Pinned
Sanna Madan
@sannam.bsky.social
· Mar 26
Can we engineer smarter CAR-T cells that target cancer with precise logic? 🎯🧬
So excited to share the heart of my PhD work:
🌟 LogiCAR designer, a framework that identifies logic-gated multi-antigen circuits for next-generation cell therapies 🧩🧵
www.biorxiv.org/content/10.1...
So excited to share the heart of my PhD work:
🌟 LogiCAR designer, a framework that identifies logic-gated multi-antigen circuits for next-generation cell therapies 🧩🧵
www.biorxiv.org/content/10.1...
Reposted by Sanna Madan
Preprint: Characterization of the dual roles of senescent-like T cells that arise during healthy and unhealthy ageing
www.biorxiv.org/content/10.1...
@drsianh.bsky.social
www.biorxiv.org/content/10.1...
@drsianh.bsky.social
June 20, 2025 at 2:23 AM
Preprint: Characterization of the dual roles of senescent-like T cells that arise during healthy and unhealthy ageing
www.biorxiv.org/content/10.1...
@drsianh.bsky.social
www.biorxiv.org/content/10.1...
@drsianh.bsky.social
Reposted by Sanna Madan
NEW: The doctor behind breakthrough Parkinson’s research was among the scientists purged from the National Institutes of Health, the US’s leading medical research agency. www.wired.com/story/doctor...
Doctor Behind Award-Winning Parkinson’s Research Among Scientists Purged From NIH
Leading scientists at the National Institutes of Health, the US’s leading medical research agency, were swept up Tuesday in the Trump administration's latest firing blitz.
www.wired.com
April 2, 2025 at 12:13 AM
NEW: The doctor behind breakthrough Parkinson’s research was among the scientists purged from the National Institutes of Health, the US’s leading medical research agency. www.wired.com/story/doctor...
Reposted by Sanna Madan
Decoding sequence determinants of gene expression in diverse cellular and disease states [updated]
Predicts gene expression from DNA via single-cell data; reveals regulation & variant effects.
Predicts gene expression from DNA via single-cell data; reveals regulation & variant effects.
April 2, 2025 at 4:49 AM
Decoding sequence determinants of gene expression in diverse cellular and disease states [updated]
Predicts gene expression from DNA via single-cell data; reveals regulation & variant effects.
Predicts gene expression from DNA via single-cell data; reveals regulation & variant effects.
Reposted by Sanna Madan
Enhancing CAR-T cell activity prediction via fine-tuning protein language models with generated CAR sequences [new]
Fine-tuning ProtLM predicts CAR-T activity. Augmented CAR seqs enable task-specific adaptation.
Fine-tuning ProtLM predicts CAR-T activity. Augmented CAR seqs enable task-specific adaptation.
April 2, 2025 at 5:11 AM
Enhancing CAR-T cell activity prediction via fine-tuning protein language models with generated CAR sequences [new]
Fine-tuning ProtLM predicts CAR-T activity. Augmented CAR seqs enable task-specific adaptation.
Fine-tuning ProtLM predicts CAR-T activity. Augmented CAR seqs enable task-specific adaptation.
Reposted by Sanna Madan
The CDC has literally been gutted today.
There’s no need for “April Fools” when reality is a nightmare for every human on this planet.
Thousand of scientists fired.
Entire departments erased.
1/
There’s no need for “April Fools” when reality is a nightmare for every human on this planet.
Thousand of scientists fired.
Entire departments erased.
1/
April 1, 2025 at 4:10 PM
The CDC has literally been gutted today.
There’s no need for “April Fools” when reality is a nightmare for every human on this planet.
Thousand of scientists fired.
Entire departments erased.
1/
There’s no need for “April Fools” when reality is a nightmare for every human on this planet.
Thousand of scientists fired.
Entire departments erased.
1/
Happy to share a blog post I wrote on our new computational approach LogiCAR Designer, which identifies logic-gated antigen circuits for precise, next-generation CAR therapies. 🎯🧬
mlandbio.substack.com/p/from-singl...
mlandbio.substack.com/p/from-singl...
