About

Shunhua Han, Ph.D.

I am a Sr. Staff Bioinformatics Scientist at Illumina, based in San Diego, CA. My work focuses on developing computational methods to detect genetic variants in medically important but algorithmically challenging regions of the genome—segmental duplications, gene families, and structurally complex loci.

Education

Ph.D. in Bioinformatics — University of Georgia (December 2021) Dissertation: Novel computational strategies for the analysis of transposable elements in Drosophila cell culture genomes Advisor: Casey Bergman

B.S. in Pharmaceutical Sciences — East China University of Science and Technology, Shanghai (June 2015)

Professional Experience

Sr. Staff Bioinformatics Scientist — Illumina (November 2025 – present) Resolving challenging and disease-causing genes using constellation mapped reads and whole-genome sequencing.

Staff Bioinformatics Scientist — Illumina (November 2023 – October 2025) Improved variant calling accuracy for PMS2 (Lynch syndrome diagnostics); published research blog on PMS2 detection.

Senior Bioinformatics Scientist — Illumina (January 2022 – October 2023) Led development of HBA1/2 copy number genotyping method for alpha-thalassemia diagnosis.

Graduate Research Assistant — University of Georgia (August 2016 – December 2021) Developed TELR (long-read TE detection), ngs_te_mapper2 (cell-line authentication), and machine learning models for P element target site prediction.

Skills

Languages: Python · R · C++ · Bash

Infrastructure: Nextflow · Docker · AWS

Specializations: Genomic variant calling in complex/repetitive regions · Long-read sequencing · Copy number analysis · Transposable element biology

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