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

This has been a really fun project and a chance to experience, thanks to the collaborative spirit of Oskar, Stephan, Ben, Clemens, Divy, and Takashi, the best side of what science can be.

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? 🧵

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

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.

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...

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

Somatic hypermutation unlocks antibody specificities beyond the primary repertoire

Initial specificity is thought to be required for somatic hypermutation (SHM)-driven antibody evolution. Zuo, Gautam, et al. demonstrate that non-cognate B cells can enter germinal centers, undergo SHM, and acquire new antigen specificities, highlighting the capacity of antibodies to generate new recognition through SHM.

dlvr.it

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]🧵

Quantifying the evolutionary dynamics of structure and content in closely-related E. coli genomes

Abstract. Bacterial genomes primarily diversify via gain, loss, and rearrangement of genetic material in their flexible accessory genome. Yet the dynamics

academic.oup.com

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!

AIRR-C Seminar Series, Sep 26, 2024 - Giulio Isacchini, Imprint Labs, USA

YouTube video by AIRR Community

youtu.be

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