Chaitanya K. Joshi
@chaitjo.bsky.social
AI researcher excited about biomolecule design 🧬
PhD student at the University of Cambridge
Prev. at FAIR, Prescient Design, and MRC LMB
📝 https://chaitjo.substack.com
PhD student at the University of Cambridge
Prev. at FAIR, Prescient Design, and MRC LMB
📝 https://chaitjo.substack.com
Pinned
Introducing gRNAde: our own little "AlphaGo Moment" for RNA design! 🧬🚀
📝: tinyurl.com/gRNAde-paper
Unlike proteins, RNA design has long relied on "wisdom of the crowd" (human experts) or the slow crawl of directed evolution — gRNAde changes that! 🧵👇
📝: tinyurl.com/gRNAde-paper
Unlike proteins, RNA design has long relied on "wisdom of the crowd" (human experts) or the slow crawl of directed evolution — gRNAde changes that! 🧵👇
Happy new year! A step change in RNA structure prediction, powered by top Kaggle-ers in a collaboration lead by Stanford University and NVIDIA
Happy to have played a small part in the new RNAPro model, significantly outperforming AlphaFold 3 as well as VFold (CASP winners)
Happy to have played a small part in the new RNAPro model, significantly outperforming AlphaFold 3 as well as VFold (CASP winners)
January 2, 2026 at 1:19 AM
Happy new year! A step change in RNA structure prediction, powered by top Kaggle-ers in a collaboration lead by Stanford University and NVIDIA
Happy to have played a small part in the new RNAPro model, significantly outperforming AlphaFold 3 as well as VFold (CASP winners)
Happy to have played a small part in the new RNAPro model, significantly outperforming AlphaFold 3 as well as VFold (CASP winners)
Merry Christmas!🎄🌟
Sharing something interesting: Friso van de Stadt created a pretty neat explainer video for our gRNAde paper and "AlphaGo moment for RNA design" blogpost!
www.youtube.com/watch?v=wDeZ...
Sharing something interesting: Friso van de Stadt created a pretty neat explainer video for our gRNAde paper and "AlphaGo moment for RNA design" blogpost!
www.youtube.com/watch?v=wDeZ...
AI vs. Humans: The "AlphaGo Moment" for RNA Design
YouTube video by Chaitanya K. Joshi
www.youtube.com
December 26, 2025 at 9:04 AM
Merry Christmas!🎄🌟
Sharing something interesting: Friso van de Stadt created a pretty neat explainer video for our gRNAde paper and "AlphaGo moment for RNA design" blogpost!
www.youtube.com/watch?v=wDeZ...
Sharing something interesting: Friso van de Stadt created a pretty neat explainer video for our gRNAde paper and "AlphaGo moment for RNA design" blogpost!
www.youtube.com/watch?v=wDeZ...
I wrote some personal reflections about being physically embedded in a world-leading molecular biology lab @mrclmb.bsky.social, learning to communicate with experimentalists, back-breaking wet lab work, scientific rigour, and skin in the game!
💌: chaitjo.substack.com/p/an-ai-rese...
💌: chaitjo.substack.com/p/an-ai-rese...
An AI Researcher in the Cathedral of Molecular Biology
How we designed catalytic RNA functions, and what I learned holding a pipette at the MRC Laboratory of Molecular Biology.
chaitjo.substack.com
December 18, 2025 at 3:38 PM
I wrote some personal reflections about being physically embedded in a world-leading molecular biology lab @mrclmb.bsky.social, learning to communicate with experimentalists, back-breaking wet lab work, scientific rigour, and skin in the game!
💌: chaitjo.substack.com/p/an-ai-rese...
💌: chaitjo.substack.com/p/an-ai-rese...
Excited to release the fully open-source code for gRNAde - our wet-lab validated, generative AI framework for 3D RNA inverse design 🚀⭐️
I pride myself on open-science & this is probably the most intense release I've done!
I pride myself on open-science & this is probably the most intense release I've done!
December 15, 2025 at 9:26 AM
Excited to release the fully open-source code for gRNAde - our wet-lab validated, generative AI framework for 3D RNA inverse design 🚀⭐️
I pride myself on open-science & this is probably the most intense release I've done!
I pride myself on open-science & this is probably the most intense release I've done!
Reposted by Chaitanya K. Joshi
Happy to have contributed to and now finally share LeMat-GenBench, a new open benchmark + leaderboard for generative crystalline materials models! ⚛️✨
It provides standardised metrics for validity, stability, & much more. Already includes results for 12 models!
