In new study led by @bdadonaite.bsky.social, we show many influenza HAs (H5, H7, H9, H1, H2, H3) can use avian or human MHC-II to enter cells. We then use novel combo of deep mutational scanning & cryoEM to define how H5 HA binds to avian MHC-II. Preprint: doi.org/10.64898/202...

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

Antibody LMs learn what looks antibody-like, but not how selection turns naive germline antibodies into strong binders. @aakarshv1.bsky.social and I are excited to share CoSiNE, a model that learns this germline-to-mature process for variant effect prediction and antibody design. (1/8)

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!

Replaying germinal center evolution on a quantified affinity landscape

Antibody affinity maturation results from a somatic evolutionary process that takes place in the germinal center. A “parallel replay” experiment on germinal center B cells reveals the evolutionary for...

cell.com

1/7 New #ecology preprint out. We’ve spent half a century searching for Arenavirus and Hantavirus reservoirs, but it turns out global surveillance is essentially just us looking under the nearest streetlight. It is decoupled from actual host biodiversity.🧵 doi.org/10.64898/202...

Andy Kern, who doesn't (really) have an account here, would like to share his group's new tool for speeding up pop gen summary stat calculations using GPUs. Check it out here: www.biorxiv.org/content/10.6... And see his thread over at the other place: x.com/pastramimach...

Marc Feldman and Jessica Riskin with another withering critique of a "sociogenomics" popularization: "...you can’t add or subtract factors that interact, such as genetic and environmental influences. How much of a rainbow’s formation is due to moisture in the air and how much to sunlight?"

Not in Your Genome | M.W. Feldman, Jessica Riskin

Generations of “sociobiologists” have tried and failed to argue that genetic analysis offers the key to understanding social inequality. A new book fares no better.

nybooks.com

Happy to share our latest preprint on the clonal dynamics of GC “refueling.” We asked what happens at the clonal level after the simple (and ubiquitous) step of delivering a second vaccine dose during an ongoing GC response. www.biorxiv.org/content/10.6...

Arc Institute’s “MULTI-evolve” learns a classical additive model, not epistasis. Preprint (w/ Gian Marco Visani and Aayush Verma): www.biorxiv.org/content/10.6... Blog: dewitt-lab.github.io/posts/2026-0...

Additivity is all you need?

Arc Institute’s “MULTI-evolve” learns a classical additive model, not epistasis.

dewitt-lab.github.io

Please share! My lab has an open fully-funded PhD position at Vilnius University's Life Sciences Center in Lithuania. The PhD project will involve identifying missing orthomyxovirus segments from public sequence data. Applicants must hold an MSc by June & have bioinformatics experience. 1/2

Excited to share our latest work in Nature. Applying single-molecule and single-cell DNA sequencing methods, we uncover an extraordinary landscape of somatic mutations in immune checkpoint genes in autoimmune B cells, suggesting that somatic mutations may be key to autoimmunity [1/n] rdcu.be/fdqbr

Results from an @sfiscience.bsky.social postdoc "research jam" now published at @prxlife.bsky.social

Ignition Criteria for Trigger Waves in Cell Signaling

Employing a minimal but biochemically relevant model of trigger waves, this study obtained an analytic expression for wave ignition thresholds in cell signaling in 1D and numerical solutions in 2D and...

journals.aps.org

William DeWitt@wsdewitt.github.io · 11mo ago

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

NEE Focus issue on "Evolution in medicine", including a comment article from @alisonfeder.bsky.social and me.

Context dependency is essential for predicting intrahost evolution - Nature Ecology & Evolution

The ability to predict rapid evolutionary processes within our bodies would advance both medical science and evolutionary biology. We discuss technologies that move us towards intrahost evolutionary p...

nature.com

Nature Ecology & Evolution@natecoevo.nature.com · 5mo ago

Our March issue is a Focus on "Evolution in medicine", out now! www.nature.com/natecolevol/... Including research & opinion on: ➡️Somatic evolution and health ➡️Predicting intrahost evolution ➡️Collateral sensitivity during antibiotic therapy Cover illustration by Alex Cagan @atjcagan.bsky.social

One more trick pulled off by antibody-mediated feedback www.cell.com/immunity/ful...

Antibody-mediated feedback modulates interclonal competition in the germinal center

Antibodies generated by prior immune responses regulate B cell responses upon recall immunization. Barbulescu et al. examine whether antibodies produced by an ongoing immune response influence the out...

cell.com

Can we simulate realistic evolutionary trajectories and “replay the tape of life”? In this work, we propose a flexible, generalizable deep learning framework for modeling how the entire protein sequence evolves over time while capturing complex interactions across sites. 1/n doi.org/10.64898/202...

How much better is an ancestral recombination graph (ARG) than a site frequency spectrum (SFS)? For recovering mutation rate history, we can answer fairly precisely because both ARG and SFS are linear transforms of mutation rate history. This blog post uses spectral analysis to clarify the picture.

This isn't in international media yet but Lithuania is in crisis. The ruling coalition is trying to seize control of our public broadcaster LRT using expedited parliamentary procedures. European & Venice Commissions are aware & we've been protesting for the last two weeks. Things are looking grim.

Over the past 5+ years I've had the honor of working with @wsdewitt.github.io @victora.bsky.social and many others on a project to "replay" affinity maturation evolution from a fixed starting point. matsen.group/general/2025...

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.

matsen.group

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

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...

Antibody-mediated feedback modulates interclonal competition in the germinal center

Serum antibodies from prior immune responses regulate B cell activation and germinal center (GC) access upon recall immunization. However, how antibodies produced by an ongoing immune response influen...

biorxiv.org

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.

T cell receptor specificity landscape revealed through de novo peptide design | PNAS

T cells play a key role in adaptive immunity by mounting specific responses against diverse pathogens. Effective bindings between T cell receptors ...

pnas.org

Armita Nourmohammad@thearmita.bsky.social · last yr.

check out our new manuscript (led by Gian Marco Visani): structure-based machine learning model for TCR-pMHC complexes, predicting T-cell affinity to peptide-MHC complexes, quantifying T-cell receptor specificity, and designing de-novo immunogenic peptides: arxiv.org/abs/2503.00648

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...

International Centre for Mathematics in Ukraine - ICMU

ICMU supports top-level research in mathematics, with special emphasis on training younger generations of scientists and the development of mathematics in Ukraine.

icmu.ua

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...

The term 'affinity maturation' understates the influence of somatic hypermutation

Three recent papers quantify how nucleotide-level mutation processes drive antibody evolution.

matsen.group

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

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...

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