Dr Michael Hall

I am a bioinformatician developing computational methods and open-source software that make pathogen genome sequencing faster, cheaper, and more clinically useful. My research applies long-read (Oxford Nanopore) and short-read whole-genome sequencing to detect antimicrobial resistance, reconstruct microbial genomes, and trace how infections spread.

A core part of my work is building widely used, open-source bioinformatics tools and reproducible analysis pipelines that researchers and laboratories around the world rely on. I also contributed to the World Health Organization catalogue of tuberculosis drug-resistance mutations, a global reference for genome-based diagnosis.

Working closely with clinical and public-health laboratories, I help translate these methods out of research and into real diagnostic and outbreak-response settings — including sequencing pathogens directly from patient samples, without the delays of laboratory culture.

My areas of expertise include:

- Pathogen genomics and genomic epidemiology - Antimicrobial resistance and drug-resistance prediction - Long-read sequencing, genome assembly, and metagenomics - Culture-free, direct-from-sample diagnostics - Open-source scientific software development (Rust and Python)

You can explore my open-source tools on my GitHub profile (https://github.com/mbhall88).