DNA sequencing for microbial surveillance in cystic fibrosis airways: advances, challenges, and clinical translation Out now: how DNA sequencing can transform microbial surveillance in lung disease and what must change for clinical use. journals.asm.org/doi/10.1128/...

DNA sequencing for microbial surveillance in cystic fibrosis airways: advances, challenges, and clinical translation | Clinical Microbiology Reviews

SUMMARYDNA sequencing has revolutionized microbial surveillance in cystic fibrosis (CF), transforming pathogen identification from culture-dependent to total microbial community identification using m...

journals.asm.org

Post issues or feature requests on GitHub and we'll deal with them

Dutchscientist (the real one)@dutchscientist.bsky.social · last wk.

OpenJDK JRE v8 and an old 2018 version of Artemis.jar on Windows. Painful indeed, but I still use it (also early adopter, not sure when). On Linux/Ubuntu it is easier. Will have a look at this.

Yep, you can install it with npm and run it completely stand alone ... Instructions to come

Dutchscientist (the real one)@dutchscientist.bsky.social · last wk.

Is there an offline version?

While this is interesting, I disagree with the observation "sequence-based tasks such as sequence searching, which do not tend to use structure even if the sequences are of proteins" #foldseek and friends are going gangbusters!

PLOS Biology@plosbiology.org · last wk.

Structural #bioinformatics aims to answer biological questions by considering biomolecular #structures at scale. This Perspective by @jgreener64.bsky.social argues that now that we have accurate predictions, we need to ask what we can learn from them. 🧪#AcademicSky plos.io/4bfgUoQ

🧬🖥️

Rob Edwards@linsalrob.bsky.social · last wk.

I've been using Sanger's Artemis to view #genomics since ... who knows (it was first published in 2000). It's still super useful, but getting harder to install. I vibe-coded a lightweight browser-only version that views #GenBank files: linsalrob.github.io/genbank_view... 🧬💻 #phagesky

#microsky #phagesky #phage The secret life of prophages journals.asm.org/doi/10.1128/...

From hijackers to architects: the role of prophages in bacterial genome evolution | Journal of Bacteriology

Bacteriophages (phages) are one of the most important drivers of bacterial evolution, regulating physiology, genetic diversity, population dynamics, and coevolution through complex host-phage interact...

journals.asm.org

Check out this fun collaboration on phages and Polyamines with the Marshall Lab! #microsky #phagesky 🧪🧫🧬🔬

Chris Marshall@sirmicrobe.bsky.social · 3w ago

This is our 2nd recently posted paper where we wanted to build off the fantastic 2023 PNAS paper by @prsecor.bsky.social group (www.pnas.org/doi/10.1073/...) 1/3

A family of lanthipeptides with anti- #phage function. Lanthivirin gene clusters in Actinobacteria yield matured peptides that block phage DNA replication, revealing new anti‑phage natural products. www.sciencedirect.com/science/arti... #bacteriophage #MicroSky

I've been using Sanger's Artemis to view #genomics since ... who knows (it was first published in 2000). It's still super useful, but getting harder to install. I vibe-coded a lightweight browser-only version that views #GenBank files: linsalrob.github.io/genbank_view... 🧬💻 #phagesky

Yep, that's why I said _almost_ We're aiming to reduce those two years to get a real cryoEM!

Trevor Lithgow@trevor-lithgow.bsky.social · 2w ago

Oh Rob, thems fightin’ words. A good and useful cryoEM structure of a phage is 2 years work from a talented postdoc. This ain’t that :-)

Starting with the DNA sequence of a #phage genome, #PholdAPhage will create a 3D reconstruction of the complete phage, almost like you did cryoEM on it! Check out Renee's awesome software github.com/reneegreen81... to assemble unknown phage particles one protein at a time

The ARC's new grant scheme table, in case you don't want to read through the details (which are here: www.arc.gov.au/system/files...)

ARC Tracker@arc-tracker.bsky.social · 2w ago

The ARC has released their new set of grant schemes ▶️ www.arc.gov.au/news-and-pub... Before implementing them, they’re now going to “consult with the sector”. Hopefully genuinely, not just with a few disengaged DVCRs. In the meantime, there’ll be another round of Discovery Projects (DP28).

Day 2 of #vom2026 starts with virus host interactions

If you’re at the Viruses of Microbes conference, interested in Pseudomonas or phage therapy, check out @hannahvpye.bsky.social ‘s poster no84. #VoM2026

The #VOM2026 keynote from @epcrocha.bsky.social was so elegant. How prophages benefit their hosts, how T6SS which is so beneficial to bacteria, evolved from phages, and how most prophages are newcomers.

