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@nipagh

Ph.d. in immunolgy. T cells, tetramers, DNA barcodes, Espresso Martini, and the Tank/Healer in my local DnD group. πŸ‡©πŸ‡°πŸ³οΈβ€πŸŒˆ.

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17.11.2024
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Latest posts by @nipagh

This is one of the most interesting developments as it appears that authors are now submitting preprints earlier in the process.

A reminder that our data suggests that the best time to post is approx 1 month prior to journal submission (which ~30% now are).

27.02.2026 14:31 πŸ‘ 5 πŸ” 3 πŸ’¬ 0 πŸ“Œ 0
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Metabolic quiescence of naive-like memory T cells precedes and maintains antigen-specific T cell memory @natimmunol.nature.com
www.nature.com/articles/s41...

24.02.2026 16:55 πŸ‘ 10 πŸ” 3 πŸ’¬ 1 πŸ“Œ 0
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What is the question? - Genome Biology Genome Biology -

A great read! link.springer.com/article/10.1...

24.01.2026 09:30 πŸ‘ 12 πŸ” 5 πŸ’¬ 1 πŸ“Œ 1

Whenever I feel bad about being responsible for wasting money on failed wet lab experiments I think about the collective failure from Novo Nordisk to pay 250 Canadian dollars to protect a key patent. I hope there's more to the story than that, honestly.

05.01.2026 16:39 πŸ‘ 1 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0
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Novo Nordisk's Canadian Mistake

πŸ’€wtf!?
""
.. the last time they paid the annual maintenance fee on it was 2018! You can even find a letter where their lawyers send a refund request for the 2017 maintenance fee ($250) because Novo apparently wanted some more time to see if they wanted to pay it...
""
www.science.org/content/blog...

05.01.2026 16:30 πŸ‘ 0 πŸ” 0 πŸ’¬ 1 πŸ“Œ 0

It's a good question whether there is HLA dependence or not for this effect in the live vaccine. But if a similar effect exists for the recombinant vaccine using glycoprotein E only, doesn't that decrease the likelihood of seeing HLA dependence? Or maybe I'm too pessimistic πŸ˜…

30.12.2025 18:12 πŸ‘ 1 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0
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.@slavov-n.bsky.social on cell size vs cell count in the human body.
Lots of white blood cells in number, lots of adipocytes (fat) in volume.

17.12.2025 16:07 πŸ‘ 7 πŸ” 1 πŸ’¬ 1 πŸ“Œ 0
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Heterogeneity of the intestinal mononuclear phagocyte compartment in health and inflammatory bowel disease Single-cell transcriptomics resolves mononuclear phagocyte diversity in the human intestine in health and inflammatory bowel disease.

Single-cell transcriptomics resolves mononuclear phagocyte diversity in the human intestine in health and inflammatory bowel disease @sciimmunology.bsky.social
www.science.org/doi/10.1126/...

12.12.2025 20:24 πŸ‘ 6 πŸ” 4 πŸ’¬ 0 πŸ“Œ 0
JCI - T-cell acute lymphoblastic leukemia exploits a neural proinflammatory pathway to colonize the meninges

Our fresh and still-steaming Journal of Clinical Investigation preprint is out! πŸš€
We explore how T-cell acute lymphoblastic leukemia (T-ALL) exploits inflammatory CXCR3–CXCL10 signaling within the meninges to drive CNS infiltration.

www.jci.org/articles/vie...

24.10.2025 04:24 πŸ‘ 9 πŸ” 3 πŸ’¬ 1 πŸ“Œ 0

I agree!

04.12.2025 17:46 πŸ‘ 1 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

Oh, I absolutely share your opinion. It sometimes feels as though people know the answer before asking the question. Though it's constructed as multiple rounds of cost/risk analysis yielding the sentiment that "hey, if we find nothing, it's a resource to others".

