Chaitanya K. Joshi @chaitjo.bsky.social · 14/04/2026Excited 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. 011
Chaitanya K. Joshi @chaitjo.bsky.social · 06/02/2026I 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... 030
Chaitanya K. Joshi @chaitjo.bsky.social · 08/01/2026New 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.comA Cambridge PhD thesis in three research questionsGeometric Deep Learning for Molecular Modelling and Design: A personal scientific journey 1112
Chaitanya K. Joshi @chaitjo.bsky.social · 02/01/2026Happy 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) 182
Chaitanya K. Joshi @chaitjo.bsky.social · 26/12/2025Merry 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.comAI vs. Humans: The "AlphaGo Moment" for RNA DesignYouTube video by Chaitanya K. Joshi 120
Chaitanya K. Joshi @chaitjo.bsky.social · 18/12/2025I 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.comAn AI Researcher in the Cathedral of Molecular BiologyHow we designed catalytic RNA functions, and what I learned holding a pipette at the MRC Laboratory of Molecular Biology. 041
Chaitanya K. Joshi @chaitjo.bsky.social · 15/12/2025Excited 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! 182
Reposted by Chaitanya K. JoshiRocío Mercado Oropeza @rociomer.bsky.social · 09/12/2025Happy 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 1/4arxiv.orgLeMat-GenBench: A Unified Evaluation Framework for Crystal Generative ModelsGenerative 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... 1103
Reposted by Chaitanya K. JoshiArc Institute @arcinstitute.org · 07/12/2025Thank 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. 281
Chaitanya K. Joshi @chaitjo.bsky.social · 08/12/2025I 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) 160
Reposted by Chaitanya K. JoshiJill Townley @jilltownley.bsky.social · 03/12/2025An 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. 😎 162
Reposted by Chaitanya K. JoshiErik Poppleton @poppleton.phd · 03/12/2025Enumerating 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! 🧬🧪 0176
Chaitanya K. Joshi @chaitjo.bsky.social · 03/12/2025Introducing 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! 🧵👇 2296
Reposted by Chaitanya K. JoshiJamie Cate @jhdcate.bsky.social · 15/11/2025To 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.govKeeping RNA happyAn official website of the United States government 041
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.comBeyond structure-based biomolecule designDynamics, black-box data, and the antedisciplinary frontier of biomolecule design 042
Chaitanya K. Joshi @chaitjo.bsky.social · 18/10/2025Why 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. 140
Reposted by Chaitanya K. JoshiDas Lab @rdaslab.bsky.social · 24/09/2025The 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... 0145
Reposted by Chaitanya K. JoshiMLSB (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. 033
Reposted by Chaitanya K. JoshiKevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 17/09/2025Genome 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... 2319
Reposted by Chaitanya K. JoshiSamuel King @samuelhking.bsky.social · 17/09/2025Many 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 🧵 35020
Reposted by Chaitanya K. JoshiJase Gehring @skyjase.bsky.social · 18/09/2025very 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 2149
Reposted by Chaitanya K. JoshiMLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 12/09/2025You 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💫 2106
Chaitanya K. Joshi @chaitjo.bsky.social · 05/09/2025The 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) 040
Reposted by Chaitanya K. JoshiRachael Kretsch @rachael-kretsch.bsky.social · 02/09/2025We 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 1134
Chaitanya K. Joshi @chaitjo.bsky.social · 31/08/2025Scaling 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 🤯 000
Reposted by Chaitanya K. JoshiNate 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.orgAccelerating Biomolecular Modeling with AtomWorks and RF3Deep learning methods trained on protein structure databases have revolutionized biomolecular structure prediction, but developing and training new models remains a considerable challenge. To facilita... 26728
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/MLSB2025mlsb.ioMLSB 2025 WorkshopWorkshop on Machine Learning in Structural Biology co-located with NeurIPS 2025 032
