Rafal Mostowy
@rafalmostowy.bsky.social
Group leader at Jagiellonian University in Krakow, cofounder of Polonium Foundation. Working on evolution of sex in bugs.
Reposted by Rafal Mostowy
Can we exploit past phage infection events (prophages) to decipher the specificity of phage receptor-binding proteins such as depolymerases?🔎 Happy to share our recent work at @natcomms.nature.com 🔽 #microsky #phagesky
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Unlocking data in Klebsiella lysogens to predict capsular type-specificity of phage depolymerases - Nature Communications
Here, the authors exploit the genetic information encoded in Klebsiella prophages to model the interplay between bacteria, prophages, and their depolymerases, using a directed acyclic graph-model and a sequence clustering-based model.
www.nature.com
October 8, 2025 at 8:59 AM
Can we exploit past phage infection events (prophages) to decipher the specificity of phage receptor-binding proteins such as depolymerases?🔎 Happy to share our recent work at @natcomms.nature.com 🔽 #microsky #phagesky
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Rafal Mostowy
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 Rafal Mostowy
🌟 Exciting news! We’re launching three fully-funded postdoc positions for "New Horizons for Synthetic Phages”
Join us in tackling antimicrobial resistance with cutting-edge synthetic biology + AI bioinformatics. Based at Flinders Uni in vibrant Adelaide.
👇 Read on for details!
#Phage
Join us in tackling antimicrobial resistance with cutting-edge synthetic biology + AI bioinformatics. Based at Flinders Uni in vibrant Adelaide.
👇 Read on for details!
#Phage
July 25, 2025 at 8:15 AM
🌟 Exciting news! We’re launching three fully-funded postdoc positions for "New Horizons for Synthetic Phages”
Join us in tackling antimicrobial resistance with cutting-edge synthetic biology + AI bioinformatics. Based at Flinders Uni in vibrant Adelaide.
👇 Read on for details!
#Phage
Join us in tackling antimicrobial resistance with cutting-edge synthetic biology + AI bioinformatics. Based at Flinders Uni in vibrant Adelaide.
👇 Read on for details!
#Phage
What determines who a phage can infect?
We tackled this question for temperate phages of Klebsiella — a bacterial pathogen — using a genome-wide association study (GWAS) and a massive protein testing effort.
👇 A thread!
We tackled this question for temperate phages of Klebsiella — a bacterial pathogen — using a genome-wide association study (GWAS) and a massive protein testing effort.
👇 A thread!
June 26, 2025 at 7:13 AM
What determines who a phage can infect?
We tackled this question for temperate phages of Klebsiella — a bacterial pathogen — using a genome-wide association study (GWAS) and a massive protein testing effort.
👇 A thread!
We tackled this question for temperate phages of Klebsiella — a bacterial pathogen — using a genome-wide association study (GWAS) and a massive protein testing effort.
👇 A thread!
I'm looking for a postdoc in computational evolutionary phage genomics, with the goal to better understand how protein innovation arises in viruses, at @jagiellonskiuni.bsky.social in Krakow (Poland).
Drop me a line if it sounds cool!
Deadline: 20.06.
Link here:
mcb.uj.edu.pl/documents/15...
Drop me a line if it sounds cool!
Deadline: 20.06.
Link here:
mcb.uj.edu.pl/documents/15...
May 20, 2025 at 7:52 AM
I'm looking for a postdoc in computational evolutionary phage genomics, with the goal to better understand how protein innovation arises in viruses, at @jagiellonskiuni.bsky.social in Krakow (Poland).
Drop me a line if it sounds cool!
Deadline: 20.06.
Link here:
mcb.uj.edu.pl/documents/15...
Drop me a line if it sounds cool!
Deadline: 20.06.
Link here:
mcb.uj.edu.pl/documents/15...
