Next Tuesday, 5/07 @ 4 pm EST, we're very excited to have Jeff Ruffolo @stephennaybach from Profluent present OpenCRISPR! Read the paper here: biorxiv.org/content/10.110… Sign up on our website to get the Zoom link via email next week!

Did you see the bridge RNA papers yesterday? Bacterial transposons promote programmable, RNA-guided DNA recombination. Remarkably, we found that the recombinase was co-opted in archaea and eukaryotes for widspread RNA-guided RNA modification, an essential function in humans!

I am thrilled to start my lab as an assistant professor Biozentrum, University of Basel & NCCR AntiResist of University of Basel this fall. I will continue my research interest in bacteria & jumbophage interactions. Equally thrilled to be closer to our families after 10+ years.

Protein structural search uncovers an ancestral Cas13 protein led by the brilliant Peter Hyungjun Yoon !! Check out the paper and thread! 👇

For gene editors, we started with a low-activity base editor previously designed using LMs, then focused design on either active site or non-active site residues. Both yielded base editors with 50% higher A-to-G editing, approaching SOTA editors in just one round of optimization.

For antibodies, we started with the clinically approved PD-1 binder nivolumab, focusing design on either the CDR loops or framework. We obtained a wide range of binders from each approach, including two antibodies with nearly 3-fold higher affinity for PD-1 than nivolumab.

Fun fact: USA men’s 4x100 have failed baton passes in the 2008, 2016, 2020, and now 2024 Olympics.

Glad this is finally out! 🛡️AntiDefenseFinder 🔎🦠 will identify over 150 defense inhibitor families across MGEs, phages, and prokaryotes. Update DefenseFinder to v1.3.0 to use. Congrats Florian and Erin Huiting!

My favorite and hardest NMR experiment ever conducted is finally out! Congrats to everyone involved, but especially Daphne for pushing the project to the end 🎉🎊

The final version of our paper on anti-CRISPRs "in disguise" as Cas proteins is out today in Nature! Congrats to Mark, Edith and the whole team! nature.com/articles/s4158…

Tomorrow, 9/17 @ 4pm ET, we'll have Jeff Ruffolo Profluent present ProseLM: Adapting protein language models for structure-conditioned design Sign up on our website to receive zoom links via email or DM us to join! Read the paper: biorxiv.org/content/10.110…

Stat news I can’t even get one free article a month?

I'm thrilled to share that I've joined Dr. Pam Ronald’s lab at UC Davis to study how plants evolve multi-pathogen resistance, and in the long-term, build upon sustainable agriculture practices. As pivot into this field, I'd love to connect w/ folks in the ag & climate space!🌱🌎

I am very proud to share our paper on Tad1/Tad2 sponges, which appeared to be multifunctional anti-defense proteins that inhibit many different signaling-based immunity systems!💫 nature.com/articles/s4158…

🌟Our latest results are now published at NAR🌟 tinyurl.com/bdfbdxt4. We hope that AntiDefenseFinder will enable scientists to further uncover the natural diversity of inhibitors (or regulators) of known bacterial defense systems. Recap below!

Can LLMs exert molecular control in modulating protein-DNA interactions? New research where we demonstrate AI can reprogram DNA recognition of gene editors-- all in single-shot without iterative laboratory screening. Incredible positive impact to unlock

Claire's paper now entitled "Multi-interface licensing of protein import into a phage nucleus" is now published here: nature.com/articles/s4158… Claire Kokontis used classic genetics to figure out how proteins are selected for import into a "phage nucleus" Some notable additions:

What could scaling unlock for biology? Introducing ProGen3- our next AI foundation models for protein generation. We develop compute-optimal scaling laws up to 46B parameters on 1.5T tokens with real evidence in the wet lab. +we solve a new set of challenges for drug discovery

Check out our new paper describing rAcrVIA1: an RNA anti-CRISPR that mimics guide RNAs to inhibit Cas13. Very fun project with stellar UW undergrad Victoria Hayes and collaboration with Ning Jia's group! science.org/doi/10.1126/sc…

Excited to share our last collab paper, now out in print Science Magazine!🎉 We reveal how dITP synthesis activates a SIR2 NADase effector to block phage infection! 🛡️🧬 science.org/doi/10.1126/sc…