Sr. Staff Bioinformatics Scientist · Illumina · San Diego
I develop computational methods to resolve genetic variation in repetitive and structurally complex genomes.
Copy-aware, haplotype-resolved analysis at Illumina. Earlier work on transposable elements and genome evolution in Drosophila.
01 / Illumina · clinical genomics research
Reconstructing gene copies and haplotypes where paralogs make short reads ambiguous. I designed and evaluated algorithms that combine joint analysis with proximity evidence.
Known pathogenic findings recovered in 31 evaluated samples across eight loci; an evaluation set, not diagnostic sensitivity.
02 / Illumina · population genomics research
Resolving common alpha-globin copy-number configurations from whole-genome sequencing. I led development of the targeted HBA caller.
Compared with long-read data in 246 samples; separately, genotype calls were Mendelian-consistent in 575 trios.
03 / Ph.D. research · genome evolution
Reconstructing transposable element insertions and estimating their allele frequencies in complex genomes. I developed the software and contributed analysis; joint first author with Guilherme B. Dias.
Insertion sequences reconstructed in Drosophila S2R+ supported family-level phylogenetic analysis.
TruPath Genome: reconstructing paralogous gene copies
Illumina Application Note, M-GL-04321.
Copy-aware variant analysis at ACMG
ACMG Annual Clinical Genetics Meeting, Baltimore, MD
Haplotype-resolved analysis at InSiGHT
Biennial Meeting of the International Society for Gastrointestinal Hereditary Tumours (InSiGHT), Dusit Thani Laguna, Singapore
Please reach out to me by email: hanshunhua0829 [at] gmail [.] com