Sofya Garushyants
@garushyants.bsky.social
Evolutionary microbiology, horizontal gene transfer, bacterial defense systems and beyond. Currently postdoc in Koonin's group. All opinions are mine
Reposted by Sofya Garushyants
Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
November 11, 2025 at 5:15 PM
Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Sofya Garushyants
Gluing a bulky host protein onto an immune surveillance complex is a wild mechanism of viral immune evasion!
@natmicrobiol.nature.com
#phagesky #phage #microsky
www.nature.com/articles/s41...
@natmicrobiol.nature.com
#phagesky #phage #microsky
www.nature.com/articles/s41...
November 12, 2025 at 5:47 PM
Gluing a bulky host protein onto an immune surveillance complex is a wild mechanism of viral immune evasion!
@natmicrobiol.nature.com
#phagesky #phage #microsky
www.nature.com/articles/s41...
@natmicrobiol.nature.com
#phagesky #phage #microsky
www.nature.com/articles/s41...
Reposted by Sofya Garushyants
Two days left to apply for a PhD or postdoc position in my lab!
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!
For more information and how to apply, see below 👇
Please RT!
📢 The #HIRI is looking for a #postdoc & a #PhD student to join the research group of @jenshoer.bsky.social. His lab focuses on understanding the molecular mechanisms of #phages with #RNA genomes during infection, host takeover & anti-phage defense. 🧫🦠 More info: www.helmholtz-hiri.de/en/jobs-tale...
November 11, 2025 at 1:37 PM
Two days left to apply for a PhD or postdoc position in my lab!
Reposted by Sofya Garushyants
Reposted by Sofya Garushyants
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
Now, a new study shows the same for a plant NLR. Another example how principles of immunity remain conserved from bacteria to eukaryotes
A wheat NLR conferring broad-spectrum resistance against powdery mildew by recognizing two structurally diverse AVR effectors. Interested? Check out our newest preprint: www.biorxiv.org/content/10.1...
Dual recognition of structurally unrelated mildew effectors underlies the broad-spectrum resistance of Pm3e in wheat
Broad-spectrum resistance genes are highly valuable for sustainable crop protection, yet the molecular basis of their activity is often unknown. The Pm3 allelic series in wheat encodes NLR receptors t...
www.biorxiv.org
November 2, 2025 at 6:34 PM
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
Now, a new study shows the same for a plant NLR. Another example how principles of immunity remain conserved from bacteria to eukaryotes
Reposted by Sofya Garushyants
New pre-print: Plasmid dependent phage effectively eliminate AMR bacteria and block plasmid transmission in the chicken gut microbiome
Fun collaboration with Tao He lab (JAAS) and @brockhurstlab.bsky.social lab (Manchester)
#phagesky#microsky
www.biorxiv.org/content/10.1...
Fun collaboration with Tao He lab (JAAS) and @brockhurstlab.bsky.social lab (Manchester)
#phagesky#microsky
www.biorxiv.org/content/10.1...
Plasmid dependent phage eliminate pathogenic bacteria and antibiotic resistance plasmids from the chicken gut microbiome
Conjugative plasmids are a key reservoir of antimicrobial resistance (AMR) in commensal and pathogenic bacteria within the gut microbiome. Plasmid-dependent phage (PDPs) are a promising therapeutic op...
www.biorxiv.org
October 27, 2025 at 8:19 AM
New pre-print: Plasmid dependent phage effectively eliminate AMR bacteria and block plasmid transmission in the chicken gut microbiome
Fun collaboration with Tao He lab (JAAS) and @brockhurstlab.bsky.social lab (Manchester)
#phagesky#microsky
www.biorxiv.org/content/10.1...
Fun collaboration with Tao He lab (JAAS) and @brockhurstlab.bsky.social lab (Manchester)
#phagesky#microsky
www.biorxiv.org/content/10.1...