🔗 Paper: arxiv.org/abs/2512.04562
1/4
It provides standardised metrics for validity, stability, & much more. Already includes results for 12 models!
🔗 Paper: arxiv.org/abs/2512.04562
1/4
LeMat-GenBench: A Unified Evaluation Framework for Crystal Generative Models
Generative machine learning (ML) models hold great promise for accelerating materials discovery through the inverse design of inorganic crystals, enabling an unprecedented exploration of chemical spac...
arxiv.org
December 9, 2025 at 5:05 PM
Happy to have contributed to and now finally share LeMat-GenBench, a new open benchmark + leaderboard for generative crystalline materials models! ⚛️✨
It provides standardised metrics for validity, stability, & much more. Already includes results for 12 models!
🔗 Paper: arxiv.org/abs/2512.04562
1/4
It provides standardised metrics for validity, stability, & much more. Already includes results for 12 models!
🔗 Paper: arxiv.org/abs/2512.04562
1/4
Reposted by Chaitanya K. Joshi
Thank you to everyone who made the inaugural Virtual Cell Challenge a success.
Over 5,000 participants from 114 countries competed to build AI models that predict cellular responses to genetic perturbations. Today we're announcing the winners and reflecting on what we learned.
Over 5,000 participants from 114 countries competed to build AI models that predict cellular responses to genetic perturbations. Today we're announcing the winners and reflecting on what we learned.
December 7, 2025 at 4:03 AM
Thank you to everyone who made the inaugural Virtual Cell Challenge a success.
Over 5,000 participants from 114 countries competed to build AI models that predict cellular responses to genetic perturbations. Today we're announcing the winners and reflecting on what we learned.
Over 5,000 participants from 114 countries competed to build AI models that predict cellular responses to genetic perturbations. Today we're announcing the winners and reflecting on what we learned.
I think the term ‘Virtual cell’ will have the same trajectory as ‘AGI’ or ‘Foundation models’: Initially opposed by rigorous scientists, while the Bay Area and Demis Hassabis are the only ones comfortable using it
→ becoming a mainstream term in academia soon, in few years (Overton window)
→ becoming a mainstream term in academia soon, in few years (Overton window)
December 8, 2025 at 7:29 AM
I think the term ‘Virtual cell’ will have the same trajectory as ‘AGI’ or ‘Foundation models’: Initially opposed by rigorous scientists, while the Bay Area and Demis Hassabis are the only ones comfortable using it
→ becoming a mainstream term in academia soon, in few years (Overton window)
→ becoming a mainstream term in academia soon, in few years (Overton window)
Reposted by Chaitanya K. Joshi
An AI researcher interested in biochemistry modeling successfully improved his RNA language model through participation in the Eterna pseudoknot design competition. Congratulations, Chaitanya! 🧬🧪 #RNAsky
The polymerase ribozyme results are pretty cool too. 😎
The polymerase ribozyme results are pretty cool too. 😎
Introducing gRNAde: our own little "AlphaGo Moment" for RNA design! 🧬🚀
📝: tinyurl.com/gRNAde-paper
Unlike proteins, RNA design has long relied on "wisdom of the crowd" (human experts) or the slow crawl of directed evolution — gRNAde changes that! 🧵👇
📝: tinyurl.com/gRNAde-paper
Unlike proteins, RNA design has long relied on "wisdom of the crowd" (human experts) or the slow crawl of directed evolution — gRNAde changes that! 🧵👇
December 3, 2025 at 6:16 PM
An AI researcher interested in biochemistry modeling successfully improved his RNA language model through participation in the Eterna pseudoknot design competition. Congratulations, Chaitanya! 🧬🧪 #RNAsky
The polymerase ribozyme results are pretty cool too. 😎
The polymerase ribozyme results are pretty cool too. 😎
Reposted by Chaitanya K. Joshi
Enumerating possible pseudoknots that a sequence can form with nearest-neighbor models is an NP-hard problem. Even evaluating these structures is challenging, let alone designing them. So it’s great to see data-based models starting to crack the RNA structural design problem! 🧬🧪
Introducing gRNAde: our own little "AlphaGo Moment" for RNA design! 🧬🚀
📝: tinyurl.com/gRNAde-paper
Unlike proteins, RNA design has long relied on "wisdom of the crowd" (human experts) or the slow crawl of directed evolution — gRNAde changes that! 🧵👇
📝: tinyurl.com/gRNAde-paper
Unlike proteins, RNA design has long relied on "wisdom of the crowd" (human experts) or the slow crawl of directed evolution — gRNAde changes that! 🧵👇
December 3, 2025 at 10:45 PM
