I'm really excited to break up the holiday relaxation time with a new preprint that benchmarks AlphaFold3 (AF3)/“co-folding” methods with 2 new stringent performance tests. Thread below - but first some links: A longer take: fraserlab.com/2025/12/29/k... Preprint: www.biorxiv.org/content/10.6...

Bacteriophages are normally classified as either virulent or temperate. Reality is, of course, more complicated! Here we show many bacterial isolates contain non-temperate phages that can persist through restreaking. Thanks to all co-authors for such a great collaboration!

So 2025 turned out to be a big year for de novo antibody design! Here are thoughts and predictions on the state of de novo antibody design heading into 2026 🧵

"By placing several phosphorus atoms within a radius of a few nanometres, they couple by means of the hyperfine interaction to a single, shared electron. Such a nuclear spin register enables high-fidelity multi-qubit control and the execution of small-scale quantum algorithms" Wow

This variability is not noise. Most systems show multi-fold expression changes across environmental (low or high temperatures🌡️), physiological (growth stage), or spatial gradients. For examples, some systems seem expressed at the center of biofilms, others on the biofilm edges

Bacterial genomes encode a rich repertoire of antiphage systems, but we still know surprisingly little about when these systems are actually expressed. In this preprint, Lucas Paoli et al, ask what shapes antiphage systems expression in native contexts. www.biorxiv.org/content/10.6...

Happy to share that I’m opening my lab at the Weizmann Institute of Science! We’ll study systems-level regulation of bacterial defense, driven by RNA-protein interactions shaping cell fate. Now recruiting PhD students & postdocs tinyurl.com/4yfa55vd Please reach out and share!

The EMBO Gold Medal 2025 was awarded to Tanmay Bharat and David Bikard: https://www.embo.org/press-releases/embo-gold-medal-2025-awarded-to-tanmay-bharat-and-david-bikard/ 🧪 At #CellBio2025, the EMBO Gold Medal was handed over to David Bikard in recognition of his pioneering work on #GeneEditing.

Phages are full of genes of unknown function that are likely adaptive in specific conditions. New preprint: Phage TnSeq identifies essential genes rapidly and knocks all non-essentials. We would like to send a pool of phiKZ mutants to anyone wanting it! Reach out tinyurl.com/bdcfrejh

Do you think transporters in E. coli contribute to metabolite release? No? Explore the effect of 66 different transporter knockout mutations on the exometabolome dynamics of ~300 metabolites yourself: keio.unil.ch Teaser: Increased proline in ΔputP #microsky #MEvoSky

Colibactin-DNA interstrand crosslinks structure reveals DNA-damaging acitivity of colibactin that is linked to colorectal cancer #MicroSky www.science.org/doi/10.1126/...

Thrilled to share that my postdoc research is published today in @science.org! We found that DNA repair uses cohesin complexes to build new chromatin loops that guide the homology search and boost accurate repair! 1/n www.science.org/doi/10.1126/...

New Thoeris systems and new bacterial TIRs, this time also producing plant and human immune signals 2'cADPR and cADPR!!! Congratulations to @erezyirmiya.bsky.social and Azita Leavitt! It was a pleasure to be involved in this project.

Preprint: Systematic discovery of TIR-based immune signaling systems in bacteria Conservation of TIR-derived signals accross the tree of life! We found bacterial TIR immune systems that signal via canonical cADPR (like in humans) and 2'cADPR (a plant immune signal). Documented 11 Thoeris types

🦠🧪🧬🚨 New paper and database alert: the new IMG/VR release is now MetaVR ! We have a new website - meta-virome.org - with quick search capabilities for the >24M viruses, >12M vOTUs, and >42M protein clusters (including >790k with predicted structures !). academic.oup.com/nar/advance-...

www.nature.com/articles/s41... Structural mechanism of the Retron-Eco7 anti-phage defense system

Looking forward to the meeting on the immune system of bacteria! Rockefeller, 5-7 May 2026. A fantastic lineup of speakers, expecting exiting science

Check out our latest paper on mirusviruses, one of the most remarkable new groups of protist viruses - extremely diverse, carry lots of spliceosomal introns (including new homing introns) and are at the evolutionary crossroads between tailed phages and herpesviruses! www.nature.com/articles/s41...

