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Ben Nicolet @bnicolet.bsky.social · 7d

Congrats !

Ben Nicolet @bnicolet.bsky.social · Aug 1

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

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Ben Nicolet @bnicolet.bsky.social · Aug 1

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…

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Ben Nicolet @bnicolet.bsky.social · Aug 1

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.

www.science.org

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Reposted by Ben Nicolet

Monika Wolkers @monikawolkers.bsky.social · Jul 23

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 [email protected]

www.science.org/doi/epdf/10....

Learning the sequence code of protein expression in human immune cells

You have to enable JavaScript in your browser's settings in order to use the eReader.

www.science.org

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Reposted by Ben Nicolet

Schumacher Lab @schumacher-lab.bsky.social · May 2

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 ...

www.biorxiv.org

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Ben Nicolet @bnicolet.bsky.social · Apr 29

Getting inspired at the EMBL sustainability event!

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Ben Nicolet @bnicolet.bsky.social · Feb 14

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

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Ben Nicolet @bnicolet.bsky.social · Jan 5

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

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Ben Nicolet @bnicolet.bsky.social · Jan 5

Thanks. Yeah amazing chance.

Ben Nicolet @bnicolet.bsky.social · Jan 5

Damn you autocorrect oppressed = opportunity. Sorry

Ben Nicolet @bnicolet.bsky.social · Jan 3

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

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Reposted by Ben Nicolet

Monika Wolkers @monikawolkers.bsky.social · Dec 12

Evelina Tutucci @anilevetu.bsky.social · Nov 12

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...

www.biorxiv.org

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Ben Nicolet @bnicolet.bsky.social · Dec 9

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

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

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Ben Nicolet @bnicolet.bsky.social · Dec 7

(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

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Reposted by Ben Nicolet

Itai Yanai @itaiyanai.bsky.social · Dec 6

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

A hypothesis is a liability - Genome Biology

genomebiology.biomedcentral.com

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Ben Nicolet @bnicolet.bsky.social · Nov 22

Looking forward to attend this great meeting!

Sander Wuyts, PhD 🧬 @swuyts.bsky.social · Nov 21

Calling 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

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Reposted by Ben Nicolet

Evelina Tutucci @anilevetu.bsky.social · Nov 12

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...

www.biorxiv.org

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Ben Nicolet @bnicolet.bsky.social · Nov 17

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

Inspired by nature – People – EMBO

Insights into projects from the shortlist for the EMBO Lab Sustainability Award and the candidates’ motivation

www.embo.org

Reposted by Ben Nicolet

Rod Rahimi @rodrahimi.bsky.social · Nov 15

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

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Ben Nicolet @bnicolet.bsky.social · Oct 26

Fascinating!

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

PNAS

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

www.pnas.org

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