#VoM2026 has started! 🎉 We were delighted to hear welcoming remarks from ISVM President Lone Brøndsted as we begin a week of exciting science, collaboration, and new connections. Here's to a fantastic week of science and networking in Prague! #VoM2026 #ISVM #Microbiology #Virology

Opening #vom2026 @isvm-society.bsky.social president Lone Brønsted encourages everyone to make new connections and find new phage phriends. Excited for the week of science to come.

#vom2026 but I am not presenting, instead I was invited to do something way more cool. Update soon

We are heading to Prague for the Viruses of Microbes 2026 conference! We will be presenting our latest research on phage formulations and delivery systems (skvortsovlab.com). Looking forward to a week of fantastic science! See you in Prague! #VoM2026 #phage

Excited to see our latest research featured in Canadian Poultry magazine! Our team is developing targeted #phage cocktail to help control #Salmonella in laying #hens to reduce bacterial colonization, #egg contamination & environmental shedding while preserving the natural gut #microbiota.

#microsky #phagesky #phage www.science.org/doi/10.1126/...

Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities

A single bacteriophage can dominate microbial communities yet only evolves when migration changes its ecological context.

science.org

If you do any work with DNA sequencing at some point, you need to assemble the reads. Usually, we just use the contigs, but that ignores important evidence from your data, so @vijinim.bsky.social wrote agtools to explore the assembly graph and learn more! academic.oup.com/bioinformati...

agtools: a software framework to manipulate assembly graphs

AbstractMotivation. Assembly graphs are a fundamental data structure used by genome and metagenome assemblers to represent sequences and their overlap info

academic.oup.com

All predicted complex structures are publicly available here: linsalrob.github.io/PHROG_struct.... Huge shoutout to Natia Geliashvili and @bedutilh.bsky.social, @linsalrob.bsky.social, @gbouras13.bsky.social, @vijinim.bsky.social, @hellmichgroup.bsky.social and Marta Bogacz! (5/n)

Enter PHLEGM! 💻🧬 We developed the Phage Homomer Level Estimate and Generation Method to infer oligomeric state using AlphaFold-Multimer and interface quality assessment. We applied it to >22,000 sequences, revealing massive structural diversity. (2/n)

New preprint! 🚨 Phage proteins don't act alone. Phages rely on homooligomerisation to assemble identical protein subunits into functional forms. But figuring out those exact configurations experimentally is tough. Learn about our approach in our new preprint! 👇 (1/n) www.biorxiv.org/content/10.6...

Huge thanks to my co-authors, including @linsalrob.bsky.social, @beardymcjohnface.bsky.social , and my co-first author Abbey Hutton! 🙏 These time-consuming experiments wouldn't have been possible without such a massive team effort!

Initial genomes from May 2026 Bundibugyo Virus Disease Outbreak in the Democratic Republic of the Congo and Uganda Great work from the teams here. virological.org/t/initial-ge...

Initial genomes from May 2026 Bundibugyo Virus Disease Outbreak in the Democratic Republic of the Congo and Uganda

Initial genomes from May 2026 Bundibugyo Virus Disease Outbreak in the Democratic Republic of the Congo and Uganda, reveal a new spillover event Context On 15 May 2026, the Ministry of Public Health, ...

virological.org

With Eugene Koonin, we wrote a rather comprehensive review on the origin, evolution and organization of the #virosphere. We describe all 10 viral realms and the logic behind them, and so much more. Check it out! comptes-rendus.academie-sciences.fr/biologies/ar...

Happy to share that our latest research on the eco-evolutionary dynamics of MDR plasmids and PDPs is now out (open access vAuthor) in The ISME Journal doi.org/10.1093/isme... Here, we explored how plasmid-dependent phages (PDPs) act as a selective pressure against the spread of multidrug resistance

Eco-evolutionary responses to plasmid-dependent phage constrain the spread of multidrug resistance plasmids

Abstract. Phage therapy offers a promising alternative to antibiotics for treating multidrug-resistant infections. Plasmid-dependent phages (PDPs) are part

doi.org

🧬 Assembly graphs are central to modern genome and metagenome assembly workflows, but working with them programmatically and reproducibly is still more difficult than it should be — at least from my experience working in this space. (2/n)