Sorek Lab
@soreklab.bsky.social
📤 3485
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The Sorek Lab Weizmann Institute of Science, Israel
https://www.weizmann.ac.il/molgen/Sorek/
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Sorek Lab
James Fraser
4 days ago
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...
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Know when to co-fold'em
This is the official web page for the James Fraser Lab at UCSF.
https://fraserlab.com/2025/12/29/know-when-to-co-fold-em/
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Peter Dougherty
4 days ago
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!
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Diego del Alamo
7 days ago
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 🧵
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"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
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10 days ago
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Aude Bernheim
18 days ago
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
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Aude Bernheim
18 days ago
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...
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Environment and physiology shape antiphage system expression
Bacteria and archaea encode on average ten antiphage systems. Quorum sensing, cellular, or transcription factors can regulate specific systems (CRISPR-Cas, CBASS). Yet, a systematic assessment of anti...
https://www.biorxiv.org/content/10.64898/2025.12.14.694197v1
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Shai Zilberzwige Tal
24 days ago
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!
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EMBO
23 days ago
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
.
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Joe Bondy-Denomy
25 days ago
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
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Snorre Sulheim
about 1 month ago
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
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Sorek Lab
Frances Yap
29 days ago
Colibactin-DNA interstrand crosslinks structure reveals DNA-damaging acitivity of colibactin that is linked to colorectal cancer
#MicroSky
www.science.org/doi/10.1126/...
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The specificity and structure of DNA cross-linking by the gut bacterial genotoxin colibactin
Accumulating evidence has connected the chemically unstable, DNA-damaging gut bacterial natural product colibactin to colorectal cancer, including the identification of mutational signatures that are ...
https://www.science.org/doi/10.1126/science.ady3571?utm_source=sfmc&utm_medium=email&utm_content=alert&utm_campaign=SCIeToc&et_rid=589019734&et_cid=5811313
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Sorek Lab
Alberto Marin
29 days ago
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/...
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Cohesin drives chromatin scanning during the RAD51-mediated homology search
Cohesin folds genomes into chromatin loops, the roles of which are under debate. We found that double-strand breaks (DSBs) induce de novo formation of chromatin loops in human cells, with the loop bas...
https://www.science.org/doi/10.1126/science.adw1928
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Osterman Ilya
29 days ago
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.
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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
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29 days ago
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Simon Roux
about 1 month ago
🦠🧪🧬🚨 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-...
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Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes
Abstract. Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is st
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf1283/8349223
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Kotaro Chihara
about 1 month ago
www.nature.com/articles/s41...
Structural mechanism of the Retron-Eco7 anti-phage defense system
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Structural mechanism of the Retron-Eco7 anti-phage defense system - Nature Communications
The Retron-Eco7 is a genetic element involved in anti-phage defense that encodes two effector proteins (PtuA and PtuB) and cleaves the host tRNA. Here, the authors solved the Retron-Eco7 complex struc...
https://www.nature.com/articles/s41467-025-66589-9
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Looking forward to the meeting on the immune system of bacteria! Rockefeller, 5-7 May 2026. A fantastic lineup of speakers, expecting exiting science
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about 1 month ago
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Mart Krupovic
about 1 month ago
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...
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Widespread and intron-rich mirusviruses are predicted to reproduce in nuclei of unicellular eukaryotes - Nature Microbiology
Environmental metagenomic explorations show that Mirusviricota lineages lack essential replication and transcription genes and contain spliceosomal introns, suggesting nuclear reproduction.
https://www.nature.com/articles/s41564-025-02190-6
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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
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about 1 month ago
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Sorek Lab
Erin Doherty
about 1 month ago
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...
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Divergent viral phosphodiesterases for immune signaling evasion
Cyclic dinucleotides (CDNs) and other short oligonucleotides play fundamental roles in immune system activation in organisms ranging from bacteria to …
https://www.sciencedirect.com/science/article/pii/S1931312825004524
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Sorek Lab
bioRxiv Microbiology
about 1 month ago
Arbitrium systems control lysis/lysogeny through the regulation of small antirepressor proteins
https://www.biorxiv.org/content/10.1101/2025.11.23.689978v1
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Sorek Lab
Plaschka lab
about 1 month ago
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)
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Michael Baym
about 1 month ago
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/...
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Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
https://www.science.org/doi/10.1126/science.adx0665
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Michael Baym
about 1 month ago
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/
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Dorentina Humolli
about 1 month ago
🚀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 (🧵)
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Alexander Harms
about 1 month ago
🚨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
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Ellinor Alseth
about 1 month ago
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/...
