PhD @Cambridge_Uni | AI in protein design & engineering | biotech & environmental applications | enzymes | geometric DL | prev. @ETH_physics

Joined April 2020
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Simon Mathis retweeted
Today we're launching Latent-Y: the world's first autonomous agent for drug design, lab-validated end to end. Give it a research goal. Latent-Y reasons, designs, iterates, and delivers lab-ready antibodies, autonomously or collaboratively, with the biological reasoning of a PhD protein design expert. Technical report: tinyurl.com/latent-y-techrep… Blog post: latentlabs.com/latent-y Apply for access: platform.latentlabs.com
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Simon Mathis retweeted
Join us next Tuesday and ask questions/discuss research!
Next Tues (3/24) at 4PM ET, @DidiKieran and Danny Reisenbach will present "Proteina-Complexa: Scaling Atomistic Protein Binder Design with Generative Pretraining and Test-Time Compute" Papers: research.nvidia.com/labs/gen… Sign up on our website for zoom links!
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Simon Mathis retweeted
📢 We’re launching Proteina-Complexa — and after the Jensen keynote mention, we definitely had to post this thread now ;) Atomistic binder design with generative pretraining test-time compute, plus large-scale wet-lab validation. Project page: research.nvidia.com/labs/gen… 🧵 1/n
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Simon Mathis retweeted
16 Dec 2025
Introducing Latent-X2 — AI-generated antibodies with drug-like developability and low immunogenicity in human panels, zero-shot. Technical report: tinyurl.com/latent-X2-report Blog: latentlabs.com/latent-x2 Apply for access: partnerships@latentlabs.com
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15 Dec 2025
Lots of gems in there - can highly recommend checking it out! Thank you for all the great work @chaitjo and for making it so accessible
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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Today at 11am I’ll present some of the exciting work in AI x Bio we’ve been up to at @Latent_Labs at the @RenPhilanthropy booth (Hall A/B, booth 1343 @NeurIPSConf - straight through the entrance at the back left). Come say hi!
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Many thanks also to the UK Sovereign AI Unit @SciTechgovuk for the invitation!
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If you can't make it at this time, we're at neurips for the next couple of days - reach out to me or any of our team if you're interested catching up over coffee. There'll also be an event on Saturday: x.com/saakohl/status/1996907… Looking forward to many interesting conversations 🙌

5 Dec 2025
We've had a whopping 500 sign-ups for our @NeurIPSConf mixer tomorrow, heavily waitlisted now! 🤩 Traveling to San Diego now and can't wait for the workshops and our mixer, electric AI fo Bio scene right now! Lots of the @Latent_Labs team are on-site already, let me know if you'd like to meet for a chat!
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Thank you @RenPhilanthropy & @charlieharris01 for hosting us!
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Simon Mathis retweeted
Today, we report a method for design of active enzymes, RFdiffusion2, in @naturemethods. For the first time, we are able to design enzymes with native-range catalytic activity. We also are releasing our next frontier model, RFdiffusion3, code 👇
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Congratulations @chaitjo - so exciting!
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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Simon Mathis retweeted
4 Nov 2025
Come do a PhD with me 😀! Promise of fun science and great coffee ☕
4 Nov 2025
I like the way @joeybos lays out his vision for PhD supervision! Seems intense and rewarding.
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Simon Mathis retweeted
🚨New package alert! 🧬 Introducing Pocketeer: A lightweight, fast protein pocket finder in pure Python! I built this as a Pythonic version of fpocket because I wanted something that could easily calculate subpockets. > pip install pocketeer Link at end of the thread 🧵(1/7)
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Super cool - congratulations Magnus & Team!
Phosphorylation on tyrosines control key pathways in immunity, cancer, and metabolism. For the first time, we can now design proteins that specifically recognize individual phosphotyrosines, even in disordered regions. (1/8) Preprint: biorxiv.org/content/10.1101/…
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Simon Mathis retweeted
We sought to make proteins both potent and FAST. We used #proteindesign to design precise control over protein interaction lifetimes, enabling us to construct rapid-response circuits, biosensors, and switchable cytokines. Now published @Nature! Links to paper and tutorial below.
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Simon Mathis retweeted
We asked ourselves what could we do if we worked cooperatively as a team to create a single model that could design any biomolecular interactions. Yesterday, we reported details of RFdiffusion3, the next step towards building functional proteins straight from the computer.
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Simon Mathis retweeted
Very excited to share our paper "De novo Design of All-atom Biomolecular Interactions with RFdiffusion3", now on BioRXiv. biorxiv.org/content/10.1101/… 1/n
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Simon Mathis retweeted
La-Proteina open source now, excited to see what people build with it!
🧬La-Proteina🧬 The first generative model demonstrating accurate co-design of fully atomistic protein structures (sequence side-chains backbone) at scale, up to 800 residues, with state-of-the-art atomistic motif scaffolding performance - has just made its code open-source! Learn more 🧵
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Simon Mathis retweeted
Thrilled to announce I'm starting as a Principal Investigator at #Aithyra in Vienna! We'll be developing generative models to understand cell biology and design proteins. I'm hiring PhDs, Postdocs, & Visiting Researchers! PhD applications by Sept 10: apply.cemm.at

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Simon Mathis retweeted
26 Aug 2025
Check out our new perspective "Illuminating the universe of enzyme catalysis in the era of artificial intelligence" now out in @CellSystemsCP ! We discuss a vision and path forward for genetically encoding almost all chemistry, powered by new AI tools: authors.elsevier.com/c/1lg4h…

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