Sorek Lab

After having to deal with fracture-related infection and its impact, up close and personal within my family during the past year, our latest research publication hits different... Deeply dedicated to see our 'Fibrilysins' developed towards clinical use in the near future.

Much of the functional biology encoded in genomes remains hidden in noncoding DNA. In a preprint out today, Patrick Hsu and team introduce COMPASS, a genomic language model-based approach to systematically map this underexplored sequence space.

IMO the paper of the year in the gene regulation field - such a clean and clear study, showing how promoter-enhancer contacts mediate transcriptional activation. www.cell.com/cell/abstrac...

Viruses have parasites too. Our new preprint shows how phages use VIPR to silence parasitic satellites, and how the satellites fight back with its own decoy VIPR RNAs that redirect VIPR to DNA REP elements in the host genome!! www.biorxiv.org/content/10.6...

Competition among viral elements for VIPR RNA-directed genome silencing https://www.biorxiv.org/content/10.64898/2026.10.15.759431v1

Very nice discovery from the Jackson, Bravo and Basel labs. Cleaved tRNA ends, loaded with an amino acid, activate a form of bacterial immunity

Aminoacylated tRNA tails trigger auxiliary bacterial immunity https://www.biorxiv.org/content/10.64898/2026.10.14.759216v1

1/1 How does a single methyl group activate bacterial defence? In my PhD work with @matthiaswilmanns.bsky.social and @typaslab.bsky.social, we reveal how this tiny DNA modification triggers retron disassembly and toxin activation. Now on bioRxiv: www.biorxiv.org/content/10.6...

Guardian obituary for biochemist and crystallographer Ada Yonath, née Lifshitz (1939-2026) who won a Nobel Prize for mapping the ribosome #chemsky 🧪 www.theguardian.com/science/2026...

LoL-align is out in @natmethods.nature.com! It aligns protein structures without superposition. More sensitive than TM-align and DALI, producing better alignments 5–20× faster. Now available in Foldseek! 📄 www.nature.com/articles/s41... 💾 github.com/steineggerlab/foldseek 🌐 search.foldseek.com

Single-site DNA methylation activates retron defence by enabling effector tetramerisation https://www.biorxiv.org/content/10.64898/2026.10.13.758329v1

1/5 Telomerase has long been linked to chromosome maintenance in eukaryotes. Now, we show that telomerase-like activity is also present in bacteria, shedding new light on its ancient origins. Excited to share that our work on DRT10 is now out in @nature.com! www.nature.com/articles/s41...

The legendary Symposium on the Immune System of Bacteria is coming to Cambridge, UK. Mark your calendars for 20-22 July 2027. Registration now open!

Congratulations to Prof. Sarel Fleishman of the Biomolecular Sciences Department, upon being awarded the Otto Meyerhof Medal at the MPI Heidelberg

The Lopatina lab is opening in Vienna on Jan 2027. Recommeded!

Massive thanks to P. Yoon and, S. Lopez, @kshulgina.bsky.social, @clangeberg.bsky.social, @knottrna.bsky.social , @doudna-lab.bsky.social and to all our collaborators. Now on @biorxivpreprint.bsky.social www.biorxiv.org/content/10.6... 11/11

Excited to share our work on bacterial immune signaling! Our preprint reveals how RNA-guided Cas13 cleaves host tRNAs to generate small-molecule messengers that activate 2TMβ, linking RNA recognition to membrane damage and phage defense. 1/11

Uncovering novel phage defense systems through genomic island analysis in Streptococcus thermophilus https://www.biorxiv.org/content/10.64898/2026.10.04.756616v1

Sam Hobbs and Philip Kranzusch show how CBASS defense systems sense phage proteases to initiate the immune response in bacteria. The bacterial cGAS becomes activated when cleaved by the phage protease. Nice!

New online! How bacterial immune systems sense phage infection

Andrew Santiago-Frangos and colleagues characterize Tiamat, a giant bacterial defense protein originally detected in the Millman 2022 study, and show that homologs of Tiamat are encoded in animals and plants. Nice to see the mystery of Tiamat starting to unravel

Eirik Lågeide, Gal Ofir and colleagues discover an antiviral protein in plants based on its homology to a bacterial antiphage defense protein called Tiamat. Cool!

Our story with @hobbslabutah.bsky.social discovering CBASS sensing of phage proteases out now in @science.org New data include CBASS recognition of diverse proteases beyond T4, and verifying CD-NTase activation loop cleavage as the trigger for defense in vivo www.science.org/doi/10.1126/...

Make natural language requests to ChimeraX with the new Pellaeon plugin developed by Yam Amir that works with many free and paid large language models. Get Pellaeon using ChimeraX menu Tools / More Tools.... cxtoolshed.rbvi.ucsf.edu/apps/chimera...

