Avigail Stokar-Avihail
@aavihail.bsky.social
HFSP postdoctoral fellow @TypasLab @EMBLHeidelberg | Alumnus of @SorekLab @WeizmannScience. Interested in microbial interactions and warfare, microbial genomics & phages 🦠🧬👩🏽🔬
Reposted by Avigail Stokar-Avihail
@sacrozhangt.bsky.social and I wrote a commentary on Jordi van Gestel and Carol Gross's latest paper, check it out!
www.pnas.org/doi/10.1073/...
Sadly, the Editors at PNAS rejected our initial introduction, which was a David Attenborough style voice over of the microbial Serengeti (included below)
www.pnas.org/doi/10.1073/...
Sadly, the Editors at PNAS rejected our initial introduction, which was a David Attenborough style voice over of the microbial Serengeti (included below)
November 13, 2025 at 2:54 PM
@sacrozhangt.bsky.social and I wrote a commentary on Jordi van Gestel and Carol Gross's latest paper, check it out!
www.pnas.org/doi/10.1073/...
Sadly, the Editors at PNAS rejected our initial introduction, which was a David Attenborough style voice over of the microbial Serengeti (included below)
www.pnas.org/doi/10.1073/...
Sadly, the Editors at PNAS rejected our initial introduction, which was a David Attenborough style voice over of the microbial Serengeti (included below)
Reposted by Avigail Stokar-Avihail
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👇
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👇
November 6, 2025 at 10:39 AM
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👇
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👇
Reposted by Avigail Stokar-Avihail
Bacteria can sense when a virus starts shredding their genome — by detecting methylated mononucleotides.
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
November 6, 2025 at 5:00 AM
Bacteria can sense when a virus starts shredding their genome — by detecting methylated mononucleotides.
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
Reposted by Avigail Stokar-Avihail
I'm happy to share the first publication from my lab @hoerlab.bsky.social, now out in @narjournal.bsky.social! I take a look at the biology of RNA phages, focusing on how meta-omics methods are discovering new RNA phage families and bacterial defense strategies.
#PhageSky
doi.org/10.1093/nar/...
#PhageSky
doi.org/10.1093/nar/...
Advancing RNA phage biology through meta-omics
Abstract. Bacteriophages with RNA genomes are among the simplest biological entities on Earth. Since their discovery in the 1960s, they have been used as i
doi.org
April 23, 2025 at 8:57 AM
I'm happy to share the first publication from my lab @hoerlab.bsky.social, now out in @narjournal.bsky.social! I take a look at the biology of RNA phages, focusing on how meta-omics methods are discovering new RNA phage families and bacterial defense strategies.
#PhageSky
doi.org/10.1093/nar/...
#PhageSky
doi.org/10.1093/nar/...
Reposted by Avigail Stokar-Avihail
It was an honor for my lab and myself to host the meeting on the Immune Systems of Bacteria. Such a high from all the incredible science and sharing with scientists from the whole world the greatness of Paris in the spring.
Vive la science, et vive Paris!
Vive la science, et vive Paris!
April 11, 2025 at 3:46 PM
It was an honor for my lab and myself to host the meeting on the Immune Systems of Bacteria. Such a high from all the incredible science and sharing with scientists from the whole world the greatness of Paris in the spring.
Vive la science, et vive Paris!
Vive la science, et vive Paris!
Reposted by Avigail Stokar-Avihail
Excited to share our paper published in @currentbiology.bsky.social that explores the consequences of having multiple genomes in a bacterial model system and it’s benefits in a multidrug environment ! www.cell.com/current-biol...
March 4, 2025 at 5:12 PM
Excited to share our paper published in @currentbiology.bsky.social that explores the consequences of having multiple genomes in a bacterial model system and it’s benefits in a multidrug environment ! www.cell.com/current-biol...
Reposted by Avigail Stokar-Avihail
Hello BlueSky! Inaugural post here from the Sternberg Lab. We're excited to share our latest work, in which we teamed up with the @WiedenheftLab to study how DRT9 reverse transcriptases provide antiviral immunity. Here’s what we found: www.biorxiv.org/content/10.1...
