Bjørn Kwee
@Bjornformatics
PhD student @Schumacher_Lab @NKI_nl | Bioinformatics | Cancer Immunology | High-Performance Computing
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.
A functionally validated TCR-pMHC database for TCR specificity model development biorxiv.org/content/10.110… #biorxiv_immuno
Alongside TCRvdb, we introduced TCRbridge - an AlphaFold3-based model for predicting TCR-pMHC specificity (built upon AlphaBridge). The code is now live on GitHub 👉github.com/schumacherlab/…
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.org/content/10.110…
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 biorxiv.org/content/10.110…
#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!
A functionally validated TCR-pMHC database for TCR specificity model development biorxiv.org/content/10.110… #biorxiv_immuno
#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 📌ow.ly/rZUO50Up0BE
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 👉 cancergrandchallenges.org/matchmakers
It's not easy to get hold of a newly awarded Nobel Prize laureate! We are happy that chemistry laureate David Baker took our call, as he turned down "100 calls" while he was on the phone with us. Hold tight for our upcoming interview with Baker.
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.
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 ➡️ bit.ly/3Ql6ObG
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!
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. biorxiv.org/content/10.110… 🧵👇
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.
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. biorxiv.org/content/10.110… 🧵👇
Follow our cancer immunology colleagues @NKI_nl
Hello world! The Schumacher lab is now also on Twitter!😃🔬
Woohoo 🙌🙌🙌! If you’re into immunology and immunotherapy, then you must know Ton Schumacher! Follow the lab’s new twitter account! @NKI_nl
Hello world! The Schumacher lab is now also on Twitter!😃🔬
Follow the Schumacher lab! (Exciting stuff coming up)
Hello world! The Schumacher lab is now also on Twitter!😃🔬
Identification of patient-specific CD4⁺ and CD8⁺ T cell neoantigens through HLA-unbiased genetic screens go.nature.com/3Ida0mm
Gene function is associated with distinct mRNA – protein levels. We show that mRNA, protein, and mRNA-protein levels are associated with sequence characteristics in human CD8+ T cells. In the lab of @WolkersMonika at @sanquin You can read more here: dx.plos.org/10.1371/journa…