Giulio Isacchini
@giulioisac.bsky.social
Machine Learning Scientist @ Imprint labs decoding the adaptive immune system, see http://giulioisac.github.io
Reposted by Giulio Isacchini
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...
looking to hire 2 postdocs to join us in this endeavor.
more details can be found here: sites.google.com/uw.edu/statp...
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...
sites.google.com
October 27, 2025 at 8:47 PM
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...
looking to hire 2 postdocs to join us in this endeavor.
more details can be found here: sites.google.com/uw.edu/statp...
Reposted by Giulio Isacchini
📢 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...
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...
October 22, 2025 at 7:09 PM
📢 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...
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...
Reposted by Giulio Isacchini
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? 🧵
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
September 18, 2025 at 10:46 PM
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? 🧵
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? 🧵
Reposted by Giulio Isacchini
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.
June 7, 2025 at 11:30 PM
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.
Reposted by Giulio Isacchini
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
May 7, 2025 at 7:55 PM
Online now: Somatic hypermutation unlocks antibody specificities beyond the primary repertoire
Reposted by Giulio Isacchini
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/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
January 6, 2025 at 5:12 PM
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/mbe/advance-...
Are you curious about how fast the genome of E.coli evolves structurally (gains, rearrangements...) ? 🧬
A summary thread [1/N]🧵
Reposted by Giulio Isacchini
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... 🧵
December 6, 2024 at 10:50 PM
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
November 26, 2024 at 10:29 AM
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!
Reposted by Giulio Isacchini
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
💻🧬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
November 19, 2024 at 6:54 PM
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
💻🧬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