Protein-primed DNA homopolymer synthesis by an antiviral reverse transcriptase
Bacteria defend themselves from viral predation using diverse immune systems, many of which sense and target foreign DNA for degradation. Defense-associated reverse transcriptase (DRT) systems provide...
www.biorxiv.org
March 26, 2025 at 10:13 PM
Hello BlueSky! Inaugural post here from the Sternberg Lab. We're excited to share our latest work, in which we teamed up with the @WiedenheftLab to study how DRT9 reverse transcriptases provide antiviral immunity. Here’s what we found: www.biorxiv.org/content/10.1...
Reposted by Avigail Stokar-Avihail
OUT NOW: Inducible transposon mutagenesis identifies bacterial fitness determinants during infection in mice
#microsky 🧪
www.nature.com/articles/s41...
#microsky 🧪
www.nature.com/articles/s41...
Inducible transposon mutagenesis identifies bacterial fitness determinants during infection in mice - Nature Microbiology
InducTn-seq, a method for inducible mutagenesis followed by transposon insertion site sequencing, enables temporal control of transposition to bypass population bottlenecks and enable the quantificati...
www.nature.com
March 27, 2025 at 4:35 PM
OUT NOW: Inducible transposon mutagenesis identifies bacterial fitness determinants during infection in mice
#microsky 🧪
www.nature.com/articles/s41...
#microsky 🧪
www.nature.com/articles/s41...
Reposted by Avigail Stokar-Avihail
I am super excited to share our work uncovering the structure and mechanism of an ATPase-associated reverse transcriptase (RT) involved in prokaryotic antiviral defense, now available as a preprint on bioRxiv!🧬🦠🔬
www.biorxiv.org/content/10.1...
🧵👇
www.biorxiv.org/content/10.1...
🧵👇
Structural basis of antiphage defense by an ATPase-associated reverse transcriptase
Reverse transcriptases (RTs) have well-established roles in the replication and spread of retroviruses and retrotransposons. However, recent evidence suggests that RTs have been conscripted by cells f...
www.biorxiv.org
March 27, 2025 at 1:59 PM
I am super excited to share our work uncovering the structure and mechanism of an ATPase-associated reverse transcriptase (RT) involved in prokaryotic antiviral defense, now available as a preprint on bioRxiv!🧬🦠🔬
www.biorxiv.org/content/10.1...
🧵👇
www.biorxiv.org/content/10.1...
🧵👇
I highly recommend attending this amazing microbiology conference!
🦠🔬👩🏼🔬🧬🧪
Only a few more days to submit your abstracts! (April 1st ).
Looking forwards! 🍻
🦠🔬👩🏼🔬🧬🧪
Only a few more days to submit your abstracts! (April 1st ).
Looking forwards! 🍻
⏳ The #EESMicrobiology abstract submission deadline is fast approaching ⏳
Submit your abstract by 1 April and don't miss the chance to present your research to top scientists working with bacteria and new technologies 👉 https://s.embl.org/ees25-06-bl
📅 24 – 26 June
📍 EMBL Heidelberg and Virtual
Submit your abstract by 1 April and don't miss the chance to present your research to top scientists working with bacteria and new technologies 👉 https://s.embl.org/ees25-06-bl
📅 24 – 26 June
📍 EMBL Heidelberg and Virtual
March 25, 2025 at 10:52 PM
I highly recommend attending this amazing microbiology conference!
🦠🔬👩🏼🔬🧬🧪
Only a few more days to submit your abstracts! (April 1st ).
Looking forwards! 🍻
🦠🔬👩🏼🔬🧬🧪
Only a few more days to submit your abstracts! (April 1st ).
Looking forwards! 🍻
Reposted by Avigail Stokar-Avihail
1/ Transposable elements are often called "jumping genes" because they mobilize within genomes. 🧬
But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯
Our new study reveals how retrotransposons invade the germline directly from somatic cells.
www.biorxiv.org/content/10.1...
A short thread 🧵👇
But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯
Our new study reveals how retrotransposons invade the germline directly from somatic cells.
www.biorxiv.org/content/10.1...