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Bacterial immune systems as causes and consequences of microbiome structure
Bacterial immune systems have evolved in response to diverse molecular "parasites", yet their ecological roles remain poorly understood. This Essay explores how interactions between mobile genetic ele...
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3003489
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Oregon 🕎🎲
about 2 months ago
Part 93 of 200 in historically interesting things to inspire your ttrpg dnd 2,700-year-old Assyrian lamassu at ancient Dur-Sharrukin
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Sorek Lab
Sergey Ovchinnikov
about 1 month ago
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)
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EMBO
6 months ago
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...
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Building bridges – People – EMBO
Meet Aude Bernheim, Institut Pasteur, Paris | EMBO Young Investigator
https://www.embo.org/people/building-bridges/
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Sorek Lab
Marcin J. Suskiewicz
about 2 months ago
Very happy to share our collaborative project on FAM118 proteins - noncanonical sirtuins that form filaments and process NAD in human and other vertebrate cells.
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Filament formation and NAD processing by noncanonical human FAM118 sirtuins
Nature Structural & Molecular Biology - Baretić and Missoury et al. identify vertebrate proteins FAM118B and FAM118A as sirtuins similar to bacterial antiphage enzymes and show that...
https://rdcu.be/eQjNK
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Owen Tuck
about 2 months ago
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...
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https://www.biorxiv.org/content/10.1101/2025.11.14.688446v1
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Sorek Lab
Janine Brunner
about 2 months ago
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.
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bioRxiv Microbiology
about 2 months ago
Surviving phage attack dynamically regulates bacterial immunity to defeat counterdefenses
https://www.biorxiv.org/content/10.1101/2025.11.13.688357v1
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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
about 2 months ago
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Osterman Ilya
about 2 months ago
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.
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Sorek Lab
bioRxiv Microbiology
about 2 months ago
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
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Owen Tuck
about 2 months ago
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
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Recurrent acquisition of nuclease-protease pairs in antiviral immunity
Antiviral immune systems diversify by integrating new genes into existing pathways, creating new mechanisms of viral resistance. We identified genes encoding a predicted nuclease paired with a trypsin...
https://www.science.org/doi/10.1126/science.aea8769
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Sorek Lab
BejaLab
about 2 months ago
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
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Lucie Etienne
about 2 months ago
📖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...
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Evolutionary characterization of antiviral SAMD9/9L across kingdoms supports ancient convergence and lineage-specific adaptations - Nature Ecology & Evolution
A search for analogues of the human SAMD9/9L antiviral genes identifies convergent evolution of this gene family in the bacterial and animal kingdoms, with species-specific and recent genomic signatur...
https://www.nature.com/articles/s41559-025-02845-x
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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👇
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about 2 months ago
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EMBL
about 2 months ago
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...
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Sorek Lab
bioRxiv Microbiology
2 months ago
A membrane-bound nuclease directly cleaves phage DNA during genome injection
https://www.biorxiv.org/content/10.1101/2025.11.03.685801v1
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Aude Bernheim
about 2 months ago
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
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Labs in bacterial immunity
https://docs.google.com/spreadsheets/d/1mKy0ALZSbGZsEmt3h20JNQ5MOpVsCQ276HybsMo-t4c/edit?gid=0#gid=0
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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
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2 months ago
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Jens Hör
3 months ago
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!
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Chen Wang
2 months ago
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...
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Phage SSB detection by retron Eco8 msDNA unleashes nuclease-mediated immunity
The cryo-EM structure of the retron Eco8 system reveals an autoinhibited 4:4:4 complex of RT, msDNA, and OLD nuclease. Phage SSB binding to msdDNA unleashes non-specific nuclease activity to restrict ...
https://www.cell.com/molecular-cell/fulltext/S1097-2765%2825%2900824-X
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Landon Getz
2 months ago
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
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Antiviral Defence is a Conserved Function of Diverse DNA Glycosylases
Bacteria are frequently attacked by viruses, known as phages, and rely on diverse defence systems like restriction endonucleases and CRISPR-Cas to survive. While phages can evade these defences by cov...
https://doi.org/10.1101/2025.10.29.685425
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bioRxiv Microbiology
2 months ago
Antiviral Defence is a Conserved Function of Diverse DNA Glycosylases
https://www.biorxiv.org/content/10.1101/2025.10.29.685425v1
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GBM (Gesellschaft für Biochemie und Molekularbiologie)
2 months ago
🎉 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
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