We (me and @benjamingvincent.bsky.social) naively assumed that heavy isotope labeled peptide synthesis for targeted MS was a solved problem. Wish I had read more before ordering so many contaminated peptides: pubmed.ncbi.nlm.nih.gov/35119480/

Listening to Shelley Earp reflect on his overall experience as a scientist following several Nobel Laureates and inspiring scientists speak about how he impacted their career. I don’t care about accolades: this is the type of legacy I aspire to have, to have uplifted so many 🤩🪜

This is a cool story that I've watched with great interest - making big steps in the field of de novo TCR generation! Great work @dkarthikey1.bsky.social / @benjamingvincent.bsky.social / @alexr.bsky.social et al

When @benjamingvincent.bsky.social and I started PIRL one of our hypotheses was that neoantigen vaccines mostly don’t work bc SNVs create low value (self-like) targets. What other mutational antigens could we use instead? @jslee.bsky.social been working on making those legible…

It’s time: @benjamingvincent.bsky.social and I are going to do a cancer immunotherapy / cool research / accelerating future medicine podcast. Any tips for getting started?

After next round of the bake-off, going to pivot to tumor antigens (once we get some mass spec validation of which ones are real). For now, read the blog post by @benjamingvincent.bsky.social: pirlblog.substack.com/p/an-experim...

Are we on the cusp of curing cancer w/ mRNA vaccines? …not quite. “…predicted tumor antigens are not actually presented by tumor…antigens included in personalized tumor vaccines are minimally immunogenic” @benjamingvincent.bsky.social lays out a path forward open.substack.com/pub/pirlblog...

(x-post from the bad place) I'm going to keep talking about this idea until @benjamingvincent.bsky.social & I do it or someone else successfully does it for us (it just needs to exist): Many cancers express reproductive proteins (aka "cancer/testis antigens"), often at very high levels 1/n

It may be a #NewYear, but our resolution remains the same: through our fiercely patient-centric approach, we are still working tirelessly to create greatly needed research infrastructure to improve the outcomes and care for #RareCancer patients. 💙💚

NEW PREPRINT A detailed overview of 32 popular predictive performance metrics for prediction models arxiv.org/abs/2412.10288

I still think about this at least once a week.

“NIH produces an astounding return on investment to the American taxpayer. In Fiscal Year 2022, NIH research funding supported 568,585 jobs and generated $96.84 billion in economic activity — that’s $2.64 of economic activity for every $1 of research funding.” www.researchamerica.org/2023-oped-us...

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...

Your periodic reminder: read the 8th Day of Creation "The basic principles of the genetic code & the molecular biology of prokaryotes were established in the years between (1953 & 1973) as documented in extraordinary detail in 1979 by Horace Freeland Judson in the “Eighth Day of Creation”

Such an interesting read from @math-rachel.bsky.social who has a remarkable gift for making complex topics (like AI ∩ immunology) accessible as well as engaging -> rachel.fast.ai/posts/2024-0... #biosky #medsky

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

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!

Is Discover feed the best default?

Your regular reminder that we, your professors, LOVE IT when you email us after the fact to let us know what you're up to. Truly one of the most gratifying parts of this work.

I can talk to them if they're interested, but essentially you have to learn a bunch of biology and ideally get deep into assay details to become a useful critical thinker

A real moonshot project in biomedical research would be a decisive legal, regulatory and IT effort to really make data access work for researchers across the world. It's not as sexy as AI, CRISPR, or ginormous sequencing projects, but more transformative and better bang for the buck.

I am very excited about guest editing a special issue in Genome Research (@genomeresearch.bsky.social ) about long reads DNA Sequencing Applications with Ana Conesa & Alexander Hoischen. This is such a timely and fast moving topic about all its applications, innovations etc. bit.ly/grcallforpap...

Huge team effort by a bunch of different people in PIRL to finish a large mouse vaccine experiment, hopefully now we get to learn something about how mRNA compares with different peptide + adjuvant vaccines.

