Mao-Jan Lin

SIFT selects reference haplotypes for genome patching using compressed indexing and pseudo-MEM queries to improve T2T imputation efficiency.

ImpuT2T patches gaps in HiFi assemblies using pangenomes, improving quality over existing methods.

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

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

IGLoo improves the analysis of immunoglobulin heavy chain locus assemblies in lymphoblastoid cell lines by characterizing somatic recombination events and enhancing germline assembly quality.

The paper introduces biastools to measure and diagnose reference bias in genomic data across different scenarios and finds that inclusive graph genomes and end-to-end alignment reduce bias.

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.