-base: Indexed pangenome file formats

The paper introduces GBZ-base and GAF-base, indexed pangenome file formats for efficient subgraph and alignment extraction.

Pangenome-resolved polymorphic transposable elements reveal human regulatory evolution in action

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

Human panepigenome represents epigenomic diversity

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.

HPRC2: A human pangenome reference with near-complete coverage of common genetic variation

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.

Population differences of chromosome 22q11.2 duplication structure predispose differentially to microdeletion and inversion.

The paper analyzes chromosome 22q11.2 haplotypes to show how structural variations in specific regions correlate with microdeletion and inversion risks across populations.

Fully T2T pedigree assemblies reveal genetic stability and epigenetic plasticity of human centromeres across inheritance and cell-fate transitions

The paper uses fully phased telomere-to-telomere assemblies and long-read epigenomes to study centromere genetic and epigenetic dynamics across inheritance and cell-fate transitions, finding positional stability of CDRs and dynamic epigenetic changes.

Pangenome discovery of missing autism variants

The paper uses long-read sequencing to identify pathogenic variants in autism cases, finding three pathogenic mutations and nine candidate structural variants missed by short-read sequencing.

Distinct Co-Methylation Patterns in African and European Populations and Their Genetic Associations

The paper identifies population-specific DNA methylation patterns in African and European populations and links them to genetic variants and disease-related genes.

Genetic Basis, Quantitative Nature, and Functional Relevance of Evolutionarily Conserved DNA Methylation

The paper identifies evolutionarily conserved DNA methylation sites in great apes and shows their association with cancer but not other diseases.

Complete Reference Genome and Pangenome Expand Biologically Relevant Information for Genome-Wide DNA Methylation Analysis Using Short-Read Sequencing and Array Data

This study shows that using updated reference genomes like T2T-CHM13 and pangenomes increases CpG detection in DNA methylation analysis and improves probe specificity in arrays, leading to more accurate findings in cancer studies.