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Giulio Isacchini

@giulioisac.bsky.social
439 followers 458 following 5 posts

Machine Learning Scientist @ Imprint labs decoding the adaptive immune system, see giulioisac.github.io

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Reposted by Giulio Isacchini
William DeWitt @wsdewitt.github.io · 05/06/2026
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!
cell.com
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...
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Giulio Isacchini @giulioisac.bsky.social · 28/03/2026
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.
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Reposted by Giulio Isacchini
Armita Nourmohammad @thearmita.bsky.social · 27/10/2025
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...
sites.google.com
SPE - join us
Postdoctoral position: In January 2026, we are relocating to Yale university to start a theory initiative at the Center for Systems and Engineering Immunology (CSEI). We are looking for talented postd...
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Reposted by Giulio Isacchini
Greifflab @victorgreiff.bsky.social · 22/10/2025
📢 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...
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Reposted by Giulio Isacchini
Frederick "Erick" Matsen @matsen.bsky.social · 18/09/2025
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? 🧵
elifesciences.org
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.
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Reposted by Giulio Isacchini
William DeWitt @wsdewitt.github.io · 08/06/2025
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.
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Reposted by Giulio Isacchini
Immunity @cp-immunity.bsky.social · 07/05/2025
Online now: Somatic hypermutation unlocks antibody specificities beyond the primary repertoire
dlvr.it
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.
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Reposted by Giulio Isacchini
Marco Molari @mmolari.bsky.social · 06/01/2025
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]🧵
academic.oup.com
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
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Reposted by Giulio Isacchini
Oskar Hallatschek @ohallats.bsky.social · 06/12/2024
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... 🧵
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Giulio Isacchini @giulioisac.bsky.social · 26/11/2024
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!
youtu.be
AIRR-C Seminar Series, Sep 26, 2024 - Giulio Isacchini, Imprint Labs, USA
YouTube video by AIRR Community
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Reposted by Giulio Isacchini
Dhuvi Karthikeyan @dkarthikey1.bsky.social · 19/11/2024
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
meme paper summary showing a fork in the road for the tcr:pmhc specificity problem: 1. pointing to binary classification 2. pointing towards gen AI
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