March 29, 2025 at 1:27 AM
Happy to share a blog post I wrote on our new computational approach LogiCAR Designer, which identifies logic-gated antigen circuits for precise, next-generation CAR therapies. 🎯🧬
mlandbio.substack.com/p/from-singl...
mlandbio.substack.com/p/from-singl...
Can we engineer smarter CAR-T cells that target cancer with precise logic? 🎯🧬
So excited to share the heart of my PhD work:
🌟 LogiCAR designer, a framework that identifies logic-gated multi-antigen circuits for next-generation cell therapies 🧩🧵
www.biorxiv.org/content/10.1...
So excited to share the heart of my PhD work:
🌟 LogiCAR designer, a framework that identifies logic-gated multi-antigen circuits for next-generation cell therapies 🧩🧵
www.biorxiv.org/content/10.1...
March 26, 2025 at 1:18 AM
Can we engineer smarter CAR-T cells that target cancer with precise logic? 🎯🧬
So excited to share the heart of my PhD work:
🌟 LogiCAR designer, a framework that identifies logic-gated multi-antigen circuits for next-generation cell therapies 🧩🧵
www.biorxiv.org/content/10.1...
So excited to share the heart of my PhD work:
🌟 LogiCAR designer, a framework that identifies logic-gated multi-antigen circuits for next-generation cell therapies 🧩🧵
www.biorxiv.org/content/10.1...
Reposted by Sanna Madan
Single-cell-guided identification of logic-gated antigen combinations for designing effective and safe CAR therapy [new]
Finds logic-gated antigen combos in single-cell data for safer CAR-T, exceeding shared methods.
Finds logic-gated antigen combos in single-cell data for safer CAR-T, exceeding shared methods.
March 19, 2025 at 9:23 PM
Single-cell-guided identification of logic-gated antigen combinations for designing effective and safe CAR therapy [new]
Finds logic-gated antigen combos in single-cell data for safer CAR-T, exceeding shared methods.
Finds logic-gated antigen combos in single-cell data for safer CAR-T, exceeding shared methods.
Reposted by Sanna Madan
Big news: we are setting up a new non-profit organization to run bioRxiv and medRxiv. It's called openRxiv [no it's not a new preprint server; it's dedicated organization to oversee the servers] openrxiv.org 1/n
Homepage - openRxiv
openRxiv is an independent non-profit, the new organizational home for bioRxiv and medRxiv, enabling researchers to instantly share groundbreaking findings with the global scientific community.
openrxiv.org
March 11, 2025 at 1:20 PM
Big news: we are setting up a new non-profit organization to run bioRxiv and medRxiv. It's called openRxiv [no it's not a new preprint server; it's dedicated organization to oversee the servers] openrxiv.org 1/n
Reposted by Sanna Madan
We are experiencing an assault on science unparalleled by anything I’ve seen in my life. It’s not one issue or another anymore, the entire institution is under attack by the most powerful individuals in the country.
This Friday, where will you be?
standupforscience2025.org
This Friday, where will you be?
standupforscience2025.org
March 2, 2025 at 4:27 PM
We are experiencing an assault on science unparalleled by anything I’ve seen in my life. It’s not one issue or another anymore, the entire institution is under attack by the most powerful individuals in the country.
This Friday, where will you be?
standupforscience2025.org
This Friday, where will you be?
standupforscience2025.org
Reposted by Sanna Madan
Bizarre tumor immunology accident. Surgeon injures hand while resecting malignant histiocytoma and finds an inflamed mass at the site of prior injury. Tumor cells transplanted, patient & surgeon HLA mismatched causing intense yet insufficient host-vs-graft response: www.nejm.org/doi/full/10....
Genetic Analysis of a Sarcoma Accidentally Transplanted from a Patient to a Surgeon | NEJM
Modern concepts of cancer immunology originated from the classic observations by Jensen,
Loeb, Tyzzer, and Little in the early years of the 20th century of the rejection of
transplanted allogeneic ...
www.nejm.org
January 5, 2025 at 6:15 PM
Bizarre tumor immunology accident. Surgeon injures hand while resecting malignant histiocytoma and finds an inflamed mass at the site of prior injury. Tumor cells transplanted, patient & surgeon HLA mismatched causing intense yet insufficient host-vs-graft response: www.nejm.org/doi/full/10....
