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New preprint: Annie Baker & Benny Chain have led the development of "FUME-TCRseq" a new T-cell receptor seq assay sensitive & robust enough to work on microdissected FFPE samples. Enables profiling of TCR clones & their tissue microenvironment together. biorxiv.org/content/10.110…

How to measure diversity with error bars? Progress on an old problem in this new preprint: an unbiased (!) estimator for the sampling variance of Simpson's index 👉arxiv.org/abs/2310.03439

Ever dreamed of clustering 10^6 TCR sequences in one second? Or 10^7 TCRs in 10 seconds? Well now you can, thanks to amazing work by Touchchai and Andreas Tiffeau-Mayer! Check it out: arxiv.org/pdf/2403.09010…

Happy to release our preprint introducing an information theory of T cell specificity! We rank TCR features by their relevance to predicting epitope specificity and bound how accurately T cell specificity can be predicted from partial information. arxiv.org/abs/2404.12565

Really proud and grateful to be part of this amazing work led by Martina Milighetti!

How to pre-train protein language model to optimize transfer learning? Yuta Nagano’s PhD work shows prior PLMs struggle to predict TCR specificty & uses contrastive learning to overcome this limitation. 👉arxiv.org/abs/2406.06397

The latest exciting step forward in T cell receptor representation ! Yuta Nagano outperforms TCR-BERT ! arxiv.org/pdf/2406.06397

Very happy to share our latest pre-print studying T cell dynamics in multiple myeloma disease evolution 🧵1/10. medrxiv.org/content/10.110…

🚨 Fresh #preprint 🚨 Targeting #DUX4 protein diffusion when designing #FSHD #therapeutics looks to be a great strategy! Read more here: biorxiv.org/content/10.110… Lovely as always working with Friends of FSH Research, Prof. Pete Zammit, and Dr Christopher Banerji.

Information theory of the T cell receptor sequence-function map -- our paper now out PNASNews ! 🔥 How informative (in bits) is the α or β chain? When does partial information limit predictions? + insights into synergy, Renyi entropy, optimal compression & more 👉

What are the rules of the immune receptor code? In my talk Kavli Institute for Theoretical Physics last Friday I summarised our recent findings, provide a perspective on why ML approaches have so far not achieved breakthrough success, and propose a path forward: online.kitp.ucsb.edu/online/viralim…

Using information theory to study the immune receptor code? 👉 check out this short popular summary of our recent PNASNews paper by first author @jhenderson_sci on Kudos growkudos.com/publications/1…

How to learn generalizable rules across complex sequence-function maps? 💡In our new preprint we propose a framework for learning two-point statistics and use it to discover biophysical rules of TCR specificity that generalize to unseen ligands ! ✨ arxiv.org/abs/2412.13722

Quant-immuno people: you should know that Andreas Tiffeau-Mayer is hiring! As his former PhD student I can attest his group is a perfect mix of brilliant minds with an open, collaborative culture and you'll have an amazing time. qimmuno.com/openings/

Our work on contrastive learning of T cell receptor representations is now out in Cell Systems! Give SCEPTR embeddings a try for your TCR analysis applications: sceptr.readthedocs.io/en/stable/