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Chaitanya K. Joshi

@chaitjo.bsky.social
1.1K followers 178 following 131 posts

AI researcher excited about biomolecule design 🧬 PhD student at the University of Cambridge Prev. at FAIR, Prescient Design, and MRC LMB 📝 chaitjo.substack.com

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Chaitanya K. Joshi @chaitjo.bsky.social · 14/04/2026
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.
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Chaitanya K. Joshi @chaitjo.bsky.social · 06/02/2026
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...
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Chaitanya K. Joshi @chaitjo.bsky.social · 08/01/2026
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...
chaitjo.substack.com
A Cambridge PhD thesis in three research questions
Geometric Deep Learning for Molecular Modelling and Design: A personal scientific journey
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Chaitanya K. Joshi @chaitjo.bsky.social · 02/01/2026
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)
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Chaitanya K. Joshi @chaitjo.bsky.social · 26/12/2025
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...
youtube.com
AI vs. Humans: The "AlphaGo Moment" for RNA Design
YouTube video by Chaitanya K. Joshi
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Chaitanya K. Joshi @chaitjo.bsky.social · 18/12/2025
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
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.
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Chaitanya K. Joshi @chaitjo.bsky.social · 15/12/2025
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!
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Rocío Mercado Oropeza @rociomer.bsky.social · 09/12/2025
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
arxiv.org
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...
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Arc Institute @arcinstitute.org · 07/12/2025
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.
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Chaitanya K. Joshi @chaitjo.bsky.social · 08/12/2025
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)
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Jill Townley @jilltownley.bsky.social · 03/12/2025
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. 😎
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Erik Poppleton @poppleton.phd · 03/12/2025
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! 🧬🧪
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Chaitanya K. Joshi @chaitjo.bsky.social · 03/12/2025
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! 🧵👇
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Chaitanya K. Joshi @chaitjo.bsky.social · 03/12/2025
Wow thank you, Jamie, for sharing! 🤗
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Jamie Cate @jhdcate.bsky.social · 15/11/2025
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
Keeping RNA happy
An official website of the United States government
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Chaitanya K. Joshi @chaitjo.bsky.social · 15/11/2025
🚀🧬 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...
chaitjo.substack.com
Beyond structure-based biomolecule design
Dynamics, black-box data, and the antedisciplinary frontier of biomolecule design
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Chaitanya K. Joshi @chaitjo.bsky.social · 18/10/2025
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.
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Das Lab @rdaslab.bsky.social · 24/09/2025
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...
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 17/09/2025
🚨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.
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 17/09/2025
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...
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Samuel King @samuelhking.bsky.social · 17/09/2025
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 🧵
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Jase Gehring @skyjase.bsky.social · 18/09/2025
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
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 12/09/2025
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💫
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Chaitanya K. Joshi @chaitjo.bsky.social · 05/09/2025
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)
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Rachael Kretsch @rachael-kretsch.bsky.social · 02/09/2025
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
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Chaitanya K. Joshi @chaitjo.bsky.social · 31/08/2025
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 🤯
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Nate Corley @ncorley.bsky.social · 15/08/2025
(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) [www.biorxiv.org/content/10.1101/202…...)
biorxiv.org
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...
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Chaitanya K. Joshi @chaitjo.bsky.social · 15/08/2025
📢 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.io
MLSB 2025 Workshop
Workshop on Machine Learning in Structural Biology co-located with NeurIPS 2025
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Chaitanya K. Joshi @chaitjo.bsky.social · 15/08/2025
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...
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Chaitanya K. Joshi @chaitjo.bsky.social · 01/08/2025
Really insightful post and responses - this is why I keep coming back to science social media!
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Chaitanya K. Joshi @chaitjo.bsky.social · 31/07/2025
🧬 Protein designers: we keep saying we're getting really good at making static, rock-like proteins... Introducing Dynamic MPNN - our first step towards truly multi-state and 'programmable' protein design! Great collaboration led by Alex Abrudan and Sebastian Pujalte!
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Martin Pacesa @martinpacesa.bsky.social · 25/07/2025
I am super excited to announce that I will be starting my lab at the Department of Pharmacology of the University of Zurich in Switzerland next year!
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Eterna @eternagame.org · 23/07/2025
Coming up this weekend, Eternacon will feature presentations about fellow #citsci platform @zooniverse.bsky.social and how participants of both Zooniverse and Eterna have created #machinelearning tools for projects. @noirlabastro.bsky.social Register for free at eternagame.org/eternacon/2025
Blue image of ROOL nanocage made of RNA with text on top noting Eternacon dates as July 26 and 27.
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Rae Radford @raeradford.bsky.social · 19/07/2025
#BookSky
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Chaitanya K. Joshi @chaitjo.bsky.social · 16/07/2025
Are we hitting a wall with scaling molecular foundation models? Some thoughts on what I think is one of the most interesting open Qs atm: chaitjo.substack.com/p/transfer-l...