Enumerating possible pseudoknots that a sequence can form with nearest-neighbor models is an NP-hard problem. Even evaluating these structures is challenging, let alone designing them. So it’s great to see data-based models starting to crack the RNA structural design problem! 🧬🧪
Introducing gRNAde: our own little "AlphaGo Moment" for RNA design! 🧬🚀
📝: tinyurl.com/gRNAde-paper
Unlike proteins, RNA design has long relied on "wisdom of the crowd" (human experts) or the slow crawl of directed evolution — gRNAde changes that! 🧵👇
📝: tinyurl.com/gRNAde-paper
Unlike proteins, RNA design has long relied on "wisdom of the crowd" (human experts) or the slow crawl of directed evolution — gRNAde changes that! 🧵👇
December 3, 2025 at 6:47 AM
Introducing gRNAde: our own little "AlphaGo Moment" for RNA design! 🧬🚀
📝: tinyurl.com/gRNAde-paper
Unlike proteins, RNA design has long relied on "wisdom of the crowd" (human experts) or the slow crawl of directed evolution — gRNAde changes that! 🧵👇
📝: tinyurl.com/gRNAde-paper
Unlike proteins, RNA design has long relied on "wisdom of the crowd" (human experts) or the slow crawl of directed evolution — gRNAde changes that! 🧵👇
Wow thank you, Jamie, for sharing! 🤗
New from @chaitjo.bsky.social and colleagues:
Generative inverse design of RNA structure and function with gRNAde
www.biorxiv.org/content/10.1...
Generative inverse design of RNA structure and function with gRNAde
www.biorxiv.org/content/10.1...
Generative inverse design of RNA structure and function with gRNAde
The design of RNA molecules with bespoke three-dimensional structures and functions is a central goal in synthetic biology and biotechnology. However, progress has been limited by the challenges of de...
www.biorxiv.org
December 3, 2025 at 6:41 AM
Wow thank you, Jamie, for sharing! 🤗
Reposted by Chaitanya K. Joshi
To make future progress it’s worth revisiting the past. From Olke Uhlenbeck, “Keeping RNA Happy”
pmc.ncbi.nlm.nih.gov/articles/PMC...
pmc.ncbi.nlm.nih.gov/articles/PMC...
November 15, 2025 at 5:49 PM
To make future progress it’s worth revisiting the past. From Olke Uhlenbeck, “Keeping RNA Happy”
pmc.ncbi.nlm.nih.gov/articles/PMC...
pmc.ncbi.nlm.nih.gov/articles/PMC...
🚀🧬 Beyond Structure-based Biomolecule Design
Its an important moment for structure-based biomolecule design: models starting to work and action shifting from academia to industry.
So what are the next scientific problems academia could be thinking about?
chaitjo.substack.com/p/beyond-str...
Its an important moment for structure-based biomolecule design: models starting to work and action shifting from academia to industry.
So what are the next scientific problems academia could be thinking about?
chaitjo.substack.com/p/beyond-str...
Beyond structure-based biomolecule design
Dynamics, black-box data, and the antedisciplinary frontier of biomolecule design
chaitjo.substack.com
November 15, 2025 at 9:39 AM
🚀🧬 Beyond Structure-based Biomolecule Design
Its an important moment for structure-based biomolecule design: models starting to work and action shifting from academia to industry.
So what are the next scientific problems academia could be thinking about?
chaitjo.substack.com/p/beyond-str...
Its an important moment for structure-based biomolecule design: models starting to work and action shifting from academia to industry.
So what are the next scientific problems academia could be thinking about?
chaitjo.substack.com/p/beyond-str...
Why do 'frontier' labs train the best models?
I think its because training deep learning models is less like science/engineering, and more like cooking. It takes some time to develop the intuitions around learning dynamics of big models.
I think its because training deep learning models is less like science/engineering, and more like cooking. It takes some time to develop the intuitions around learning dynamics of big models.
October 18, 2025 at 5:30 AM
Why do 'frontier' labs train the best models?
I think its because training deep learning models is less like science/engineering, and more like cooking. It takes some time to develop the intuitions around learning dynamics of big models.
I think its because training deep learning models is less like science/engineering, and more like cooking. It takes some time to develop the intuitions around learning dynamics of big models.
Reposted by Chaitanya K. Joshi
The results are in: top codes in Stanford #RNA 3D Folding @kaggle.com competition are competitive with CASP16-leading humans Vfold, beat AlphaFold 3. Top team’s trick was template-based modeling, not #DeepLearning. Congrats: john, odat, Eigen, + all 1706 participants! www.kaggle.com/competitions...
