Dhuvi Karthikeyan
@dkarthikey1.bsky.social
Shape rotator and vibes curator at UNC’s Personalized Immunotherapy Research Lab. Generative modeling and representation learning in biology. 👨🏫👨🔬
Pinned
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
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
Reposted by Dhuvi Karthikeyan
This is so friggin cool. You don't have to rewrite all that FORTRAN to do autodiff on it. "Enzyme"
Found the paper
arxiv.org/abs/2010.01709
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
October 12, 2025 at 9:00 PM
This is so friggin cool. You don't have to rewrite all that FORTRAN to do autodiff on it. "Enzyme"
Reposted by Dhuvi Karthikeyan
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...
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
October 8, 2025 at 6:06 AM
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...
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...
Reposted by Dhuvi Karthikeyan
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
September 10, 2025 at 8:16 PM
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
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
September 9, 2025 at 9:25 AM
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
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
Reposted by Dhuvi Karthikeyan
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.
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.
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 9, 2025 at 12:33 AM
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.
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.
Reposted by Dhuvi Karthikeyan
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.
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.
September 9, 2025 at 12:32 AM
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.
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.
Reposted by Dhuvi Karthikeyan
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 Dhuvi Karthikeyan
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...
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
May 19, 2025 at 1:58 AM
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...
www.cbsnews.com/amp/news/art...
Reposted by Dhuvi Karthikeyan
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...
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
May 9, 2025 at 11:38 PM
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...
www.science.org/content/arti...
Reposted by Dhuvi Karthikeyan
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.
May 8, 2025 at 2:04 PM
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.
Reposted by Dhuvi Karthikeyan
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.
May 3, 2025 at 10:22 PM
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.
Reposted by Dhuvi Karthikeyan
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
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
April 24, 2025 at 10:58 AM
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
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
Reposted by Dhuvi Karthikeyan
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
April 21, 2025 at 8:41 PM
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.
Reposted by Dhuvi Karthikeyan
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 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
April 10, 2025 at 3:57 PM
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 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
Reposted by Dhuvi Karthikeyan
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_...
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
March 31, 2025 at 2:41 PM
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_...
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_...
Reposted by Dhuvi Karthikeyan
HHS's Office of Long COVID Research and Practice has been DOGEd. Closing this week.
March 24, 2025 at 9:23 PM
HHS's Office of Long COVID Research and Practice has been DOGEd. Closing this week.
Reposted by Dhuvi Karthikeyan
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/content/10.1...
www.biorxiv.org
February 26, 2025 at 9:15 PM
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/content/10.1...
Reposted by Dhuvi Karthikeyan
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
You can leave a sign w me and i can bring it up to DC!
@standupforscience.bsky.social
February 25, 2025 at 3:41 AM
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
You can leave a sign w me and i can bring it up to DC!
@standupforscience.bsky.social
Reposted by Dhuvi Karthikeyan
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/
jamieheather.github.io/stitchr/
stitchr — stitchr documentation
jamieheather.github.io
February 25, 2025 at 4:24 AM
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/
jamieheather.github.io/stitchr/
Reposted by Dhuvi Karthikeyan
🚨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.
February 4, 2025 at 1:26 AM
🚨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
February 1, 2025 at 5:07 AM
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
Reposted by Dhuvi Karthikeyan
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 ...
www.biorxiv.org
January 12, 2025 at 10:41 PM
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...
On the merits of reading papers, attending conferences, preprinting manuscripts… Overseen at the Library of Congress.
December 30, 2024 at 2:17 AM
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
December 21, 2024 at 5:41 AM
Unsure if people on bsky are aware of o3s existence. But if anyone wants to talk I’ve been itching all day