Ben Nicolet

Congrats !

Very proud of our team @sanquin & @oncodeinstitute.bsky.social (yet now im at @nkinl.bsky.social ) and especially my mentor @monikawolkers.bsky.social

Then we used that knowledge to boost or dampen the expression of different proteins.
There are many exciting applications!! e.g.
enhance (protein) drug production,
enhance mRNA expression in vaccines,
boost T cell immunotherapy efficacy…

Learning the sequence code of protein expression in human immune cells SONAR informs the design of cell type–specific protein expression in human cells.

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/...

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....

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 ...

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...

Getting inspired at the EMBL sustainability event!

Same here. My eyes are bleeding and crying due to the color mess of my ab boxes…

Tackling one of immunology’s greatest questions Future Leaders Spotlight: Meet MATCHMAKERS with Benoit Nicolet.

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!)

Thanks. Yeah amazing chance.

Damn you autocorrect oppressed = opportunity. Sorry

Tackling one of immunology’s greatest questions Future Leaders Spotlight: Meet MATCHMAKERS with Benoit Nicolet.

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!)

Rethinking sustainability in science – People – EMBO Shortlisted candidates for the EMBO Lab Sustainability Award are reshaping how science addresses consumption and waste

www.embo.org/people/rethi...

(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

A hypothesis is a liability - Genome Biology

genomebiology.biomedcentral.com/articles/10....

Looking forward to attend this great meeting!

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...

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...

Inspired by nature – People – EMBO Insights into projects from the shortlist for the EMBO Lab Sustainability Award and the candidates’ motivation

www.embo.org/people/inspi...

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

Fascinating!

www.pnas.org/doi/full/10....