Jacob Shujui Hsu

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

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

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.

The paper evaluates somatic mutation detection methods across different sequencing and analysis pipelines to identify false negatives in drug-resistant mutations.

This study uses long-read sequencing to identify STRC variants in patients with hereditary hearing impairment, finding 11% diagnostic yield and highlighting LRS's ability to detect complex variants missed by conventional NGS.

This study analyzes mitochondrial DNA variation in the Taiwan Biobank, identifying pathogenic variants and associations with complex traits like myopia and renal function.

This paper evaluates the concordance of variant annotations from three tools on ClinVar variants, highlighting inconsistencies in pathogenicity interpretation.

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

This study evaluates variant calling pipelines for tumor whole exome sequencing, finding no single combination outperforms all variants and recommending merged and ensemble approaches.

This study reanalyzes 1,496 Taiwanese whole genome sequences to identify novel variants and clinically relevant genetic markers with potential medical implications.

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.

The paper uses whole exome sequencing to identify ciliary gene mutations in nonsyndromic biliary atresia, finding significant enrichment of deleterious variants in liver-expressed ciliary genes.

variant2literature searches biomedical literature for genetic variants by processing images and normalizing variant formats to improve recall.