Reposted by Sanna Madan
One main pain point: interdisciplinary work is often judged by the highest standards in *both* disciplines. This creates an almost impossible burden, effectively extinguishing creative work. Sure, some standards are there for a reason, but more often than not, they are just stock critiques.
💯. Most aspects of the system subtly (or not-so-subtly) push you back in your lane, making interdisciplinary work very hard.
Expert's Dilemma: the more specialized you become, the less open you are to creative solutions from other fields. But the more you explore other fields, the more you risk losing credibility in your home field.
Interdisciplinary work is still not really embraced by academia.
Interdisciplinary work is still not really embraced by academia.
January 5, 2025 at 5:00 PM
One main pain point: interdisciplinary work is often judged by the highest standards in *both* disciplines. This creates an almost impossible burden, effectively extinguishing creative work. Sure, some standards are there for a reason, but more often than not, they are just stock critiques.
Reposted by Sanna Madan
This paper is the result of an incredibly fun collaboration with Sandro Santagata and Peter Sorger. Led by an amazing postdoc @tanjinakader.bsky.social and JiaRen Lin, we provide a pre-cancer atlas of Fallopian tube precursors to High-Grade Serous Ovarian Cancer. The data is also on cbioportal!
Now online in Cancer Discovery: Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma - by Tanjina Kader, Jia-Ren Lin, Clemens Hug, Ronny Drapkin, Sandro Santagata, et al. doi.org/10.1158/2159...
December 24, 2024 at 5:40 PM
This paper is the result of an incredibly fun collaboration with Sandro Santagata and Peter Sorger. Led by an amazing postdoc @tanjinakader.bsky.social and JiaRen Lin, we provide a pre-cancer atlas of Fallopian tube precursors to High-Grade Serous Ovarian Cancer. The data is also on cbioportal!
Reposted by Sanna Madan
Wouldn't have guessed that a PCSK9 blocker (used for LDL cholesterol lowering) might someday be indicated to prevent breast cancer in individuals with a common genomic variant
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
December 11, 2024 at 10:58 PM
Wouldn't have guessed that a PCSK9 blocker (used for LDL cholesterol lowering) might someday be indicated to prevent breast cancer in individuals with a common genomic variant
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
Reposted by Sanna Madan
Could one envision a synthetic receptor technology that is fully programmable, able to detect diverse extracellular antigens – both soluble and cell-attached – and convert that recognition into a wide range of intracellular responses, from gene expression and real-time fluorescence to modulation..
December 4, 2024 at 4:05 PM
Could one envision a synthetic receptor technology that is fully programmable, able to detect diverse extracellular antigens – both soluble and cell-attached – and convert that recognition into a wide range of intracellular responses, from gene expression and real-time fluorescence to modulation..
Reposted by Sanna Madan
One of the alluring and theoretical strategies for extending healthspan and longevity is to rejuvenate the thymus gland, promote an intact immune system. Now there's a way to do that in aged mice.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
December 4, 2024 at 9:20 PM
One of the alluring and theoretical strategies for extending healthspan and longevity is to rejuvenate the thymus gland, promote an intact immune system. Now there's a way to do that in aged mice.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Sanna Madan
WaPo Edito: Be thankful for the applications of AI in medicine.
More accurate detection of cancers (breast, prostate, skin, brain), faster diagnosis of strokes, sepsis, heart attacks, faster MRIs, full-body in 40 minutes.
Much more to come over the next years.
www.washingtonpost.com/opinions/202...
More accurate detection of cancers (breast, prostate, skin, brain), faster diagnosis of strokes, sepsis, heart attacks, faster MRIs, full-body in 40 minutes.
Much more to come over the next years.
www.washingtonpost.com/opinions/202...
November 28, 2024 at 7:54 PM
WaPo Edito: Be thankful for the applications of AI in medicine.
More accurate detection of cancers (breast, prostate, skin, brain), faster diagnosis of strokes, sepsis, heart attacks, faster MRIs, full-body in 40 minutes.
Much more to come over the next years.
www.washingtonpost.com/opinions/202...
More accurate detection of cancers (breast, prostate, skin, brain), faster diagnosis of strokes, sepsis, heart attacks, faster MRIs, full-body in 40 minutes.
Much more to come over the next years.
www.washingtonpost.com/opinions/202...
