Martina's elegant new paper defines an important and under-appreciated role for molecular interactions between CDR loops of the TCR !

Our new work! The 3D affinities of the OT-I TCR to foreign and self-antigens predict their 2D affinities and reveal imperfect antigen discrimination biorxiv.org/content/10.110…

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/

ImmuneLENS characterizes systemic immune dysregulation in aging and cancer | Nature Genetics nature.com/articles/s4158…

🚀 What do Bayesian inference and skydiving have in common? Both demand trust under uncertainty. Our CTO bvdmitri used RxInfer to clean up noisy pose estimates from his 500th skydive — showing how probabilistic inference fills the gaps where standard ML fails #Bayes #Skydiving

"Enhancing sequence alignment of adaptive immune receptors through multi-task deep learning" by Gur Yaari lab. Very promising: speed boost from GPU acceleration + solving problems of greedy aligners in capturing V(D)J rearrangement uncertainty academic.oup.com/nar/article/53…

TCR2HLA: calibrated inference of HLA genotypes from TCR repertoires enables identification of immunologically relevant metaclonotypes biorxiv.org/content/10.110… #biorxiv_immuno

One of the most complex regions in the human genome revealed. To me, it was fascinating to combine genome assembly and pangenome graphs (PGR-TK in Fig. 3e) algorithm techniques to uncover the hidden diversity across human populations. #genomics #bioinformatics

Now looking forward to "CMV DNAemia")

For innate immune cells, the lack of diverse receptor rearrangements has prevented the study of clonal evolution of the innate immune system in human tissues and tumors. With @satpathology and @caleblareau, I’m delighted to share my PhD work that tackles this challenge:

Our study on human T cell aging across blood, lymphoid and mucosal tissues reveals continuous turnover across sites with longer-lived cells in spleen and tissue resident memory T cells protected from immunosenescence. with Yates lab cell.com/immunity/abstr…

Our paper is out: the first genetic treatment response biomarker in MS. A finding only made possible by AIRRseq. This was a truly collaborative effort with Joe Sabatino Heinz Wiendl Adaptive Biotech and is a huge step towards personalized medicine. thelancet.com/journals/ebiom…

De novo identification of the specificities of recurrent human T cell receptors biorxiv.org/content/10.110… #biorxiv_immuno

Predicting TCR antigen specificity at proteome‑scale with synthetic immune cells and machine learning. I’m pleased to share our group's collaborative effort with Engimmune in this new pre‑print: biorxiv.org/content/10.110…

I'm excited to share that our latest research, "Sensitive neoantigen discovery by real-time mutanome-guided immunopeptidomics," has just been published in Nature Communications! nature.com/articles/s4146…

New preprint on a surprising question - with a pangenome reference, *what is a genetic variant?* biorxiv.org/content/10.110… With Pouria Salehi Nowbandani, Shenghan Zhang, Haoyang Hu, and Heng Li Heng Li

Interact-omics is a high-throughput cytometry-based framework for cellular interaction mapping. Haas Lab nature.com/articles/s4159…

Single-cell, Spatially-Resolved TCR Profiling Links T Cell Phenotype and Clonality in Human Tumors. -honored to have contributed a tiny bit to this innovative work from the twitterless Hudson lab biorxiv.org/content/10.110…

Our study on immune cell aging across tissue compartments that was part of the CZI Chan Zuckerberg Initiative networks for the human cell atlas is out! Longterm collaborations with Peter Sims @yoseflab @Teichlab Cambridge University Columbia Medicine nature.com/articles/s4159…

Perhaps we can finally evaluate stability of receptor-antigen complexes without spending days of MD simulations?