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 short—any way to lower the length limit or workaround?

Which output is on when both switches are open? And can you guess why ChatGPT's 03 reinforcement learning model got this wrong initially? #reinforcementlearning #ai

"We are speaking on behalf of hundreds of NIH staff who are standing up together to say: WE DISSENT.

I am so scared about doing this but I am trying to be brave for my kids because it's only gonna get harder to speak up."

Thank you to Dr. Jenna Norton and NIH scientists for your courage!

At Posit, we love @typst.app:

⚡ Make PDFs in milliseconds, not minutes
✨ The power of LaTeX with today's technologies
✍️ Modern typography (including emojis!)
🧠 Clear mental model

So I'm thrilled to announce that we're now supporting its development: posit.co/blog/posit-a...

#rstats

I've been developing a semantic search tool that covers not just bioRxiv and medRxiv, but the entire PubMed database. This means you can search across a massive collection of biomedical research using keywords, questions, hypotheses, or even full abstracts. Try it out: mssearch.xyz

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

The measles vaccine is given as a shot but it is surprisingly good at inducing protective immunity in the respiratory tract (mucosal IgA). Our new study provides some clues about why...a thread (1/8) #IDSky #MedSky #lungs #immunology #ImmunoSky academic.oup.com/jid/advance-...

Best #Nikolaus 🎅! Our paper on how the 🫁 microenvironment can shape #innate immunity against #viruses is out @sciimmunology.bsky.social This was a herculean effort brilliantly led by @pauljbaker.bsky.social who singlehandedly established the model in the lab during the pandemic. 🧪 #Immunosky 1/9

Parse Bio GigaLab and Vevo Therapeutics Tahoe-100 experiment open.substack.com/pub/albertvi...

Re-pinging for new arrivals: here's a starter pack of researchers who work on variable immune receptors: let's all have nice repertoire chats together.

go.bsky.app/Gi2dcGd

Prioritized mass spec data acquisition increases proteomic data completeness & coverage depth.

The increase is largest for the most challenging proteins.

When using TMTpro, data completeness reaches 93% for all proteins across multiple sets.

nature.com/articles/s41...

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...

Nice paper using an inverse covariance / partial correlation network analysis with graphical Lasso to identify direct associations with an outcome variable.

Hello, world! We don’t routinely measure the immune system in the clinical laboratory. I’m working to make immune-based clinical tests a cornerstone of treatment selection, prognostication, and strategies to reprogram immunity across immune-mediated disease. Snapshot of my past work so far:

New in #ScienceImmunology:

Research from @boztugk.bsky.social and team identifies an inborn error of #immunity caused by human LTβR deficiency, resulting in defective stromal cell signaling and impaired humoral immune responses.

Read more: www.science.org/doi/10.1126/...

Anyone knows a good set of validated T-cell epitopes? Meaning epitopes that definitely showed a good T-cell response.

I've used IEDB in the past but maybe there are other valuable resources?

#Immunosky

Curious about what a blood sample can reveal about humoral immunity? Our latest work combined sequencing methods and mass spectrometry to explore BCR and antibody repertoires and assess their synergistic potential. www.biorxiv.org/content/10.1...

I created a starter pack for systems immunology - let me know if you would like to be added. Excited to be here on
@bsky.app

go.bsky.app/PjH2Fuj