B and T cells—the organizing principle of the adaptive immune system - Lasker Foundation For their discovery of the two distinct classes of lymphocytes, B and T cells – a monumental achievement that provided the organizing principle of the adaptive immune system and launched the course of...

Renewing my yearly bet on Cooper/Miller for the Nobels.

One might think that I would learn after being wrong so many times, but one would be mistaken.

laskerfoundation.org/winners/b-an...

Excited to present at the ASHI Annual Meeting next week on Predicting TCR Specificity in the Age of Single-Cell Sequencing. See you on Monday!

ashiannualmeeting2025.eventscribe.net/agenda.asp?p...

GitHub - BorchLab/immReferent: An Interface for Immune Receptor and HLA Gene IMGT Reference Data An Interface for Immune Receptor and HLA Gene IMGT Reference Data - BorchLab/immReferent

Excited to announce ImmReferent - A one stop shop for getting and handling IMGT immune receptor and HLA sequences in R.

github.com/BorchLab/imm...

I could not find it this morning - I sent him an email to see where his project ended up and will get back to you.

I am not sure if anyone has looked at this in a systematic way - I know Andrew Malone (malonelab.com) had some interesting data suggest T cell doublets in transplant biopsies might be doing this. You will probably need to know the HLA typing for the sample (not great typing in single-cell data)

GitHub - myADLM/ADLM-2025-Data-Challenge: Build an AI Tool for Extracting Information from Laboratory Documentation Build an AI Tool for Extracting Information from Laboratory Documentation - myADLM/ADLM-2025-Data-Challenge

Anyone interested in medical/laboratory information systems and language models - Check out the 2025 ADLM Data Science Challenge:

github.com/myADLM/ADLM-...

Researching at the intersection of HLA and viral infections - check out the special issue from Viruses.

www.mdpi.com/journal/viru...

scRepertoire now supports exporting clones directly into the immunarch workflow. Removing barriers like it's an anti-PD1.

vignette: www.borch.dev/uploads/scre...

dandelionR: Single-cell immune repertoire trajectory analysis in R Integration of single-cell RNA-sequencing (scRNA-seq) and adaptive immune receptor (AIR) sequencing (scVDJ-seq) is extremely powerful in studying lymp…

dandelionR: Single-cell immune repertoire trajectory analysis in R is out! www.sciencedirect.com/science/arti...

Checkout our package at github.com/tuonglab/dan... and on Bioconductor 3.21 onwards!

Thanks to everyone involved! @thehumanborch.bsky.social

Schematic figure showing divergent evolution of malignant subclones and how they migrate to different tissue compartments (blood vs skin), respond differently to extrinsic stimuli such as Staphylococcus aureus enterotoxins, and how subclones differ in their intrinsic resistance to anti-cancer drugs.

❗How can a cancer exploit its environment and still resist treatment?
✅The answer: co-existing malignant subclones.

Let me walk you through our latest study investigating how divergent evolution drives adaptability, aggressiveness, and drug resistance of T cell cancer. 1/🧵

doi.org/10.1158/2159...

Just resubmited the scRepertoire manuscript. Favorite part of the reviewer suggestions was benchmarking - scRepertoire v2 (yellow) can assign > 1 million TCR clonotypes in 30 seconds! Let's not talk about scRepertoire v1 (green line).

Preprint: www.biorxiv.org/content/10.1...

GitHub - BorchLab/Ibex: Using BCR and expression for sequence embedding Using BCR and expression for sequence embedding . Contribute to BorchLab/Ibex development by creating an account on GitHub.

Ibex update!
Our single-cell BCR deep learning package just got a major overhaul!
✅ Now supports CDR3 & full CDR1/2/3 embeddings
✅ Human & mouse models available
✅ Trained on 2–10M unique sequences for high accuracy
Check it out! github.com/BorchLab/Ibex

Human Leukocyte Antigen (HLA) in Viral Infections Special Issue in journal Viruses: Human Leukocyte Antigen (HLA) in Viral Infections

If you are interested in HLA, adaptive immunity, or viral infections, please see the special issue I am guest editor for: www.mdpi.com/journal/viru...

1/2 Every #rstats user, interested in #reproducible analysis should try the new version of #rix. It's much more robust than just using renv. With this update rix allows to use date specific versions and improves using github packages.
bsky.app/profile/brod...

Awesome! Please thank Ksenia for all her help!!

GitHub - ncborcherding/scRepertoire: A toolkit for single-cell immune profiling A toolkit for single-cell immune profiling. Contribute to ncborcherding/scRepertoire development by creating an account on GitHub.

Package Repo: github.com/ncborcherdin...
Code for Figure: github.com/ncborcherdin...

scRepertoire 2: Enhanced and Efficient Toolkit for Single-Cell Immune Profiling
www.biorxiv.org/content/10.1...

