ORCiD: 0009-0007-4163-6928. Email: first initial + last name @ ucsc.edu
UC Santa Cruz BMEB PhD student. Advisor: Dr. Benedict Paten (UCSC Computational Genomics Lab)
About me
I’m Faith Okamoto, a bioinformatics PhD student who loves algorithms. I work on methods to better handle complex genomic regions. To that end I’m extending and applying the vg toolkit. Pangenome sequence-graph references are supposed to better represent genetic variation compared to linear references. But pangenomic algorithms aren’t quite as mature as we’d like them to be, so they still struggle with those complex regions. My job? Fix that.
Publications
- Chang et al. [including Okamoto F] 2025. Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe. bioRxiv. doi:10.1101/2025.09.29.678807
- Okamoto et al. 2024. Y and Mitochondrial Chromosomes in the Heterogeneous Stock Rat Population. G3: Genes|Genomes|Genetics. doi:10.1093/g3journal/jkae213
- Chen et al. [including Okamoto F] 2024. A Cost-effective, High-throughput, Highly Accurate Genotyping Method for Outbred Populations. G3: Genes|Genomes|Genetics. doi:10.1093/g3journal/jkae291
Talks
- “Y and mitochondrial chromosomes in the heterogeneous stock rat population”, Complex Trait Community, October 2024
- “Rapid, accurate long-read mapping to large pangenome graphs with vg Giraffe”, UC Santa Cruz Long Reads Group, October 2025 (Also presented part of an identically named talk at the HPRC 2025 Annual Meeting)
Posters
- “Improved Chaining in non-DAG Regions for Long Read Giraffe”, HPRC 2025 Annual Meeting, October 2025
Awards
- NHGRI T32 Trainee: Award to support PhD students working in the genome sciences
- Regents Fellowship: Extra stipend for first-year UCSC graduate students
Service
Work experience
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Graduate researcher, UCSC Computational Genomics Lab (March 2025—present). Developing and using vg for pangenomic research.
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Student research assistant, Palmer Lab (September 2022—August 2024). Published a journal article. Also, several blog posts.
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NREIP intern, Naval Environmental Preventative Medicine Unit 5 (June 2022—August 2022). Code (sans classified data) on GitHub.
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Freelance tutor, Wyzant (July 2021—December 2024).
Education
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PhD, Biomolecular Engineering & Bioinformatics, University of California, Santa Cruz (2024—present)
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BS, Biology with a Specialization in Bioinformatics, University of California, San Diego (2021—2024)
Graduated summa cum laude. Performed extracurricular research in the lab of Dr. Abraham Palmer. Member of the Undergraduate Bioinformatics Club.