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

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 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

❗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

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...

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🧵

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

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...

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...

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.

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...

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

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/...

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!

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/...

in case this is useful to someone in this massive platform migration: a starting pack for single-cell omics computational methods go.bsky.app/GmS1cH

The one science tweet that I still think about regularly, posting here for posterity.

New de-novo TCR design preprint from @dkarthikey1.bsky.social just dropped: TCR-TRANSLATE: Conditional Generation of Real Antigen Specific T-cell Receptor Sequences www.biorxiv.org/content/10.1...

New TCR + Expression multimodal integration approach for single-cell sequencing. www.embopress.org/doi/full/10....

New R package immApex for deep learning with immune receptor sequences: repo: github.com/ncborcherdin... vignette: www.borch.dev/uploads/scre...

scRepertoire v2 beta is out and stable, Rccp integration from means its 30x faster. Please check it out, kick the tires, find the edge cases: GitHub: github.com/ncborcherdin... website: www.borch.dev/uploads/scre...

scRepertoire v2 is coming - reach out if you have a feature request and even better, if you want to contribute (and authorship!!). New feature - clonal-based rarefaction analysis. Find out more at: github.com/ncborcherdin...

Trex now has 16 total CNN models for single-cell TRA and TRB chains + geometric transformations. Next stop, dual chains!

🧪🔬🦠🩺Pls share. We are evaluating postdoc candidates with interests computational or experimental immunology, or tumor biology, immunotherapy, T cell immunology, or genome engineering. ccr.cancer.gov/careers/post...

#HiSciSky I work on machine learning x genomics x immunology for personalized cancer vaccine design. Background: CS PhD (ML + GPU compilers), pivoted to biomedicine, helped start 3 neoantigen vaccine trials. Now at UNC (pirl.unc.edu) trying to improve basic design of neoantigen therapies. 🧪🧬🖥️⚕️

Preprint for Trex is up, check out a framework for combining sc-GEX and TCR data - www.researchsquare.com/article/rs-3.... Like Ibex, the CNN encoders for TCR sequences are up and integrated into the Seurat/Bioconductor pipeline at github.com/ncborcherdin...

New version of Ibex up later today for single-cell GEX and BCR sequencing. Now at 16 convolutional neural network-based autoencoders trained on over 1.5 million heavy and light chain sequences with more to come: github.com/ncborcherdin...

Coder life hack - loop testing parameters now auto-idents the step it is on and emails me the top 10 iterations when it is done:

First few day on bsky - I am Nick a MD/PhD working on developing computational frameworks to bring TCR sequencing into the clinic at Omniscope. My free time is mostly spent running after my daughter and writing open-source R packages for single-cell sequencing. Excited to meet new people here!