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
Excited to have Edric Choi present his latest work on RNA chemical mapping at the CASP Nucleic Acids Reading Group! Thursday April 16 2026 on Zoom; Pacific Daylight Saving Time 8 am / Eastern Daylight Saving Time 11 am -- free to attend and full of interactive discussions.
I recently joined The Pauling Principle podcast to discuss our research on RNA design, hot takes on architecture research in BioML, origins of life, and being in a wet lab! Feels pretty surreal that I'm interesting enough to be on a podcast (?) www.youtube.com/watch?v=ftrQ...
New blog 💙: I reflect on why I worked on what I worked on... I think a PhD is a very special time. You get to challenge yourself, push your boundaries, and grow. My thoughts go against the current AI/academia narrative online, so I hope you find it interesting. chaitjo.substack.com/p/phd-thesis...
A Cambridge PhD thesis in three research questions
Geometric Deep Learning for Molecular Modelling and Design: A personal scientific journey
chaitjo.substack.com
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)
Das Lab@rdaslab.bsky.social · 7mo agoPreprint on the Stanford #RNA 3D folding Kaggle challenge is out. My scientific new year’s resolution is to brush up on template-based modeling. #gofai www.biorxiv.org/content/10.6...
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...
AI vs. Humans: The "AlphaGo Moment" for RNA Design
YouTube video by Chaitanya K. Joshi
youtube.com
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...
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
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!
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
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
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.
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)
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. 😎
Chaitanya K. Joshi@chaitjo.bsky.social · 8mo agoIntroducing 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! 🧵👇
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! 🧬🧪
Chaitanya K. Joshi@chaitjo.bsky.social · 8mo agoIntroducing 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! 🧵👇
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! 🧵👇
To make future progress it’s worth revisiting the past. From Olke Uhlenbeck, “Keeping RNA Happy” pmc.ncbi.nlm.nih.gov/articles/PMC...
Keeping RNA happy
An official website of the United States government
pmc.ncbi.nlm.nih.gov
Chaitanya K. Joshi@chaitjo.bsky.social · 9mo ago🚀🧬 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...
🚀🧬 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...
Beyond structure-based biomolecule design
Dynamics, black-box data, and the antedisciplinary frontier of biomolecule design
chaitjo.substack.com
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.
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...
🚨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.
MLSB (in San Diego + Copenhagen)@workshopmlsb.bsky.social · 12mo ago📢The submission portal for MLSB 2025 is live! Submissions are due September 26, 2025 11:59 pm AoE. cmt3.research.microsoft.com/MLSB2025
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...
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 🧵
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
Samuel King@samuelhking.bsky.social · 11mo agoMany 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 🧵
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💫
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)
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 🤯
(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...)
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...
biorxiv.org
📢 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
MLSB 2025 Workshop
Workshop on Machine Learning in Structural Biology co-located with NeurIPS 2025
mlsb.io
RosettaFold 3 is here! 🧬🚀 AtomWorks (the foundational data pipeline powering it) is perhaps the really most exciting part of this release! Congratulations @simonmathis.bsky.social and team!!! ❤️ bioRxiv preprint: www.biorxiv.org/content/10.1...
Really insightful post and responses - this is why I keep coming back to science social media!
Kresten Lindorff-Larsen@lindorfflarsen.bsky.social · 2y agoWe’re getting more and more papers on de novo protein design, but I still don’t really know what it means What’s your definition of de novo design?
