This is so friggin cool. You don't have to rewrite all that FORTRAN to do autodiff on it. "Enzyme"

Adrien Corenflos@adriencorenflos.bsky.social · 10mo ago

Found the paper arxiv.org/abs/2010.01709

When a T cell carries both its natural TCR and an engineered CAR, do these two receptors cooperate - or compete? Our new preprint on bioRxiv shows that TCR activation can enhance CAR-T activation but impairs CAR-mediated killing when targets are on separate cells. www.biorxiv.org/content/10.1...

TCR activation impairs CAR-T cytotoxicity against separate target cells

Chimeric antigen receptor T cells (CAR-T) are effective therapeutics against cancer and autoimmunity, but whether the endogenous T cell receptor (TCR) is beneficial, detrimental or irrelevant for CAR ...

biorxiv.org

No Distinct Gut Microbiome Signature in Alzheimer's Disease: A Reanalysis with Modern Tools https://www.biorxiv.org/content/10.1101/2025.09.09.675220v1

Now out in @natmachintell.nature.com TCRT5 is a rapid generator of target-conditioned CDR3b, leads SoTA, and yields the first AI-designed self-tolerant binder to an OOD non-viral epitope (w val) 📑: www.nature.com/articles/s42... 🤗: huggingface.co/dkarthikeyan1 👨‍💻: github.com/pirl-unc/tcr_translate

Dhuvi Karthikeyan@dkarthikey1.bsky.social · 2y ago

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

tl;dr T5 style translation model to generate T cell receptors from targets actually kinda works Caveats: not full TCR (CDR3b), strong signal that public data biased towards “polyspecific” TCRs — lo and behold, generated TCR-T is polyspecific in vitro. Open weights, go wild.

Jamie Heather@jamieheather.bsky.social · 11mo ago

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

With some key contributions by Sarah Bennet in actually turning predicted TCRs into TCR-Ts and testing them! Hopefully this raises the bar on TCR generation evals, I think we the best in silico metrics and 1 in 20 TCRs just kinda works.

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

Waggoner Lab@labwaggoner.bsky.social · 11mo ago

Conditional generation of real antigen-specific T cell receptor sequences @natmachintell.nature.com www.nature.com/articles/s42...

Today’s news about Joe Biden makes it almost difficult not to reflect on the unrealistic promises from AI leaders who claim AI could end disease and usher in radical abundance. Disease will persist. AI is a tool, not a cure-all. People deserve truth, not hype. www.cbsnews.com/amp/news/art...

Artificial intelligence could end disease, lead to "radical abundance," Google DeepMind CEO Demis Hassabis says

At Google DeepMind, researchers are chasing what's called artificial general intelligence: a silicon intellect as versatile as a human's, but with superhuman speed and knowledge.

cbsnews.com

NSF to ONLY fund research in five areas: artificial intelligence, quantum information science, biotechnology, nuclear energy, and translational science. Can this be happening? www.science.org/content/arti...

NSF slashes number of ‘rotators’ and well-paid managers as part of restructuring

Smaller future budgets will require fewer people, NSF official tells staff

science.org

what do you teach at the first-year graduate course on machine learning, in this era of LLM and large-scale compute? here's my experiment on answering this question: let's teach everything that admits SGD and that is not LLM, and ask students to read old papers.

We hadn’t won World War II by May 8th. I know because my family and I were still in an internment camp in Tule Lake, California.

Your immune system gradually loses it top team players when we get older 👱➡️👵 Our study in @ebiomedicine.bsky.social investigates how long good immune cells stay around – a 🧵⬇️ go.unimelb.edu.au/4sep @katherinekedz.bsky.social @thedohertyinst.bsky.social #Influenza #AgingResearch #Immunity #TCR

My PhD student's NSF grant was terminated today. Her dissertation investigates why air pollution monitoring, metrics, and regulations don't properly capture the harms experienced by marginalized communities--esp in the most polluted Detroit neighborhoods. She and I are happy to talk with press etc.

