📢 Hiring a Postdoc in Computational Phage Biology (Kraków, Poland) We study the evolution & structural modularity of prophage-encoded glycan-degrading enzymes in Klebsiella pneumoniae — combining genomics and AlphaFold-based analyses. Details in attached PDF 👇

Phold's manuscript is now available @narjournal.bsky.social thanks to @susiegriggo.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @linsalrob.bsky.social @martinsteinegger.bsky.social @milot.bsky.social @eunbelivable.bsky.social & others not on bsky #phagesky academic.oup.com/nar/article/...

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...

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

🌟 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

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!

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...

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! 🧵

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/...

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!

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...

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

Running rapidNJ on M1 macs: johnlees.me/posts/rapidnj/ (and fork github.com/johnlees/rap...)

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

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...

AlphaFind: Discover structure similarity across the entire known proteome https://www.biorxiv.org/content/10.1101/2024.02.15.580465v1

Every figure in this work is an absolute banger. Here is just one:

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!

A wonderful postdoc opportunity in a temple for microbial evolution in Paris!

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

#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....

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...

Make sure you follow tomaszlab.bsky.social for some great science of the human microbiome.

Can anyone put me in the direction of a paper that synthesizes microbiome diversity across systems? Do we have any idea how variable the number of taxa in microbiomes is? I feel like I have seen this graph in a presentation but I’m not sure if there’s a publication looking at this. Thanks!!!!

#PhDSky #Academia

Very important and exciting work. Must read for any microbiologist. Congrats to Fanny and the entire team!

1st post on a ms just out in #MBE. We have been playing with the idea that horizontal gene transfer by shaping genetic backgrounds can affect patterns of adaptation by point mutations (or other changes) in core genes. We apply a recent method to identify significant chronologies HGT -> mutation. 1/3

Our group had a great time at the Local Pangenome conference in Alicante. Very proud of Janusz and Bogna for giving great talks.

I do take credit for convincing @epcrocha.bsky.social to give Bluesky a try. Make sure you follow him for some delicious science! :-)

Recently gave some reflections on getting (and not getting) research grants. Sharing here as well in case useful to others starting out: kucharski.substack.com/p/some-tips-...

PhD studentship with myself and Ed Feil at the University of Bath looking at the evolution and epidemiology of plasmids - in particular looking at plasmid fusions/hybrids/recombinants. Lots of fun bioinformatics! Open to UK or international students. #microsky www.findaphd.com/phds/project...

We have a PhD vacancy. Structural and functional protein bioinformatics, with a focus on bacteria-phage interactions lu.varbi.com/en/what:job/...

Bacteriophage ecology: Getting a head start on genomic competitors www.cell.com/current-biol...