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Paul Thomas

@pgtimmune.bsky.social
3.1K followers 630 following 97 posts

Division of Vaccine and Infectious Disease, Fred Hutchinson Cancer Center TCRs, influenza virus, anti-tumor immunity, books, dogs, Venice

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Paul Thomas @pgtimmune.bsky.social · 04/09/2026
TCR specificity prediction is advancing rapidly. The central question is not only which TCR sequence recognizes an antigen, but also which TCR pairings make recognition possible & where is the binding boundary? Our new paper tackles these questions. 🧵 www.science.org/doi/10.1126/...
science.org
Uneven TCR chain pairing constraints govern epitope recognition
Combinatorial pairing of independently recombined T cell receptor (TCR) α- and β-chains is central to diversifying the TCR repertoire. Although sequence motifs in one chain correlate with epitope reco...
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Fred Hutch @fredhutch.org · 03/09/2026
“We know both chains are critical for what the TCR sees,” said @pgtimmune.bsky.social, the senior author on new work in the journal @science.org that lays out some of the rules that govern the dance of the TCR chains. “But how much play do we have between the two chains?”
science.org
Uneven TCR chain pairing constraints govern epitope recognition
Combinatorial pairing of independently recombined T cell receptor (TCR) α- and β-chains is central to diversifying the TCR repertoire. Although sequence motifs in one chain correlate with epitope reco...
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Joe Sabatino @jsabatino37.bsky.social · 05/02/2026
Overjoyed to share our new work exploring the antigen specificity of CSF-expanded CD8+ T cells in #multiplesclerosis #EBV in @natimmunol.nature.com #immunology 🧪🧵1/ www.nature.com/articles/s41...
nature.com
Antigen specificity of clonally enriched CD8+ T cells in multiple sclerosis - Nature Immunology
Sabatino and colleagues examine expanded CD8+ T cell clonotypes from a small cohort of multiple sclerosis patients. They identified several cognate peptide epitopes that derive from Epstein–Barr virus...
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Paul Thomas @pgtimmune.bsky.social · 10/03/2026
Are you a fan of #fibroblasts? Do you think about the lung ECM in your quiet moments? Then join David Boyd & a panel discussion as he presents “Integrated Longitudinal Transcriptomic & Proteomic Analysis of the Murine Lung Response to Influenza A Virus" t.co/2IdbWJVNDQ
t.co
https://thoracic.zoom.us/webinar/register/WN_KiZv45vNRe6bpnnXXJG9nQ
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Harry Wallop @harrywallop.co.uk · 02/12/2025
Great culture can save lives. Literally. Amazing letter in today’s @thetimes.com about Tom Stoppard
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Mikhail Pogorelyy @pogorely.bsky.social · 25/11/2025
Excited to see our TIRTL-seq method published in Nature Methods www.nature.com/articles/s41...! Some updates after the revision: (1/4)
nature.com
TIRTL-seq: deep, quantitative and affordable paired TCR repertoire sequencing - Nature Methods
TIRTL-seq is a high-throughput method for paired T cell receptor sequencing at the cohort scale.
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Waggoner Lab @labwaggoner.bsky.social · 25/11/2025
A therapeutic peptide vaccine for fibrolamellar hepatocellular carcinoma @naturemedicine.bsky.social @markyarchoan.bsky.social @hopkinspress.bsky.social @pgtimmune.bsky.social @fredhutch.org @stjude.bsky.social www.nature.com/articles/s41...
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Waggoner Lab @labwaggoner.bsky.social · 25/11/2025
@natmethods.nature.com TIRTL-seq: deep, quantitative and affordable paired TCR repertoire sequencing www.nature.com/articles/s41... @pogorely.bsky.social @fredhutch.org @stjude.bsky.social @pgtimmune.bsky.social
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Sylvain Simon @sylvainsimon.bsky.social · 25/11/2025
We are hiring! We have a postdoc position opened @fredhutch.org to join our team to design next gen cellular therapies for cancer. Heavy focus on T cell signaling and understanding how synthetic receptors instruct T cells to fight cancer.
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Paul Thomas @pgtimmune.bsky.social · 24/11/2025
Two complementary studies from our group out today: a therapeutic peptide vaccine trial for fibrolamellar carcinoma (FLC) & TIRTL-Seq, our robust method for deep quantitative paired TCR sequencing a🧵w/ @markyarchoan.bsky.social & @pogorely.bsky.social www.nature.com/articles/s41...
nature.com
TIRTL-seq: deep, quantitative and affordable paired TCR repertoire sequencing - Nature Methods
TIRTL-seq is a high-throughput method for paired T cell receptor sequencing at the cohort scale.
