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Rob Edwards

@linsalrob.bsky.social
2.5K followers 1.9K following 220 posts

Bioinformatician and microbiologist at Flinders University in Adelaide. @linsalrob on all your socials

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Reposted by Rob Edwards
Vivek Mutalik @vivekmutalik.bsky.social · 19/09/2026
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 🧵👇
Schematics of how single strand RNA and DNA phages infect bacteria with F-pilus
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Rob Edwards @linsalrob.bsky.social · 17/08/2026
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.
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Reposted by Rob Edwards
Vijini Mallawaarachchi @vijinim.bsky.social · 17/08/2026
Prof Rob Edwards talking about the use of AI to learn from Cystic Fibrosis metagenomic data. #ISME20 @linsalrob.bsky.social
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Rob Edwards @linsalrob.bsky.social · 17/08/2026
We're having fun developing post-cloud bioinformatics tools: reimagining some of the bioinformatics canon as local, browser-native applications so your data never has to leave your laptop. Here's the first set: edwards.flinders.edu.au/viz/ Let us know if you want other tools local to your laptop
edwards.flinders.edu.au
-viz
Welcome to the -viz suite of tools: classic bioinformatics tools, reimagined for the browser. agviz · bamviz · genbankviz · phispyviz Each of our tools is a classic bioinformatics tool, but reimagi…
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Rob Edwards @linsalrob.bsky.social · 09/08/2026
Vibe coding, vibe analysing, and the singularity. Has the singularity occurred yet? fame.flinders.edu.au/blog/2026/08...
fame.flinders.edu.au
Vibe coding, vibe analysing, and the singularity.
Recently, we’ve been vibe coding bioinformatics projects and vibe analysing bioinformatics data. Have we reached the singularity yet?
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Rob Edwards @linsalrob.bsky.social · 04/08/2026
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/...
journals.asm.org
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...
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Rob Edwards @linsalrob.bsky.social · 29/07/2026
Post issues or feature requests on GitHub and we'll deal with them
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Rob Edwards @linsalrob.bsky.social · 29/07/2026
Yep, you can install it with npm and run it completely stand alone ... Instructions to come
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Rob Edwards @linsalrob.bsky.social · 29/07/2026
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!
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Rob Edwards @linsalrob.bsky.social · 29/07/2026
🧬🖥️
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Reposted by Rob Edwards
Emmanuele Severi @emmseveri.bsky.social · 17/07/2026
#microsky #phagesky #phage The secret life of prophages journals.asm.org/doi/10.1128/...
journals.asm.org
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...
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Reposted by Rob Edwards
Patrick R. Secor @prsecor.bsky.social · 17/07/2026
Check out this fun collaboration on phages and Polyamines with the Marshall Lab! #microsky #phagesky 🧪🧫🧬🔬
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Current Research in Microbial Sciences @microbesinfect.bsky.social · 26/07/2026
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
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Rob Edwards @linsalrob.bsky.social · 29/07/2026
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
linsalrob.github.io
genbank_viewer
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Rob Edwards @linsalrob.bsky.social · 24/07/2026
Yep, that's why I said _almost_ We're aiming to reduce those two years to get a real cryoEM!
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Rob Edwards @linsalrob.bsky.social · 22/07/2026
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
A computer generated 3D reconstruction of a phage, based solely on its genome sequence. For this image, we started with the genome, and used PholdAPhage to create the structures. Colours are based on pLDDT scores.
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ARC Tracker @arc-tracker.bsky.social · 22/07/2026
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...)
Screenshot of a table (black text on variously shaded backgrounds) showing some main aspects of the new grant schemes announced by the ARC.
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Rob Edwards @linsalrob.bsky.social · 07/07/2026
Day 2 of #vom2026 starts with virus host interactions
The introduction to viruses of microbes 2026
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Reposted by Rob Edwards
Evelien Adriaenssens @evelienadri.bsky.social · 07/07/2026
If you’re at the Viruses of Microbes conference, interested in Pseudomonas or phage therapy, check out @hannahvpye.bsky.social ‘s poster no84. #VoM2026
Woman standing in front of science poster
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Rob Edwards @linsalrob.bsky.social · 06/07/2026
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.
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ISVM @isvm-society.bsky.social · 06/07/2026
#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
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Rob Edwards @linsalrob.bsky.social · 06/07/2026
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.
ISVM President Lone Brønsted opening #vom2026
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Pavol Bardy @pavol.bsky.social · 06/07/2026
#vom2026 but I am not presenting, instead I was invited to do something way more cool. Update soon
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Timofey Skvortsov @timskvortsov.bsky.social · 05/07/2026
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