Reposted by Sofya Garushyants
@prczhaoyansong.bsky.social’s deep dive into the dark matter of compost communities is now out 🎉 Genomic islands hijack jumbo phages—whose capsids enable transfer of large tracts of DNA—shedding new light on the scale & scope of phage-mediated gene flow 😎
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
Jumbo phage–mediated transduction of genomic islands | PNAS
Bacteria acquire new genes by horizontal gene transfer, typically mediated by mobile
genetic elements (MGEs). While plasmids, bacteriophages, and c...
www.pnas.org
October 28, 2025 at 6:36 PM
@prczhaoyansong.bsky.social’s deep dive into the dark matter of compost communities is now out 🎉 Genomic islands hijack jumbo phages—whose capsids enable transfer of large tracts of DNA—shedding new light on the scale & scope of phage-mediated gene flow 😎
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
Reposted by Sofya Garushyants
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!
For more information and how to apply, see below 👇
Please RT!
📢 The #HIRI is looking for a #postdoc & a #PhD student to join the research group of @jenshoer.bsky.social. His lab focuses on understanding the molecular mechanisms of #phages with #RNA genomes during infection, host takeover & anti-phage defense. 🧫🦠 More info: www.helmholtz-hiri.de/en/jobs-tale...
Working at HIRI
At the HIRI, we do not just value excellent research. Short distances, an open door policy, and a good working atmosphere—this is what distinguishes us from others. Have a look at our current job…
www.helmholtz-hiri.de
October 17, 2025 at 12:52 PM
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!
For more information and how to apply, see below 👇
Please RT!
Reposted by Sofya Garushyants
BREAKING: Friday night massacre underway at CDC. Doznes of "disease detectives," high-level scientists, entire Washington staff and editors of the MMWR (Morbidity and Mortality Weekly Report) have all been RIFed and received the following notice:
October 11, 2025 at 2:10 AM
BREAKING: Friday night massacre underway at CDC. Doznes of "disease detectives," high-level scientists, entire Washington staff and editors of the MMWR (Morbidity and Mortality Weekly Report) have all been RIFed and received the following notice:
Reposted by Sofya Garushyants
Thoughtful and well-informed op-ed from @ianlmorgan.bsky.social
Definitely worth a read!
www.the-scientist.com/nih-leadersh...
1/2
Definitely worth a read!
www.the-scientist.com/nih-leadersh...
1/2
NIH Leadership Is Failing Early Career Researchers
Halted training programs, funding chaos, and hiring freezes jeopardize advancement options for early career researchers.
www.the-scientist.com
October 10, 2025 at 12:01 PM
Thoughtful and well-informed op-ed from @ianlmorgan.bsky.social
Definitely worth a read!
www.the-scientist.com/nih-leadersh...
1/2
Definitely worth a read!
www.the-scientist.com/nih-leadersh...
1/2
Reposted by Sofya Garushyants
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
Thread 1/n
September 25, 2025 at 9:29 PM
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
Thread 1/n
Reposted by Sofya Garushyants
Reminder: a large (2.5M+) sibling control study found "no evidence of increased risk of autism, ADHD, or intellectual disability associated with acetaminophen use". Precisely the kind of data that requires serious consideration before declaring mission accomplished.
jamanetwork.com/journals/jam...
jamanetwork.com/journals/jam...
Acetaminophen Use During Pregnancy and Children’s Risk of Autism, ADHD, and Intellectual Disability
This nationwide cohort study with sibling control analysis examines the association of acetaminophen use during pregnancy with children’s risk of autism, ADHD, and intellectual disability.
jamanetwork.com
September 22, 2025 at 9:03 PM
Reminder: a large (2.5M+) sibling control study found "no evidence of increased risk of autism, ADHD, or intellectual disability associated with acetaminophen use". Precisely the kind of data that requires serious consideration before declaring mission accomplished.
jamanetwork.com/journals/jam...
jamanetwork.com/journals/jam...
Reposted by Sofya Garushyants
Now hiring a computational postdoc (evolutionary genomics, molecular evolution) in my lab at Emory University.
If you’re interested in population genetics, fitness landscapes, and viral evolution — get in touch.
faculty-emory.icims.com/jobs/151181/...
If you’re interested in population genetics, fitness landscapes, and viral evolution — get in touch.
faculty-emory.icims.com/jobs/151181/...
Careers | Emory University | Atlanta GA
faculty-emory.icims.com
September 18, 2025 at 3:38 PM
Now hiring a computational postdoc (evolutionary genomics, molecular evolution) in my lab at Emory University.
