Erez Yirmiya
@erezyirmiya.bsky.social
PhD student @soreklab.bsky.social. Researching the arms race between bacteria and phages 🦠🛡⚔️ A proud father of 3 cats. 🏳️🌈
Pinned
Erez Yirmiya
@erezyirmiya.bsky.social
· Jan 23
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...
Such a beautiful and well-rounded discovery, yet another exciting strategy in bacterial immunity. Congrats, Ilya!
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 6:13 AM
Such a beautiful and well-rounded discovery, yet another exciting strategy in bacterial immunity. Congrats, Ilya!
Reposted by Erez Yirmiya
📢 New preprint alert!
We designed synthetic proteins that can block bacterial immune systems, allowing phages + plasmids to overcome natural defenses.
This could transform phage therapy + genetic engineering.
Here’s what we found 🧵
Preprint🔗: www.biorxiv.org/content/10.1...
We designed synthetic proteins that can block bacterial immune systems, allowing phages + plasmids to overcome natural defenses.
This could transform phage therapy + genetic engineering.
Here’s what we found 🧵
Preprint🔗: www.biorxiv.org/content/10.1...
Synthetically designed anti-defense proteins overcome barriers to bacterial transformation and phage infection
Bacterial defense systems present considerable barriers to both phage infection and plasmid transformation. These systems target mobile genetic elements, limiting the efficacy of bacteriophage-based t...
www.biorxiv.org
September 2, 2025 at 7:36 AM
📢 New preprint alert!
We designed synthetic proteins that can block bacterial immune systems, allowing phages + plasmids to overcome natural defenses.
This could transform phage therapy + genetic engineering.
Here’s what we found 🧵
Preprint🔗: www.biorxiv.org/content/10.1...
We designed synthetic proteins that can block bacterial immune systems, allowing phages + plasmids to overcome natural defenses.
This could transform phage therapy + genetic engineering.
Here’s what we found 🧵
Preprint🔗: www.biorxiv.org/content/10.1...
Reposted by Erez Yirmiya
Preprint: De-novo design of proteins that inhibit bacterial defenses
Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications
Congrats Jeremy Garb!
tinyurl.com/Syttt
🧵
Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications
Congrats Jeremy Garb!
tinyurl.com/Syttt
🧵
Synthetically designed anti-defense proteins overcome barriers to bacterial transformation and phage infection
Bacterial defense systems present considerable barriers to both phage infection and plasmid transformation. These systems target mobile genetic elements, limiting the efficacy of bacteriophage-based t...
www.biorxiv.org
September 2, 2025 at 10:48 AM
Preprint: De-novo design of proteins that inhibit bacterial defenses
Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications
Congrats Jeremy Garb!
tinyurl.com/Syttt
🧵
Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications
Congrats Jeremy Garb!
tinyurl.com/Syttt
🧵
Congrats @romihadary.bsky.social and @reneechang.bsky.social for dissecting the functional diversity of ALL Sponges! 🧽
📢 Preprint out!
Together with @reneechang.bsky.social @kranzuschlab.bsky.social and the amazing @soreklab.bsky.social, we explored viral sponges to map their diversity and function.
Discovered huge diversity, including sponges that inhibit Pycsar & Type IV Thoeris!
www.biorxiv.org/content/10.1...
Together with @reneechang.bsky.social @kranzuschlab.bsky.social and the amazing @soreklab.bsky.social, we explored viral sponges to map their diversity and function.
Discovered huge diversity, including sponges that inhibit Pycsar & Type IV Thoeris!
www.biorxiv.org/content/10.1...
Functional diversity of phage sponge proteins that sequester host immune signals
Multiple bacterial immune systems, including CBASS, Thoeris, and Pycsar, employ signaling molecules that activate the immune response following phage infection. Phages counteract bacterial immune sign...
www.biorxiv.org
August 25, 2025 at 1:16 PM
Congrats @romihadary.bsky.social and @reneechang.bsky.social for dissecting the functional diversity of ALL Sponges! 🧽
An absolute masterpiece by the talented @dinahoch.bsky.social on nucleotide-based immunity
Read my review with @soreklab.bsky.social on the nucleotide pool as a central playground in antiviral immunity across humans, bacteria and plants! 🧍♀️🦠🌿
& how viruses overcome these nucleotide-based immune mechanisms 🗡️
www.nature.com/articles/s41...
& how viruses overcome these nucleotide-based immune mechanisms 🗡️
www.nature.com/articles/s41...
Manipulation of the nucleotide pool in human, bacterial and plant immunity - Nature Reviews Immunology
Modification of the nucleotide pool is emerging as key to innate immunity in animals, plants and bacteria. This Review explains how immune pathways conserved from bacteria to humans manipulate the nuc...
www.nature.com
August 1, 2025 at 7:17 PM
An absolute masterpiece by the talented @dinahoch.bsky.social on nucleotide-based immunity
Amazing work identifying novel immune inhibitors based on structural and genomic traits.
Congrats Nitzan and everyone!
Congrats Nitzan and everyone!
📢Preprint out!
