Chia‐Lang Hsu

CyriPanel for CYP2D6 Genotyping from Targeted Capture Panels Using Assay-Matched Diploid References

CyriPanel improves CYP2D6 genotyping accuracy using assay-matched diploid references and structural inference, achieving higher concordance than Aldy 4 in benchmark tests.

Graph-KIR: Graph-based KIR Copy Number Estimation and Allele Calling Using Short-read Sequencing Data

Graph-KIR estimates KIR gene copy numbers and calls 7-digit alleles from WGS data with high accuracy, outperforming existing tools.

Unmasking Human T Cell Receptor Germline Diversity: 335 Novel Alleles Identified in 47 Pangenome Reference Individuals Using the gAIRR Suite

The paper identifies 335 novel T cell receptor alleles in 47 pangenome reference individuals using the gAIRR Suite, significantly expanding the IMGT database.

deCYPher: Star Allele-Resolution Computational Framework of Pharmacogenes for Haplotype-Resolved Long-Read Assemblies

deCYPher is a computational framework for pharmacogene analysis using haplotype-resolved assemblies, demonstrating high accuracy in resolving complex gene structures and identifying allele variations.

gAIRR-wgs: An Algorithm to Genotype T Cell Receptor Alleles Using Whole Genome Sequencing Data

gAIRR-wgs accurately calls T cell receptor alleles from whole genome sequencing data, identifying novel alleles and population-specific diversity patterns.

TypeAssembly: Copy number estimation and allele typing for haplotype assemblies

TypeAssembly annotates complex genes in haplotype assemblies by estimating copy numbers and typing alleles, successfully applied to 41 genes, 17 KIR genes, and 15 pharmacogenes across 466 assemblies.

Airway microbiome-host transcriptome networks link microbial dysbiosis to survival outcomes and therapeutic opportunities in severe COVID-19

The paper links airway microbiome dysbiosis to survival outcomes in severe COVID-19 and identifies potential therapeutic compounds that may modulate host gene expression to favor beneficial microbial signatures.

Genetic Diversity and Structural Complexity of the Killer-Cell Immunoglobulin-Like Receptor Gene Complex: A Comprehensive Analysis using Human Pangenome Assemblies

The paper develops a tool to analyze KIR gene diversity using pangenome assemblies and identifies novel alleles and structural variants in human genomes.

Profiling Germline Adaptive Immune Receptor Repertoire with gAIRR Suite

The paper introduces gAIRR Suite, a toolset for profiling germline adaptive immune receptor repertoire, achieving high accuracy in allele calling and discovering novel alleles across multiple datasets.

Mitochondrial ATP Synthase Trafficking along Microtubules to Cell Surface Depends on KIF5B and DRP1

This study identifies KIF5B and DRP1 as key factors in mitochondrial ATP synthase trafficking to the cell surface via microtubules in cancer cells.