Coupling antigens from multiple subtypes of influenza can broaden antibody and T cell responses The seasonal influenza vaccine contains strains of viruses from distinct subtypes that are grown independently and then combined. However, most individuals exhibit a more robust response to one of the...

There's a really interesting new paper out in Science for people who care about immunity to flu (which should be everyone because flu is a VERY big problem):
www.science.org/doi/10.1126/...

Here's my thread explaining this work🧵

Palleon Pharmaceuticals and Henlius Collaborate to Advance Glycan Editing as a Treatment for Autoimmune Diseases Palleon Pharmaceuticals, a company pioneering glyco-immunology drug development to treat autoimmune diseases and cancer, today announced a collaborati

Exciting news from Palleon Pharma. Engineered sialidases remove glyco-immune checkpoint ligands from B cells, thereby potentiating antibody-mediated B cell depletion for treatment of autoimmune disease. Clinical studies gearing up in partnership with Henlius Biotech #glycotime

Distinct T-cell receptor (TCR) gene segment usage and MHC-restriction between foetal and adult thymus The foetal thymic T-cell receptor (TCR) repertoire is distinct from adult, and it is less governed by MHC-restriction, more closely encoded by genomic sequence with distinct gene-segment usage includi...

Our paper has now been published @elife.bsky.social 🎉🎉🎉

Check it out, especially if you are interested in the TCR repertoire and T cell development in the thymus
doi.org/10.7554/eLif...

totally second R for Data Science!

The 3 things that helped me the most was: 1) working in markdown to add context to my code (as well as annotated code), 2) working towards writing functions over scripts, and 3) getting comfortable with git.

Also I also found it easier to learn things when it was relevant to a research project.

Method of the Year 2024: spatial proteomics - Nature Methods Approaches for profiling the spatial proteome in tissues are the basis of atlas-scale projects that are delivering on their promise for understanding biological complexity in health and disease.

I could not be more thrilled to announce the Nature Methods @naturemethods.bsky.social Method of the Year is Spatial Proteomics! Please see our editorial as a roadmap to the fantastic content in this special issue! www.nature.com/articles/s41...

T cell receptor–centric perspective to multimodal single-cell data analysis T cell receptor–centric perspective improves single-cell analysis.

Our massive effort to recontextualize #single #T-cell data is now out in Science Advances! We developed a new system, STEGO, to do a TCR-first analysis, and reanalyzed 12 studies and more than 500 000 individual T-cells.
Supported by @cziscience.bsky.social !
doi.org/10.1126/scia...

Rather than immune suppression, CD206+ TAMs recruit a tumor-reactive network of CD8 T cells, cDC1s, and NK cells
doi.org/10.1084/jem....
@maxkrummel.bsky.social @jexpmed.bsky.social

I had zero luck with grants. People really didn’t get why what I did was important and never figured out how to explain it to them.

Solution structure and synaptic analyses reveal determinants of bispecific T cell engager potency Bispecific T-cell engagers (TcEs) link T cell receptors to tumor-associated antigens on cancer cells, forming cytotoxic immunological synapses (IS). Close membrane-to-membrane contact (≤13 nm) has bee...

Cool preprint by ⁦Dustin and coworkers on how various T cell engager formats, w/varying geometries/rigidities, impact synapse structure and potency

www.biorxiv.org/content/10.1...

TIRTL-seq: Deep, quantitative, and affordable paired TCR repertoire sequencing α/β T cells are key players in adaptive immunity. The specificity of T cells is determined by the sequences of the hypervariable T cell receptor (TCR) α and β chains. Although bulk TCR sequencing offe...

We keep improving TIRTL-seq, see the updated preprint (www.biorxiv.org/content/10.1...)! New additions include: a manual 96-well protocol, code and raw data now available, and successful in vitro validation of EBV and SARS-CoV-2 TCRs.

🎨 In case anyone need…

The NIH BioArt Source is an awesome library of *free* professionally drawn illustrations for scientific presentations or figures. Downloadable in HD. Thank you NIH for this invaluable tool 🙏!

Check it out 👇
bioart.niaid.nih.gov

A B cell screen against endogenous retroviruses identifies glycan-reactive IgM that recognizes a broad array of enveloped viruses Profiling of ERV-reactive B-1 cells in mice reveals natural antibodies against terminal N-acetylglucosamine on multiple viral envelope proteins.

This #glycotime work by @virusesimmunity.bsky.social is intriguing; terminal GlcNAc is a viral epitope recognized by Abs that keep endogenous retroviruses at bay. Must be something about the context of that GlcNAc, would love to see some followup structural biology.

www.science.org/doi/10.1126/...