Reposted by Rafal Mostowy
We're looking for a PhD student to join us at Vilnius University in Lithuania. We work on RNA virus evolution computationally but we'd like to generate more mosquito RNA virus sequence data. Official ad: www.gmc.vu.lt/en/doctoral-.... Please share & continue reading if interested.
April 3, 2025 at 5:46 AM
We're looking for a PhD student to join us at Vilnius University in Lithuania. We work on RNA virus evolution computationally but we'd like to generate more mosquito RNA virus sequence data. Official ad: www.gmc.vu.lt/en/doctoral-.... Please share & continue reading if interested.
🚀 Follow-up on my recent MANIAC tweet: our new MMseqs2-blased tool is optimised for ANI and alignment fraction (AF) calculation in viral genomes. Unlike many other tools, it excels at ANI ~70%, an important range for viral taxonomy & evolution.
Here’s why that matters ➡️ a thread! 🧵
Here’s why that matters ➡️ a thread! 🧵
January 30, 2025 at 9:50 AM
🚀 Follow-up on my recent MANIAC tweet: our new MMseqs2-blased tool is optimised for ANI and alignment fraction (AF) calculation in viral genomes. Unlike many other tools, it excels at ANI ~70%, an important range for viral taxonomy & evolution.
Here’s why that matters ➡️ a thread! 🧵
Here’s why that matters ➡️ a thread! 🧵
Reposted by Rafal Mostowy
It was a pleasure working with you and Wanangwa on this project and I'm happy to see it published. Congratulations all!
January 29, 2025 at 3:28 PM
It was a pleasure working with you and Wanangwa on this project and I'm happy to see it published. Congratulations all!
And now with the working link!
journals.asm.org/doi/10.1128/...
journals.asm.org/doi/10.1128/...
January 30, 2025 at 8:33 AM
And now with the working link!
journals.asm.org/doi/10.1128/...
journals.asm.org/doi/10.1128/...
Our new paper out in mSystems!
journals.asm.org/eprint/ISRAZ...
We created a tool called MANIAC to estimate ANI between virus pairs. We found that:
1) MANIAC can reliably estimate ANI ~70%,
2) dsDNA phages exhibit ANI gap around 80%,
3) taxonomic assignment in temperate phages is tricky.
Try it!
journals.asm.org/eprint/ISRAZ...
We created a tool called MANIAC to estimate ANI between virus pairs. We found that:
1) MANIAC can reliably estimate ANI ~70%,
2) dsDNA phages exhibit ANI gap around 80%,
3) taxonomic assignment in temperate phages is tricky.
Try it!
January 29, 2025 at 2:26 PM
Our new paper out in mSystems!
journals.asm.org/eprint/ISRAZ...
We created a tool called MANIAC to estimate ANI between virus pairs. We found that:
1) MANIAC can reliably estimate ANI ~70%,
2) dsDNA phages exhibit ANI gap around 80%,
3) taxonomic assignment in temperate phages is tricky.
Try it!
journals.asm.org/eprint/ISRAZ...
We created a tool called MANIAC to estimate ANI between virus pairs. We found that:
1) MANIAC can reliably estimate ANI ~70%,
2) dsDNA phages exhibit ANI gap around 80%,
3) taxonomic assignment in temperate phages is tricky.
Try it!
If bacteria can be "good", so can viruses!
We made a short clip to explain to the public what phages are and why we should study them. The film also tells how our research on viral mosaicism could be socially and medically revelant.
🎥 Watch the film here:
www.youtube.com/watch?v=wXnx...
We made a short clip to explain to the public what phages are and why we should study them. The film also tells how our research on viral mosaicism could be socially and medically revelant.
🎥 Watch the film here:
www.youtube.com/watch?v=wXnx...
Bacteriophages, or good viruses: hope in the age of antimicrobial resistance POB
YouTube video by Uniwersytet Jagielloński
www.youtube.com
December 19, 2024 at 4:06 PM
If bacteria can be "good", so can viruses!
We made a short clip to explain to the public what phages are and why we should study them. The film also tells how our research on viral mosaicism could be socially and medically revelant.