September 24, 2025 at 4:21 PM
The results are in: top codes in Stanford #RNA 3D Folding @kaggle.com competition are competitive with CASP16-leading humans Vfold, beat AlphaFold 3. Top team’s trick was template-based modeling, not #DeepLearning. Congrats: john, odat, Eigen, + all 1706 participants! www.kaggle.com/competitions...
Reposted by Chaitanya K. Joshi
🚨To accommodate the addition of EuroMLSB, we have extended the submission deadline to October 1, 2025 11:59pm AoE.
Find information on paper guidelines at mlsb.io. Submissions will be made through CMT.
Find information on paper guidelines at mlsb.io. Submissions will be made through CMT.
📢The submission portal for MLSB 2025 is live! Submissions are due September 26, 2025 11:59 pm AoE. cmt3.research.microsoft.com/MLSB2025
September 17, 2025 at 2:59 PM
🚨To accommodate the addition of EuroMLSB, we have extended the submission deadline to October 1, 2025 11:59pm AoE.
Find information on paper guidelines at mlsb.io. Submissions will be made through CMT.
Find information on paper guidelines at mlsb.io. Submissions will be made through CMT.
Reposted by Chaitanya K. Joshi
Genome language models can generate new, high-fitness bacteriophages!
@samuelhking.bsky.social @claudiadriscoll.bsky.social
@david-li.bsky.social @danguo.bsky.social @adititm.bsky.social Garyk Brixi @maxewilkinson.bsky.social @brianhie.bsky.social
www.biorxiv.org/content/10.1...
@samuelhking.bsky.social @claudiadriscoll.bsky.social
@david-li.bsky.social @danguo.bsky.social @adititm.bsky.social Garyk Brixi @maxewilkinson.bsky.social @brianhie.bsky.social
www.biorxiv.org/content/10.1...
September 17, 2025 at 9:15 PM
Genome language models can generate new, high-fitness bacteriophages!
@samuelhking.bsky.social @claudiadriscoll.bsky.social
@david-li.bsky.social @danguo.bsky.social @adititm.bsky.social Garyk Brixi @maxewilkinson.bsky.social @brianhie.bsky.social
www.biorxiv.org/content/10.1...
@samuelhking.bsky.social @claudiadriscoll.bsky.social
@david-li.bsky.social @danguo.bsky.social @adititm.bsky.social Garyk Brixi @maxewilkinson.bsky.social @brianhie.bsky.social
www.biorxiv.org/content/10.1...
Reposted by Chaitanya K. Joshi
Many of the most complex and useful functions in biology emerge at the scale of whole genomes.
Today, we share our preprint “Generative design of novel bacteriophages with genome language models”, where we validate the first, functional AI-generated genomes 🧵
Today, we share our preprint “Generative design of novel bacteriophages with genome language models”, where we validate the first, functional AI-generated genomes 🧵
September 17, 2025 at 3:03 PM
Many of the most complex and useful functions in biology emerge at the scale of whole genomes.
Today, we share our preprint “Generative design of novel bacteriophages with genome language models”, where we validate the first, functional AI-generated genomes 🧵
Today, we share our preprint “Generative design of novel bacteriophages with genome language models”, where we validate the first, functional AI-generated genomes 🧵
Reposted by Chaitanya K. Joshi
very cool work and a milestone in synthetic biology. how impressive are the new phage genomes?
with generative bioML, i'm always looking at how similar the generated sequences are to known sequences. let's take a look
with generative bioML, i'm always looking at how similar the generated sequences are to known sequences. let's take a look
Many of the most complex and useful functions in biology emerge at the scale of whole genomes.
Today, we share our preprint “Generative design of novel bacteriophages with genome language models”, where we validate the first, functional AI-generated genomes 🧵
Today, we share our preprint “Generative design of novel bacteriophages with genome language models”, where we validate the first, functional AI-generated genomes 🧵
September 18, 2025 at 3:30 AM
very cool work and a milestone in synthetic biology. how impressive are the new phage genomes?
