New paper! How do RNAs "know" where to go inside a cell? We dug into the sequence elements that route RNAs to the right place. It turns out that, in mammals, they're surprisingly massive (>200 nt), multipartite, and wonderfully complicated. 🧵

Excited to share our work uncovering SNOR, a ribosome-associated factor that promotes translation restart after dormancy published in Nature!! This was, as usual, a wonderful collaborative effort between our group and the Mattei Lab @simonemattei.bsky.social @embl.org www.nature.com/articles/s41...

Our lab is proud to present our latest work harnessing Bridge Recombinase for genome-scale editing in diverse bacteria, microbiome editing, and programmable horizontal gene transfer.

The best thing since *before* sliced bread... VIPRs. www.biorxiv.org/content/10.6... www.biorxiv.org/content/10.6...

"Use it or lose it." This is great advice for exercise, but when cells need to slow down or go dormant, they need to store ribosomes to recover growth in the future. They use hibernation factors to do this. Here is our latest story on how archaea hibernate ribosomes (1/7): doi.org/10.64898/202...

Excited to share our first work on protein design! Huge thanks to the entire team, and especially to Bel, Evan, to the Doudna, Jacobsen, Cate, Banfield labs, all co-authors, and my D-lab mates! 💫

A very nice Preview of our work in @cp-cellhostmicrobe.bsky.social this morning from Chrishan Fernando & Nicole D. Marino! www.cell.com/cell-host-mi...

Our study from the Steckelberg lab is out now in @narjournal.bsky.social !! We dove into a new nuclease-blocking viral #RNA structure important for viral infection, which provided evidence of similar structure-based strategies across diverse viral families. academic.oup.com/nar/article/...

Archaeal virus entry and egress Archaea also have viruses and they are cool! #microbiology #virology #virus #viruses @femsmicro.org @femsjournals.bsky.social academic.oup.com/microlife/ar...

Our work, co-led by @alfredo0712.bsky.social and @nlue8.bsky.social is out in @natsmb.nature.com Shout out to coauthors P.Grob, B. Kaeser, J.Fang, and S. Kassube for their contributions and thanks to the reviewers for the suggestions that led to the final work. www.nature.com/articles/s41...

We are happy to share that our snR30 story is finally out in @natureportfolio.nature.com 🥳 We report the first structure of a H/ACA snoRNP acting in ribosome synthesis thereby providing a detailed structural and biochemical view of the snR30 snoRNP guiding local 18S rRNA subdomain folding. 👇👇👇

Final grad paper is officially out! Grateful for the incredible team and all the support along the way! www.nature.com/articles/s41...

Preprint alert! ✨ In this project that I co-led with @benadler.bsky.social, we show that a miniature CRISPR-Cas10-like enzyme, mCpol, uses a novel inverse signaling mechanism to prevent the spread of viruses that attempt immune evasion by depleting host cyclic nucleotides. Check it out:

Giving a seminar for the Genome Engineering Seminar Series at Harvard this Monday, April 7 at 1pm EST / 10am PST! 🎙️ I’ll be talking about our Cas9 work—if you’ve ever wondered what the recipe is for high-efficiency CRISPR genome editing, come hang out!🧬💥 📍 Zoom link: harvard.zoom.us/j/94394339529

Really nice issue of RNA this month featuring many Perspective pieces on RNA in disease. rnajournal.cshlp.org/content/31/3...

We present Rfam-based RNA structural alignments and other structure-based inputs for RNA 3D structure prediction by deep learning. www.biorxiv.org/content/10.1...

Single-molecule live-cell RNA imaging with CRISPR–Csm - @doudna-lab.bsky.social @qb3-berkeley.bsky.social @innovativegenomics.bsky.social go.nature.com/3EJPKsM

Latent Labs comes out of stealth today with $50M funding. Our goal? To push the frontiers of generative biology, giving partners instant access to tools capable of accelerating drug design

I had the pleasure of co-hosting this new career exploration podcast from ASBMB- tune in to hear from my fellow committee member Tom Kiselak about being a patent attorney!

Excited to see this work finally out, it was a pleasure to be involved!

Excited🚨to share our first work on the human gut phageome doi.org/10.1101/2025... Always inspiring to work with @epcrocha.bsky.social , Erick D, Camille d'H and everyone else within this super dynamic consortium @inrae-france.bsky.social[email protected][email protected]! Many thanks for this great journey!🙌

Today, the IGI turns 10! We’ve grown from a fledgling initiative focused around developing #CRISPR tools to a full-blown research institute bringing together leaders in basic & translational research! ⚕️💊🌱☀️ Take a look at our timeline & key achievements from our first decade: ow.ly/GzVt50UTsbP

A conserved class of viral RNA structures regulates translation reinitiation through dynamic ribosome interactions pubmed.ncbi.nlm.nih.gov/39893634/ #cryoem

Thrilled to have been involved in this work and looking forward to what the Sherlock Lab has in store!

✨ New from C-GEM in ACS Central Science: Thioesters Support Efficient Protein Biosynthesis by the Ribosome pubs.acs.org/doi/10.1021/... Congrats to Alexandra & Jacob, along with Isaac, Jess, @alexsolivan.bsky.social, @nxhamlish.bsky.social, Katie, Alanna, Jamie, and Scott! #NSFfunded @pubs.acs.org

Out today @ Science: TIR signaling activates caspase-like immunity in bacteria We report a new immune signaling molecule: N7-cADPR. Produced by phage-induced TIRs and activates a defensive bacterial caspase Congrats Francois Rousset, Ilya Osterman and coauthors! www.science.org/doi/10.1126/...