chaitjo.substack.com
Towards transfer learning in molecular foundation models
Are multi-modal molecular foundation models learning transferable representations across biology and chemistry?
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Quanta Magazine @quantamagazine.org · 14/07/2025
How does a cell know when it’s been damaged? A molecular alarm, set off by mutated RNA and colliding ribosomes, signals danger. @dsamorod.bsky.social reports: www.quantamagazine.org/rna-is-the-c...
quantamagazine.org
RNA Is the Cell’s Emergency Alert System | Quanta Magazine
How does a cell know when it’s been damaged? A molecular alarm, set off by mutated RNA and colliding ribosomes, signals danger.
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Phil Holliger @philholliger.bsky.social · 14/07/2025
We are looking to recruit a tenure track group leader in the field of Chemical/Synthetic Biology (in the broadest sense) to lead a research program within the Division of Protein & Nucleic Acid Chemistry ( www.jobs.ac.uk/job/DNW809/r... ) at the MRC Laboratory of Molecular Biology (LMB).
jobs.ac.uk
Research Group Leader in Chemical/Synthetic Biology at MRC Laboratory of Molecular Biology
Start your UK & international job search for academic jobs, research jobs, science jobs and managerial jobs in leading universities and top...
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Kelly Nguyen @kellythd-nguyen.bsky.social · 11/07/2025
Highly collaborative efforts that involved 6 lab members and the labs of @yiliangding.bsky.social and @rdaslab.bsky.social. We uncovered a telomerase dimer and its potential role in telomere maintenance.
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Gina El Nesr @ginaelnesr.bsky.social · 07/07/2025
Unfortunately, the MLSB Workshop @ NeurIPS (@workshopmlsb.bsky.social) was rejected this year. Feedback from the deciding committee indicates it was a coin flip decision, with 283 proposals & a number related to “computational biology” More on the future of MLSB soon…
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Chaitanya K. Joshi @chaitjo.bsky.social · 30/06/2025
Needing a permanent doi was a forcing function to revisit this article on Transformers and Graph Neural Networks: arxiv.org/abs/2506.22084 This is (very) old news, so what's new?
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Chaitanya K. Joshi @chaitjo.bsky.social · 28/06/2025
This was posed by a VC (@dreidco.bsky.social ) on LinkedIn. Just a thought: Maybe Boltz-2 is also a moment similar to GPT-3 where a sizeable part of the community moves on from academic publishing and to the world of capabilities, tech reports, and shipping models
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Chaitanya K. Joshi @chaitjo.bsky.social · 20/06/2025
Check out this post from @ffabffrasca.bsky.social and the GLOW reading group on the future of graph learning! I’ve also contributed and my main take is - its actually working and its an exciting moment to work on applications! open.substack.com/pub/glowread...
open.substack.com
Community Takes on the Future of Graph Learning
On drifting goals, fresh frontiers, and a bittersweet lesson we are slowly learning
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Joe Greener @jgreener64.bsky.social · 16/06/2025
Interested in a postdoc position combining computational protein design and molecular simulation? There is an open position in my group at the MRC-LMB in Cambridge, UK. www.nature.com/naturecareer... Feel free to message me with any questions.
nature.com
Postdoctoral Scientist - Structural Studies - Dr Joe Greener - LMB 2633 - Cambridgeshire job with MRC Laboratory of Molecular Biology (LMB) | 12840475
Postdoctoral Scientist Salary £41,344 per annum  Fixed Term – 3 years MRC Laboratory of Molecular Biology, Cambridge, UK We are looking for a postd...
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Chaitanya K. Joshi @chaitjo.bsky.social · 13/06/2025
Have you ever been frustrated by how hard it is to tinker with AlphaFold 3? Here's a (hopefully) simple repo to instal locally on laptop/single-GPU and a handy notebook to play around with! github.com/chaitjo/alph...
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Chaitanya K. Joshi @chaitjo.bsky.social · 01/06/2025
After a long hiatus, I've started blogging again! My first post was a difficult one to write, because I don't want to keep repeating what's already in papers. chaitjo.substack.com/p/transforme...
chaitjo.substack.com
Equivariance is dead, long live equivariance?
When should you bake symmetries into your architecture versus just scaling up — an attempt at a nuanced take.
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MRC Laboratory of Molecular Biology @mrclmb.ac.uk · 29/05/2025
How did life on Earth begin? 🌍🧬 New #LMBResearch from Phil Holliger’s group, including James Attwater (now @uclchemistry.bsky.social‬‬ @uclnews.bsky.social) shows how pH-freeze-thaw cycles enables RNA self-replication, overcoming a key evolutionary hurdle.‬ Read more: www.ucl.ac.uk/news/2025/ma...
ucl.ac.uk
Chemists recreate how RNA might have reproduced for first time
Chemists at UCL and the MRC Laboratory of Molecular Biology have demonstrated how RNA (ribonucleic acid) might have replicated itself on early Earth – a key process in the origin of life.
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Phil Holliger @philholliger.bsky.social · 29/05/2025
New paper from my group rdcu.be/eoaRr "Trinucleotide substrates under pH–freeze–thaw cycles enable open-ended exponential RNA replication by a polymerase ribozyme" in Nature Chemistry — great collaboration with attwaterlab.uk.
rdcu.be
Trinucleotide substrates under pH–freeze–thaw cycles enable open-ended exponential RNA replication by a polymerase ribozyme
Nature Chemistry - Models of abiotic RNA replication suffer from inherent product inhibition arising from the high stability of RNA duplexes. Now, it has been shown that RNA trinucleotide...
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Chaitanya K. Joshi @chaitjo.bsky.social · 22/05/2025
Sharing a surprising result on AI molecule generation with Transformers: All-atom DiT with minimal molecular inductive bias is on par with SOTA equivariant diffusion (SemlaFlow, a very strong and optimized model) Scaling pure Transformers can alleviate explicit bond prediction!
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Rachael Kretsch @rachael-kretsch.bsky.social · 20/05/2025
What is the status of nucleic acid structure prediction? Our analysis of CASP16 (doi.org/10.1101/2025...) reveals human expertise is still necessary for the most accurate prediction, but accuracy still heavily relies on templates; having seen a similar structure already.
doi.org
Assessment of nucleic acid structure prediction in CASP16
Consistently accurate 3D nucleic acid structure prediction would facilitate studies of the diverse RNA and DNA molecules underlying life. In CASP16, blind predictions for 42 targets canvassing a full ...
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Chaitanya K. Joshi @chaitjo.bsky.social · 06/05/2025
Happy to be a small part of this humongous effort by the inimitable Srijit!
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