Population DNA methylome analyses remain largely confined to reference-defined genomic space despite extensive human genetic diversity. A central challenge is therefore to define comparable methylation phenotypes across diverse genomes and map the genetic architecture of methylome variation. Here, using 460 haplotypes...
Tian-Jie Liu, Juan F. Macias-Velasco, X. Zhuo et al.· bioRxiv· 0 citations
Evaluating multiple callers showed that telomere-to-telomere CHM13 alignment improves structural variant detection and offers advantages in difficult-to-map regions compared to GRCh38, and a binomial-based model was developed to estimate coverage requirements for variant detection.
Nahyun Kong, Zi-Tian Tang, Andrew Ruttenberg et al.· Cell Genomics· 1 citation
This work establishes a framework and best practices for reliably detecting low-VAF mutations in non-cancer tissues and provides a valuable resource for the community.
Y.-J. Ha, Dominika Maziec, J. Markowski et al.· Cell Genomics· 3 citations
This work resolved segregating transposable-element alleles as sequences, epigenetic states, and transcript components using 231 haplotype-resolved human pangenomes with matched long-read multi-omics.
Juan Jiang, X. Zhuo, Rong-Han Li et al.· bioRxiv· 0 citations
The human pangenome captures genetic diversity beyond a single linear reference, yet conventional DNA methylome maps largely assume that the underlying CpG substrate is fixed. Here we present a first draft of the human panepigenome on DNA methylation, generated from 440 haplotype-resolved long-read methylomes spanning...
Zheng Dong, Juan F. Macias-Velasco, X. Zhuo et al.· bioRxiv· 0 citations
Diploid genomes carry millions of heterozygous variants in cis-regulatory DNA, yet most genes produce similar RNA output from two parental alleles. How this balance is maintained is unclear. We developed Nanopore-HiChIP, a long-read method that maps high-order enhancer hubs on each haplotype. Over half of these enhance...
Jiang Tan, M. Sentmanat, Yu-Qing Wu et al.· bioRxiv· 0 citations
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