Frederick "Erick" Matsen
matsen.bsky.social
Frederick "Erick" Matsen
@matsen.bsky.social
I ♥ evolution, immunology, math, & computers. Professor at Fred Hutch & Investigator at HHMI. http://matsen.fredhutch.org/
... and second is to have a map from the figures to where they are made in the associated "experiments" code repository (github.com/matsengrp/dn...):
September 25, 2025 at 6:03 PM
I forgot to post two things I liked doing in this paper that I hope catch on. First is to have links in the methods section to the model fitting code (in a tagged version github.com/matsengrp/ne... as the code continues to evolve):
September 25, 2025 at 6:03 PM
Oh, and here is a picture of a cyborg-Darwin (cooked up by Gemini), after he realized how useful transformers are. For some reason MBE didn't want it as a cover image!
September 24, 2025 at 10:24 PM
And because natural selection is predicted for individual sequences, we can also investigate changes in selection strength as a sequence evolves down a tree:
September 24, 2025 at 10:24 PM
Because this model isn't constrained to work with a fixed-width multiple sequence alignment we can do things like look at per-site selection factors on sequences with varying CDR3 length:
September 24, 2025 at 10:24 PM
The final version of our transformer-based model of natural selection has come out in MBE. I hope some molecular evolution researchers find this interesting & useful as a way to express richer models of natural selection. doi.org/10.1093/mol... (short 🧵)
September 24, 2025 at 10:24 PM
Solution: first embed 3-mers and then the number of parameters goes up only linearly with the context width.
September 18, 2025 at 10:46 PM
Here are some useful subagents we've developed for Claude Code.
github.com/matsengrp/c...
(description in README if you don't know what I'm talking about)

Example uses:
August 14, 2025 at 1:40 PM
Working with Claude Code has been transformative. Yes, it does great on new code and refactoring. VSCode integration is 👍.

But the big surprise: it can seamlessly edit notebooks and then view the plots to plan next steps. Time to update my blog post matsen.group/general/202...
June 4, 2025 at 6:27 PM
Paper 3: doi.org/10.1101/2024... (in revision for NAR.) Clear evidence for the effects of microhomology in VDJ recombination: if there is a little homology between the two trimmed ends, then the sequence is more likely to ligate. This was a very challenging project; Maggie crushed it!
February 26, 2025 at 12:46 AM
Paper 2: dx.doi.org/10.7554/eLif... Sequence determinants of VDJ recombination trimming. VDJ trimming distributions have all these crazy shapes yet are consistent between individuals. Why? Maggie modeled sequence dependence with a handful of parameters and got a model that fits beautifully (orange)
February 26, 2025 at 12:46 AM
Paper 1: dx.doi.org/10.7554/eLif... . GWAS finding first examples of trans genetic variants associated with VDJ recombination outcome. Look, there's Artemis (DCLRE1C), providing an independent line of evidence for Artemis being the agent of VDJ recombination trimming.
February 26, 2025 at 12:46 AM
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.)
February 26, 2025 at 12:46 AM