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?

Check out our latest preprint on the effects of antibody-mediated feedback on ongoing germinal center reactions, led by Alex Barbulescu and @janabilanovic.bsky.social

www.biorxiv.org/content/10.1...

excited that this paper is finally out in @pnas.org :
www.pnas.org/doi/10.1073/...

Led by Gian Marco Visani (effort initiated by Michael Pun), fantastic collaboration with @pgtimmune.bsky.social @asya-minervina.bsky.social and Phil Bradley.

In another display of incredible resilience, Ukrainian mathematicians in 2022(❗) opened a new International Centre for Mathematics in Ukraine (ICMU): icmu.ua/en

It was pleasure to give an online mini-course on Bayesian Statistics to Ukrainian students and scientists: icmu.ua/en/events/in...

We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)

My MSc student Indrė Blagnytė has a #preprint up on @biorxivpreprint.bsky.social on influenza D virus: www.biorxiv.org/content/10.1.... Flu D was discovered back in 2011, mostly circulating in cattle. Despite lots of research, a comprehensive analysis of its phylogeography had been missing. 1/6

A short blog post about a recent preprint (work hatched as a very fun all-postdoc collaboration at @sfiscience.bsky.social)

Why does selection feel so weak relative to mutation in affinity maturation? A new blog post giving three perspectives, including our new transformer-based model of natural selection on antibodies: matsen.group/general/202...

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 🧵

Antibodies are highly diverse, but most possible sequences are unstable or polyreactive. In this work, just published in Cell Syst., we propose a new source of data for modeling constraints from these properties. Our models show clear improvements in predicting Ab dysfunction. (1/n)
t.co/qCZERPUMPF

Excited to share my new preprint developed with @matsen.bsky.social, in collaboration with Marius Brusselmans, Luiz Carvalho, @msuchard.bsky.social, and @guybaele.bsky.social, on the biological causes and impacts of tree space ruggedness in phylodynamic inference. 1/
www.biorxiv.org/content/10.1...

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...

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...

matsen.group/general/2025...

I have a new paper about these cute little guys (and some girls)!

White-necked Jacobins are interesting because all males and some but not all (!) females are brightly colored. The scientific question is why some but not all females?

(Img credit: Kate & Sam)

Kudos to NIH for getting rid of the odious 12 month delay in public access (a capitulation to the demands of scientific societies). But, as the new policy assumes grantees will continue to publish their work in traditional scientific journals, it remains unacceptable.

grants.nih.gov/grants/guide...

Where do our rights come from? Believe it or not, the United States has been rolling back our rights for 40 years. The biggest expansion of the peoples' rights in American history actually occurred between 1953 and 1969, during the period of American history known as the "Warren Court."

THREAD.