I am so excited to share that our new paper is out! A model of intratumor and interpatient heterogeneity explains clinical trials of curative combination therapy for lymphoma Out in Blood Cancer Discovery doi.org/10.1158/2643-3230.BCD-24-0230 #mathonc #lymsm #BloodCancer 1/n

Do you analyze large BCR and TCR sequencing datasets? Answer our survey for improving nf-core/airrflow, a Nextflow pipeline to analyze bulk and single-cell AIRRseq data (doi.org/10.1371/jour...). We’re interested in your opinion on useful new features! yalesurvey.ca1.qualtrics.com/jfe/form/SV_...

nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework

Author summary We have created nf-core/airrflow, a workflow to help researchers study the immune system in healthy and disease states, such as infections, autoimmunity, and cancer. The adaptive immune...

doi.org

HHS's Office of Long COVID Research and Practice has been DOGEd. Closing this week.

We @prescientdesign.bsky.social Genentech pre-printed our "Lab-in-the-loop for therapeutic antibody design." We built a general ML system to accelerate molecule design for challenging, therapeutically relevant targets. www.biorxiv.org/content/10.1...

You in the Triangle area and thinking about standing up for science? Come to my beloved 2nd workplace and make a sign 😊🍻 supplies provided! You can leave a sign w me and i can bring it up to DC! @standupforscience.bsky.social

Dear TCR researchers of #immunosky, you may be interested to know that our tool Stitchr - for the automated production of full-length T cell receptor sequences - has just had a nice little update: jamieheather.github.io/stitchr/

🚨BREAKING. From a program officer at the National Science Foundation, a list of keywords that can cause a grant to be pulled. I will be sharing screenshots of these keywords along with a decision tree. Please share widely. This is a crisis for academic freedom & science.

Musks method of ruthlessly enforcing efficiency by removing things and adding them back if the system breaks has worked well for pruning complexity of products, pipelines and entire companies. But applying this methodology to govt is dangerous and will result in greater harm to the American people

Good combo! A nasal vaccine with self-amplifying RNA (much less dose required for v potent immune response), complete protection effective vs both H5N1 and H7N9 viruses in experimental models www.biorxiv.org/content/10.1...

An intranasal, NLC-delivered self-amplifying RNA vaccine establishes protective immunity against pre-pandemic H5N1 and H7N9 influenza

Seasonal and pandemic influenzas are continuous threats to human health, requiring rapid development of vaccines to multiple evolving viral strains. New RNA vaccine technologies have the adaptability ...

biorxiv.org

On the merits of reading papers, attending conferences, preprinting manuscripts… Overseen at the Library of Congress.

Unsure if people on bsky are aware of o3s existence. But if anyone wants to talk I’ve been itching all day

How to learn generalizable rules across complex sequence-function maps? 💡In our new preprint we propose a framework for learning two-point statistics and use it to discover biophysical rules of TCR co-specificity that generalize to unseen ligands ! ✨ arxiv.org/abs/2412.13722

Ideal test is antibody CDRH3s which often conformationally rigidify during affinity maturation. MSAs only report inter-species evolution, not intra-species maturation, so existing methods fail. Pics from doi.org/10.3389/fimmu.2018.03065 & doi.org/10.3389/fmolb.2020.00182

Given the subtext here I wouldn’t be surprised if both X and Bsky develop extremely close but distinct niches: the former to blast information and reach broader audiences, and the latter as a place of discourse with members of a particular community.

Hank Green@hankgreen.bsky.social · 2y ago

The deep goal of bluesky is to decentralize the social internet so that every individual controls their experience of it rather than having it be controlled by 5 random billionaires. Everyone thinks they signed up for a demuskified twitter...we actually signed an exciting and bizarre experiment.

🧙🪄Summoning Alex to 💙🦋 so the Bio x ML community can celebrate ESM-C with him on here as well

My usual go to is VDJdb. Set antigen species to human, minimal confidence score to 3, and paired A+B. It's not perfect, but it filters out most of the cruft. There's also a new DB called TRAIT which has a nice pack of TCRs that are being/have been trialed, which are mostly against human epitopes.