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Reposted by Dhuvi Karthikeyan

Eric Kernfeld @ekernf01.bsky.social · 2d

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 · 2d

Found the paper
arxiv.org/abs/2010.01709

Instead of Rewriting Foreign Code for Machine Learning, Automatically Synthesize Fast Gradients

Applying differentiable programming techniques and machine learning algorithms to foreign programs requires developers to either rewrite their code in a machine learning framework, or otherwise provid...

arxiv.org

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Kilian Schober @kischober.bsky.social · 6d

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 ...

www.biorxiv.org

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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · Sep 10

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

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Dhuvi Karthikeyan @dkarthikey1.bsky.social · Sep 9

Thanks Professor!

Dhuvi Karthikeyan @dkarthikey1.bsky.social · Sep 9

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

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Alex Rubinsteyn @alexr.bsky.social · Sep 9

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 · Sep 8

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 · Sep 8

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

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Dhuvi Karthikeyan @dkarthikey1.bsky.social · Sep 9

This story is nothing without its reviewers 🩵

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Alex Rubinsteyn @alexr.bsky.social · Sep 9

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.

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Jamie Heather @jamieheather.bsky.social · Sep 8

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 · Sep 8

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

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AlphaFold Unofficial @alphafold.bsky.social · May 19

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.

www.cbsnews.com

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Dustin Rubenstein @dustinrubenstein.com · May 9

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

www.science.org

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kyunghyuncho.bsky.social @kyunghyuncho.bsky.social · May 8

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.

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George Takei @georgetakei.bsky.social · May 3

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.

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Carolien van de Sandt @cvandesandt.bsky.social · Apr 24

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

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Shobita Parthasarathy @shobitap.org · Apr 21

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.

NSF Award Search: Award # 2240343 - Constructing Credible Knowledge and Expertise in Air Pollution Regulation and Monitoring: The Problem of Quantification Lock

www.nsf.gov

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Amy Pomeroy @amypomeroy.bsky.social · Apr 10

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

A model of intra-tumor and inter-patient heterogeneity explains clinical trials of curative combination therapy for lymphoma

Abstract. Models of tumor drug response have illuminated important concepts in oncology, but there remains a need for theory that combines intra-tumor and inter-patient heterogeneity to explain patien...

doi.org

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Gisela Gabernet @ggabernet.bsky.social · Mar 31

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

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Eric Topol @erictopol.bsky.social · Mar 24

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

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Nathan C. Frey @ncfrey.bsky.social · Feb 26

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...

www.biorxiv.org

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jp flores (he/him) @jpflores.rbind.io · Feb 25

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

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Jamie Heather @jamieheather.bsky.social · Feb 25

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/

stitchr — stitchr documentation

jamieheather.github.io

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Darby Saxbe @darbysaxbe.bsky.social · Feb 4

🚨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.

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Dhuvi Karthikeyan @dkarthikey1.bsky.social · Feb 1

Arguably well*

Dhuvi Karthikeyan @dkarthikey1.bsky.social · Feb 1

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

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Dhuvi Karthikeyan @dkarthikey1.bsky.social · Jan 27

Tagging in @pranam.bsky.social

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