Bjørn Kwee

PhD student @Schumacher_Lab @NKI_nl | protein LLMs | Bioinformatics | Cancer Immunology

[Bjørn Kwee @Bjornformatics]

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.

[bioRxiv Immunology @biorxiv_immuno]

A functionally validated TCR-pMHC database for TCR specificity model development https://t.co/POIaG8vO2P #biorxiv_immuno

[Bjørn Kwee @Bjornformatics]

@BingxuL @ragoninstitute @harvardmed Ready for take-off 🛫
Congrats!

[Bjørn Kwee @Bjornformatics]

Incredibly excited and grateful for the opportunity to present at Antwerp TCR in 3 weeks. There’s no place more relevant to showcase what we have been up to.

If you want to have a sneak preview; check out the thread of @MariusMessemak1 & our pre-print https://t.co/1eiGdkUdGj

[Pieter Meysman @chevaliersf]

#ATCR25 acceptance notifications just went out! We had 76 abstracts of very high quality, but could only accept 8! for short talks (so 10%). Huge thanks to our review committee for making though decisions. Really excited where the #TCR field is going based on the abstracts I saw!

[Bjørn Kwee @Bjornformatics]

@iskander I would suggest looking at 3D, supplemental 3D and 4B. I am not entirely convinced that measuring CDR1 and CDR2 would solve the data quality problem, but happy to hear your thoughts.

[bioRxiv Immunology @biorxiv_immuno]

A functionally validated TCR-pMHC database for TCR specificity model development https://t.co/POIaG8vO2P #biorxiv_immuno

[Bjørn Kwee @Bjornformatics]

@Paimaamu Thank you Ajey, you are the best.

[Bjørn Kwee @Bjornformatics]

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.

[bioRxiv Immunology @biorxiv_immuno]

A functionally validated TCR-pMHC database for TCR specificity model development https://t.co/POIaG8vO2P #biorxiv_immuno

[Bjørn Kwee @Bjornformatics]

@andimscience Thank you Andreas!
Are you coming to TCR Antwerp this year? Would be great to catch up.

[ESMO - Eur. Oncology @myESMO]

#ESMOImmuno24: According to the 2024 ESMO Immuno-Oncology Awardee, @Schumacher_lab, tackling the T-cell receptor challenge w/ vast datasets and cutting-edge high-throughput methods may pave the way for advances in #immunotherapy.
#ESMODailyReporter
📌https://t.co/FyknBm6pAB

[Bjørn Kwee @Bjornformatics]

@BingxuL Very interesting work Bingxu, congrats!

[Cancer Grand Challenges @CancerGrand]

Congratulations David Baker (@UW, member of #CancerGrandChallenges team MATCHMAKERS), who's won the 2024 Nobel Prize in Chemistry for his pioneering work building new kinds of proteins! 👏

More about MATCHMAKERS, funded by @CR_UK @theNCI @TheMarkFdn 👉 https://t.co/VypvhxCknh

[Science and Innovation at Cancer Research UK @CRUKresearch]

Ton Schumacher is closing #CancerHostTI24 discussing neoantigens and neoadjuvant therapy. With his research group he created technologies to dissect T cell responses in cancer and contributed to the development of adoptive T cell therapies and neoadjuvant cancer immunotherapy.

[The Netherlands Cancer Institute @NKI_nl]

Researchers from the group of @HaanenJohn and @Schumacher_lab have successfully developed a novel method that enables the identification of T cell receptors at an unprecedented scale ➡️ https://t.co/EqLZlbmzOd

[The Netherlands Cancer Institute @NKI_nl]

We’re excited to reveal that Team MATCHMAKERS has been selected by @CancerGrand to receive up to $25m over five years to take on one of cancer’s toughest challenges. Congratulations to Ton Schumacher @schumacher_lab and all the #CancerGrandChallenges teams!

[Bjørn Kwee @Bjornformatics]

@chevaliersf Thanks!
I find the last point especially interesting. Would you say that your case (5000 epitopes with 100 TCRs) is preferred over, let's say, 50000 epitopes with 10 TCRs?

[Bjørn Kwee @Bjornformatics]

@chevaliersf Very interesting!
I watched the seminar, hoping that you would elaborate on these two numbers. Could you reference a paper or share the calculation you made to estimate these numbers? And how would the TCRs (ideally) be shared over the epitopes?

[Ton Schumacher Lab @Schumacher_lab]

Excited to share STAPLER, a language model to predict TCR – pMHC reactivity that outperforms prior models.

And for ML aficionados: Description of a new data leakage problem inherent to a common negative data generation strategy.

https://t.co/dsLeYJoT7v
🧵👇

[Bjørn Kwee @Bjornformatics]

@Paimaamu @MariusMessemak1 Thanks Ajey 😁

[Bjørn Kwee @Bjornformatics]

Preprint alert 🚨🚨

Large language models can predict TCR - pMHC reactivity!🧬🔬

Proud to have worked on this project with @MariusMessemak1 and all other amazing co-authors.

[Ton Schumacher Lab @Schumacher_lab]

Excited to share STAPLER, a language model to predict TCR – pMHC reactivity that outperforms prior models.

And for ML aficionados: Description of a new data leakage problem inherent to a common negative data generation strategy.

https://t.co/dsLeYJoT7v
🧵👇

[AI for Oncology Lab @AI4Oncology]

Follow our cancer immunology colleagues @NKI_nl

[Myriam Chalabi @MyriamChalabi]

Woohoo 🙌🙌🙌! If you’re into immunology and immunotherapy, then you must know Ton Schumacher! Follow the lab’s new twitter account! @NKI_nl