If you’re interested in population genetics, fitness landscapes, and viral evolution — get in touch.
faculty-emory.icims.com/jobs/151181/...
If you’re interested in population genetics, fitness landscapes, and viral evolution — get in touch.
faculty-emory.icims.com/jobs/151181/...
Reposted by Sofya Garushyants
PIWI clade Argonautes are essential for transposon silencing. Without them, animals are sterile due to massive transposon activity.
But how does piRNA-guided target interaction translate into silencing?
PhD student Júlia Portell Montserrat has an intriguing answer
www.cell.com/molecular-ce...
But how does piRNA-guided target interaction translate into silencing?
PhD student Júlia Portell Montserrat has an intriguing answer
www.cell.com/molecular-ce...
September 17, 2025 at 10:39 AM
PIWI clade Argonautes are essential for transposon silencing. Without them, animals are sterile due to massive transposon activity.
But how does piRNA-guided target interaction translate into silencing?
PhD student Júlia Portell Montserrat has an intriguing answer
www.cell.com/molecular-ce...
But how does piRNA-guided target interaction translate into silencing?
PhD student Júlia Portell Montserrat has an intriguing answer
www.cell.com/molecular-ce...
Reposted by Sofya Garushyants
Three new kids on the block. ARMADA, BRIGADE, and TALON. Impressive how multiple labs all come together to contribute to discovery. Great collaboration with Simon, Chase, and Eugene. From the very talented Ryan Bell, together with Thomas Gaudin and our own Yi Wu.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
YprA family helicases provide the missing link between diverse prokaryotic immune systems
Bacteria and archaea possess an enormous variety of antivirus immune systems that often share homologous proteins and domains, some of which contribute to diverse defense strategies. YprA family helic...
www.biorxiv.org
September 16, 2025 at 4:56 PM
Three new kids on the block. ARMADA, BRIGADE, and TALON. Impressive how multiple labs all come together to contribute to discovery. Great collaboration with Simon, Chase, and Eugene. From the very talented Ryan Bell, together with Thomas Gaudin and our own Yi Wu.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
YprA is a helicase popping up in multiple defense systems. In our new preprint (led by Ryan Bell), we investigate YprA clades and describe new defense systems. Importantly, ARMADA II synergizes with Druantia III; and Zorya II, Druantia III, and ARMADA II often travel together on various MGEs.
YprA family helicases provide the missing link between diverse prokaryotic immune systems
Bacteria and archaea possess an enormous variety of antivirus immune systems that often share homologous proteins and domains, some of which contribute to diverse defense strategies. YprA family helic...
www.biorxiv.org
September 17, 2025 at 3:37 AM
YprA is a helicase popping up in multiple defense systems. In our new preprint (led by Ryan Bell), we investigate YprA clades and describe new defense systems. Importantly, ARMADA II synergizes with Druantia III; and Zorya II, Druantia III, and ARMADA II often travel together on various MGEs.
Sanasar has been digging into how bacterial defense systems shift under different phage attack modes – from long-term infections by similar phages to constantly changing phage assaults. Glad to be part of that story, out today
Evolution of antivirus defense in prokaryotes, depending on the environmental virus prevalence and virome dynamics | mBio
The virus-host arms race is a major component of the evolutionary process in all organisms
that drove the evolution of a broad variety of immune mechanisms. In the last few
years, over 200 distinct an...
journals.asm.org
September 16, 2025 at 10:52 PM
Sanasar has been digging into how bacterial defense systems shift under different phage attack modes – from long-term infections by similar phages to constantly changing phage assaults. Glad to be part of that story, out today
hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!
September 15, 2025 at 5:26 PM
hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!
Reposted by Sofya Garushyants
Reposted by Sofya Garushyants
An inspiring read!
academic.oup.com/genetics/adv...
A beautiful historical perspective on Ester Lederberg's legacy from @ccwendling.bsky.social & @zacharybailey.bsky.social
academic.oup.com/genetics/adv...
A beautiful historical perspective on Ester Lederberg's legacy from @ccwendling.bsky.social & @zacharybailey.bsky.social
Pioneer of bacterial genetics: the legacy of Esther Miriam Lederberg
Abstract. Esther Miriam Lederberg's brilliant scientific lifework, from the discovery of phage lambda, bacterial conjugation, and replica plating, provided
academic.oup.com
August 28, 2025 at 10:52 PM
An inspiring read!
academic.oup.com/genetics/adv...
