Preprint: Bacteria sense virus-induced genome degradation via methylated mononucleotides tinyurl.com/ch3damp We show how molecular byproducts released during virus-induced cell exploitation are used as signals to trigger host immunity Revealed by the amazing Ilya Osterman. See his thread below👇

HT-PELSA, a new proteomics tool by EMBL researchers, processes samples 100x faster and works directly with complex crude cell, tissue, and bacterial lysates – developments which could accelerate drug discovery and basic biological research 💊 🔗 www.embl.org/news/science...

A membrane-bound nuclease directly cleaves phage DNA during genome injection https://www.biorxiv.org/content/10.1101/2025.11.03.685801v1

Hi everyone, a few years ago, we started a list of labs studying bacterial immunty for students, editors, conference organizers... (currently n=79). Update time ! Send me a message to 1) add your lab or others 2) Correct info docs.google.com/spreadsheets... #Phagesky #Microsky

Last year it was discovered that a single bacterial NLR-like protein can recognize multiple, structurally unrelated phage proteins (Béchon et al, Kibby et al) Now, a new study shows the same for a plant NLR. Another example how principles of immunity remain conserved from bacteria to eukaryotes

Are you interested in studying RNA phages? We are looking for a PhD student and a postdoc to join the lab! For more information and how to apply, see below 👇 Please RT!

I’m thrilled to share our Retron Eco8 paper published in Molecular Cell today. Thanks all Fu lab members and our collaborators. 👉Phage SSB detection by retron Eco8 msDNA unleashes nuclease-mediated immunity. www.cell.com/molecular-ce...

Excited to share: DNA glycosylases are diverse antiviral effectors. They recognize phage base modifications and initiate genome destruction. A structure‑guided approach made the scope of this discovery possible! 🧪 #phagesky doi.org/10.1101/2025... #phage #microbiology

Antiviral Defence is a Conserved Function of Diverse DNA Glycosylases https://www.biorxiv.org/content/10.1101/2025.10.29.685425v1

🎉 Huge congrats to Maya Schuldiner from the Weizmann Institute (Israel) for the 🏅 Otto Warburg Medal 2026! Her work on how proteins find their way to organelles and how these organelles talk to each other has reshaped how we think about cells 🧬✨ #OWM #WeizmannInstitute @elsevierconnect.bsky.social

Everything is integrated in one easy to use end-to-end pipeline! Just type up your design specification and try it out!

Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!

New article alert: Bacterial TIR-based immune systems sense phage capsids to initiate defense Out now in Nature Microbiology by Cameron G. Roberts, Chloe B. Fishman, Zhiying Zhang, Dalton V. Banh, Dinshaw J. Patel & Luciano A. Marraffini #microsky www.nature.com/articles/s41...

Been working on a really strange retron bacterial immune system, here's the preprint: www.biorxiv.org/content/10.1... Type VI retrons are unlike any other. Phage infection triggers reverse transcription of a DNA fragment that activates translation of a toxin to kill the infected cell.

Now published in PLOS Biology! We found new retron containing bacteria in the wild, figured out defense mechanisms, and turned them into genome editors. From a cupful of dirt to new parts for genome editing in one story! journals.plos.org/plosbiology/...

New biology: stink bugs inoculate their eggs with a fungus that protects them from parasitoids www.sciencemagazinedigital.org/sciencemagaz...

Super excited about first Shendure/Baker Lab collaboration & preprint on a multiplex sequencing-based strategy for screening de novo proteome editors in mammalian cells. Kudos to the brilliant Chase Suiter (not here) & @greenahn.bsky.social on the work! Preprint here: www.biorxiv.org/content/10.1...

NAD+ is a central molecule in bacterial immunity. An excellent and timely review by Hugo Vausset and Aude Bernheim

A new study from the Sternberg lab suggests that the telomerase function evolved from a defense system that protects bacteria against phages. Amazing!

Perfect timing in the field for a beautiful review on NAD+ in bacterial immunity by @hugovaysset.bsky.social and @audeber.bsky.social @cp-molcell.bsky.social #MicroSky www.cell.com/molecular-ce...

🦖 Something HUGE just hatched. Plasmidsaurus now offers RNA sequencing for gene expression analysis: • As fast as 3 day turnaround • $50/sample for academia, $80 for industry • Up to ~10M unique transcript 3’ end reads per sample • Interactive results Explore Plasmidsaurus RNA-Seq today.

Wow, a significant expansion of what we know about BREX. www.biorxiv.org/content/10.1...

Happy that the final version of our Lamassu work @yli18smc.bsky.social is now out: www.nature.com/articles/s41... Thanks again to our awesome collaborators @mblokesch.bsky.social and David and co and Mark Szczelkun and @steven-shaw.bsky.social and the DCI Lausanne @fbm-unil.bsky.social

Thank you to the Blavatnik Family Foundation and The New York Academy of Sciences for honoring our research uniting human innate immunity and bacterial anti-phage defense at @danafarber.bsky.social @harvardmicro.bsky.social @harvard.edu bit.ly/4pZUDkF blavatnikawards.org/news/items/t...

