Tsung-Yu Tony Lu

This paper develops a pangenome-based method to improve trait association and genomic prediction by capturing complex genetic variation missed by traditional approaches.

The paper introduces Minigraph-Cactus, a pangenome pipeline that constructs pangenome graphs directly from whole-genome alignments, demonstrating improved performance in mapping and variant calling across human and Drosophila data.

The paper presents a draft human pangenome reference that improves variant discovery and structural variant detection compared to existing references.

The paper shows recombination between heterologous human acrocentric chromosomes using pangenome data, revealing pseudo-homologous regions linked to Robertsonian translocations.

The paper identifies VNTR motifs linked to gene expression using a repeat-pangenome graph, showing motif variation explains more associations than VNTR length.

The paper develops a repeat-pangenome graph to analyze VNTR variation across populations and identifies population-specific VNTRs and expression quantitative trait loci.

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