A short thread 🧵👇
March 17, 2025 at 11:56 AM
1/ Transposable elements are often called "jumping genes" because they mobilize within genomes. 🧬
But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯
Our new study reveals how retrotransposons invade the germline directly from somatic cells.
www.biorxiv.org/content/10.1...
A short thread 🧵👇
But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯
Our new study reveals how retrotransposons invade the germline directly from somatic cells.
www.biorxiv.org/content/10.1...
A short thread 🧵👇
Reposted by Avigail Stokar-Avihail
🚀 Thrilled to share our latest work from Zhang Lab, now published in Science (www.science.org/doi/10.1126/...)
We introduce TIGR-Tas, a PAM-free, compact, modular RNA-guided DNA-targeting system in prokaryotes & their viruses.
More details coming soon 👀
#TIGR #RNA #GeneEditing #CRISPR
We introduce TIGR-Tas, a PAM-free, compact, modular RNA-guided DNA-targeting system in prokaryotes & their viruses.
More details coming soon 👀
#TIGR #RNA #GeneEditing #CRISPR
February 28, 2025 at 10:41 PM
🚀 Thrilled to share our latest work from Zhang Lab, now published in Science (www.science.org/doi/10.1126/...)
We introduce TIGR-Tas, a PAM-free, compact, modular RNA-guided DNA-targeting system in prokaryotes & their viruses.
More details coming soon 👀
#TIGR #RNA #GeneEditing #CRISPR
We introduce TIGR-Tas, a PAM-free, compact, modular RNA-guided DNA-targeting system in prokaryotes & their viruses.
More details coming soon 👀
#TIGR #RNA #GeneEditing #CRISPR
The cool papers just keep coming 🙃 Interesting regulation of anti-bacterial and anti-phage systems by danger sensing!
Pseudomonads coordinate innate defense against viruses and bacteria with a single regulatory system https://www.biorxiv.org/content/10.1101/2025.02.26.640152v1
February 28, 2025 at 8:44 AM
The cool papers just keep coming 🙃 Interesting regulation of anti-bacterial and anti-phage systems by danger sensing!
A newly discovered antiphage defense system prevents phage DNA packaging leading to the release of empty non-infectious virions upon bacterial lysis. How many more cool new bacterial immune systems are still out there? 🤓
Congrats Gil & @AnatHerskovits et al! 🥂
Congrats Gil & @AnatHerskovits et al! 🥂
A prophage-encoded anti-phage defense system that prevents phage DNA packaging by targeting the terminase complex https://www.biorxiv.org/content/10.1101/2025.02.27.640495v1
February 28, 2025 at 8:30 AM
A newly discovered antiphage defense system prevents phage DNA packaging leading to the release of empty non-infectious virions upon bacterial lysis. How many more cool new bacterial immune systems are still out there? 🤓
Congrats Gil & @AnatHerskovits et al! 🥂
Congrats Gil & @AnatHerskovits et al! 🥂
Reposted by Avigail Stokar-Avihail
Legitmately thrilled to share our latest work, in which @fernpizza.bsky.social solved an experimental challenge in plasmid biology as old as the field: measuring how plasmids compete and evolve within individual cells!
February 21, 2025 at 8:42 PM
Legitmately thrilled to share our latest work, in which @fernpizza.bsky.social solved an experimental challenge in plasmid biology as old as the field: measuring how plasmids compete and evolve within individual cells!
Reposted by Avigail Stokar-Avihail
Excited to share our opinion piece with the KC Huang Lab.
Check it out here:
Harnessing gut microbial communities to unravel microbiome functions
doi.org/10.1016/j.mi...
@typaslab.bsky.social
Check it out here:
Harnessing gut microbial communities to unravel microbiome functions
doi.org/10.1016/j.mi...
@typaslab.bsky.social
January 13, 2025 at 3:08 PM
Excited to share our opinion piece with the KC Huang Lab.
Check it out here:
Harnessing gut microbial communities to unravel microbiome functions
doi.org/10.1016/j.mi...
@typaslab.bsky.social
Check it out here:
Harnessing gut microbial communities to unravel microbiome functions
doi.org/10.1016/j.mi...
