Jacob West-Roberts

Hi, I'm Jacob West-Roberts

Computational Biologist & Environmental Scientist

I work to understand biological sequences, describe new and rare organisms, and develop tools to further biological research.

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 PublicationsGoogle 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.