Our paper out @Nature: CARD domains mediate anti-phage defense in bacterial gasdermin systems CARDs are essential for caspase recruitment during human inflammasome activation. We now find them in bacterial immune systems Congrats Tana Wein! Thank you Kranzusch lab! www.nature.com/articles/s41...

scary but fascinating - cells have a degradation pathway that hunts down C-terminal scars (amides!) on damaged proteins. just wow. chemical biology plus CRISPR at its best. big congrats to all authors! www.nature.com/articles/s41...

In addition to today's posted work by @cryoclem.bsky.social on Archaeal ribosomes we further expanded RAPPL (www.biorxiv.org/content/10.1...) on multiple other complexes that work with ribosomes, subunits or even off the ribosome. Soon more...

Nature research paper: CARD domains mediate anti-phage defence in bacterial gasdermin systems https://go.nature.com/3CvoD3W

It’s out! Brand new work from my PostDoc in @themaxwelllab.bsky.social exploring anti-phage defence in V. parahaemolyticus: Integrons are anti-phage defence libraries in Vibrio parahaemolyticus rdcu.be/d7EsN

New Title Alert: AlphaFlow- a modified version of AlphaFold, fine-tuned with a flow matching objective, designed for generative modeling of protein conformational ensembles. Learn more here: https://buff.ly/4gwVW5o #SBGrid #SBGridsoftware #StructuralBiology

Happy to share our latest findings on Kiwa. Foundational work from Thomas, with Zhiying and Yi providing beautiful structures and molecular insights. Ever grateful for the collaborations with Eugene and Dinshaw. More to come 🙃 doi.org/10.1101/2023...

Our paper out @CellCellPress: Structure guided discovery of viral proteins that inhibit host immunity Congrats Erez Yirmiya, Azita Leavitt, Gil Amitai, our collaborators at the Kranzusch lab, and coauthors A 🧵 1/10 www.cell.com/cell/abstrac...

Congratulations to Dan Haack and Boris Rudolfs on the new paper from our lab about the development of a scaffold enabling high resolution cryo-EM structure determination of protein-free RNAs. www.nature.com/articles/s41...

Foldseek 10 with 4-27x (1-8 GPUs) faster search through MMseqs2-GPU. Faster ProstT5 protein search w/o structure prediction through multi-GPU/Apple Metal, new BFVD/BFMD databases and multimer clustering (preview). 💾 github.com/steineggerla... 📄 www.biorxiv.org/content/10.1... 🐍 available in bioconda

In Science Advances: "We took a deep dive into over 1.8 million bacterial and archaeal genomes to see how much of their diversity we’ve actually captured. Turns out that despite all the genomes we’ve sequenced, we’ve only scratched the surface." -Dongying Wu 🖥️🧬🦠 biosciences.lbl.gov/2025/01/17/t...

🧬🗓️ Mon, Jan 20, 2025, 16:00-17:00 GMT 3D-BioInfo Webinar with insights from AlphaFold Database Register: https://elixir-europe.org/events/3d-bioinfo-webinar-infrastructure-and-functional-annotations Hosted by Elixir By Prof. David Jones Recent pub: www.science.org/doi/10.1126/science.adq4946

Nature research paper: De novo designed proteins neutralize lethal snake venom toxins https://go.nature.com/4fZU9EI

by now you probably know that #giantviruses have #histones, but some also have histone variants! Check out our latest preprint on an essential H2B-H2A histone variant in Melbournevirus - a fantastic collaboration with the Abergel Lab, spearheaded by Ale Villalta. www.biorxiv.org/content/10.1...

So without further ado, HERE is the preprint: www.biorxiv.org/content/10.1.... The answer is YES—water masses do structure microbial communities for both prokaryotes and eukaryotes. In fact, they seem to be the single most important factor structuring microbial communities in the pelagic ocean.

Very cool! As Harry already pointed out!

And it’s been a while since I dipped my toe into the questions of what ‘species’ might mean for bacteria, and how they relate to ecology. But still interests me! genomebiology.biomedcentral.com/articles/10....

We are down to 2.32A and 2.61A for these specific ribosome complexes using tandem purification using RAPPL and tagged protein enrichment. In this case it was and hour and 45 minutes prep and 20-50 ml bacterial culture. www.biorxiv.org/content/10.1...

The Cryo-EM: the next 50 years Symposium held yesterday at @ucberkeleyofficial.bsky.social was a smashing success!!

Congrats to Johannes Linder, David Kelley et al. on the journal publication of Borzoi - a long context sequence models of RNA-seq coverage profiles with many nice applications for transcriptional & post-transcriptional regulation & variant effect prediction. www.nature.com/articles/s41... 1/

Excited to share our work using machine learning to predict anti-phage defense systems! 1/n

What is the diversity of antiphage systems out there ? We used protein and genomic language models (and defense score!) to start bringing some answers: >45 000 protein families. Leb by E. Mordret. www.biorxiv.org/content/10.1... Interactive UMAP to have fun mdmparis.github.io/antiphage-la...

RNA control of reverse transcription in a diversity-generating retroelement www.nature.com/articles/s41...