04.12.2025 17:45 πŸ‘ 1 πŸ” 0 πŸ’¬ 1 πŸ“Œ 0

πŸ˜… but I admit that I'm probably super biased here from studying for the PhD at an engineering department, where I was the applicationist (is that a word?). I'm traumatized by the responsibility of proving the applicability of a method haha.

04.12.2025 17:24 πŸ‘ 1 πŸ” 0 πŸ’¬ 1 πŸ“Œ 0

Idk, maybe there's a young doctor that will use a method created by a physicist and go on to win the Nobel prize! This was the case for Jens Skou, if I get his speech. www.nobelprize.org/uploads/2018...

I don't see biologists or computational folks generating an abundance of tools as a bad thing.

04.12.2025 17:04 πŸ‘ 0 πŸ” 0 πŸ’¬ 1 πŸ“Œ 0

But it could also be collective delusion for all I know πŸ™ˆ

04.12.2025 15:51 πŸ‘ 1 πŸ” 0 πŸ’¬ 1 πŸ“Œ 0

If every single field in academia is fundamentally a pyramid scheme with the most renowned individuals at the top. Proposing a method seems more likely to generate a new field, in my opinion, compared to proposing an interesting application using a method others are already experts on.

04.12.2025 15:38 πŸ‘ 1 πŸ” 0 πŸ’¬ 1 πŸ“Œ 0
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A microenvironment-driven HLA-II-associated insulin neoantigen elicits persistent memory T cell activation in diabetes - Nature Immunology The authors identify a Cysβ†’Ser transformation (C19S) in insulin leading to neoepitope presentation and CD4⁺ T cell autoreactivity in type 1 diabetes. Inflammation and oxidative stress enhanced C19S tr...

A very interesting read. I wonder how one could replicate this in other autoimmune disorders. www.nature.com/articles/s41...

29.11.2025 10:42 πŸ‘ 3 πŸ” 1 πŸ’¬ 0 πŸ“Œ 0
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Deep profiling of human T cells defines compartmentalized clones and phenotypic trajectories across blood and tonsils Human T cell responses are often studied using blood, yet most T cells reside in tissues. By comparing T cell receptor repertoires from millions of T cells from autologous tonsils and blood, Sureshcha...

We are #absolutely #thrilled to #present @cp-immunity.bsky.social - Deep profiling of human T cells defines compartmentalized clones and phenotypic trajectories across blood and tonsils: Immunity www.cell.com/immunity/ful...

26.11.2025 15:47 πŸ‘ 17 πŸ” 11 πŸ’¬ 1 πŸ“Œ 1
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Tumour-reactive heterotypic CD8 T cell clusters from clinical samples - Nature Tumour-reactive CD8+ T cells are enriched in functional clusters with tumour cells and/or antigen-presenting cells and can be isolated and expanded from clinical samples.

Our new paper is out in Nature - online today!
Huge congrats to shared first authors Sofía IbÑñez-Molero & Johanna Veldman, the whole team & all collaborators.
πŸ“„ Open-access paper: www.nature.com/articles/s41...

19.11.2025 21:00 πŸ‘ 21 πŸ” 8 πŸ’¬ 2 πŸ“Œ 0

Super interesting how conflated the ABC and DN nomenclatures are in B cell biology. Wouldn't it make sense to pick a different acronym for age-associated B cells, and atypical B cells? And "atypical" seems risky to use as models in immunology can become outdated as paradigms shift, no?

16.11.2025 08:57 πŸ‘ 1 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0
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A roadmap for defining β€œextrafollicular” B cell responses The term β€œextrafollicular” is now being used expansively to describe a variety of B cell processes beyond the original use of the term, potentially obscuring important distinct immunological processes...

Sunday reading. I aspire to write something like this for T cells one day. www.cell.com/immunity/ful...

