Happy to announce the release of IggyTop, a metadatabase for immune receptor–epitope interactions. It's integrated with scirpy v0.24 so you can readily use it to annotate your single-cell TCR datasets. iggytop.readthedocs.io/en/latest/

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...

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...

laskerfoundation.org

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...

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

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

github.com

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

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

github.com

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 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

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…

sciencedirect.com

❗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...

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

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.

github.com

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...

Human Leukocyte Antigen (HLA) in Viral Infections

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

mdpi.com

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...

Bruno Rodrigues@brodriguesco.bsky.social · 2y ago

rix v0.14.3 is on CRAN with many new features and improvements! cran.r-project.org/web/packages... Thanks to the many contributors for this release (credited in the DESCRIPTION file) Here is a sneak peak of what awaits you: 1/4

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

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🧵

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...

science.org

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

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

businesswire.com

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...

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...

doi.org

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...

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.

nature.com

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...

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

T cell receptor–centric perspective improves single-cell analysis.

doi.org

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.

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...

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...

biorxiv.org

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.

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...

biorxiv.org

🎨 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

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/...

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.

science.org

VDJ space-based trajectory analysis for single-cell immune profiling is coming to R! Check the dandelionR package (in progress): github.com/tuonglab/dan... Original Publication: www.nature.com/articles/s41...

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

Congrats to Qile and the R package: APackOfTheClones to visualize single-cell immune profiling! Fully compatible with scRepertoire too!

Journal of Open Source Software@joss-openjournals.bsky.social · 2y ago

Just published in JOSS: 'APackOfTheClones: Visualization of clonal expansion with circle packing' https://doi.org/10.21105/joss.06868

Inspired by @rodrahimi.bsky.social 's noble efforts linking immunologists together over here, let's try and get more specifically TCR/BCR/AIRR/repertoire chat going with this starter park go.bsky.app/Gi2dcGd Drop me a beep to get added or suggest others!

I am excited to share our latest paper. We profiled CD8+ TILs from HPV- HNSCC patients using scRNA/TCRseq. In addition, we performed an ex vivo stimulation of cells to capture their transcriptional response. 1/n onlinelibrary.wiley.com/doi/10.1002/...

Type I Interferon Drives a Cellular State Inert to TCR‐Stimulation and Could Impede Effective T‐Cell Differentiation in Cancer

Multimodal single-cell RNA sequencing identified a population of CD8+ T cells elevated in tumor tissue enriched for interferon-stimulated genes (ISG). These ISG cells are clonally related to a popula...

onlinelibrary.wiley.com