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 candidate who loves algorithms. I work
on methods to better handle complex genomic regions. To that end I’m extending
and applying the vg toolkit, in particular vg giraffe’s long-read mode.
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
- Eizenga et al. [including me] 2026. Pangenome alignment reveals global diversity and evolution of human centromeric regions. bioRxiv. doi: 10.64898/2026.09.03.749043
- Lukas et al. [including me] 2026. HPRC2: A human pangenome reference with near-complete coverage of common genetic variation. bioRxiv. doi: 10.64898/2026.07.21.739710
- Nakamoto et al. [including me] 2026. Genome sequence of Ceratocystis huliohia, a fungal pathogen of the native ‘Ōhi‘a tree in Hawai‘i. Microbiology Resource Announcements. doi: 10.1128/mra.00236-26
- Jacobs et al. [including me] 2026. Complete de novo assembly of Wolbachia endosymbiont of contemporary Drosophila simulans using long-read genome sequencing. Microbiology Resource Announcements. doi: 10.1128/mra.00992-25
- Chang et al. [including me] 2025. Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe. bioRxiv. doi: 10.1101/2025.09.29.678807
- Chen et al. [including me] 2024. A Cost-effective, High-throughput, Highly Accurate Genotyping Method for Outbred Populations. G3: Genes|Genomes|Genetics. doi: 10.1093/g3journal/jkae291
- Okamoto et al. 2024. Y and Mitochondrial Chromosomes in the Heterogeneous Stock Rat Population. G3: Genes|Genomes|Genetics. doi: 10.1093/g3journal/jkae213
Talks
- “How (not) to code into the void”, UCSC PBSE Retreat 2026
- “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)
- “Y and mitochondrial chromosomes in the heterogeneous stock rat population”, Complex Trait Community, October 2024
Posters
- “Long Read Giraffe: Past, Present, Future, presented at UC Systemwide Bioengineering Symposium (August 2026) and Telomere-to-Telomere “Face-to-Face” (September 2026)
- “Improved Chaining in non-DAG Regions for Long Read Giraffe”, presented at NHGRI Training Conference, March 2026 (prior version presented at 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
- Reviewer for Bioinformatics (2025)
- Graduate Student Association Representative on UC Santa Cruz’s Police Accountability Board (2025—)
Work experience
-
Graduate researcher, UCSC Computational Genomics Lab (March 2025—present). Developing and using vg for pangenomic research.
-
Student research assistant, Palmer Lab (September 2022—August 2024). Published a journal article. Also, several blog posts.
-
NREIP intern, Naval Environmental Preventative Medicine Unit 5 (June 2022—August 2022). Code (sans classified data) on GitHub.
-
Freelance tutor, Wyzant (July 2021—December 2024).
Education
-
PhD, Biomolecular Engineering & Bioinformatics, University of California, Santa Cruz (2024—present)
-
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.