Xian H. Chang

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.

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.

Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe

The paper updates Giraffe to map both long and short reads to large pangenome graphs, showing improved speed and accuracy compared to existing tools.

Personalized Pangenome References

The paper introduces a personalized pangenome approach to improve short-read mapping and variant calling by reducing reference bias and errors.

Pangenome Graph Construction from Genome Alignment with Minigraph-Cactus

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.

A Draft Human Pangenome Reference

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

Recombination between heterologous human acrocentric chromosomes

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

Haplotype-aware pantranscriptome analyses using spliced pangenome graphs

This paper introduces a toolchain for haplotype-aware transcript analysis using spliced pangenome graphs, improving RNA-seq mapping accuracy and enabling haplotype-specific expression quantification without prior haplotype characterization.

Genotyping common, large structural variations in 5,202 genomes using pangenomes, the Giraffe mapper, and the vg toolkit

The paper introduces Giraffe, a pangenome mapper that improves genotyping of SNVs, indels, and SVs in 5,202 human genomes using the vg toolkit.

Distance Indexing and Seed Clustering in Sequence Graphs

The paper develops efficient algorithms for distance calculation and seed clustering on sequence graphs to improve mapping algorithms.