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(Fred)erick Matsen @ematsen

I ♥ evolution, immunology, math, & computers. Professor at Fred Hutch & Investigator at HHMI. matsen.fredhutch.org

Joined August 2010
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(Fred)erick Matsen @ematsen
13 Nov 2025
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?

Agentic Coding For Scientists

A series on using coding agents like Claude Code for scientific programming, covering fundamentals, workflows, best practices, the human side of AI-assisted development, and spec-driven development.

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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…

Bipartite: manuscript-driven development with a team of agents

Bipartite is an agent orchestration system built around a simple idea: the manuscript is the source of truth, so understanding a project should mean reading its paper.

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Looking forward to the next AIRR immune repertoire meeting tinyurl.com/airrcmeeting8 . Hope to see you there! (Note there is a hybrid option too.)
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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…

Spec-Driven Development with spec-kit

A walkthrough of using GitHub's spec-kit for spec-driven development on a bioinformatics pipeline.

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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.

Replaying evolution to learn about the fitness landscape of affinity maturation

A five year collaboration with the Victora lab is bearing fruit for evolutionary biology.

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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. youtube.com/watch?v=Rbhs7CoL…

Agentic Coding For Scientists

A series on using coding agents like Claude Code for scientific programming, covering fundamentals, workflows, best practices, the human side of AI-assisted development, and spec-driven development.

matsen.group
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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…
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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 🧵)
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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):
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... 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…):
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Open AI Engineer position on next-generation protein evolution models! Join HHMI's AI initiative at Janelia Farm, Virginia, (an amazing place) and work closely with our team. This is going to be fun. hhmi.wd1.myworkdayjobs.com/e…
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