Xiao Chen

The paper introduces Kivvi, a tool to genotype D4Z4 repeats using HiFi sequencing, enabling accurate detection of FSHD-related alleles and revealing genetic diversity across populations.

The paper introduces a computational model to quantify tandem repeat instability using long-read sequencing data and applies it to identify unstable alleles in 256 HPRC cell lines.

The paper creates a long-read benchmark for genetic variants using a large pedigree, improving variant calling performance and introducing new truth sets for tandem repeats and structural variants.

The paper develops Paraphase, a HiFi-based method to resolve highly similar paralogous genes, revealing genetic diversity and de novo events in segmental duplications.

This paper uses long-read sequencing to comprehensively identify pathogenic variants in the CYP21A2 locus for Congenital Adrenal Hyperplasia, including phasing and module counts, improving diagnostic accuracy.

StarPhase diplotypes 21 pharmacogenes using long-read sequencing with high accuracy, updating 26.2% of existing diplotypes and highlighting gaps in pharmacogenomic databases.

The paper introduces a CN caller for KIV-2 repeats using short reads, showing high accuracy and demonstrating its correlation with Lp(a) levels and population-specific CN distributions.

The paper develops Paraphase, a method using long-read sequencing to accurately determine SMN1 and SMN2 haplotypes and copy numbers, improving silent carrier detection in spinal muscular atrophy.

Cyrius accurately genotypes CYP2D6 using whole-genome sequencing data, outperforming existing methods and improving accuracy to 99.3%.

This paper develops a method to accurately determine SMN1 and SMN2 copy numbers from whole-genome sequencing data, enabling SMA diagnosis and carrier screening with high precision and recall.