Excited to share my final work from the @soreklab.bsky.social!
We mined phage dark matter using structural features shared by anti-defense proteins (viral tools that help phages bypass bacterial immunity) to guide discovery.
Found 3 new families targeting immune signaling!
Excited to share my final work from the @soreklab.bsky.social!
We mined phage dark matter using structural features shared by anti-defense proteins (viral tools that help phages bypass bacterial immunity) to guide discovery.
Found 3 new families targeting immune signaling!
July 13, 2025 at 1:55 PM
Amazing work identifying novel immune inhibitors based on structural and genomic traits.
Congrats Nitzan and everyone!
Congrats Nitzan and everyone!
Reposted by Erez Yirmiya
Hello everyone! I am pleased to share information on the first ever Computational Structural Virology Symposium, conducted August 4th on zoom and highlighting work in this emerging field. You can register for this event here: forms.gle/CNiqskMwQEuV.... Please re-post!
June 12, 2025 at 8:31 PM
Hello everyone! I am pleased to share information on the first ever Computational Structural Virology Symposium, conducted August 4th on zoom and highlighting work in this emerging field. You can register for this event here: forms.gle/CNiqskMwQEuV.... Please re-post!
Reposted by Erez Yirmiya
This was our latest journal-club paper. Nice use of large-scale AlphaFold modelling & various experiments. Phage proteins’ ability to recognise eukaryotic homologues of their bacterial targets is striking - suggests these proteins evolved to recognise their targets in a fairly mutation-resistnt way.
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...
April 14, 2025 at 7:24 AM
This was our latest journal-club paper. Nice use of large-scale AlphaFold modelling & various experiments. Phage proteins’ ability to recognise eukaryotic homologues of their bacterial targets is striking - suggests these proteins evolved to recognise their targets in a fairly mutation-resistnt way.
Reposted by Erez Yirmiya
A fun collaboration with the Whitney, Prehna, and Bosis labs, in which we reveal the role of DUF2169 proteins: assisting PAAR-like domains in forming spike complexes and #T6SS assembly. 🦠
search.app/jDxaUi5yJK9B...
search.app/jDxaUi5yJK9B...
A conserved chaperone protein is required for the formation of a non-canonical type VI secretion system spike tip complex
Type VI secretion systems (T6SS) are dynamic protein nanomachines found in Gram-negative
bacteria that deliver toxic effector proteins into target cells in a contact-dependent
manner. Prior to secreti...
search.app
January 27, 2025 at 1:18 PM
A fun collaboration with the Whitney, Prehna, and Bosis labs, in which we reveal the role of DUF2169 proteins: assisting PAAR-like domains in forming spike complexes and #T6SS assembly. 🦠
search.app/jDxaUi5yJK9B...
search.app/jDxaUi5yJK9B...
Reposted by Erez Yirmiya
Check out our latest paper using protein structures to uncover immune inhibitors hidden among millions of phage genes! These inhibitors block immune proteins from bacteria, plants and even humans, highlighting how immunity and counter-immunity mechanisms are conserved across the tree of life! 🦠🌿🧍♀️
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 24, 2025 at 1:39 PM
Check out our latest paper using protein structures to uncover immune inhibitors hidden among millions of phage genes! These inhibitors block immune proteins from bacteria, plants and even humans, highlighting how immunity and counter-immunity mechanisms are conserved across the tree of life! 🦠🌿🧍♀️
Reposted by Erez Yirmiya
Incredbile work from @soreklab.bsky.social demonstrating how to mine viral genomes to identify immune-modulatory proteins that work across bacteria, plants and animals 😱.
Bacteria have been amazing ressources of molecular diversity for biotech and medicine, now viral diversity can be explored too!
Bacteria have been amazing ressources of molecular diversity for biotech and medicine, now viral diversity can be explored too!
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 24, 2025 at 8:45 AM
Incredbile work from @soreklab.bsky.social demonstrating how to mine viral genomes to identify immune-modulatory proteins that work across bacteria, plants and animals 😱.
Bacteria have been amazing ressources of molecular diversity for biotech and medicine, now viral diversity can be explored too!
Bacteria have been amazing ressources of molecular diversity for biotech and medicine, now viral diversity can be explored too!
Reposted by Erez Yirmiya
Really cool!
Remarkable that phage proteins can inhibit human and plant TIR proteins and human cGAS. Conservation of function across such long evolutionary distances identifies new immunomodulators
Congrats to @soreklab.bsky.social and Kranzusch labs! What a great collaboration that is 😍
🧪
Remarkable that phage proteins can inhibit human and plant TIR proteins and human cGAS. Conservation of function across such long evolutionary distances identifies new immunomodulators
Congrats to @soreklab.bsky.social and Kranzusch labs! What a great collaboration that is 😍
🧪
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 24, 2025 at 5:53 AM
Really cool!
