Benjamin Vincent
@benjamingvincent.bsky.social
PIRL Co-PI (https://pirl.unc.edu/). Trying to figure out adaptive immunity to cancer, at least enough to develop better immunotherapies.
Reposted by Benjamin Vincent
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/35119480/
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...
pubmed.ncbi.nlm.nih.gov
September 25, 2025 at 1:17 AM
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/35119480/
Reposted by Benjamin Vincent
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 🤩🪜
I don’t care about accolades: this is the type of legacy I aspire to have, to have uplifted so many 🤩🪜
September 10, 2025 at 4:43 PM
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 🤩🪜
I don’t care about accolades: this is the type of legacy I aspire to have, to have uplifted so many 🤩🪜
Reposted by Benjamin Vincent
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
Conditional generation of real antigen-specific T cell receptor sequences @natmachintell.nature.com
www.nature.com/articles/s42...
www.nature.com/articles/s42...
September 8, 2025 at 8:17 PM
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
Reposted by Benjamin Vincent
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…
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.
pirlblog.substack.com
June 23, 2025 at 2:18 PM
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…
Reposted by Benjamin Vincent
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?
Any tips for getting started?
May 17, 2025 at 4:12 PM
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?
Any tips for getting started?
Reposted by Benjamin Vincent
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...
For now, read the blog post by @benjamingvincent.bsky.social: pirlblog.substack.com/p/an-experim...
pirlblog.substack.com
May 16, 2025 at 2:50 PM
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...
For now, read the blog post by @benjamingvincent.bsky.social: pirlblog.substack.com/p/an-experim...
Reposted by Benjamin Vincent
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...
“…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...
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...
open.substack.com
May 4, 2025 at 12:31 AM
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...
“…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...
Reposted by Benjamin Vincent
(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
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
April 30, 2025 at 1:55 AM
(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
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
Reposted by Benjamin Vincent
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. 💙💚
January 3, 2025 at 3:00 PM
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. 💙💚
Reposted by Benjamin Vincent
NEW PREPRINT
A detailed overview of 32 popular predictive performance metrics for prediction models
arxiv.org/abs/2412.10288
A detailed overview of 32 popular predictive performance metrics for prediction models
arxiv.org/abs/2412.10288
December 16, 2024 at 8:44 AM
NEW PREPRINT
A detailed overview of 32 popular predictive performance metrics for prediction models
arxiv.org/abs/2412.10288
A detailed overview of 32 popular predictive performance metrics for prediction models
arxiv.org/abs/2412.10288
Reposted by Benjamin Vincent
I still think about this at least once a week.
December 8, 2024 at 3:14 PM
I still think about this at least once a week.
Reposted by Benjamin Vincent
“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...
www.researchamerica.org/2023-oped-us...
Research supported by NIH has led more than 100 Nobel Prizes and has supported more than 99% of drugs approved by federal regulators from 2010 to 2019.
But come January, NIH may face a wrecking ball
nytimes.com/2024/12/01/h...
But come January, NIH may face a wrecking ball
nytimes.com/2024/12/01/h...
Long a ‘Crown Jewel’ of Government, N.I.H. Is Now a Target
nytimes.com
December 1, 2024 at 11:58 PM
“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...
www.researchamerica.org/2023-oped-us...
Reposted by Benjamin Vincent
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...
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
December 2, 2024 at 8:30 AM
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...
Supported by @cziscience.bsky.social !
doi.org/10.1126/scia...
Reposted by Benjamin Vincent
Reposted by Benjamin Vincent
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”
"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”
https://www.cell.com/cell/fulltext/S0092-8674%2824%2901219-4"
November 24, 2024 at 6:29 AM
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”
"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”
Reposted by Benjamin Vincent
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 Thomas, PhD - AI’s Quest to Predict T Cell Binding– The Holy Grail of Immunology
an AI researcher going back to school for immunology
rachel.fast.ai
November 20, 2024 at 1:39 AM
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
Reposted by Benjamin Vincent
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
💻🧬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
November 19, 2024 at 6:54 PM
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
💻🧬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
Reposted by Benjamin Vincent
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!
go.bsky.app/Gi2dcGd
Drop me a beep to get added or suggest others!
November 18, 2024 at 5:21 AM
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!
go.bsky.app/Gi2dcGd
Drop me a beep to get added or suggest others!
Reposted by Benjamin Vincent
Is Discover feed the best default?
November 15, 2024 at 3:10 PM
Is Discover feed the best default?
Reposted by Benjamin Vincent
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.
December 9, 2023 at 4:15 AM
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.
Reposted by Benjamin Vincent
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
December 5, 2023 at 3:35 PM
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
Reposted by Benjamin Vincent
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.
November 27, 2023 at 1:51 PM
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.
Reposted by Benjamin Vincent
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...
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...
November 6, 2023 at 2:26 PM
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...
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...