Yuta Nagano

Quantitative immunology, machine learning, medicine MBBS PhD @UCL @UCLMS

[Yuta Nagano @YutaNotUtah]

Excited to announce that our work on #TCR representation modelling is now out on @CellSystemsCP! You can try our model SCEPTR at https://t.co/kCq6NUKSBx 🚀

[Yuta Nagano @YutaNotUtah]

If anyone uses #Prettier to auto-format #Markdown notes, and wishes there was an auto-bullet list plugin for #NeoVim that has the same formatting conventions, you might like https://t.co/Onl2qlBozU

[Andreas Tiffeau-Mayer @andimscience]

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: https://t.co/IpFJrvRkiR

[Yuta Nagano @YutaNotUtah]

Quant-immuno people: you should know that @andimscience 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. https://t.co/DXQqA1eK44

[Andreas Tiffeau-Mayer @andimscience]

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 ! ✨ https://t.co/bonytcnVW9

[Andreas Tiffeau-Mayer @andimscience]

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 @GrowKudos https://t.co/xQ2XrWWc18

[Andreas Tiffeau-Mayer @andimscience]

What are the rules of the immune receptor code? In my talk @KITP_UCSB 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:
https://t.co/ClmNVKi8Ri

[Andreas Tiffeau-Mayer @andimscience]

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 👉

[Matthew V. Cowley @mvcowley]

🚨 Fresh #preprint 🚨

Targeting #DUX4 protein diffusion when designing #FSHD #therapeutics looks to be a great strategy!

Read more here: https://t.co/KCRJH7tSeN

Lovely as always working with @FSHresearch, Prof. Pete Zammit, and Dr Christopher Banerji.

[Yuta Nagano @YutaNotUtah]

@drchristhorpe Thank you so much for the shout-out @drchristhorpe! Very happy to hear it's been helpful.

[Kane Foster @KaneFos]

Very happy to share our latest pre-print studying T cell dynamics in multiple myeloma disease evolution 🧵1/10.
https://t.co/xqtVNDRgDI

[Yuta Nagano @YutaNotUtah]

A huge and sincere thank you to my supervisors @BennyChain @andimscience and co-authors Andrew Pyo @Martina_Milig @jhenderson_sci and Prof. John Shawe-Taylor. It's been great fun and I've learned so much working on this with all of you 🙏💪

[Yuta Nagano @YutaNotUtah]

How can we better align protein language model (PLM) pre-training with downstream tasks of interest? For TCR specificity prediction, it turns out that autocontrastive learning is really beneficial! Check out our preprint: https://t.co/ffDkCdRUiU

[Yuta Nagano @YutaNotUtah]

We also find that performance on TCR specificity prediction is not currently bottlenecked by model size.

[Benny Chain @BennyChain]

The latest exciting step forward in T cell receptor representation ! @YutaNotUtah outperforms TCR-BERT ! https://t.co/1OMhRsckRw

[Andreas Tiffeau-Mayer @andimscience]

How to pre-train protein language model to optimize transfer learning? @YutaNotUtah’s PhD work shows prior PLMs struggle to predict TCR specificty & uses contrastive learning to overcome this limitation. 👉https://t.co/sOov8EdpQG

[Yuta Nagano @YutaNotUtah]

Really proud and grateful to be part of this amazing work led by @Martina_Milig!

[Martina Milighetti @Martina_Milig]

New preprint!

We investigated the molecular interactions between the TCR CDR loops and find that these may be important in shaping TCR specificity and sequence

https://t.co/bvnZMPr2LR

[Andreas Tiffeau-Mayer @andimscience]

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.

https://t.co/fHRPP0Vjd8

[Trevor Graham @trevoragraham]

New preprint: Annie Baker & @BennyChain 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. https://t.co/tY8L4aFljH