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Armita Nourmohammad @thearmita.bsky.social · 16/10/2025
excited that this paper is finally out in @pnas.org : www.pnas.org/doi/10.1073/... Led by Gian Marco Visani (effort initiated by Michael Pun), fantastic collaboration with @pgtimmune.bsky.social @asya-minervina.bsky.social and Phil Bradley.
pnas.org
T cell receptor specificity landscape revealed through de novo peptide design | PNAS
T cells play a key role in adaptive immunity by mounting specific responses against diverse pathogens. Effective bindings between T cell receptors ...
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Paul Thomas @pgtimmune.bsky.social · 07/11/2025
After many rewarding years at @StJudeResearch surrounded by exceptional colleagues & groundbreaking science, I’m delighted to join @fredhutch to push boundaries in viral & cancer immunology. Grateful to St. Jude and looking forward to what’s next at FH! More here: www.fredhutch.org/en/news/cent...
fredhutch.org
Viral immunologist taps ‘incredible potential’ of immune system
New Fred Hutch Cancer Center viral immunologist Dr. Paul Thomas is working to turn the "incredible potential" of the immune system into real-life diagnostic and therapeutic applications. He studies ho...
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Fred Hutch @fredhutch.org · 07/11/2025
Viral immunologist @pgtimmune.bsky.social, who recently joined Fred Hutch's Vaccine and Infectious Diseases Division, aims to harness the "incredible potential" of the immune system to advance diagnostics, vaccines and cancer therapies. bit.ly/3WJVpos
bit.ly
Viral immunologist taps ‘incredible potential’ of immune system
New Fred Hutch Cancer Center viral immunologist Dr. Paul Thomas is working to turn the "incredible potential" of the immune system into real-life diagnostic and therapeutic applications. He studies ho...
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Paul Thomas @pgtimmune.bsky.social · 15/07/2025
How much of the TCR repertoire can we make sense of? Can your TCR and GEX data be put in the context of other conditions/tissues? How many varieties of T cells are in the repertoire zoo? All these questions (& more) addressed in our latest preprint: MetaCoNGA www.biorxiv.org/content/10.1... . a 🧵
biorxiv.org
Diverse modes of T cell receptor sequence convergence define unique functional and cellular phenotypes
Single-cell techniques allow concurrent study of gene activity and T cell receptor (TCR) sequences, identifying connections between TCR structure and cell traits. Expanding on our CoNGA software, we p...
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David M. Perry @lollardfish.bsky.social · 14/04/2025
For transporting us beyond Seas to be tried for pretended offences
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Thomas Ramey Watson, Ph.D. @thomasrameywatson.bsky.social · 28/03/2025
Now is a uniquely terrible time to cut funding for HIV www.motherjones.com/politics/202...
motherjones.com
Now is a uniquely terrible time to cut funding for HIV
New breakthrough drugs could eradicate AIDS. Why are we hobbling their distribution?
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Waggoner Lab @labwaggoner.bsky.social · 28/03/2025
Hematopoietic aging drives lung fibrosis and profibrotic macrophage influx, stalling their maturation via reduced Treg-derived IL-10 @sciimmunology.bsky.social @asmafarhat.bsky.social www.science.org/doi/10.1126/...
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Stacey Ogden 🦔 @labogden.bsky.social · 28/03/2025
Eric Skaar presented this week's hospital-wide Danny Thomas Lecture, and it was a spectacular talk! So far outside what I normally think about and my mind was blown 🤯 Such innovative use of imaging modalities! THIS is why it is important for all of us to attend talks outside our usual science lanes🧪
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smtflu.bsky.social @smtflu.bsky.social · 28/03/2025
A collaborative work resulting in an exciting paper on influenza B virus and the differential immunity elicited by the Vic and Yam lineages. Neuraminidase-specific antibodies drive differential cross-protection between contemporary FLUBV lineages | Science Advances www.science.org/doi/10.1126/...
science.org
Neuraminidase-specific antibodies drive differential cross-protection between contemporary FLUBV lineages
FLUBV Victoria infection elicits NA-specific antibodies that provide cross-lineage protection, possibly driving Yamagata decline.
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TRAstonDrs @castltrastondrs.medsky.network · 28/03/2025
#MedSky🧪 #IDsky #immunosky #publichealth Age-associated changes to the bone marrow impact immune regulation in the lungs, which promotes inflammation and #fibrosis after lung injury. @knapplab.bsky.social via @sciimmunology.bsky.social www.science.org/doi/10.1126/...
science.org
An aging bone marrow exacerbates lung fibrosis by fueling profibrotic macrophage persistence
Hematopoietic aging drives lung fibrosis and profibrotic macrophage influx, stalling their maturation via reduced Treg-derived IL-10.
