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Epitope landscape in autoimmune neurological disease and beyond sciencedirect.com/science/articl…

CD45RA/RO isoforms are crucial markers for T-cell phenotyping. We have developed a handy tool IDEIS to extract this information from scRNAseq data. Works well for 10x 5' seq. Also, we used IDEIS to reveal CD45 splicing patterns in mouse leukocyte subsets. tinyurl.com/72cne76c

BREAKING NEWS The Royal Swedish Academy of Sciences has decided to award the 2024 #NobelPrize in Chemistry with one half to David Baker “for computational protein design” and the other half jointly to Demis Hassabis and John M. Jumper “for protein structure prediction.”

Tumor-reactive T cell clonotype dynamics underlying clinical response to TIL therapy in melanoma dlvr.it/TF9VW3

New online! Epstein–Barr virus as a potentiator of autoimmune diseases go.nature.com/3Y1UVKL

PSA: R packages on CRAN now have DOIs (fx 10.32614/CRAN.package.ggplot2)! Huge development for people who want to cite R packages in papers but think regular URLs in reference lists are not aesthetically pleasing.

Guardians of the brain galaxy: Endogenous self-peptides guard immune privilege of the central nervous system nature nature.com/articles/s4158…

TCR lovers, we are delighted to share our benchmarking of TCR specificity tools using an harmonized aggregation of public databases. biorxiv.org/content/10.110…

Why do some patients who get immune checkpoint inhibit develop immune-related myocarditis, which carries a mortality rate of 20-50%? New insights nature nature.com/articles/s4158… Steve Blum Mass General Cancer Center Alexandra-Chloé Villani Lab MassGeneral Medicine

1/10 PREPRINT MONDAY at the SchubertLab Benchmarking TCR-Epitope Predictors with ePytope-TCR (doi.org/10.1101/2024.1…) Short-Summary: - 18 pre-trained public methods - evaluated on 2 benchmarking datasets - for repertoire annotation & cross-reactivity prediction

I definitely want to test this tool in the near future 👀! Thank you Felix Drost and Benjamin Schubert !

The REAL Superpower of Deep T Cell Sequencing! We tracked #singlecell from Tumor to Blood. We identified ICI-induced T cells. We quantified T cell memory. We designed personalized TCR-T therapy. Amazing collab Omniscope CNAG Hospital Sant Joan de Déu Barcelona ES biorxiv.org/content/10.110…

A suggestion for an improved BLOSUM-like substitution matrix. COVID epitopes identified with the proposed substitution matrix for TCRb covered larger edit distance but smaller physicochemical similarity than BLOSUM62 @oxfordjournals | doi.org/10.1093/bib/bb…

The combination of nivolumab and ipilimumab in patients with metastatic colorectal cancer led to 24-month progression-free survival of 72%, as compared with 14% with chemotherapy. Read the full CheckMate 8HW trial results: nej.md/4eGp1tj

If you do nested loops in #Rstats, then you've taken a wrong turn somewhere 😆 Functional programming to the rescue...

🚀 Precision Cancer Immunotherapy with AI-Designed pMHC Binders 🧬 In collaboration with DTU Bioengineering, @DTUHealthTech, and Scripps Research, we developed a de novo binder design pipeline for #pMHCs biorxiv.org/content/10.110…

TCR-pMHC prediction is tough. So, we took a fresh approach: AI-driven protein design. 🤯 With @DarianSWolff & @TPJenkinsDTU, we engineered NY-ESO-1-pMHC binders, integrating them into CARs for cancer cell targeting. 🚀 biorxiv.org/content/10.110…

Modex's EBV vaccine given to first participant in Phase 1 trial multiplesclerosisnewstoday.com/news-posts/202…

Deep learning methods aid in de novo design of proteins to neutralize lethal snake venom toxins in vitro and protect mice from a lethal neurotoxin challenge. nature.com/articles/s4158… #NBThighlight

Hyperreactive B cells instruct their elimination by T cells to curb autoinflammation and lymphomagenesis dlvr.it/THPHtC