Hello again, internet

For humans, written by a human

Welcome to the new site. The old one dated from early grad school and had started to feel like someone else’s homepage, so I rebuilt it from scratch — still Quarto, now with a hand-rolled theme (thanks Claude!).

This blog is where I put whatever I’m thinking about at the moment that I might want to share with the world. This post doesn’t really count, but stick around and hopefully I’ll post a thing or two soon.

A few things I’m deep in at the moment:

• AI agent tools for bioinformatics research We all are or should be using AI to write our analysis code these days, but the inherent randomness of LLMs makes it hard to achieve our goals of reliability and reproducibility in research. I’m trying to fix that with stringency…more to come soon!
• Segmentation benchmarking. Comparing cell segmentation algorithms for Xenium data across a multi-organ mouse atlas, and building CRISP to measure segmentation purity without ground truth.
• Spatial pipelines. Nextflow and Seurat workflows that take Xenium runs from raw output to annotated cells reproducibly.

I don’t know what purpose blogs have anymore in this new AI-slop-soaked internet but if you’re human and reading this maybe we’ll find out.