🎥 Watch the film here:
www.youtube.com/watch?v=wXnx...
We made a short clip to explain to the public what phages are and why we should study them. The film also tells how our research on viral mosaicism could be socially and medically revelant.
🎥 Watch the film here:
www.youtube.com/watch?v=wXnx...
Reposted by Rafal Mostowy
New job offer: we search a postdoc (bioinformatics) to work on mobile genetic elements and gene flow in bacteria, with a focus on antibiotic resistance within a consortium including bioinformatics, synthetic biology, epidemiology & biochemistry. See research.pasteur.fr/en/job/postd... #MicroSky
April 4, 2024 at 4:33 PM
New job offer: we search a postdoc (bioinformatics) to work on mobile genetic elements and gene flow in bacteria, with a focus on antibiotic resistance within a consortium including bioinformatics, synthetic biology, epidemiology & biochemistry. See research.pasteur.fr/en/job/postd... #MicroSky
Reposted by Rafal Mostowy
First step in a community project to provide a uniformly assembled, annotated and searchable set of bacterial genomes, our preprint on our initial release of 1.9 million genome assemblies+taxonomic estimates. (figure compares with previous 661k dataset)
www.biorxiv.org/content/10.1...
#microsky
www.biorxiv.org/content/10.1...
#microsky
March 11, 2024 at 1:45 PM
First step in a community project to provide a uniformly assembled, annotated and searchable set of bacterial genomes, our preprint on our initial release of 1.9 million genome assemblies+taxonomic estimates. (figure compares with previous 661k dataset)
www.biorxiv.org/content/10.1...
#microsky
www.biorxiv.org/content/10.1...
#microsky
Reposted by Rafal Mostowy
Our latest on phage-plasmids(PP) is out! Two main findings. PP recombine more with (other) plasmids and phages than the latter, thereby connecting them. PP can become just phages or plasmids, which may then transition to be conjugative. All the world’s an MGE! www.nature.com/articles/s41...
February 21, 2024 at 11:34 AM
Our latest on phage-plasmids(PP) is out! Two main findings. PP recombine more with (other) plasmids and phages than the latter, thereby connecting them. PP can become just phages or plasmids, which may then transition to be conjugative. All the world’s an MGE! www.nature.com/articles/s41...
Reposted by Rafal Mostowy
AlphaFind: Discover structure similarity across the entire known proteome https://www.biorxiv.org/content/10.1101/2024.02.15.580465v1
AlphaFind: Discover structure similarity across the entire known proteome https://www.biorxiv.org/content/10.1101/2024.02.15.580465v1
AlphaFind is a web-based search engine that provides fast structure-based retrieval in the entire se
www.biorxiv.org
February 18, 2024 at 10:48 PM
AlphaFind: Discover structure similarity across the entire known proteome https://www.biorxiv.org/content/10.1101/2024.02.15.580465v1
Reposted by Rafal Mostowy
Every figure in this work is an absolute banger. Here is just one:
February 8, 2024 at 2:07 PM
Every figure in this work is an absolute banger. Here is just one:
Reposted by Rafal Mostowy
Have a look at our paper on a new group of pleomorphic viruses infecting marine hyperthermophilic #archaea of the class Archaeoglobi. The virus coexists in a stable relationship with its host. Congrats to Diana Baquero and Eduardo Bignon. @ISMEJ doi.org/10.1093/isme...
January 25, 2024 at 5:14 PM
Have a look at our paper on a new group of pleomorphic viruses infecting marine hyperthermophilic #archaea of the class Archaeoglobi. The virus coexists in a stable relationship with its host. Congrats to Diana Baquero and Eduardo Bignon. @ISMEJ doi.org/10.1093/isme...
It looks like PhiSpy has evolved into a new, exciting tool called Phables!
January 23, 2024 at 8:35 AM
It looks like PhiSpy has evolved into a new, exciting tool called Phables!