16.11.2025 08:53 πŸ‘ 2 πŸ” 0 πŸ’¬ 1 πŸ“Œ 0
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Epstein-Barr virus–mediated B cell reprogramming may initiate systemic lupus erythematosus
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/... @stanfordmedicine.bsky.social @shady-myounis.bsky.social

12.11.2025 23:21 πŸ‘ 25 πŸ” 5 πŸ’¬ 0 πŸ“Œ 1

Dear single-cell bluesky community: We’re running Cell Ranger (5’ scRNA-seq) on sorted human CD8+ T cells with a custom library. Custom seqs (27–133 bp) appear in FASTQs + BAM but aren’t mapped. They are filtered out by STAR for being too shortβ€”any way to lower the length limit or workaround?

03.11.2025 10:16 πŸ‘ 2 πŸ” 2 πŸ’¬ 1 πŸ“Œ 0

Me as a PhD student:"I hate how useful this is".
Me as a Postdoc: "I LOVE HOW USEFUL THIS IS".

30.10.2025 11:34 πŸ‘ 0 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

Mapping of CD8 T-cell recognition to latent EBV infection and neuroantigens reveals HLA-specific depletion of T-cell responses in multiple sclerosis https://www.biorxiv.org/content/10.1101/2025.10.23.682742v1

24.10.2025 13:15 πŸ‘ 6 πŸ” 4 πŸ’¬ 0 πŸ“Œ 0
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If the immune system is an army...
...
would you rather rely on one β€œsuper warrior” β€” or on a diverse team of fighters, even if none of them is the single strongest?

I’d go with the team.

Why? Check out our new study, just published in Science Immunology: www.science.org/doi/10.1126/...

03.10.2025 18:07 πŸ‘ 73 πŸ” 21 πŸ’¬ 5 πŸ“Œ 1
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TCR activation impairs CAR-T cytotoxicity against separate target cells Chimeric antigen receptor T cells (CAR-T) are effective therapeutics against cancer and autoimmunity, but whether the endogenous T cell receptor (TCR) is beneficial, detrimental or irrelevant for CAR ...

When a T cell carries both its natural TCR and an engineered CAR, do these two receptors cooperate - or compete?

Our new preprint on bioRxiv shows that TCR activation can enhance CAR-T activation but impairs CAR-mediated killing when targets are on separate cells.

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

08.10.2025 06:05 πŸ‘ 12 πŸ” 5 πŸ’¬ 2 πŸ“Œ 0
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Sometimes, knocking out a gene isn't a good way to figure out the function of that gene ...

In our new @jcellsci.bsky.social paper, we report potent transcriptional adaptation by cytotoxic T lymphocytes (CTLs) in response to CRISPR/Cas9-mediated deletion of the important polarity protein CDC42 πŸ§΅β¬‡οΈ

04.08.2025 19:30 πŸ‘ 44 πŸ” 14 πŸ’¬ 2 πŸ“Œ 3

De novo identification of the specificities of recurrent human T cell receptors https://www.biorxiv.org/content/10.1101/2025.08.03.668342v1

05.08.2025 04:22 πŸ‘ 2 πŸ” 3 πŸ’¬ 0 πŸ“Œ 0
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Technical blogging for growth and learning Writing a technical blog improves your writing, forces you to learn new things, helps others and yourself, and helps your career. This post: why blog, what to blog about, how to start, and using AI.

Writing a technical blog improves your writing, forces you to learn new things, helps others and yourself, and helps your career. In this essay: (1) why blog, (2) what to blog about, (3) how to get started, and (4) using AI. https://doi.org/10.59350/bqnfd-7p249 πŸ§ͺ

25.01.2025 16:00 πŸ‘ 54 πŸ” 11 πŸ’¬ 2 πŸ“Œ 3

Double negative T cells can act as professional APCs capable of tolerance induction? How fascinating - I'm picturing a western stand-off between two T cells (both equipped with granzymes btw) unwilling to let go of the other!

02.08.2025 07:28 πŸ‘ 2 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0