with generative bioML, i'm always looking at how similar the generated sequences are to known sequences. let's take a look
with generative bioML, i'm always looking at how similar the generated sequences are to known sequences. let's take a look
Reposted by Chaitanya K. Joshi
You asked and we listened... @workshopmlsb.bsky.social is excited to be expanding to Copenhagen, DK at @euripsconf.bsky.social 🎉
Two workshops (San Diego & Copenhagen) will run concurrently to support broader attendance. You can indicate your location preference(s) in the submission portal💫
Two workshops (San Diego & Copenhagen) will run concurrently to support broader attendance. You can indicate your location preference(s) in the submission portal💫
September 12, 2025 at 12:43 PM
You asked and we listened... @workshopmlsb.bsky.social is excited to be expanding to Copenhagen, DK at @euripsconf.bsky.social 🎉
Two workshops (San Diego & Copenhagen) will run concurrently to support broader attendance. You can indicate your location preference(s) in the submission portal💫
Two workshops (San Diego & Copenhagen) will run concurrently to support broader attendance. You can indicate your location preference(s) in the submission portal💫
The 3D structure of biomolecules are nature's 'thinking tokens' enroute to the output that we actually truly want to understand: Function.
(Slide from Denny Zhou's Stanford talk on LLM Reasoning)
(Slide from Denny Zhou's Stanford talk on LLM Reasoning)
September 5, 2025 at 4:01 AM
The 3D structure of biomolecules are nature's 'thinking tokens' enroute to the output that we actually truly want to understand: Function.
(Slide from Denny Zhou's Stanford talk on LLM Reasoning)
(Slide from Denny Zhou's Stanford talk on LLM Reasoning)
Reposted by Chaitanya K. Joshi
We have restarted our global Nucleic Acid Strcuture webinar series to bring the expiremental and computational communities together to discuss new developments in the field. Join us this Thursday for the next webinar. Sign up to our mailing list here: groups.google.com/g/casp-rna-sig
September 2, 2025 at 5:50 PM
We have restarted our global Nucleic Acid Strcuture webinar series to bring the expiremental and computational communities together to discuss new developments in the field. Join us this Thursday for the next webinar. Sign up to our mailing list here: groups.google.com/g/casp-rna-sig
Scaling laws for BioML and wet lab data will eventually work out in the right setting! After all, language data for LLMs was acquired by the largest wet lab experiment ever conducted: Human civilisation 🤯
August 31, 2025 at 5:31 AM
Scaling laws for BioML and wet lab data will eventually work out in the right setting! After all, language data for LLMs was acquired by the largest wet lab experiment ever conducted: Human civilisation 🤯
Reposted by Chaitanya K. Joshi
(1/7)
Training biomolecular foundation models shouldn't be so hard. And open-source structure prediction is important. So today we're releasing two software packages: AtomWorks and RosettaFold3 (RF3)
[https://www.biorxiv.org/content/10.1101/2025.08.14.670328v2](www.biorxiv.org/content/10.1...)
Training biomolecular foundation models shouldn't be so hard. And open-source structure prediction is important. So today we're releasing two software packages: AtomWorks and RosettaFold3 (RF3)
[https://www.biorxiv.org/content/10.1101/2025.08.14.670328v2](www.biorxiv.org/content/10.1...)
Accelerating Biomolecular Modeling with AtomWorks and RF3
Deep learning methods trained on protein structure databases have revolutionized biomolecular structure prediction, but developing and training new models remains a considerable challenge. To facilita...
www.biorxiv.org
August 15, 2025 at 5:17 PM
(1/7)
Training biomolecular foundation models shouldn't be so hard. And open-source structure prediction is important. So today we're releasing two software packages: AtomWorks and RosettaFold3 (RF3)
[https://www.biorxiv.org/content/10.1101/2025.08.14.670328v2](www.biorxiv.org/content/10.1...)
Training biomolecular foundation models shouldn't be so hard. And open-source structure prediction is important. So today we're releasing two software packages: AtomWorks and RosettaFold3 (RF3)
[https://www.biorxiv.org/content/10.1101/2025.08.14.670328v2](www.biorxiv.org/content/10.1...)
📢 Submissions for MLSB 2025 are officially open! We invite researchers to submit their work on the intersection of AI and structural biology.
🗓️ Deadline: September 26, 2025 🔗 More info: cmt3.research.microsoft.com/MLSB2025
🗓️ Deadline: September 26, 2025 🔗 More info: cmt3.research.microsoft.com/MLSB2025
MLSB 2025 Workshop
Workshop on Machine Learning in Structural Biology co-located with NeurIPS 2025
www.mlsb.io
August 15, 2025 at 6:10 PM
📢 Submissions for MLSB 2025 are officially open! We invite researchers to submit their work on the intersection of AI and structural biology.
🗓️ Deadline: September 26, 2025 🔗 More info: cmt3.research.microsoft.com/MLSB2025
🗓️ Deadline: September 26, 2025 🔗 More info: cmt3.research.microsoft.com/MLSB2025