Anne Nakamoto
PhD Candidate
Department of Biomolecular Engineering and Bioinformatics | Genomics Institute
University of California, Santa Cruz
Education
2023-
PhD Biomolecular Engineering & Bioinformatics, University of California,
Santa Cruz, USA
2018-22
BA Molecular & Cell Biology, University of California, Berkeley, USA
- Emphasis in Genetics, Genomics, and Development
- Minor in Computer Science
Research Experience
2024-
Graduate Student Researcher, Dissertation research
- Dr. Russ Corbett-Detig Lab, Department of Biomolecular Engineering, University of California, Santa Cruz
2023-24
Graduate Student Researcher, Research rotations
- Dr. Russ Corbett-Detig Lab, Department of Biomolecular Engineering
- Dr. Joanna Kelley Lab, Department of Ecology and Evolutionary Biology
- Dr. Shelbi Russell Lab, Department of Biomolecular Engineering, University of California, Santa Cruz
2022-23
Staff Research Associate II, Dr. Ksenia Krasileva Lab, Department of
Plant and Microbial Biology, University of California, Berkeley
2020-22
Undergraduate Researcher, Dr. Ksenia Krasileva Lab, Department of
Plant and Microbial Biology, University of California, Berkeley
Fellowships
2024
T32 Genome Sciences Training Fellowship, University of California, Santa Cruz
2023
National Science Foundation Graduate Research Fellowship (NSF-GRFP)
2021
Summer Undergraduate Research Fellowship (SURF), University of California, Berkeley
2021
Undergraduate Research Apprenticeship Program Summer Award, University of California, Berkeley (not accepted due to accepting SURF Award)
Awards & Honors
2025
Graduate Dean’s Research Travel Grant, University of California, Santa Cruz
2025
Advancement to PhD Candidacy with Honors, Department of Biomolecular Engineering & Bioinformatics, University of California, Santa Cruz. Thesis Proposal: “Conservation genomics at the landscape scale.”
Publications
(*authors contributed equally)
Preprints
2026
Anne Nakamoto, Lisa Keith, Qingyi Yu, Lionel Sugiyama, Xiaohua Wu, Blaine Luiz, MaryAnn Villalun, Jodie Jacobs, Russ Corbett-Detig, Ariana Cisneros, Harrison D. Heath, Cole Shanks, Faith Okamoto, Alexis Abigail Aroma Albura, Kyle Henricson, Yi Jun Lan, Henry Moore, William Seligmann, Yulia Zybina. Genome sequence of Ceratocystis huliohia, a fungal pathogen of the native ‘ōhi‘a tree in Hawai‘i. In review at Microbiology Resource Announcements.
2025
Jodie Jacobs, Alexandra Lum, Darren D. Lee, Emry L Gutierrez, Jonah A Dionisio, Camryn N. Morey, Cade Mirchandani, Luke Sylvester, Hailey Loucks, Anne Nakamoto, Ciara Wanket, Ariana Cisneros, Alessandro Calicchio, Alexis Enstrom, Camille Headrick, Faith Okamoto, Kseniya Malukhina, Harrison D Heath, Petria Russell, Sagorika Nag, Thomas Gillespie, William Sobolewski, Zia Truong, Shelbi L. Russell. Complete de novo assembly of Wolbachia endosymbiont of contemporary Drosophila simulans using long-read genome sequencing. EcoEvoRxiv.
Journals
2025
Landen Gozashti, Anne Nakamoto, Shelbi Russell, Russell Corbett-Detig. Horizontal transmission of functionally diverse transposons is a major source of new introns. Proc. Natl. Acad. Sci., 122 (21) e2414761122.
2024
Lionel Sugiyama, Brian Bushe, Eva Brill, MaryAnn Villalun, Anne Nakamoto, Lisa Keith. First Report of Leaf Spot Caused by Paramyrothecium roridum on Coffea arabica in Hawai‘i, U.S.A. Plant Disease, 108 (10), 3198.
