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Benjamin Vincent

@benjamingvincent.bsky.social
164 followers 98 following 20 posts

PIRL Co-PI (pirl.unc.edu). Trying to figure out adaptive immunity to cancer, at least enough to develop better immunotherapies.

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Reposted by Benjamin Vincent
Alex Rubinsteyn @alexr.bsky.social · 25/09/2025
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/
pubmed.ncbi.nlm.nih.gov
Light contamination in stable isotope-labelled internal peptide standards is frequent and a potential source of false discovery and quantitation error in proteomics - PubMed
In mass spectrometry-based proteomics, heavy internal standards are used to validate target peptide detections and to calibrate peptide quantitation. Here, we report light contamination present in hea...
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Chrystal Starbird @drstarbird.bsky.social · 10/09/2025
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 🤩🪜
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Jamie Heather @jamieheather.bsky.social · 08/09/2025
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
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Alex Rubinsteyn @alexr.bsky.social · 23/06/2025
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…
pirlblog.substack.com
A Unifying Grammar for DNA Variants
A unified framework and toolkit for standardizing DNA variants at scale. Part 1 of the neoantigen discovery with long-read sequencing series.
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Alex Rubinsteyn @alexr.bsky.social · 17/05/2025
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?
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Alex Rubinsteyn @alexr.bsky.social · 16/05/2025
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...
pirlblog.substack.com
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Alex Rubinsteyn @alexr.bsky.social · 04/05/2025
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...
open.substack.com
Three Axes of Innovation in Personalized Cancer Vaccines
The personalized cancer vaccine field had its first true clinical success with the KEYNOTE-942 study, where patients with resected melanoma were treated with Merck’s PD-1 inhibitor pembrolizumab (Keyt...
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Alex Rubinsteyn @alexr.bsky.social · 30/04/2025
(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
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Rare Cancer Research Foundation + Pattern.org @rarecancerrf.bsky.social · 03/01/2025
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. 💙💚
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Maarten van Smeden @maartenvsmeden.bsky.social · 16/12/2024
NEW PREPRINT A detailed overview of 32 popular predictive performance metrics for prediction models arxiv.org/abs/2412.10288
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Daniel Probst @skepteis.bsky.social · 08/12/2024
I still think about this at least once a week.
A tweet:

Alex Blechman @AlexBlechman

Sci-Fi Author: In my book I invented the Torment Nexus as a cautionary tale

Tech Company: At long last, we have created the Torment Nexus from classic sci-fi novel Don't Create The Torment Nexus

5:49 PM Nov 8, 2021 Twitter Web App
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Prasad Jallepalli, MD, PhD @prasad.bsky.social · 01/12/2024
“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...
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Pieter Meysman @pmeysman.bsky.social · 02/12/2024
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...
doi.org
T cell receptor–centric perspective to multimodal single-cell data analysis
T cell receptor–centric perspective improves single-cell analysis.
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Reader of Banned Books @readerofbannedbook.bsky.social · 26/11/2024
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Thiago Carvalho @cyrilpedia.bsky.social · 24/11/2024
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”
cell.com
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David Shaywitz @dshaywitz.bsky.social · 20/11/2024
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
rachel.fast.ai
Rachel Thomas, PhD - AI’s Quest to Predict T Cell Binding– The Holy Grail of Immunology
an AI researcher going back to school for immunology
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Dhuvi Karthikeyan @dkarthikey1.bsky.social · 19/11/2024
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
meme paper summary showing a fork in the road for the tcr:pmhc specificity problem: 1. pointing to binary classification 2. pointing towards gen AI
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Jamie Heather @jamieheather.bsky.social · 18/11/2024
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!
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Alex Rubinsteyn @alexr.bsky.social · 15/11/2024
Is Discover feed the best default?
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Holden Thorp @holdenthorp.bsky.social · 18/12/2023
Eric Montross was the best of the best. So sorry for his family and us all. Love to all Tar Heels.
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Alex Rubinsteyn @alexr.bsky.social · 05/12/2023
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
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Tuuli Lappalainen @tuuliel.bsky.social · 27/11/2023
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.
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Fritz Sedlazeck @sedlazeck.bsky.social · 06/11/2023
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...
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Alex Rubinsteyn @alexr.bsky.social · 27/10/2023
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.
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Baker Lab UNC @bakerlabms.bsky.social · 11/10/2023
Welcome to our Bluesky account! Follow us to see updates on what’s latest in #massspec and the accomplishments of the Baker lab! 🧪
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Stacey Ogden 🦔 @labogden.bsky.social · 09/10/2023
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. 🧪
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Naim Rashid @naimurashid.bsky.social · 05/10/2023
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
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Alex Rubinsteyn @alexr.bsky.social · 03/10/2023
It has begun.
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Per Engzell @pengzell.bsky.social · 03/10/2023
Katalin Karikó on the status economy of academia. She’s the hero we don’t deserve. Source: josephnoelwalker.com/147-katalin-...
There is a “centre” where the money, the fame, is; most likely your proposal gets funded because it’s on the most favourable topic. Maybe today, RNA is [most favourable]. If you are working with mRNA, maybe that's the centre there.