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Caroline Bartman @cbartman.bsky.social · 27/03/2025
great thread on a great podcast!
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Mike Barnkob @mikebarnkob.bsky.social · 27/03/2025
Assessing CAR T cells cytotoxic capacity at the single-cell level can be tricky. Here we provide a method for encapsulating >500.000 single CAR T cells with single target cells in droplets together with reagents to examine killing using standard flow cytometry: app.jove.com/t/67657/drop...
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Adam Kucharski @adamjkucharski.bsky.social · 27/03/2025
I've got a new book extract in Wired! The book also has lots of stories about the history of controlled trials, case-control studies, cohort studies, confounding, causal inference and more - most of which I suspect you won't have heard before! You can order from: proof.kucharski.io
wired.com
How a Cup of Tea Laid the Foundations for Modern Statistical Analysis
Scientific experiments run today are based on research practices that evolved out of a British tea-tasting experiment in the 1920s.
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Jacek Debiec, MD, PhD, DPhil 🌎 🧠 @drjacekdebiec.bsky.social · 26/03/2025
"Nothing which was being done, no matter how stupid, no matter how many people knew and foretold the consequences, could be undone or prevented." - Hannah Arendt about Germany sliding to fascism in the 1920s and 30s.
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Q-Immuno lab at UCL @qimmuno.bsky.social · 27/03/2025
Two weeks to go for our London Quantitative Immunology day on April 10th! Last chance to submit abstracts for contributed talks is today 👉 qimmuno.com/ldnday/
qimmuno.com
LDNQImmuno · April 10th
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Waggoner Lab @labwaggoner.bsky.social · 27/03/2025
Long-term B cell memory emerges at uniform relative rates in the human immune response www.pnas.org/doi/10.1073/... @stephenquake.bsky.social
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Waggoner Lab @labwaggoner.bsky.social · 27/03/2025
Ectopic germinal centers in the nasal turbinates contribute to B cell immunity to intranasal viral infection and vaccination @angelettilab.bsky.social www.pnas.org/doi/10.1073/...
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WIRED @wired.com · 27/03/2025
Modern science wouldn’t exist without the online research repository known as arXiv. Three decades in, its creator still can’t let it go.
wrd.cm
Inside arXiv—the Most Transformative Platform in All of Science
Modern science wouldn’t exist without the online research repository known as arXiv. Three decades in, its creator still can’t let it go.
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Ryan Flynn @raflynn5.bsky.social · 26/03/2025
A nearly 9 year effort to design and implement new CLIP-based technologies to define multimeric protein assemblies on RNA. Enables ‘watching’ of RNP assemblies inside living cells Special congrats to Luca Ducoli, Brian Zarnegar, and Paul Khavari @nature.com www.nature.com/articles/s41...
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Aaron Reichlin-Melnick @reichlinmelnick.bsky.social · 26/03/2025
NEW: @motherjones.com reports that one of the men renditioned to El Salvador is Neri Alvarado, who was working in Dallas as a baker. An ICE agent told him they were questioning all men with tattoos. Neri has an AUTISM AWARENESS TATTOO in honor of his 15-year-old brother with autism.
A picture of Neri Alvarado, a young man, standing next to his brother, who is a young teenager. Both are smiling for the camera and wearing matching shirts. Neri has his arm around his brother.A picture of Neri's tattoo, which is an autism ribbon in rainbow colors with his brother's name "Neryelson" written on it.
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karanormal activity 💜 @deadontheoutside.bsky.social · 26/03/2025
it's propagander
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Jake Yeston @jakeyeston.bsky.social · 10/03/2025
Part of what’s good about this piece of writing is the clarity of thought, which is deceptively hard to achieve even when the language is otherwise stylistically impressive. Kevin was above all a clear thinker in an extraordinarily broad range of subjects. Even in disagreement he was worth reading.
