Simon Mathis

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

[Simon Mathis @SimMat20]

@goodwin_ml Wow fantastic - congratulations to the fractile team!

[Simon Kohl @saakohl]

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: https://t.co/E7IHfkvvD3
Blog post: https://t.co/GfJAfzj0Qx
Apply for access: https://t.co/E0SR9znZiP

[Kieran Didi @DidiKieran]

Join us next Tuesday and ask questions/discuss research!

[Kieran Didi @DidiKieran]

📢 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: https://t.co/aT8Lz2VhSJ
🧵 1/n

[Simon Kohl @saakohl]

Introducing Latent-X2 — AI-generated antibodies with drug-like developability and low immunogenicity in human panels, zero-shot.

Technical report: https://t.co/9uU6GQCdM7
Blog: https://t.co/TFyCzlZ4qN
Apply for access: [email protected]

[Simon Mathis @SimMat20]

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

[Chaitanya K. Joshi @chaitjo]

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!

[Simon Mathis @SimMat20]

@Latent_Labs @RenPhilanthropy @NeurIPSConf Many thanks also to the UK Sovereign AI Unit
@SciTechgovuk for the invitation!

[Simon Mathis @SimMat20]

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!

[Simon Mathis @SimMat20]

@Latent_Labs @RenPhilanthropy @NeurIPSConf 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:
https://t.co/NteoHewFDs

Looking forward to many interesting conversations 🙌

[Simon Kohl @saakohl]

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!

[Simon Mathis @SimMat20]

@Latent_Labs @RenPhilanthropy @NeurIPSConf Thank you @RenPhilanthropy & @charlieharris01 for hosting us!

[Rohith Krishna @r_krishna3]

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 👇

[Simon Mathis @SimMat20]

Congratulations @chaitjo - so exciting!

[Chaitanya K. Joshi @chaitjo]

Introducing gRNAde: our own little "AlphaGo Moment" for RNA design! 🧬🚀

📝: https://t.co/vZCLiPg99O

Unlike proteins, RNA design has long relied on "wisdom of the crowd" (human experts) or the slow crawl of directed evolution — gRNAde changes that! 🧵👇

[Joey Bose @bose_joey]

Come do a PhD with me 😀! Promise of fun science and great coffee ☕

[Charlie Harris @charlieharris01]

🚨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)

[Simon Mathis @SimMat20]

Super cool - congratulations Magnus & Team!

[Magnus Bauer @kinasekid]

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: https://t.co/iIucGbMSDp

[Adam Broerman @adam_broerman]

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.

[Rohith Krishna @r_krishna3]

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.

[Jasper Butcher @butcher_jasper]

Very excited to share our paper "De novo Design of All-atom Biomolecular Interactions with RFdiffusion3", now on BioRXiv. https://t.co/ry7b17DHgy 1/n

[Kieran Didi @DidiKieran]

La-Proteina open source now, excited to see what people build with it!

[Alex Tong @AlexanderTong7]

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: https://t.co/jYG60pfPX6