Curriculum Vitae
Education
2018 – 2023
Ph.D. in Environmental Science, Policy and Management
University of California, Berkeley
2016 – 2017
M.S. in Computational Biology
Carnegie Mellon University
2012 – 2016
B.A. in Molecular, Cellular & Developmental Biology
University of Colorado Boulder · Minors in Math & Chemistry
Technical Proficiencies
Programming Languages
- Python
- Bash
- R
- Julia
- C++
Fields of Expertise
- Metagenomics & Metatranscriptomics
- Phylogenetics
- Protein Language Models
- Machine Learning
- Metaproteomics
Professional Experience
2024 – Present
Consulting Computational Biologist
Sift Biosciences · San Carlos, CA
- Built pipelines to identify peptide targets for cancer immunotherapy vaccine development.
2024
Computational Biologist
Tatta Bio · Remote
- Developed genome-context-aware similarity search tooling for internal web application.
- Created benchmarks for assessing state-of-the-art protein language models.
2018 – 2023
Ph.D. Researcher · Banfield Lab
University of California, Berkeley
- Led metagenomic and metatranscriptomic analyses of montane soil microbial communities.
- Characterized giant genes in candidate phylum Omnitrophota and their ecological roles.
- Engineered scalable HMM-based annotation pipelines for large metagenome datasets.
Selected Publications Google Scholar
- West-Roberts, J.A. et al. (2024). “Diverse genomic embedding benchmark for functional evaluation across the tree of life.” bioRxiv.
- West-Roberts, J.A. et al. (2023). “Giant genes are rare but implicated in cell wall degradation by predatory bacteria.” bioRxiv.
- Al-Shayeb, B. et al. (2021). “Borgs are giant extrachromosomal elements with the potential to expand metabolic capacity.” Nature.
Contact
Reach out if you’d like to collaborate or learn more about my work.