PAIR-Scan: Single-step identification of highly potent TCR-neoantigen pairs through library-on-library screening https://www.biorxiv.org/content/10.64898/2026.09.07.749948v1
Ben Nicolet
@bnicolet.bsky.social
Postdoc @ Schumacher lab, immunology, ML, TCR, Amsterdam
Can you boost the protein expression in specific cell types? That is what we asked in our study published a week ago in @scienceadvances We used machine learning (AI) to learn the code for protein expression in immune cells. www.science.org/doi/10.1126/...
Learning the sequence code of protein expression in human immune cells
SONAR informs the design of cell type–specific protein expression in human cells.
science.org
it is finally out! 👇 our #ML pipeline SONAR, which can predict the protein abundance in #immune cells. Using sequence features present in the #RNA. With @bnicolet.bsky.social Supported by the @erc.europa.eu and@oncodeinstitute.bsky.social www.science.org/doi/epdf/10....
Learning the sequence code of protein expression in human immune cells
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science.org
It's not the models, it's the data! We show that a substantial proportion of a widely used TCR-pMHC database does not functionally validate, causing underestimation of performance of TCR-pMHC prediction models. www.biorxiv.org/content/10.1...
A functionally validated TCR-pMHC database for TCR specificity model development
Accurate prediction of TCR specificity forms a holy grail in immunology and large language models and computational structure predictions provide a path to achieve this. Importantly, current TCR-pMHC ...
biorxiv.org
Super grateful and happy to be part of MATCHMAKERS team of @cancergrand.bsky.social : bit.ly/4iN1dY9 (And thanks to CGC for the opportunity to talk about my work!)
Tackling one of immunology’s greatest questions
Future Leaders Spotlight: Meet MATCHMAKERS with Benoit Nicolet.
bit.ly
Super grateful and happy to be part of MATCHMAKERS team of @cancergrand.bsky.social : bit.ly/4iN1dY9 (And thanks to CGC for the oppressed to talk about my work!)
Tackling one of immunology’s greatest questions
Future Leaders Spotlight: Meet MATCHMAKERS with Benoit Nicolet.
bit.ly
Evelina Tutucci@anilevetu.bsky.social · 2y agoNew preprint 📣📣 Together with Monika Wolker's lab @sanquin Amsterdam, we optimized a smFISH protocol for T cells. We measured cytokines IFNG/TNF expression and localization during T cell activation and optimized an imaging pipeline for quantification. www.biorxiv.org/content/10.1...
(Repost from EMBO on x) Rethinking #sustainability in #science: read about three projects on consumption and waste of shortlisted candidates for the EMBO Lab Sustainability Award embo.org/people/rethink… @CanigovaNikola @bnicolet.bsky.social @SELS_Network
Looking forward to attend this great meeting!
Sander Wuyts, PhD 🧬@swuyts.bsky.social · 2y agoCalling all T-cell aficionado's. Come and join us next year (27-28 May 2025) for the fourth Antwerp T-Cell Receptor conference organised by @pmeysman.bsky.social, @krislaukens.bsky.social and Benson Ogunjimi. I'll also be there! www.uantwerpen.be/en/conferenc... #ImmunoSky
New preprint 📣📣 Together with Monika Wolker's lab @sanquin Amsterdam, we optimized a smFISH protocol for T cells. We measured cytokines IFNG/TNF expression and localization during T cell activation and optimized an imaging pipeline for quantification. www.biorxiv.org/content/10.1...
Single molecule imaging of transcription dynamics, RNA localization and fate in T cells
T cells are critical effector cells against infections and malignancies. To achieve this, they produce pro-inflammatory cytokines, including IFN-gamma and TNF. Cytokine production is a tightly regulat...
biorxiv.org
Wonderful to see the #immunology community growing here. The first starter pack is full (they cap at 150), so I created a second one. Let me know if you'd like to be added go.bsky.app/PY5tCas go.bsky.app/FmERUoD