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Hi, I'm Tom 👋

I'm a Research Fellow in Microbial Bioinformatics in the Wyres Lab at Monash University (Melbourne, Australia). I started out as a wet-lab molecular microbiologist at UKHSA (formerly Public Health England) and completed my PhD at the University of Edinburgh before moving full-time into computational biology.

Read more about my path from wet-lab agar dilution MICs to computational genomics in How I got to where I am now 🔬.

🔬 What I Work On

  • In Silico Serotyping & Surface Antigens

    Lead developer of Kaptive, a tool and curated database ecosystem for rapid in silico typing of bacterial surface polysaccharides (K and O antigens) in Klebsiella pneumoniae, Acinetobacter baumannii, and beyond.

  • Antimicrobial Resistance (AMR) & Virulence

    Investigating the evolutionary dynamics, iron-uptake receptors (SideroScanner), plasmid defense systems, and genetic determinants of hypervirulence and last-line antibiotic resistance (such as cefiderocol).

  • Fast Bioinformatics Tooling

    Building ergonomic, high-throughput command-line tools and Python/Rust libraries (pyfgs, rammappy, bart, eris) using modern data-oriented architectures like Polars.

  • Open Collaborations

    Always keen to collaborate on in silico serotyping databases, bacterial glycan structure curation, and vaccine target discovery for global priority pathogens.

💻 Tech Stack & Tooling

Languages & Core
Python • Rust • R • Bash • SQL
Data & Scientific Computing
Polars • NumPy • SciPy • Pandas • scikit-learn • PyTorch • Biopython • PyO3
Visualisation & Apps
Matplotlib • Plotly • Seaborn • ggplot2 • Shiny • Streamlit • FastAPI
Workflows & Reproducibility
Nextflow • Snakemake • uv • Git • GitHub Actions • Docker / Apptainer • Linux / HPC

🌐 Connect & Elsewhere