I ♥ evolution, immunology, math, & computers. Professor at Fred Hutch & Investigator at HHMI. matsen.fredhutch.org
Seattle
- Tweets 1,690
- Following 473
- Followers 2,263
- Likes 1,099
Pinned Tweet
The last five months with Claude Code have completely changed how we work.
matsen.group/agentic.html details:
• How agents work (& why it matters)
• Git Flow with agents
• Using agents for science
• The human-agent interface
Questions? What has your experience been?
6
423
Phylogenetic inference should be impossible, and yet it works. Lena Collienne led a project to build deep learning on the classical ideas that make it work. Now out in Systematic Biology.
matsen.group/general/2026/10…
2
15
86
5,974
Coding tools are great at producing code. But they don't fit how I do science, where the manuscript is the central artifact. So I built bipartite: manuscript-driven development with a team of agents, directed the way a PI directs a group.
matsen.fredhutch.org/general…
1
6
705
Looking forward to the next AIRR immune repertoire meeting tinyurl.com/airrcmeeting8 . Hope to see you there!
(Note there is a hybrid option too.)
1
284
Spec-kit points to the future of software development. New post: when I use it, how it's changed my dev flow overall, and a complete walkthrough building a bioinformatics pipeline from scratch. matsen.group/general/2026/02…
3
295
Over the past 5+ years we've had the honor of working with the Victora lab on a project to "replay" affinity maturation evolution from a fixed starting point.
My summary
matsen.group/general/2025/11…
is for both immunologists and evolutionary biologists.
1
7
482
The era of coding agents is here. How do we approach this as scientists?
Wednesday Dec 10th at 9am PT I'll livestream an interactive demo of what I have learned (matsen.group/agentic.html) about how to leverage agentic coding to do rigorous science.
piped.video/watch?v=Rbhs7CoL…
2
4
422
The Mahan postdoctoral fellowship offers 21 months of support to develop your own research with Fred Hutch computational biology faculty-- lots of excellent labs to choose from!
Apply: apply.interfolio.com/172697
Faculty: fredhutch.org/en/research/di…
1
2
368
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/molbev/msaf1… (short 🧵)
1
6
368
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/netam/r… as the code continues to evolve):
1
129
... and second is to have a map from the figures to where they are made in the associated "experiments" code repository (github.com/matsengrp/dnsm-ex…):
106