I’m a Sr. Staff Bioinformatics Scientist at Illumina in San Diego, where I develop computational methods to resolve genetic variation in repetitive and structurally complex regions of the genome. My current focus is copy-aware, haplotype-resolved analysis for TruPath Genome and DRAGEN: TruPath Genome is an on-flowcell proximity sequencing chemistry, and I work on the multi-region joint detection algorithms that turn its long-range linkage into per-copy variant calls in segmental duplications. Before that I built targeted callers for the alpha-globin locus and for PMS2, two of the harder targets in carrier screening and hereditary cancer research.
I came to this problem through transposable elements. During my Ph.D. with Casey Bergman at the University of Georgia, I studied how TEs reshape the genomes of Drosophila cell lines, and built the software (TELR, ngs_te_mapper2) to find insertions that standard tools miss. Repetitive DNA has a way of breaking every assumption a pipeline makes, and I found I liked working exactly where things break.
The through-line of my work is simple: a lot of medically important genetic variation sits in places where the genome carries two nearly identical copies of the same sequence, and someone has to figure out which copy a read came from. That puzzle, in different forms, has kept me busy for a decade.
Education
2016 – 2021
Ph.D. in Bioinformatics
University of Georgia
Dissertation: Novel computational strategies for the analysis of transposable elements in Drosophila cell culture genomes (Dissertation PDF). Advisor: Casey Bergman.
2011 – 2015
B.S. in Pharmaceutical Sciences
East China University of Science and Technology, Shanghai
Professional experience
2025 – now
Sr. Staff Bioinformatics Scientist
Illumina
Copy-aware, haplotype-resolved variant analysis for paralogous genes, using multi-region joint detection with TruPath Genome proximity data and standard whole-genome sequencing.
2023 – 2025
Staff Bioinformatics Scientist
Illumina
Improved small-variant calling accuracy in the PMS2/PMS2CL high-homology region for standard whole-genome sequencing, work relevant to Lynch syndrome research.
2022 – 2023
Senior Bioinformatics Scientist
Illumina
Led development of the HBA1/2 copy-number genotyping method, which genotypes common alpha-globin configurations from whole-genome sequencing. Released for research use.
2016 – 2021
Graduate Research Assistant
University of Georgia
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
Focus
Variant calling in complex and repetitive regions · Long-read sequencing · Copy number analysis · Transposable element biology