@typaslab.bsky.social
Reposted by Avigail Stokar-Avihail
Happy to share our latest piece of work on the PARIS bacterial immune system. We performed a detailed characterization of the AriB Toprim nuclease, the effector of PARIS immunity.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Specificity and Mechanism of tRNA cleavage by the AriB Toprim nuclease of the PARIS bacterial immune system
Transfer RNA molecules have been recently recognized as widespread targets of bacterial immune systems. Translation inhibition through tRNA cleavage or modification inhibits phage propagation, thereby...
www.biorxiv.org
February 5, 2025 at 2:43 PM
Happy to share our latest piece of work on the PARIS bacterial immune system. We performed a detailed characterization of the AriB Toprim nuclease, the effector of PARIS immunity.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Avigail Stokar-Avihail
Exciting to see our paper now published 🙌
www.science.org/doi/10.1126/...
In this project co-led with @ostermanilya.bsky.social at @soreklab.bsky.social , we show that a bacterial immune system employs a TIR protein and a caspase-like protease, two typical immune components seen in eukaryotes. 🧵👇
www.science.org/doi/10.1126/...
In this project co-led with @ostermanilya.bsky.social at @soreklab.bsky.social , we show that a bacterial immune system employs a TIR protein and a caspase-like protease, two typical immune components seen in eukaryotes. 🧵👇
January 31, 2025 at 11:41 AM
Exciting to see our paper now published 🙌
www.science.org/doi/10.1126/...
In this project co-led with @ostermanilya.bsky.social at @soreklab.bsky.social , we show that a bacterial immune system employs a TIR protein and a caspase-like protease, two typical immune components seen in eukaryotes. 🧵👇
www.science.org/doi/10.1126/...
In this project co-led with @ostermanilya.bsky.social at @soreklab.bsky.social , we show that a bacterial immune system employs a TIR protein and a caspase-like protease, two typical immune components seen in eukaryotes. 🧵👇
Reposted by Avigail Stokar-Avihail
Our paper is finally published in Science! 🎉The HPLC, NMR, MS, purification, and characterization of the new molecule felt like a real detective story. I was especially thrilled to use and reference my grandfather, Lev Osterman's, 1966 paper—he was the main reason I became a scientist.
January 31, 2025 at 7:00 AM
Our paper is finally published in Science! 🎉The HPLC, NMR, MS, purification, and characterization of the new molecule felt like a real detective story. I was especially thrilled to use and reference my grandfather, Lev Osterman's, 1966 paper—he was the main reason I became a scientist.
Congratulations to my dear friend Tana Wein on another beautiful discovery: showing (yet another!) example of a fundamental player in human immunity, now discovered to function in bacterial immunity.
Congrats Tana et al @SorekLab and Kranzusch lab! 🥂
Congrats Tana et al @SorekLab and Kranzusch lab! 🥂
Our paper out @Nature: CARD domains mediate anti-phage defense in bacterial gasdermin systems
CARDs are essential for caspase recruitment during human inflammasome activation. We now find them in bacterial immune systems
Congrats Tana Wein! Thank you Kranzusch lab!
www.nature.com/articles/s41...
CARDs are essential for caspase recruitment during human inflammasome activation. We now find them in bacterial immune systems
Congrats Tana Wein! Thank you Kranzusch lab!
www.nature.com/articles/s41...
January 30, 2025 at 10:45 AM
Congratulations to my dear friend Tana Wein on another beautiful discovery: showing (yet another!) example of a fundamental player in human immunity, now discovered to function in bacterial immunity.
Congrats Tana et al @SorekLab and Kranzusch lab! 🥂
Congrats Tana et al @SorekLab and Kranzusch lab! 🥂
Reposted by Avigail Stokar-Avihail
Our paper out @CellCellPress: Structure guided discovery of viral proteins that inhibit host immunity
Congrats Erez Yirmiya, Azita Leavitt, Gil Amitai, our collaborators at the Kranzusch lab, and coauthors
A 🧵 1/10
www.cell.com/cell/abstrac...
Congrats Erez Yirmiya, Azita Leavitt, Gil Amitai, our collaborators at the Kranzusch lab, and coauthors
A 🧵 1/10
www.cell.com/cell/abstrac...
