Sorek Lab
@soreklab.bsky.social
Reposted by Sorek Lab
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...
Thread below - but first some links:
A longer take:
fraserlab.com/2025/12/29/k...
Preprint:
www.biorxiv.org/content/10.6...
Know when to co-fold'em
This is the official web page for the James Fraser Lab at UCSF.
fraserlab.com
December 29, 2025 at 10:25 PM
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...
Thread below - but first some links:
A longer take:
fraserlab.com/2025/12/29/k...
Preprint:
www.biorxiv.org/content/10.6...
Reposted by Sorek Lab
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!
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!
[1/3] Is your favorite bacterial isolate hiding a surprise lytic virus with a VERY different lifestyle? Finally I can proudly say that our paper on persistent phages is out in Nature Microbiology. rdcu.be/eWJEp. Well done @peterdoug.bsky.social
Persistent virulent phages exist across bacterial isolates
Nature Microbiology - The long-term existence of diverse virulent phages within cultures of Escherichia coli and others challenges the virulent–temperate dichotomy and points to non-canonical...
rdcu.be
December 29, 2025 at 3:18 PM
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!
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!
Reposted by Sorek Lab
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 🧵
December 26, 2025 at 11:49 PM
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
Wow
December 23, 2025 at 3:49 PM
"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
Wow
Reposted by Sorek Lab
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
For examples, some systems seem expressed at the center of biofilms, others on the biofilm edges
December 15, 2025 at 9:49 PM
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
For examples, some systems seem expressed at the center of biofilms, others on the biofilm edges
Reposted by Sorek Lab
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...
In this preprint, Lucas Paoli et al, ask what shapes antiphage systems expression in native contexts.
www.biorxiv.org/content/10.6...
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...
www.biorxiv.org
December 15, 2025 at 9:49 PM
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...
In this preprint, Lucas Paoli et al, ask what shapes antiphage systems expression in native contexts.
www.biorxiv.org/content/10.6...
Reposted by Sorek Lab
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!
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!
December 9, 2025 at 9:35 PM
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!
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!
Reposted by Sorek Lab
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.
At #CellBio2025, the EMBO Gold Medal was handed over to David Bikard in recognition of his pioneering work on #GeneEditing.
December 10, 2025 at 1:40 PM
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.
At #CellBio2025, the EMBO Gold Medal was handed over to David Bikard in recognition of his pioneering work on #GeneEditing.
Reposted by Sorek Lab
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
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
December 8, 2025 at 3:04 PM
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
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
Reposted by Sorek Lab
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
Teaser: Increased proline in ΔputP
#microsky #MEvoSky
December 3, 2025 at 11:11 AM
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
Teaser: Increased proline in ΔputP
#microsky #MEvoSky
Reposted by Sorek Lab
Colibactin-DNA interstrand crosslinks structure reveals DNA-damaging acitivity of colibactin that is linked to colorectal cancer #MicroSky www.science.org/doi/10.1126/...
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 ...
www.science.org
December 4, 2025 at 10:07 PM
Colibactin-DNA interstrand crosslinks structure reveals DNA-damaging acitivity of colibactin that is linked to colorectal cancer #MicroSky www.science.org/doi/10.1126/...
Reposted by Sorek Lab
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/...
www.science.org/doi/10.1126/...
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...
www.science.org
December 4, 2025 at 9:50 PM
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/...
www.science.org/doi/10.1126/...
Reposted by Sorek Lab
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.
I’m happy to share our new preprint! We uncovered the full diversity of bacterial TIR-based antiviral immune signaling, massively expanded the known diversity of Thoeris systems, and revealed conservation of TIR-derived immune signals across the tree of life.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Systematic discovery of TIR-based immune signaling systems in bacteria
Toll/interleukin-1 receptor (TIR) domains are important for immune signaling across humans, plants and bacteria. These domains were recently found to produce immune signaling molecules in plant immuni...
www.biorxiv.org
December 4, 2025 at 9:56 AM
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
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
December 4, 2025 at 1:56 PM
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
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
Reposted by Sorek Lab
🦠🧪🧬🚨 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-...
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
academic.oup.com
December 3, 2025 at 2:34 AM
🦠🧪🧬🚨 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-...
Reposted by Sorek Lab
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 this out for the 2026 SISB (phage defense) meeting in NYC. Mark your calendar! (and note the Zoom option, if needed)
sisb2026.rockefeller.edu
sisb2026.rockefeller.edu
SISB2026
sisb2026.rockefeller.edu
December 2, 2025 at 6:52 AM
Looking forward to the meeting on the immune system of bacteria! Rockefeller, 5-7 May 2026. A fantastic lineup of speakers, expecting exiting science
Reposted by Sorek Lab
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...
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.
www.nature.com
November 28, 2025 at 4:43 PM
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
Lamassu evolved from a DNA repair complex
Beautiful study from the Patel, Bernheim and Sternberg labs
🧬🛡️How are new immune mechanisms created?
We show how Lamassu antiphage system, originated from a DNA-repair complex and evolved into a compact and modular immune machine, wt Dinshaw Patel lab in @pnas.org.
👏 @matthieu-haudiquet.bsky.social, Arpita Chakravarti & all authors!
doi.org/10.1073/pnas...
We show how Lamassu antiphage system, originated from a DNA-repair complex and evolved into a compact and modular immune machine, wt Dinshaw Patel lab in @pnas.org.
👏 @matthieu-haudiquet.bsky.social, Arpita Chakravarti & all authors!
doi.org/10.1073/pnas...
November 27, 2025 at 7:08 PM
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
Lamassu evolved from a DNA repair complex
Beautiful study from the Patel, Bernheim and Sternberg labs
Reposted by Sorek Lab
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...
@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...
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 …
www.sciencedirect.com
November 25, 2025 at 9:10 PM
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...
@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...
Reposted by Sorek Lab
Arbitrium systems control lysis/lysogeny through the regulation of small antirepressor proteins https://www.biorxiv.org/content/10.1101/2025.11.23.689978v1
November 25, 2025 at 2:17 AM
Arbitrium systems control lysis/lysogeny through the regulation of small antirepressor proteins https://www.biorxiv.org/content/10.1101/2025.11.23.689978v1
Reposted by Sorek Lab
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)
November 21, 2025 at 5:37 PM
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)
Reposted by Sorek Lab
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/...
www.science.org/doi/10.1126/...
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...
www.science.org
November 20, 2025 at 9:42 PM
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/...
www.science.org/doi/10.1126/...
Reposted by Sorek Lab
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/
November 20, 2025 at 9:42 PM
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/
Reposted by Sorek Lab
🚀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 (🧵)
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 (🧵)
November 20, 2025 at 6:52 PM
🚀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 (🧵)
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 (🧵)