Jim Shaw

Hi there! I am an NSERC Postdoctoral Fellow at Harvard Medical School and Dana-Farber Cancer Institute. I work with Heng Li.

I obtained my PhD in Math at the University of Toronto, where I was advised by Yun William Yu. Previously, I studied Engineering Physics + Mathematics at the University of British Columbia.

Research interests

I develop algorithms/software/theory for biological sequence analysis and apply these bioinformatics approaches to investigate microbiome genomics.

I like to approach computational biology with a “full-stack approach”: start from an interesting biology question, create algorithms backed by theory, engineer widely-used bioinformatics software, and then (hopefully!) discover something interesting about how microbes evolve.

More specifically, two intertwined themes define my work:

1. Obtaining novel insights about microbiome genome evolution (especially due to mobile genetic elements) through principled computational and analytical methods.
2. Building sophisticated bioinformatics algorithms to democratize and improve the analysis of massive microbial and meta-omics data.

For example, see my work on ultrafast microbial divergence computation, rapid metagenome profiling, and long-read metagenome assembly.