Structure-guided discovery of viral proteins that inhibit host immunity
Large-scale, structure-guided computational pipeline sifts through millions of phage
proteins to identify those that bind and antagonize host immune proteins. Detected
proteins are shown to inhibit no...
www.cell.com
January 23, 2025 at 4:12 PM
Our paper out @CellCellPress: Structure guided discovery of viral proteins that inhibit host immunity
Congrats Erez Yirmiya, Azita Leavitt, Gil Amitai, our collaborators at the Kranzusch lab, and coauthors
A 🧵 1/10
www.cell.com/cell/abstrac...
Congrats Erez Yirmiya, Azita Leavitt, Gil Amitai, our collaborators at the Kranzusch lab, and coauthors
A 🧵 1/10
www.cell.com/cell/abstrac...
I'm excited to see the published version of this amazing work.
@erezyirmiya et al identified viral proteins that inhibit host immunity using structural predictions of protein-protein interactions.
Congrats to you all @soreklab & Kranzusch lab! 🥂
@erezyirmiya et al identified viral proteins that inhibit host immunity using structural predictions of protein-protein interactions.
Congrats to you all @soreklab & Kranzusch lab! 🥂
I'm thrilled to announce our latest work is now published in Cell! Viruses encode numerous proteins that inhibit host defenses, but identifying immune-modulatory proteins among millions of viral sequences has been nearly impossible - until now! www.cell.com/cell/fulltex...
January 23, 2025 at 6:25 PM
I'm excited to see the published version of this amazing work.
@erezyirmiya et al identified viral proteins that inhibit host immunity using structural predictions of protein-protein interactions.
Congrats to you all @soreklab & Kranzusch lab! 🥂
@erezyirmiya et al identified viral proteins that inhibit host immunity using structural predictions of protein-protein interactions.
Congrats to you all @soreklab & Kranzusch lab! 🥂
Reposted by Avigail Stokar-Avihail
Excited to share our work using machine learning to predict anti-phage defense systems!
1/n
1/n
DefensePredictor: A Machine Learning Model to Discover Novel Prokaryotic Immune Systems https://www.biorxiv.org/content/10.1101/2025.01.08.631726v1
January 9, 2025 at 7:32 PM
Excited to share our work using machine learning to predict anti-phage defense systems!
1/n
1/n
Cool new preprint on prediction of new anti-phage systems using language models from @mdmlab.bsky.social
I'm really looking forward to a great read 🤓(as usual).
Congrats Ernest & Aude et al!!! 🥂
I'm really looking forward to a great read 🤓(as usual).
Congrats Ernest & Aude et al!!! 🥂
What is the diversity of antiphage systems out there ?
We used protein and genomic language models (and defense score!) to start bringing some answers: >45 000 protein families.
Leb by E. Mordret.
www.biorxiv.org/content/10.1...
Interactive UMAP to have fun
mdmparis.github.io/antiphage-la...
We used protein and genomic language models (and defense score!) to start bringing some answers: >45 000 protein families.
Leb by E. Mordret.
www.biorxiv.org/content/10.1...
Interactive UMAP to have fun
mdmparis.github.io/antiphage-la...
January 9, 2025 at 5:44 PM
Cool new preprint on prediction of new anti-phage systems using language models from @mdmlab.bsky.social
I'm really looking forward to a great read 🤓(as usual).
Congrats Ernest & Aude et al!!! 🥂
I'm really looking forward to a great read 🤓(as usual).
Congrats Ernest & Aude et al!!! 🥂
Reposted by Avigail Stokar-Avihail
1/11 - With Karin Mitosch and Clément Potel + colleagues in Savitski lab and @typaslab.bsky.social @embl.org, I’m very happy to share our discovery of a hyper-promiscuous phage protein kinase (T7K) which broadly deactivates bacterial defenses! 🦠
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
December 23, 2024 at 7:29 AM
1/11 - With Karin Mitosch and Clément Potel + colleagues in Savitski lab and @typaslab.bsky.social @embl.org, I’m very happy to share our discovery of a hyper-promiscuous phage protein kinase (T7K) which broadly deactivates bacterial defenses! 🦠
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...