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Armita Nourmohammad @thearmita.bsky.social · 04/03/2025
check out our new manuscript (led by Gian Marco Visani): structure-based machine learning model for TCR-pMHC complexes, predicting T-cell affinity to peptide-MHC complexes, quantifying T-cell receptor specificity, and designing de-novo immunogenic peptides: arxiv.org/abs/2503.00648
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samuel mehr @mehr.nz · 21/02/2025
I chatted with a program director at NIH for a half hour just now It's clear that the people who make American science happen are doing everything they can to keep making it happen in a very difficult environment They deserve our respect and gratitude
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Nicole La Gruta @niclag.bsky.social · 21/02/2025
Please enjoy our paper showing that Lck- coreceptor association is important for repertoire diversity and lineage fidelity in T cells ☺️
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Jeremy Berg @jeremymberg.bsky.social · 21/02/2025
I agree. It seems extremely unlikely that they are trying to get grants flowing again. One of my concerns is that they may be hoping to delay things enough that NIH will not have time to get appropriated funds issued by September 30th, the end of the fiscal year. 1/n
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Susie Dent @susiedentwords.bsky.social · 21/02/2025
Word discovery of the day is ‘yoke-devil’ (17th century): an accomplice in a villainous or immoral undertaking.
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BWJones @bwjones.bsky.social · 21/02/2025
We all owe @jeremymberg.bsky.social a debt of gratitude for his work in clarifying, connecting, and advocating for science in this chaotic time. 🙏🏼
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@LaBonneLaB @labonnelab.bsky.social · 17/02/2025
HHS blocked posting indefinitely. Not enough press is being given to this back door approach to blocking NIH grants. If and when it is lifted will still be 35 days before study sections can be held
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Harmit Singh Malik @harmitmalik.bsky.social · 20/02/2025
But many people were not new employees. They were long time employees who had recently been promoted because of their experience and good work, landing on probationary status (don’t ask me why the govt does this) purely because of their ‘good fortune’. Letting these folks go is stupid and cruel. /3
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Waggoner Lab @labwaggoner.bsky.social · 20/02/2025
Disease diagnostics using machine learning of B cell and T cell receptor sequences @science.org www.science.org/doi/10.1126/... @zazius.bsky.social @anshulkundaje.bsky.social @scottboydlab.bsky.social
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Max Delbrück Center @mdc-berlin.bsky.social · 21/02/2025
Ever heard of "systems immunology"? On March 3, Sai Reddy from @ethzurich.bsky.social will give an "MDC Lecture" at the @mdc-berlin.bsky.social exploring this emerging field. Check out our interview and get a sneak peek into his world! ➡️ www.mdc-berlin.de/news/news/en... #mdcBerlin | #mdcBIMSB
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Anshul Kundaje @anshulkundaje.bsky.social · 21/02/2025
Disease diagnostics using machine learning of B cell and T cell receptor sequences www.science.org/doi/10.1126/... TL;DR: BCRs ARE ALL YOU NEED! (Well actually .... keep reading) 1/
science.org
Disease diagnostics using machine learning of B cell and T cell receptor sequences
Clinical diagnosis typically incorporates physical examination, patient history, various laboratory tests, and imaging studies but makes limited use of the human immune system’s own record of antigen ...
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Infectious Diseases @infectiousdz.bsky.social · 21/02/2025
Amid the chaos over USAID funding and waivers, one thing is clear: PrEP (pre-exposure prophylaxis) for HIV prevention is not funded—unless you're pregnant or breastfeeding. 2025 could have marked the start of an HIV-free generation. 🧵
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Paul Thomas @pgtimmune.bsky.social · 21/02/2025
It seems like study sections for the Feb cycle are being pushed back until May. There will be a pile up of reviews in the “best” case scenario that something “normal” happens again. We will all need to step up & ad hoc our hearts out to help the SROs with the backlog (assuming things do get better)
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Ákos T Kovács @evolvedbiofilm.bsky.social · 21/02/2025
Experimental evolution of evolvability @science.org by Michael Barnett, Lena Meister, and paul Rainey at @mpi-evolbio.bsky.social www.science.org/doi/10.1126/...
science.org
Experimental evolution of evolvability
Evolvability—the capacity to generate adaptive variation—is a trait that can itself evolve through natural selection. However, the idea that mutation can become biased toward adaptive outcomes remains...
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Stacey Ogden 🦔 @labogden.bsky.social · 17/02/2025
Special shout out this AM to NIH 🧪 grant mgmt specialists, POs, and SROs during this chaotic time - THANK YOU for caring for our grants and uploading scores/summary statements despite the unprecedented challenges you may be facing. You are science warriors and we APPRECIATE & SUPPORT YOU 🫶
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John Scalzi @scalzi.com · 13/02/2025
The Oregon Trail generation speaks
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Undervalued Vagina MD (she/her)🦄 @undervaluedvagina.medsky.social · 15/02/2025
#flu #nec #medsky
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bioRxiv Immunology @biorxiv-immuno.bsky.social · 16/02/2025
Functional memory T cells are derived from exhausted clones and expanded by checkpoint blockade www.biorxiv.org/content/10.1101/202…
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