Ulrik Stervbo (he/him)

Can someone explain to me the rationale behind every single journal requiring their own login and account information while completely ignoring the fact that a single person may hold more than one email address? I just added the 5th username to my *.nature.com keychain because... different email.

Getting ready for #ATCR25. A fantastic location for two days of amazing talks and science.

New exciting paper by Mikhail Shugay! TCREMP: a bioinformatic pipeline for efficient embedding of T-cell receptor sequences from immune repertoire and single-cell sequencing data - ScienceDirect | doi.org/10.1016/j.jm...

Hello world!

Have you heard of the AIRR Knowledge Commons yet? The AKC is being established as an integrated resource immune receptors, repertoires, antigen specificity and germline gene information.

Want to know more? We have recently updated our website: airr-knowledge.org

The IMMREP25 TCR specificity prediction challenge is now live on Kaggle!

Get involved: kaggle.com/competitions...

Huge thanks to: Matthew Noakes, @the-dee-em.bsky.social, @everichardson.bsky.social, @bjoernpeters.bsky.social , @adaptivebiotech.bsky.social , IEDB, @airr-community.bsky.social

Listen to Maxim and Scott discuss their work on #OnAIRR episode 13

www.podbean.com/ew/pb-9qkk6-...

Disease diagnostics using machine learning of B cell and T cell receptor sequences Clinical diagnosis typically incorporates physical examination, patient history, various laboratory tests, and imaging studies but makes limited use of the human immune system’s own record of antigen ...

Happy to see the fantastic work by @maximzaslavsky.bsky.social , @scottboydlab.bsky.social and coworkers finally out in Science. Great demonstration of the potential of AIRR-Seq based diagnostics |
www.science.org/doi/10.1126/...

Antigen-driven T cell responses in rheumatic diseases: insights from T cell receptor repertoire studies - Nature Reviews Rheumatology Garrido-Mesa and Brown review findings from TCR profiling studies in rheumatic diseases and discuss how improved study design might help elicit information about autoreactive T cell clones and their c...

Great overview of AIRR-seq in rheumatic diseases | @natrevrheumatol.bsky.social www.nature.com/articles/s41...

Molecular determinants of cross-strain influenza A virus recognition by αβ T cell receptors TCR-peptide-HLA ternary structures define molecular mechanisms of TCR cross-reactivity toward natural influenza variants.

Timely study by Katherine Kedzierska and Jamie Rossjohn and colleagues defining key structural features of #Tcell binding to circulating #influenza strains from 1918 to ~present #ImmunoSky www.science.org/doi/10.1126/...

Emergence of collective oscillations in massive human crowds - Nature Analysis of the confined crowds at the San Fermín festival in Spain shows that dense crowds can self-organize into macroscopic chiral oscillators, coordinating the orbital motion of hundreds of indivi...

Nature is amazing (and science too)! When the density becomes high enough, crowds of humans become a liquid | @nature.com doi.org/10.1038/s415...

Interested in B cell receptor repertoire analysis? We have a great set of speakers lined up for the “2025 Immcantation Users Group Meeting!” Check out the program and register for this free virtual meeting 1/30/25 10AM-1:40PM (ET) at: immcantation.github.io/users-meetin...

The Guardian view on the Pelicot rape trial: Merci, Gisèle, from women everywhere | Editorial Editorial: Gisèle Pelicot’s extraordinary courage and composure has forced a reckoning in France and elsewhere. We must act on her demand for change

Gisèle Pelicot - a tower of strength and a beacon of hope. #OnlyYesMeansYes www.theguardian.com/commentisfre...

I keep seeing ads for #OpenR and get excited thinking it’s about R... until I remember it’s not. Guess it is also confusing for the algorithm - maybe I should just give in and check it out openrfestival.de

The nasal anti-S. epidermidis IgA observed by @mfgrp.bsky.social is interesting as a potential strategy to induce pathogen-specific antibodies in mucosal respiratory areas

Exciting papers from @mfgrp.bsky.social and Belkaid Lab! IgG antibodies specific to the commensal bacterium Staphylococcus epidermidis are generated in tertiary lymphoid organs in the skin | #Nature
doi.org/10.1038/s415...
doi.org/10.1038/s415...

Can we predict T cell specificity with digital biology and machine learning? - Nature Reviews Immunology Koohy and co-workers discuss how we must turn to machine-learning approaches to define the antigen specificity of the many millions of possible T cell receptors. They review the models and methods cur...

Re-visiting this @natrevimmunol.bsky.social paper on challenges in TCR specificity prediction. Call to action: Build a unified TCR data library, expand antigen coverage, ensure unbiased model evaluation, and foster collaboration across immunology, AI, and industry experts. | doi.org/10.1038/s415...

A new paper, led by Kerry Mullan from Pieter Meysman’s (@pmeysman.bsky.social) group, advocates for a TCR-centric approach to analyzing scRNA data from T cells. One highlight is the identification of melanoma- and colitis-specific TCR clusters. | #ImmuneWatch #ScienceAdvances doi.org/10.1126/scia...

Bluesky for Science Bluesky starter packs for genomics, bioinformatics, R, and Nextflow

Bluesky for Science

Starter packs for genomics, bioinformatics, #Rstats, Nextflow. Moderation lists. Feeds. Let's rebuild the old scitwitter community and keep this place nice

blog.stephenturner.us/p/bluesky-fo... 🧬🖥️🧪

Calling all T-cell aficionado's.

Come and join us next year (27-28 May 2025) for the fourth Antwerp T-Cell Receptor conference organised by @pmeysman.bsky.social, @krislaukens.bsky.social and Benson Ogunjimi.

I'll also be there!

www.uantwerpen.be/en/conferenc...
#ImmunoSky

Re-pinging for new arrivals: here's a starter pack of researchers who work on variable immune receptors: let's all have nice repertoire chats together.

go.bsky.app/Gi2dcGd

meme paper summary showing a fork in the road for the tcr:pmhc specificity problem: 1. pointing to binary classification 2. pointing towards gen AI

My first Skeetorial!

💻🧬TCR-TRANSLATE - A new framework for thinking about the TCR:pMHC specificity problem.

TLDR:
We pretrained LLMs on ~8M TCR & pMHC seqs
Finetuned on sparse pMHC->TCR pair data
Validated CDR3b sequences to unseen antigens
>> random performance on IMMREP2023 "private" antigens

The First NFDI BioMed Workshop was a great success. Nearly two days with great colleagues and focused discussions finding out how NFDI consortia with a biomedical focus can synergise and support each other #NFDI

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 | doi.org/10.1093/bib/...