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matsen.bsky.social
I ♥ evolution, immunology, math, & computers. Professor at Fred Hutch & Investigator at HHMI. http://matsen.fredhutch.org/
10 posts 397 followers 81 following
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Congratulations to Maggie Russell @magdalenarussell.bsky.social for graduating from @mcbseattle.bsky.social with a phenomenal thesis. I will retell the story of her thesis through images from her papers. 🧵 (Here we are with Phil Bradley, who co-advised Maggie.)

submitted 1 day ago • 1 comment

Big news from Sebastien Roch and collabs on phylogenetic likelihood function: "... we show that the expected log-likelihood is strongly concave and smooth in a box around the true parameter whose size is independent of both the tree topology and number of leaves." arxiv.org/abs/2501.17622

submitted 24 days ago • 0 comments

Building on the UShER tree of millions of SARS-CoV-2 genomes maintained by Angie Hinrichs, Hugh Haddox and Georg Angehrn (and others in @matsen.bsky.social lab and @jbloomlab.bsky.social) have looked into how the neutral mutation rate varies along the genome: [1/N] www.biorxiv.org/content/10.1...

submitted 46 days ago • 1 comment

Large protein language models can learn complex epistatic interactions, but how much does that help with predicting variant effects? In this NeurIPS article, we show that classical independent-sites phylogenetic models can outperform pLMs on this task. 1/7 openreview.net/forum?id=H7m...

submitted 102 days ago • 2 comments

We are here! All future seminar announcements will be posted here.

submitted 102 days ago • 0 comments