Rob Edwards

Some of the smallest 😎 viruses on Earth are all around us. Three or four genes 😍 each, in nearly every environment. We keep finding thousands by sequencing, yet don't know who they infect, can't easily isolate them, or even how the few we have infect a cell. Our new preprint takes this on 🧵👇

Sitting in the #ISME20 round table discussion about whether we can use AI in microbiome science, meanwhile chatting with my agents that are vibe-analysing microbiome data for me.

Prof Rob Edwards talking about the use of AI to learn from Cystic Fibrosis metagenomic data. #ISME20 @linsalrob.bsky.social

Vibe coding, vibe analysing, and the singularity. Has the singularity occurred yet? fame.flinders.edu.au/blog/2026/08...

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/...

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

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

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!

🧬🖥️

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

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

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!

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...)

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/...

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...

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...

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

🧬 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)

🎉 Excited to share that our paper, “agtools: A Software Framework to Manipulate Assembly Graphs”, has been accepted in Bioinformatics Advances. (1/n) 🔗 GitHub: github.com/Vini2/agtools 📄 Paper: academic.oup.com/bioinformati... #bioinformatics #genomics #openscience

During my PhD, @milja001.bsky.social and I started counting phage genomes, and tried to make them available in useful formats with useful metadata. We also described the extent of sequenced phage genomes at the time. Five years on, we've had a look at what's changed www.biorxiv.org/content/10.6...

When they say "The EOI process did not lead to an overall increase in the number of competitive applications submitted to the ARC compared to pre-EOI rounds.” it's very disingenuous since competitiveness is completely limited by dollars. We always have more great grants than they can support

Want to find #prophage in your #bacteria genomes? We built PhiSpy a long time ago, and now we've created a new web page for it: linsalrob.github.io/PhiSpyWeb/ Best of all, the data never leaves your computer! #phage #phagesky

Phage community: our plasmids for executing phage transposon mutagenesis are now on AddGene and I would love for you to try it out! It is powerful for ID'ing all essential genes and knocking out all non-essentials in a single experiment :) New exp here: www.addgene.org/browse/artic...

Aren't we all just having AI rewrite the original perl implementations in rust these days?

How every layer of science's "self-correcting machinery" failed when Iva Veseli and I simply wanted to reproduce the findings of a high-profile study on gut microbiome and autism: merenlab.org/2026/04/15/u...

The correct link: lh3.github.io/2026/04/17/t...

The almost best thing about this is that Bioinformatics Twitter is back!

Excited to share our new paper out today in @science.org 🎉 We show that HGT via natural competence drives diversification of chromosomal integrons in V. cholerae 🤩 Below a 🧵 on key findings incl. background on natural competence in V. cholerae 1/ #microsky #phagesky www.science.org/doi/10.1126/...

Have you developed a new #bioinformatics tool to understand #phage or #virus? Make sure you add it to #awesome-virome github.com/shandley/awe...