A wonderful postdoc opportunity in a temple for microbial evolution in Paris!
Last few days to apply for a postdoc position on the evolution and dynamics of microbial genomes !
New postdoc position in our lab for a project led by Marie Touchon (bioinformatics) and with O Tenaillon (experiments) on the evolution and dynamics of microbial genomes to understand their diversification by gene flow. Check research.pasteur.fr/en/job/postd...
January 11, 2024 at 1:53 PM
A wonderful postdoc opportunity in a temple for microbial evolution in Paris!
Reposted by Rafal Mostowy
Happy to see my new paper with @bjesseshapiro.bsky.social published! www.nature.com/articles/s41....
Bonus of this great News and Views article that was a surprise to us both: www.nature.com/articles/s41...
Along with our own blog post on the topic where we summarize the work: tinyurl.com/34r87kr9
Bonus of this great News and Views article that was a surprise to us both: www.nature.com/articles/s41...
Along with our own blog post on the topic where we summarize the work: tinyurl.com/34r87kr9
January 4, 2024 at 8:23 PM
Happy to see my new paper with @bjesseshapiro.bsky.social published! www.nature.com/articles/s41....
Bonus of this great News and Views article that was a surprise to us both: www.nature.com/articles/s41...
Along with our own blog post on the topic where we summarize the work: tinyurl.com/34r87kr9
Bonus of this great News and Views article that was a surprise to us both: www.nature.com/articles/s41...
Along with our own blog post on the topic where we summarize the work: tinyurl.com/34r87kr9
Reposted by Rafal Mostowy
#Microsky community have a look 🧫🦠: If you are interested in bacterial toxins, check out this paper from Asaf Levy lab: Toxinome—the bacterial protein toxin database. An interactive database of 1.4M toxins and 491K antitoxins encoded in 59,475 bacterial genomes ▶️ journals.asm.org/doi/epub/10....
Toxinome—the bacterial protein toxin database
journals.asm.org
December 21, 2023 at 7:43 AM
#Microsky community have a look 🧫🦠: If you are interested in bacterial toxins, check out this paper from Asaf Levy lab: Toxinome—the bacterial protein toxin database. An interactive database of 1.4M toxins and 491K antitoxins encoded in 59,475 bacterial genomes ▶️ journals.asm.org/doi/epub/10....
Reposted by Rafal Mostowy
Any advice on the best nanopore bacterial (Ecoli ideally) datasets which have the same isolate sequenced with both R9 and R10 and basecalled with multiple different versions of basecaller and sup/hac and methylation-aware on/off? Wanted to look at effect on AMR gene detection.
November 29, 2023 at 12:41 PM
Any advice on the best nanopore bacterial (Ecoli ideally) datasets which have the same isolate sequenced with both R9 and R10 and basecalled with multiple different versions of basecaller and sup/hac and methylation-aware on/off? Wanted to look at effect on AMR gene detection.
Our paper looking into the phenomenon of domain mosaicism in phages is now out in Nature Communications. Work led by Bogna Smug together with Krzysztof Szczepaniak, @epcrocha.bsky.social and @staszekdh.bsky.social. See a short thread. 1/7
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Ongoing shuffling of protein fragments diversifies core viral functions linked to interactions with ...
Proteins are composed of distinct functional domains, each serving a specific role. Here, Smug et al. show that phages are able to shuffle fragments of their proteins and this predominantly occurs in ...
www.nature.com
November 28, 2023 at 1:51 PM
Our paper looking into the phenomenon of domain mosaicism in phages is now out in Nature Communications. Work led by Bogna Smug together with Krzysztof Szczepaniak, @epcrocha.bsky.social and @staszekdh.bsky.social. See a short thread. 1/7
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Make sure you follow tomaszlab.bsky.social for some great science of the human microbiome.
November 15, 2023 at 8:21 AM
Make sure you follow tomaszlab.bsky.social for some great science of the human microbiome.