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 and Developmental Biology
University of Colorado at Boulder
Minors in Math and Chemistry
Technical Proficiencies
Programming Languages
- Python
- Bash
- R
- Javascript
- Julia
- Matlab
- C/C++
Fields of Expertise
- Metagenomics
- Phylogenetics
- Metatranscriptomics
- Machine Learning
- Metaproteomics
- Web Development
Professional Experience
2024 - Present
Computational Biologist
Sift Biosciences, San Carlos, CA
- Pipeline construction for identifying peptide targets for cancer immunotherapy vaccine development
2024
Computational Biologist
Tatta Bio, Remote
- Development of genome context-aware similarity search webapp
- Creation of benchmarks for protein language model assessment
2018 - 2023
Ph.D. Candidate
UC Berkeley - Banfield Lab
- Analysis of proteins from giant genes in candidate phylum Omnitrophota
- Metatranscriptomic and metagenomic analysis of montane soil datasets
- Development of scalable HMM-based metagenome annotation pipeline
Selected Publications
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.