A beautiful historical perspective on Ester Lederberg's legacy from @ccwendling.bsky.social & @zacharybailey.bsky.social
academic.oup.com/genetics/adv...
A beautiful historical perspective on Ester Lederberg's legacy from @ccwendling.bsky.social & @zacharybailey.bsky.social
Reposted by Sofya Garushyants
New paper alert! We suggest caution in the analyses of viral auxiliary metabolic genes and propose a new overarching term - 'auxiliary viral genes' (AVGs) to describe different types of such genes. @simrouxvirus.bsky.social #phagesky #Microsky www.nature.com/articles/s41...
A call for caution in the biological interpretation of viral auxiliary metabolic genes - Nature Microbiology
This Perspective discusses virus-encoded auxiliary metabolic genes and provides a framework for the biological interpretation of these genes.
www.nature.com
August 27, 2025 at 12:24 PM
New paper alert! We suggest caution in the analyses of viral auxiliary metabolic genes and propose a new overarching term - 'auxiliary viral genes' (AVGs) to describe different types of such genes. @simrouxvirus.bsky.social #phagesky #Microsky www.nature.com/articles/s41...
Reposted by Sofya Garushyants
Preprint: We discovered phage proteins that sequester diverse immune signaling molecules, including cUMP, cCMP, and N7-cADPR
The first viral sponges to inhibit Pycsar and type IV Thoeris
Congrats to talented leading author Romi Hadary! Read her thread to learn more about our findings
The first viral sponges to inhibit Pycsar and type IV Thoeris
Congrats to talented leading author Romi Hadary! Read her thread to learn more about our findings
August 25, 2025 at 1:00 PM
Preprint: We discovered phage proteins that sequester diverse immune signaling molecules, including cUMP, cCMP, and N7-cADPR
The first viral sponges to inhibit Pycsar and type IV Thoeris
Congrats to talented leading author Romi Hadary! Read her thread to learn more about our findings
The first viral sponges to inhibit Pycsar and type IV Thoeris
Congrats to talented leading author Romi Hadary! Read her thread to learn more about our findings
Reposted by Sofya Garushyants
Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Protein Structure Informed Bacteriophage Genome Annotation with Phold
Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here we introduce Phold, an annotation framework utilis...
www.biorxiv.org
August 8, 2025 at 7:11 AM
Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Sofya Garushyants
It was a great pleasure to contribute to this work by Jemma Fendley, @mmolari.bsky.social, and Boris Shraiman on pan-genomes, linkage, and recombination in phage genomes.
We analyzed data collected by the fantastic SEA-PHAGES program in phagesdb.org.
[1/6]
www.biorxiv.org/content/10.1...
We analyzed data collected by the fantastic SEA-PHAGES program in phagesdb.org.
[1/6]
www.biorxiv.org/content/10.1...
The Actinobacteriophage Database | Home
phagesdb.org
August 23, 2025 at 4:21 PM
It was a great pleasure to contribute to this work by Jemma Fendley, @mmolari.bsky.social, and Boris Shraiman on pan-genomes, linkage, and recombination in phage genomes.
We analyzed data collected by the fantastic SEA-PHAGES program in phagesdb.org.
[1/6]
www.biorxiv.org/content/10.1...
We analyzed data collected by the fantastic SEA-PHAGES program in phagesdb.org.
[1/6]
www.biorxiv.org/content/10.1...
Reposted by Sofya Garushyants
RFdiffusion2 is now live!
github.com/RosettaCommo...
You can now design proteins, and in particular enzymes from just partially defined amino acid side chains, and without defining their sequence position or order!
github.com/RosettaCommo...
You can now design proteins, and in particular enzymes from just partially defined amino acid side chains, and without defining their sequence position or order!
August 22, 2025 at 12:51 AM
RFdiffusion2 is now live!
github.com/RosettaCommo...
You can now design proteins, and in particular enzymes from just partially defined amino acid side chains, and without defining their sequence position or order!
github.com/RosettaCommo...
You can now design proteins, and in particular enzymes from just partially defined amino acid side chains, and without defining their sequence position or order!