Chaitanya K. Joshi @chaitjo.bsky.social · 15/08/2025RosettaFold 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... 05418
Chaitanya K. Joshi @chaitjo.bsky.social · 01/08/2025Really insightful post and responses - this is why I keep coming back to science social media! 010
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! 191
Reposted by Chaitanya K. JoshiMartin Pacesa @martinpacesa.bsky.social · 25/07/2025I 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! 2321839
Reposted by Chaitanya K. JoshiEterna @eternagame.org · 23/07/2025Coming 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 052
Chaitanya K. Joshi @chaitjo.bsky.social · 16/07/2025Are 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.comTowards transfer learning in molecular foundation modelsAre multi-modal molecular foundation models learning transferable representations across biology and chemistry? 111
Reposted by Chaitanya K. JoshiQuanta Magazine @quantamagazine.org · 14/07/2025How 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.orgRNA Is the Cell’s Emergency Alert System | Quanta MagazineHow does a cell know when it’s been damaged? A molecular alarm, set off by mutated RNA and colliding ribosomes, signals danger. 0205
Reposted by Chaitanya K. JoshiPhil Holliger @philholliger.bsky.social · 14/07/2025We 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.ukResearch Group Leader in Chemical/Synthetic Biology at MRC Laboratory of Molecular BiologyStart your UK & international job search for academic jobs, research jobs, science jobs and managerial jobs in leading universities and top... 12733
Reposted by Chaitanya K. JoshiKelly Nguyen @kellythd-nguyen.bsky.social · 11/07/2025Highly 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. 15917
Reposted by Chaitanya K. JoshiGina El Nesr @ginaelnesr.bsky.social · 07/07/2025Unfortunately, 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… 285
Chaitanya K. Joshi @chaitjo.bsky.social · 30/06/2025Needing 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? 161
Chaitanya K. Joshi @chaitjo.bsky.social · 28/06/2025This 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 100
Chaitanya K. Joshi @chaitjo.bsky.social · 20/06/2025Check 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.comCommunity Takes on the Future of Graph LearningOn drifting goals, fresh frontiers, and a bittersweet lesson we are slowly learning 082
Reposted by Chaitanya K. JoshiJoe Greener @jgreener64.bsky.social · 16/06/2025Interested 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.comPostdoctoral Scientist - Structural Studies - Dr Joe Greener - LMB 2633 - Cambridgeshire job with MRC Laboratory of Molecular Biology (LMB) | 12840475Postdoctoral Scientist Salary £41,344 per annum Fixed Term – 3 years MRC Laboratory of Molecular Biology, Cambridge, UK We are looking for a postd... 02725
Chaitanya K. Joshi @chaitjo.bsky.social · 13/06/2025Have 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... 1222
Chaitanya K. Joshi @chaitjo.bsky.social · 01/06/2025After 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.comEquivariance is dead, long live equivariance?When should you bake symmetries into your architecture versus just scaling up — an attempt at a nuanced take. 170
Reposted by Chaitanya K. JoshiMRC Laboratory of Molecular Biology @mrclmb.ac.uk · 29/05/2025How 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.ukChemists recreate how RNA might have reproduced for first timeChemists 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. 12912
Reposted by Chaitanya K. JoshiPhil Holliger @philholliger.bsky.social · 29/05/2025New 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.beTrinucleotide substrates under pH–freeze–thaw cycles enable open-ended exponential RNA replication by a polymerase ribozymeNature 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... 03013
Chaitanya K. Joshi @chaitjo.bsky.social · 22/05/2025Sharing 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! 170
Reposted by Chaitanya K. JoshiRachael Kretsch @rachael-kretsch.bsky.social · 20/05/2025What 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.orgAssessment of nucleic acid structure prediction in CASP16Consistently 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 ... 142
Chaitanya K. Joshi @chaitjo.bsky.social · 06/05/2025Happy to be a small part of this humongous effort by the inimitable Srijit! 020