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Frederick "Erick" Matsen

@matsen.bsky.social

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

53 Posts639 Follower152 Folgt
Gabriel Victora@victora.bsky.social · 2mo ago

This was one of the most complex projects I have ever been involved in. Took us the better part of a decade, but I thoroughly enjoyed every minute of it. Especially the intensive and extensive interactions with @wsdewitt.github.io, @matsen.bsky.social, and @tylernstarr.bsky.social

William DeWitt@wsdewitt.github.io · 2mo ago

This started in 2019 as daydreamy PhD student musings with Tatsuya Araki. We're as excited as ever about germinal centers as a platform for experimental evolution. Many thanks to PIs @victora.bsky.social @matsen.bsky.social, co-1st authors Ashni Vora and Tatsuya, and many other key collaborators!

Frederick "Erick" Matsen@matsen.bsky.social · last mo.

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/202...

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.

matsen.fredhutch.org

Joshua Fein@joshuafein.bsky.social · 9mo ago

Outstanding articles. I’ve only just begun experimenting with Claude and Gemini CLIs and they’re incredibly powerful. This is extremely valuable best practice advice.

Frederick "Erick" Matsen@matsen.bsky.social · 9mo ago

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?

Frederick "Erick" Matsen@matsen.bsky.social · 9mo ago

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

matsen.group

Stephan Saalfeld@herrsaalfeld.bsky.social · 11mo ago

We are looking for an #AIEngineer to help build protein language models that capture evolutionary constraints with @matsen.bsky.social and @jbloomlab.bsky.social at #AI@HHMI @hhmijanelia.bsky.social hhmi.wd1.myworkdayjobs.com/en-US/Extern...

AI Engineer - Evolutionary Protein Language Models

Primary Work Address: 19700 Helix Drive, Ashburn, VA, 20147 Current HHMI Employees, click here to apply via your Workday account. Intro: AI@HHMI: HHMI is investing $500 million over the next 10 years ...

hhmi.wd1.myworkdayjobs.com

Frederick "Erick" Matsen@matsen.bsky.social · 11mo ago

The final version of our "Thrifty" paper is up now: elifesciences.org/articles/10... . We were motivated to fit wide-context mutation models based on previous analyses showing "mesoscale" effects and a position-specific effect. But, how to avoid exploding the number of parameters? 🧵

Thrifty wide-context models of B cell receptor somatic hypermutation

Convolutional embedding models efficiently capture wide sequence context in antibody somatic hypermutation, avoiding exponential k-mer parameter scaling and eliminating the need for per-site modeling.

elifesciences.org

@psathyrella.bsky.social · 12mo ago

In a new preprint we use deep learning on lineage trees to infer the functional form of the relationship between affinity and fitness that controls antibody evolution in germinal centers: arxiv.org/abs/2508.09871 🧵

Inference of germinal center evolutionary dynamics via simulation-based deep learning

B cells and the antibodies they produce are vital to health and survival, motivating research on the details of the mutational and evolutionary processes in the germinal centers (GC) from which mature...

arxiv.org

Gabriel Victora@victora.bsky.social · last yr.

Wanted to highlight our latest preprint--a huge effort by multiple people and labs, but led primarily by @wsdewitt.github.io, Tatsuya Araki, and Ashni Vora, in a very close wet-dry collaboration with @matsen.bsky.social’s lab at the Hutch www.biorxiv.org/content/10.1...

Replaying germinal center evolution on a quantified affinity landscape

Darwinian evolution of immunoglobulin genes within germinal centers (GC) underlies the progressive increase in antibody affinity following antigen exposure. Whereas the mechanics of how competition be...

biorxiv.org

Frederick "Erick" Matsen@matsen.bsky.social · last yr.

Many of my favorite collaborators are immigrants who face double threats of funding cuts and the anti-immigrant political climate. To them and immigrants generally: we need you, and we want you here. I understand if you want to leave but I hope you will stay and reach out.

Frederick "Erick" Matsen@matsen.bsky.social · last yr.

New blog post: our recent work to understand the somatic hypermutation process that enables antibodies to incrementally improve. A story of running into the limitations of deep learning, but still gaining biological insight along the way. matsen.group/general/2025...

Two new approaches to learn about antibody somatic hypermutation

We try to learn about SHM mechanism and do so by directly using mechanistic models, and by exploring deep architectures.

matsen.group