The mechanism of Lamassu, an abundant bacterial immune system, is now solved Lamassu evolved from a DNA repair complex Beautiful study from the Patel, Bernheim and Sternberg labs

Work I co-led with @jnoms.bsky.social is now online at @cp-cellhostmicrobe.bsky.social ! We revealed a previously unrealized diversity of viral immune-evasion proteins that selectively destroy different cyclic nucleotide signals used in bacterial immunity. www.sciencedirect.com/science/arti...

Arbitrium systems control lysis/lysogeny through the regulation of small antirepressor proteins https://www.biorxiv.org/content/10.1101/2025.11.23.689978v1

How does messenger RNA (mRNA) get out of the nucleus to become a protein? Eukaryotic mRNA is packaged, exported, and then translated in the cytoplasm. But how do these steps work? And what are open questions? Check out our new review for our take: www.annualreviews.org/content/jour... (1/3)

Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/ www.science.org/doi/10.1126/...

With this working, as a first test we took two plasmids, identical save for 8 point mutations changing the color, and competed them against one another. Here’s a video of what it looked like when we activated the recombinase. You can see the two compete in real time: 4/

🚀New preprint from our lab! I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡 Continue reading (🧵)

🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages. Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms. A thread 1/8

Very happy to see this piece out in @plosbiology.org, on the bacterial immune systems and microbial communities. It was a great team effort with Rafael Custodio, @brockhurstlab.bsky.social , @brownlab.bsky.social, and Edze Westra! 🦠🧫 #phagesky #mevosky journals.plos.org/plosbiology/...

Part 93 of 200 in historically interesting things to inspire your ttrpg dnd 2,700-year-old Assyrian lamassu at ancient Dur-Sharrukin

A few py2Dmol updates 🧬 py2dmol.solab.org Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)

Meet Aude Bernheim @audeber.bsky.social, EMBO Young Investigator at @pasteur.fr #France: “The EMBO Young Investigator Programme has been developed by and for researchers,” she says. “It gives us access to some of the best #research infrastructures in the world.” 🧪 www.embo.org/people/build...

Very happy to share our collaborative project on FAM118 proteins - noncanonical sirtuins that form filaments and process NAD in human and other vertebrate cells.

Beautiful preprint from Simone Evans et al. in Alex Gao's group looking at MBL/nuclease and other cool zymogens (pepco, EACC1) in antiphage defense systems. Great to see this paradigm extended - probably many more proteolytically activated effectors out there... www.biorxiv.org/content/10.1...

MISO: microfluidic protein isolation enables single-particle cryo-EM structure determination from a single cell colony. Or from a single dish of HEK cell culture in the case of two membrane proteins. Out in Nature Methods now! lnkd.in/gpyBSceg Wonderful collaboration with the Efremov lab.

Surviving phage attack dynamically regulates bacterial immunity to defeat counterdefenses https://www.biorxiv.org/content/10.1101/2025.11.13.688357v1

Congratulations to Sorek lab alumnus Nitzan Tal, who won the prestigious 2025 Science & SciLifeLab prize for the best PhD thesis in Systems Biology! 💫 Read her Prize Assay, published in the journal Science today www.science.org/doi/10.1126/... @nitzantal.bsky.social

Fascinating discovery - anti-phage defense protein is a proenzyme that is cleaved by partner protease after phage infection and all three! products of cleavage form active nuclease.

Cap1 forms a cyclic tetra-adenylate-induced membrane pore during the type III-A CRISPR-Cas immune response https://www.biorxiv.org/content/10.1101/2025.11.13.688252v1

Our nuclease-protease story is out! We explored a fascinating case of coevolution and modularity in prokaryotic immune systems: www.science.org/doi/10.1126/... Thanks to wonderful coauthors/collaborators/friends, the whole @doudna-lab.bsky.social and everyone at @innovativegenomics.bsky.social

Viral NblA proteins negatively affect oceanic cyanobacterial photosynthesis www.nature.com/articles/s41... this project was led by @omernadel.bsky.social and is a joint work between the labs of @bejalab.bsky.social, Debbie Lindell and Oded Kleifeld from @biologytechnion.bsky.social

📖Latest from the lab: Evo. characterization #antiviral #SAMD9/9L across #kingdoms🚶‍♀️🦍🦠🧫🖥️: ancient #convergence + #adaptations @natecoevo.nature.com Led by amazing Alexandre Legrand +major contributions by Rémi Demeure & Amandine Chantharath @ciri-lyon.bsky.social 1/n www.nature.com/articles/s41...

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