And then there are people in the periphery. There is no fame, there is no money, no nothing there. The only thing in the periphery is freedom. You can do what you like to do, what you feel is important.

Here’s what a proposal is: why they should give me money. And they should question that. “She came from university nobody knew about.” “She never had a mentor who was famous.”

And somehow it gravitates always to the same people, same circle. They get published there, they get the money. And that's another explanation: I was not famous enough or didn't have anybody who would support me in a way that somebody that’s a famous and well-established scientist stands behind you and says, “Oh, look at this, it’s good.”
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Nick Borcherding @thehumanborch.bsky.social · 03/10/2023
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...
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Jamie Heather @jamieheather.bsky.social · 30/09/2023
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?
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Sri Krishna (Krish) @tellkrish.bsky.social · 29/09/2023
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. 🩺🦠🔬🧪
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Alexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 28/09/2023
IMHO, this is amazing Protein sequencing using nanopore-based strategy 🧶🧬 www.nature.com/articles/s41...
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👾Jasmin Schreiber @tiredmegafauna.com · 26/09/2023
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 🎮) 👋👋👋
Me with a beetle on my hand (Phyllopertha horticola)A rove beetle under the microscopeSelfie: me and a beeMe drawing a fox
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kevin @kevinng.bsky.social · 27/09/2023
Plasma cells in human pancreatic ductal adenocarcinoma secrete antibodies to self-antigens
insight.jci.org
JCI Insight - Plasma cells in human pancreatic ductal adenocarcinoma secrete antibodies to self-ant...
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Rebecca Bekker @rebeccabekker.bsky.social · 23/09/2023
#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!
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Alex Rubinsteyn @alexr.bsky.social · 23/09/2023
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?
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Michael Hoffman @michaelhoffman.bsky.social · 22/09/2023
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.
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Camille Marchet ⚡ @camillemrcht.bsky.social · 21/09/2023
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?
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Naim Rashid @naimurashid.bsky.social · 18/09/2023
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
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Jamie Heather @jamieheather.bsky.social · 19/09/2023
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.
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Benjamin Vincent @benjamingvincent.bsky.social · 19/09/2023
(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?
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GenomeTDCC @genometdcc.org · 19/09/2023
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... 🧪🧬🖥️
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Naim Rashid @naimurashid.bsky.social · 18/09/2023
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
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Benjamin Vincent @benjamingvincent.bsky.social · 18/09/2023
PIRL mission: Figuring out how to target the right antigens, with the right therapies, at the right time.
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Michal Caspi Tal, PhD @immunofever.bsky.social · 16/09/2023
Thank you @alexr.bsky.social for making an #immunosky feed! I've been wanting to connect with the Immunologists on here!!!
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Garth Marenghi's Catbus @catbus.phd · 16/09/2023
Kierkegaard was a poster
excerpt from Kierkegaard's diary reading 

LIFE MOOD

i have just returned from a party of which I was the life and soul; witty banter flowed from my lips, everyone laughed and admired me-- but I came away, indeed that dash should be as long as the radii of the earth's orbit -----------------------------wanting to shoot myself.
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