Super excited to share my postdoctoral work at @imbavienna.bsky.social @viennabiocenter.bsky.social - We discovered that some retrotransposons, or "jumping genes" 🧬, are able to spread from cell to cell via a new viral infectivity route. A short thread: 🧵👇 (1/7)

AlphaFold Database is expanding into pandemic preparedness. Together with NVIDIA, DeepMind, EBI et al. we exhaustively predicted ~1.7 million homo- & heterodimers across 2,812 viral proteomes, resulting in 8,028 high-confidence predictions. 📄 research.nvidia.com/labs/dbr/ass... 🌐 alphafold.ebi.ac.uk

Can “jumping genes” spread like viruses? New research from the Brennecke lab at IMBA shows that, in fruit flies, certain transposable elements can break out of their own cell and slip into developing eggs—securing their passage to the next generation. Published in Cell: https://imba.science/4jdMuYQ

A phage DUF669 protein mediates post-cleavage DNA repair against host CRISPR immunity | Nature Communications

Many important bacterial non-coding RNAs and structural elements remain undiscovered. To help, David Li, Garyk Brixi, Michael Fischbach, @brianhie.bsky.social & team introduce Minerva, which uses a genome language model to predict RNA base pairing, repeats, & other interactions from sequence alone.

Claude has discovered a previously unknown enzyme system hidden in the DNA of bacteriophages. Beside the enzyme’s gene sits a long array of repeating DNA—a structure that looks somewhat similar to CRISPR. We don’t yet understand what this system does, but only a handful of known systems share it...

Excited to share this part of my research as a part of @multidefence.bsky.social: meet viPAO1 - the very best Pseudomonas strain for phage research😉 Also check out our temperate phage collection featuring PAnicatthedisco, PAthetic and some other new fun names🎉 www.biorxiv.org/content/10.6...

Great work led by @jmouradesousa.bsky.social, where we find that phage and satellite defense hotspots change by recombination exceedingly fast, producing novel defenses. Oddly, phage & their satellites exchange defenses with lots of elements from theirs and other types, but not among the two.

New preprint from PhD student Yu Sun. TSR1 is a TIR effector specialised for CRISPR defence. It is an obligate dimer activated by cA3 and degrades its own activator using a ring nuclease domain. Perhaps the first confirmed dimeric TIR effector? www.biorxiv.org/content/10.6...

BFVD v3 contains 5.8M viral protein structures, 16× more than v2; 75% high quality, filling a major gap in AFDB coverage. It fully covers 72.6% of reference proteomes and spans 72.7% of ICTV species. Great work by @eunbelivable.bsky.social et al. 📄 www.biorxiv.org/content/10.6... 🌐 bfvd.foldseek.com

Thank you, Jack Bravo, for the accompanying Science Perspective, “A viral origin for RNA-guided immunity.” www.science.org/doi/10.1126/...

Out now in Science: Two papers from our lab reveal VIPR, an RNA-guided DNA-targeting system in bacteriophages, providing clues to the origins of CRISPR www.science.org/doi/10.1126/... www.science.org/doi/10.1126/... Congrats to Peter Yoon, @kenjmloi.bsky.social @terryzzy.bsky.social, T.Docter & team

Most #bacterial #immune systems raise an alarm when they sense a #phage. This Primer explores a @plosbiology.org study showing how type II Panoptes reverses this logic by maintaining a quiet signal & sensing infection through its sudden disappearance 🧪 Paper: buff.ly/1ixwg9v Primer: buff.ly/WmnHZBp

New enzymes that create natural phosphorothioate modifications in RNA share homology with proteins in bacterial DndABCDE anti-phage defense! www.cell.com/cell/abstrac...

Our paper on type II Panoptes is now published at PLOS Biology with new data on phage escapers - quite a step up in microbiology for our lab, led by Sabine Gruschow. Thanks to @erc.europa.eu for funding dx.plos.org/10.1371/jour...

#TrendingNow | Using a modified host, this study adds 36 new phages to the BASEL collection of phages that infect E. coli, revealing key roles of the O-antigen barrier in host recognition and restriction-modification systems in bacterial immunity. #ICYMI #MicroSky 🧪 buff.ly/grvuhX2

Congratulations to @francoisrousset.bsky.social and colleagues, who discovered NIR—“NADase in bacterial immunity and vault ribonucleoproteins”—a new NAD⁺-depleting domain! NAD⁺ is involved in defense yet again, while its reconstitution by NARP1 was shown to help phages overcome this defense :)

Gabija restricts phage circularization & DNA replication Gabija prevents phage genome circularization & replication w/out impacting bacterial host. Exposed DNA ends & phage end-binding proteins license DNA targeting while RecBCD protects host from Gabija www.cell.com/cell-host-mi...

Wow, this is getting fascinating with these NADases - seems pretty widespread - three BioRxivs on this exciting antiviral system in a matter of months from the Ibarra-Chavez lab www.biorxiv.org/content/10.6... and Tagliabracci lab www.biorxiv.org/content/10.6...

An exciting study showing how understanding bacterial immunity reveals new functions in human biology. Congratulations François and colleagues!