Reposted by Sanna Madan
Medically adapted foundation models (think Med-*) turn out to be more hot air than hot stuff. Correcting for fatal flaws in evaluation, the current crop are no better on balance than generic foundation models, even on the very tasks for which benefits are claimed.
arxiv.org/abs/2411.04118
arxiv.org/abs/2411.04118
Medical Adaptation of Large Language and Vision-Language Models: Are We Making Progress?
Several recent works seek to develop foundation models specifically for medical applications, adapting general-purpose large language models (LLMs) and vision-language models (VLMs) via continued pret...
arxiv.org
November 26, 2024 at 6:12 PM
Medically adapted foundation models (think Med-*) turn out to be more hot air than hot stuff. Correcting for fatal flaws in evaluation, the current crop are no better on balance than generic foundation models, even on the very tasks for which benefits are claimed.
arxiv.org/abs/2411.04118
arxiv.org/abs/2411.04118
Reposted by Sanna Madan
Happy to share our new paper, which was just published in Nature Communications. In-context learning enables general-purpose vision language models to perform well on medical image analysis tasks. We don't need to train a neural network at all - just provide a handful of examples at inference time.
November 23, 2024 at 8:39 PM
Happy to share our new paper, which was just published in Nature Communications. In-context learning enables general-purpose vision language models to perform well on medical image analysis tasks. We don't need to train a neural network at all - just provide a handful of examples at inference time.
Incredible experience at the
NCI HTAN Data Jamboree! Grateful to work with a brilliant team to develop HTANalyzer, a multi-agent LLM that helps researchers query and analyze HTAN spatial transcriptomics data through natural language queries. Check out our project github: github.com/NCI-HTAN-Jam...
NCI HTAN Data Jamboree! Grateful to work with a brilliant team to develop HTANalyzer, a multi-agent LLM that helps researchers query and analyze HTAN spatial transcriptomics data through natural language queries. Check out our project github: github.com/NCI-HTAN-Jam...
November 22, 2024 at 8:25 PM
Incredible experience at the
NCI HTAN Data Jamboree! Grateful to work with a brilliant team to develop HTANalyzer, a multi-agent LLM that helps researchers query and analyze HTAN spatial transcriptomics data through natural language queries. Check out our project github: github.com/NCI-HTAN-Jam...
NCI HTAN Data Jamboree! Grateful to work with a brilliant team to develop HTANalyzer, a multi-agent LLM that helps researchers query and analyze HTAN spatial transcriptomics data through natural language queries. Check out our project github: github.com/NCI-HTAN-Jam...
Reposted by Sanna Madan
—Please give me an A.I. that automatically detects, interprets all types of medical. images (scans, retina, endoscopy, skin) that I can interact with, can integrate data from other sources, saves a lot of time, and improves accuracy
—Sure, here it is
www.nature.com/articles/s41...
—Sure, here it is
www.nature.com/articles/s41...
November 20, 2024 at 2:28 PM
—Please give me an A.I. that automatically detects, interprets all types of medical. images (scans, retina, endoscopy, skin) that I can interact with, can integrate data from other sources, saves a lot of time, and improves accuracy
—Sure, here it is
www.nature.com/articles/s41...
—Sure, here it is
www.nature.com/articles/s41...
Reposted by Sanna Madan
A genome-scale map of genetic interaction profiles building upon cell morphology. Great work by Florian Heigwer and collaborators. #Genomics #Imaging
“A global genetic interaction network by single-cell imaging and machine learning”
www.sciencedirect.com/science/arti...
“A global genetic interaction network by single-cell imaging and machine learning”
www.sciencedirect.com/science/arti...
A global genetic interaction network by single-cell imaging and machine learning
Cellular and organismal phenotypes are controlled by complex gene regulatory networks. However, reference maps of gene function are still scarce acros…
www.sciencedirect.com
September 18, 2023 at 11:34 AM
A genome-scale map of genetic interaction profiles building upon cell morphology. Great work by Florian Heigwer and collaborators. #Genomics #Imaging
“A global genetic interaction network by single-cell imaging and machine learning”
www.sciencedirect.com/science/arti...
“A global genetic interaction network by single-cell imaging and machine learning”
www.sciencedirect.com/science/arti...