Our TRM modeling paper is now published in PLOS Computational Biology! In this paper, we fit dynamical (ODE) models to single-cell flow cytometry data using a variational autoencoder that has a GMM with time-dependent weights as prior. journals.plos.org/ploscompbiol...

Our manuscript on the effect of school closure on pre-vaccination SARS-CoV-2 transmission is now available on MedRxiv. Congrats to first authors Benedetta and Rey! www.medrxiv.org/content/10.1...

StanConnects are a series of one-day online conferences for the application of Stan to specific areas. This year, we're kicking off with Stan for biology (broadly defined), co-organized by @ericnovik.bsky.social and @vianeylb.bsky.social, on 30 May '25!! stanbio.org

Nearly 20 years ago, theory predicted that evolution can evolve “mutation sensors” to improve evolvability. Michael Barnett et all et al. now show this in a beautiful experiment! ❤️ www.science.org/doi/10.1126/...

In this preprint we quantify how resident-memory CD4 T cells are maintained in skin and lamina propria, and where they come from. We did this with a fate reporter mouse model, and of course Bayesian ODE models implemented in Stan. doi.org/10.1101/2024...

Our CD4 memory T cell paper is finally published in PLOS Biology (doi.org/10.1371/jour...). Congratulations to Elise Bullock and other co-authors!

I this preprint we model lung memory T cell dynamics following influenza infection, and fit such models to "single cell" flow cytometry data directly. The idea is to identify T cell populations and their dynamics simultaneously. www.biorxiv.org/content/10.1...

Our Science paper is finally published! www.science.org/doi/10.1126/...

My first publication of 2024! Thanks to Michiel van Boven and all other co-authors. This work required some creative Stan programming. doi.org/10.1371/jour...

I wrote a blog post about my efforts to add a distribution to Stan. It's work in progress. Check it out here: tbz533.blogspot.com/2023/12/cont...

What would Alanis say about this?