2024
Jodie Jacobs,* Anne Nakamoto,* Mira Mastoras, Hailey Loucks, Cade Mirchandani, Lily Karim, Gabriel Penunuri, Ciara Wanket, Shelbi L Russell. Complete de novo assembly of Wolbachia endosymbiont of Drosophila willistoni using long-read genome sequencing. Scientific Reports, 14 (1), 17770.
2023
Anne Nakamoto,* Pierre Joubert,* Ksenia Krasileva. Intraspecific variation of transposable elements reveals differences in the evolutionary history of fungal phytopathogen pathotypes. Genome Biology and Evolution, 15 (12), evad206.
Conference Presentations
2026
Biomolecular Engineering Research Retreat, University of California, Santa Cruz. Talk: “Comparative mutation load in the California Conservation Genomics Project.”
2025
Evolution Conference, Athens, GA. Talk: “Investigating deleterious mutation burden across populations and landscapes in the California Conservation Genomics Project.”
2024
Joint Idaho and Washington Chapters of the Wildlife Society Meeting, Coeur d’Alene, Idaho. Talk: “Investigating Mammalian Hibernation Phenotypes using Comparative Transcriptomics.”
2022
Plant and Microbial Biology Department Retreat, University of California, Berkeley. Speed Talk: “Investigating the role of transposable elements in fungal plant pathogen genome evolution.”
2021
Summer Undergraduate Research Fellowship Program Conference, University of California, Berkeley. Talk: “Investigating the role of transposable elements in fungal plant pathogen genome evolution.”
Poster Presentations
2026
NHGRI Training Conference, St. Louis, MO. Poster: “From orientation to publication: training in genome sequencing and assembly for new graduate students.”
2025
Bay Area Population Genomics Conference, Stanford University, CA. Poster: “Comparative mutation load in the California Conservation Genomics Project.”
2025
The 12th Wolbachia Conference, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan. Poster: “Mining for novel bacterial symbiont genomes of invertebrate metazoan hosts through de novo assembly.”
2023
Biology of Genomes, Cold Spring Harbor Laboratory. Poster: “Investigating the role of transposable elements in fungal plant pathogen genome evolution.”
2022
Center for Computational Biology Retreat, University of California, Berkeley. Poster: “Investigating the role of transposable elements in fungal plant pathogen genome evolution.”
2022 Plant and Microbial Biology Department Retreat, University of California, Berkeley. Poster: “Investigating the role of transposable elements in fungal plant pathogen genome evolution.”
Seminars
2025
Biomolecular Engineering Seminar Series, University of California, Santa Cruz. Seminar: “Investigating deleterious mutation burden across populations and landscapes in the California Conservation Genomics Project.”
2025
Dr. Peter Sudmant Lab, University of California, Berkeley. Seminar: “Investigating deleterious mutation burden across populations and landscapes in the California Conservation Genomics Project.”
2021
Dr. Daniel Croll Lab, University of Neuchâtel. Virtual seminar: “Investigating the role of transposable elements in fungal plant pathogen genome evolution.”
Teaching Experience
2024,25
Instructor for the BMEB Bootcamp, a two-week orientation for incoming PhD
and Masters students led by the T32 Genome Sciences Fellows. Led hands-on genome sequencing and assembly tutorials. Department of Biomolecular Engineering & Bioinformatics, University of California, Santa Cruz, USA
2022,23
Instructor for the Genomes and Plant Health Workshop, Summer 2022 and
Summer 2023, hosted by Ksenia Krasileva Lab, Department of Plant and Microbial Biology, University of California, Berkeley
Mentorship
2026-
Rebecca Abraham - undergraduate student, bioinformatics techniques for
transposable element analysis
2025-26
Faith Okamoto - Science Support Network mentee, Program in Biomedical
Sciences & Engineering, University of California, Santa Cruz
Work Experience
2019-21
Intermittent Lab Assistant at Daniel K. Inouye U.S. Pacific Basin Agricultural
Research Center, Hilo, Hawaii, USA