How do SMC complexes load onto DNA to get ready for loop extrusion? @roisnehamelinf.bsky.social & co discovered that Wadjet, an SMC complex involved in bacterial DNA immunity, performs some impressive molecular gymnastics 🤸‍♂️🤸‍♂️🤸‍♂️. Check out the new paper: www.cell.com/molecular-ce...

Congratulations to Philip J. Kranzusch, Ph.D., Professor of Cancer Immunology and Virology, who was one of three scientists awarded top honors at the 2025 Blavatnik National Awards for Young Scientists. Watch to learn more about his work: bit.ly/4pZUDkF

You can get MSAs directly from AlphaFold DB now (alphafold.ebi.ac.uk). I also missed the FoldSeek implementation, which lets you search for structurally similar proteins direktly. This saves some clicking around. Neat!

My pleasure @erinedoherty.bsky.social and @benmorehouse.bsky.social - for me this was the stand-out discovery of the last year in the field

Our story describing the Panoptes bacterial immune defense system is now finally peer-reviewed and published today! www.nature.com/articles/s41...

Today in @nature.com , we highlight how a cousin of CRISPR-Cas10, mCpol, establishes an evolutionary trap in anti-phage immune systems. Check out @erinedoherty.bsky.social and my work from @doudna-lab.bsky.social lab here: www.nature.com/articles/s41...

www.nature.com/articles/s41... #phagesky #phage defence

In reporting this piece on the new trial for a Huntington's treatment, I was struck by one thing in particular: The joy. One of my sources wept for joy. He has spent his entire career studying this disease, he said it was the happiest day. www.sciencenews.org/article/hunt...

I found this fascinating! Termites build and tend a fungal garden. www.science.org/doi/10.1126/...

You’ve heard of ubiquitination, meet deazaguanylation: Doug Wassarman in our lab discovered phage defense pathways have co-opted Q nucleobase biosynthetic enzymes to catalyze a new form of protein conjugation chemistry @science.org www.science.org/doi/10.1126/...

Still boggles my mind that we can leave frameworks as-is and only edit CDRs and still reliably get nM binders. Complete opposite of what I would have expected given how hard it is to graft CDRs from one FW to another (such as humanizing mouse mAbs). First RFantibody and now this

A recent cool preprint by John Whitney's lab on a new family of antibacterial proteins secreted by Gram-positive bacteria that enter and kill a broad spectrum of bacteria. Cell entry is receptor-independent and relies on cleavage by a co-secreted protease and the PMF. www.biorxiv.org/content/10.1...

MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n 📄 www.nature.com/articles/s41... 💿 mmseqs.com

De novo design of All-atom biomolecular interactions with RFdiffusion3 www.biorxiv.org/content/10.1...

GPU-accelerated MMseqs2 offers tremendous speedup for homology retrieval, protein structure prediction with ColabFold, and protein structure search with Foldseek. @martinsteinegger.bsky.social @milot.bsky.social @machine.learning.bio www.nature.com/articles/s41...

PIWI clade Argonautes are essential for transposon silencing. Without them, animals are sterile due to massive transposon activity. But how does piRNA-guided target interaction translate into silencing? PhD student Júlia Portell Montserrat has an intriguing answer www.cell.com/molecular-ce...

YprA family helicases provide the missing link between diverse prokaryotic immune systems https://www.biorxiv.org/content/10.1101/2025.09.15.676423v1

Excited to share our latest paper - now out in @science.org - we showed how oxytocin modulates maternally-directed behavior in young mice (P15).

Phage "satellites" that produce capsids but have no genes to produce tails have puzzled scientists for a long time. These are abundant as prophages in bacteria, but it was unclear how they can infect without tails Now, Penadés & co show that they hijack tails from other phages. Incredible!

Looking for a new approach to studying or eliminating phages? Check out our study introducing anti-phage ASOs (antisense oligos) out in @Nature today. nature.com/articles/s4158…

Cool preprint! 🚨 Lanternfish lack MHC I and functional MHC II — yet still produce antibodies! 🧬🐟 www.biorxiv.org/content/10.1...

Sometimes you meet absolutely incredible bioinfo-magicians. It was a huge privilege when @shenwei356.bsky.social joined our group for a year on an @embl.org sabbatical. While here, he developed a new way of aligning to millions of bacteria, called LexicMap 1/n www.nature.com/articles/s41...

Thrilled to share our two latest papers with the @tcostalab.bsky.social lab! In the first, we uncover a new mechanism of satellite transfer: cf-PICIs hijack tails from diverse phages to spread across species. @imperialcollegeldn.bsky.social www.cell.com/cell/fulltex...

Update: RareFold 🧬 Our AI framework for protein design with 29 noncanonical AAs now shows designed binders (linear + cyclic) are non-immunogenic in patient-derived assays — paving the way for safe next-gen peptide therapeutics. 👉https://www.biorxiv.org/content/10.1101/2025.05.19.654846v2

Harnessing the anti-phage defense system DarTG for single-base editing in human cells - an impressive method developed by Chase Beisel and colleagues

Excited to share my latest review, now published in the Royal Society theme issue on ‘The ecology and evolution of bacterial immune systems' (available OA): Defence systems encoded by core genomic islands of seventh pandemic Vibrio cholerae royalsocietypublishing.org/doi/10.1098/...