Remarkable that phage proteins can inhibit human and plant TIR proteins and human cGAS. Conservation of function across such long evolutionary distances identifies new immunomodulators
Congrats to @soreklab.bsky.social and Kranzusch labs! What a great collaboration that is 😍
🧪
Remarkable that phage proteins can inhibit human and plant TIR proteins and human cGAS. Conservation of function across such long evolutionary distances identifies new immunomodulators
Congrats to @soreklab.bsky.social and Kranzusch labs! What a great collaboration that is 😍
🧪
Reposted by Erez Yirmiya
Viral immune evasion proteins are widespread and block both bacterial and human immune proteins! Go check out Erez’s paper using AlphaFold-multimer to screen for new anti-defense proteins!!🤩🤩
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 8:46 PM
Viral immune evasion proteins are widespread and block both bacterial and human immune proteins! Go check out Erez’s paper using AlphaFold-multimer to screen for new anti-defense proteins!!🤩🤩
Reposted by Erez Yirmiya
Been waiting a long time to see this in print - phage proteins are capable of inhibiting immune systems across host-domain boundaries 🤯
Big congrats @erezyirmiya.bsky.social et al!!
Big congrats @erezyirmiya.bsky.social et al!!
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 6:35 PM
Been waiting a long time to see this in print - phage proteins are capable of inhibiting immune systems across host-domain boundaries 🤯
Big congrats @erezyirmiya.bsky.social et al!!
Big congrats @erezyirmiya.bsky.social et al!!
Reposted by Erez Yirmiya
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 Erez Yirmiya
A high-throughput AlphaFold screen reveals phage proteins that bind and inhibit bacterial immune proteins 🤯 Some of them even bind and inhibit eukaryotic immune proteins as well !
Congrats @erezyirmiya.bsky.social @soreklab.bsky.social et al for these beautiful discoveries 👌
Congrats @erezyirmiya.bsky.social @soreklab.bsky.social et al for these beautiful discoveries 👌
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 4:26 PM
A high-throughput AlphaFold screen reveals phage proteins that bind and inhibit bacterial immune proteins 🤯 Some of them even bind and inhibit eukaryotic immune proteins as well !
Congrats @erezyirmiya.bsky.social @soreklab.bsky.social et al for these beautiful discoveries 👌
Congrats @erezyirmiya.bsky.social @soreklab.bsky.social et al for these beautiful discoveries 👌
Reposted by Erez Yirmiya
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 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 3:35 PM
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...
Reposted by Erez Yirmiya
Finally moved to #Bluesky
and happy to share our recent work about a new phage anti-defense system, based on NAD reconstitution by new enzymatic reactions.
www.nature.com/articles/s41...
and happy to share our recent work about a new phage anti-defense system, based on NAD reconstitution by new enzymatic reactions.
www.nature.com/articles/s41...
November 21, 2024 at 4:40 PM
Finally moved to #Bluesky
and happy to share our recent work about a new phage anti-defense system, based on NAD reconstitution by new enzymatic reactions.
www.nature.com/articles/s41...
and happy to share our recent work about a new phage anti-defense system, based on NAD reconstitution by new enzymatic reactions.
www.nature.com/articles/s41...
Reposted by Erez Yirmiya
Seems like a good time to finally move here !
Taking the opportunity to share our most recent work :
www.biorxiv.org/content/10.1...
Taking the opportunity to share our most recent work :
www.biorxiv.org/content/10.1...
TIR signaling activates caspase-like immunity in bacteria
Proteases of the caspase family, as well as Toll/Interleukin-1 Receptor (TIR)-domain proteins, have central roles in innate immunity and regulated cell death in humans. In this study we describe a bac...
www.biorxiv.org
November 11, 2024 at 4:58 PM
Seems like a good time to finally move here !
Taking the opportunity to share our most recent work :
www.biorxiv.org/content/10.1...
Taking the opportunity to share our most recent work :
www.biorxiv.org/content/10.1...
Reposted by Erez Yirmiya
Happy to see our paper out @ Nat Comm
We discovered a bacterial NLR-like pattern recognition receptor that can sense 3 different viral proteins as a signature for infection. This explains its broad defense against different phage families
Congrats Nathalie Béchon!
www.nature.com/articles/s41...
We discovered a bacterial NLR-like pattern recognition receptor that can sense 3 different viral proteins as a signature for infection. This explains its broad defense against different phage families
Congrats Nathalie Béchon!
www.nature.com/articles/s41...
Diversification of molecular pattern recognition in bacterial NLR-like proteins - Nature Communications
Avs proteins are bacterial anti-phage pattern recognition receptors evolutionarily related to eukaryotic NLRs. Here, Béchon et al show that a single bacterial Avs can recognize different phage protein...
www.nature.com
November 14, 2024 at 4:45 PM
Happy to see our paper out @ Nat Comm
We discovered a bacterial NLR-like pattern recognition receptor that can sense 3 different viral proteins as a signature for infection. This explains its broad defense against different phage families
Congrats Nathalie Béchon!
www.nature.com/articles/s41...
We discovered a bacterial NLR-like pattern recognition receptor that can sense 3 different viral proteins as a signature for infection. This explains its broad defense against different phage families
Congrats Nathalie Béchon!
www.nature.com/articles/s41...