Welcome to our Bluesky account! Follow us to see updates on what’s latest in #massspec and the accomplishments of the Baker lab! 🧪

Trainees - This is a reminder that your PIs want to see ALL the data. We want to see the experiments that "worked" and the experiments that "didn't work". You can learn a lot from results that do not fit your hypothesis. Resist the urge to curate what you show your advisor. 🧪

Excited to share the news of my appointment to associate prof with tenure @uncbiostat! Milestones like this don’t happen alone, and are made possible by amazing mentors, colleagues, collaborators, students, and especially family Thank you for everything, and for believing in me

It has begun.

Katalin Karikó on the status economy of academia. She’s the hero we don’t deserve. Source: josephnoelwalker.com/147-katalin-...

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...

Every couple of years I try to figure out how simple it would be to self-host a Zotero database on my home server, and the answer is always 'not very'. Anyone got any simpler ideas for hosting a database of papers (PDFs + metadata, optional annotations/notes) for working with on multiple devices/OS?

As probably one of the few NIH researchers on here, I feel obligated to note that a US federal govt shutdown will also impact the approx 1500 clinical trials being conducted at the NIH, including those against cancer, Alzheimer's, and many other diseases. Hopefully it is averted. 🩺🦠🔬🧪

IMHO, this is amazing Protein sequencing using nanopore-based strategy 🧶🧬 www.nature.com/articles/s41...

I am a biologist researching rove beetles at Uni Hamburg. My bread job is writer of fiction and non fiction books, but I went back to university as side hustle because I missed science so much 😅. And I also illustrate my books! (And I am a passionate gamer 🎮) 👋👋👋

Plasma cells in human pancreatic ductal adenocarcinoma secrete antibodies to self-antigens

#HiSciSky! I'm in the 5th year of my PhD looking at the immunological consequences of radiotherapy using mathematical oncology 👩‍💻☢️ Starting to look for #postdocs in #mathonco if you know anyone who's hiring!

I have a great target (NUTM1), luciferase expressing NUTM1 onco-fusion cell lines, and have identified areas of NUTM1 shared between isoforms & fusion breakpoints but not shared with any paralogs. So...how do I actually design ASOs (antisense oligos) to target these regions?

There's a Genomics/Bioinformatics feed available now thanks to @afreeparticle.com! Thank you!!! To post, you need to: 1/be an approved What's Science 🧪 poster (ask @danirabaiotti.bsky.social) 2/Use 🖥️🧬 in your post.

Engagement dropped a lot on the doomed birdsite. So trying my luck here. I'm looking for a quite exhaustive list of seminal papers introducing the de Bruijn graph in Bioinformatics (dating back to SGS assembly I believe)/resources such as books on bioinformatics history during this period. Anybody?

Come join us! UNC Biostatistics is one of the top bios depts in the country, with amazing students and a stellar research environment. You will also be a part of high profile and impactful work at the top ranked Department of Genetics This position will remain open until filled

Brings me back to my favorite drum to bang: we🥁need🥁more🥁data! In terms of high confidence TCR:pMHC interactions we have ~100-1000s of viral peptides, and dozens-100s of cancer peptides (depending on how you slice it). Almost all HLA-A2. We've barely dipped our toes in the interaction space.

(5) What is the precursor frequency of Tc with this TCR? (6) Will Tc with this TCR be shut down by peripheral tolerance? (7) What will be the function of Tc with this TCR (upon antigen stimulation)? (8) How will the presence of Tc with this TCR affect function of Tc with that TCR?

Unidirectional transport of native proteins through an engineered #nanopore! Giovanni Maglia and colleagues use fixed charges to engineer a strong electroosmotic flow to thread and stretch proteins across a nanopore. Out now in NatureBiotech doi.org/10.1038/s415... 🧪🧬🖥️

Please spread the word! UNC biostatistics and UNC Genetics are recruiting a tenure-track assistant professor to engage in statistical genetics/genomics methodological and collaborative research Apply here: unc.peopleadmin.com/postings/265... Details below

PIRL mission: Figuring out how to target the right antigens, with the right therapies, at the right time.

Thank you @alexr.bsky.social for making an #immunosky feed! I've been wanting to connect with the Immunologists on here!!!

Kierkegaard was a poster