excited to announce that this January we are relocating to Yale to start a theory initiative at the Center for Systems and Engineering Immunology (CSEI): @yalecsei.bsky.social looking to hire 2 postdocs to join us in this endeavor. more details can be found here: sites.google.com/uw.edu/statp...

📢 We are announcing the Adaptive Immune Profiling Challenge 2025! Can you predict immune state labels from adaptive immune receptor repertoires? 💰 $10,000 prize pool! 🗓️ Launches Nov 5 on @kaggle.com More Info: uio-bmi.github.io/adaptive_imm...

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? 🧵

I'm stoked to have this long-term and highly collaborative effort out in the wild. We present an experimental evolution system to quantitatively study the rapid evolutionary dynamics of B-cell affinity maturation. These evolutionary mechanisms underpin antibody responses and immune memory formation.

Online now: Somatic hypermutation unlocks antibody specificities beyond the primary repertoire

Thrilled to announce that our work (w. with fantastic @neher.io and Liam Shaw) has been published on Molecular Biology and Evolution! 🎉 academic.oup.com/mbe/advance-... Are you curious about how fast the genome of E.coli evolves structurally (gains, rearrangements...) ? 🧬 A summary thread [1/N]🧵

After a long and winding odyssey, excited to finally drop anchor in open-access waters. This preprint shows how neutral allele frequency time series can illuminate disease transmission rates between communities— key for epidemic fore- & backcasting. medrxiv.org/content/10.1... 🧵

Curious about generative modeling for T and B cell receptor repertoires and its role in understanding immune system diversity? Watch my talk here youtu.be/HVUYG-UmRH8?.... Thanks to the @airr-community.bsky.social and @victorgreiff.bsky.social for the opportunity to share our work!

My first Skeetorial! 💻🧬TCR-TRANSLATE - A new framework for thinking about the TCR:pMHC specificity problem. TLDR: We pretrained LLMs on ~8M TCR & pMHC seqs Finetuned on sparse pMHC->TCR pair data Validated CDR3b sequences to unseen antigens >> random performance on IMMREP2023 "private" antigens