Lightnews — Scholar-powered news

Reposted by Nick Borcherding

Gabriel Victora @victora.bsky.social · 4d

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

6 7 43

Nick Borcherding @thehumanborch.bsky.social · 5d

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...

1

Nick Borcherding @thehumanborch.bsky.social · Aug 20

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

3 8

Nick Borcherding @thehumanborch.bsky.social · Aug 20

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.

Nick Borcherding @thehumanborch.bsky.social · Aug 20

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)

1 1

Nick Borcherding @thehumanborch.bsky.social · Jul 28

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

2

Nick Borcherding @thehumanborch.bsky.social · Jul 18

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

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

1 1 2

Nick Borcherding @thehumanborch.bsky.social · Jul 17

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

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

1 6

Reposted by Nick Borcherding

Kelvin (Zewen) Tuong @kelvintuong.bsky.social · Jul 1

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…

www.sciencedirect.com

1 7

Reposted by Nick Borcherding

Terkild Brink Buus @terkild.bsky.social · Jun 19

❗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...

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.

2 8 19

Nick Borcherding @thehumanborch.bsky.social · Apr 20

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...

1 9

Nick Borcherding @thehumanborch.bsky.social · Feb 15

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

1 10

Nick Borcherding @thehumanborch.bsky.social · Jan 15

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

www.mdpi.com

1 3

Reposted by Nick Borcherding

mheming.bsky.social @mheming.bsky.social · Jan 10

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 · Jan 10

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

NEWS

cran.r-project.org

1 5 9

Nick Borcherding @thehumanborch.bsky.social · Jan 1

Awesome! Please thank Ksenia for all her help!!

1

Nick Borcherding @thehumanborch.bsky.social · Dec 31

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

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.

github.com

2

Nick Borcherding @thehumanborch.bsky.social · Dec 31

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

2 13 46

Reposted by Nick Borcherding

Edward Nirenberg @enirenberg.bsky.social · Dec 20

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...

www.science.org

10 70 240

Reposted by Nick Borcherding

Carolyn Bertozzi @carolynbertozzi.bskyverified.social · Dec 19

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

www.businesswire.com

2 9 64

Reposted by Nick Borcherding

Jasmine Rowell, PhD @jasminerowell.bsky.social · Dec 6

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

2 6 23

Nick Borcherding @thehumanborch.bsky.social · Dec 7

totally second R for Data Science!

1

Nick Borcherding @thehumanborch.bsky.social · Dec 7

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.

1 4

Reposted by Nick Borcherding

Rita Strack @ritastrack.bsky.social · Dec 6

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.

www.nature.com

3 170 620

Reposted by Nick Borcherding

Pieter Meysman @pmeysman.bsky.social · Dec 2

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

5 16 49

Reposted by Nick Borcherding

Waggoner Lab @labwaggoner.bsky.social · Nov 28

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

8 24