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Hany Anany @guelphage-lab.bsky.social · 20/05/2026
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.
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Emmanuele Severi @emmseveri.bsky.social · 30/05/2026
#microsky #phagesky #phage www.science.org/doi/10.1126/...
science.org
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.
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Rob Edwards @linsalrob.bsky.social · 02/06/2026
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...
academic.oup.com
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
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Reposted by Rob Edwards
Susie Grigson @susiegriggo.bsky.social · 26/05/2026
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)
linsalrob.github.io
PHROG Structure Gallery
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Reposted by Rob Edwards
Susie Grigson @susiegriggo.bsky.social · 26/05/2026
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)
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Susie Grigson @susiegriggo.bsky.social · 26/05/2026
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...
biorxiv.org
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Susie Grigson @susiegriggo.bsky.social · 20/05/2026
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!
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Rob Edwards @linsalrob.bsky.social · 19/05/2026
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...
virological.org
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, ...
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Reposted by Rob Edwards
Mart Krupovic @mkrupovic.bsky.social · 11/05/2026
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...
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Daniel Cazares @danielcazares.bsky.social · 11/05/2026
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
doi.org
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
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Reposted by Rob Edwards
Vijini Mallawaarachchi @vijinim.bsky.social · 08/05/2026
🧬 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)
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Reposted by Rob Edwards
Vijini Mallawaarachchi @vijinim.bsky.social · 08/05/2026
🎉 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
academic.oup.com
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
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Reposted by Rob Edwards
Ryan Cook @ryancook94.bsky.social · 08/05/2026
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...
biorxiv.org
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Rob Edwards @linsalrob.bsky.social · 07/05/2026
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
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Rob Edwards @linsalrob.bsky.social · 06/05/2026
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
linsalrob.github.io
PhiSpyWeb – Browser-based Prophage Prediction
Browser-based prophage prediction using PhiSpy, Pyodide, and WebAssembly
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Reposted by Rob Edwards
Joe Bondy-Denomy @jbdsf.bsky.social · 24/04/2026
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...
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Rob Edwards @linsalrob.bsky.social · 21/04/2026
Aren't we all just having AI rewrite the original perl implementations in rust these days?
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A. Murat Eren (Meren) @merenbey.bsky.social · 16/04/2026
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...
merenlab.org
Unfalsifiable by Design: A Year of Trying and Failing to Reproduce a Human Microbiome and Autism Study
The myth of open data, reproducibility, responsibility, and accountability in science, and your role in it
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Heng Li @lh3lh3.bsky.social · 17/04/2026
The correct link: lh3.github.io/2026/04/17/t...
lh3.github.io
The AI Rewrite Dilemma
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Dr Andrew Lonsdale @lonsbio.bsky.social · 11/04/2026
The almost best thing about this is that Bioinformatics Twitter is back!
Sickos meme, with "rewrites.bio flamewars" caption
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Melanie Blokesch @mblokesch.bsky.social · 10/04/2026
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/...
science.org
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Rob Edwards @linsalrob.bsky.social · 08/04/2026
Have you developed a new #bioinformatics tool to understand #phage or #virus? Make sure you add it to #awesome-virome github.com/shandley/awe...
The awesome virome logo of a phage above a strand of DNA
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Vivek Mutalik @vivekmutalik.bsky.social · 03/04/2026
📣Huge preprint 🔔 Today we share something our group has been working toward for a long time, led by @lucasmoriniere.bsky.social We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something I had only dreamed of.
Phage receptor prediction from genome sequencing alone. Bacterial receptor (blue) interacting with phage proteins (purple) is shown here
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Vivek Mutalik @vivekmutalik.bsky.social · 03/04/2026
www.biorxiv.org/content/10.6... There is so much to explore in this data that one can spend life time going through. To make it easier to go through the data, @miloj.bsky.social put together this beautiful “Phage Datasheet”🤩 iseq.lbl.gov/PhageDataShe...
iseq.lbl.gov
Phage Foundry Data Browser
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George O'Toole (he/him/his) @geiselbiofilm.bsky.social · 04/04/2026
Pls share: A postdoctoral researcher position is available in the Scharf lab in the Department of Biological Sciences at Virginia Tech to study motility and chemotaxis in the symbiotic soil bacterium Sinorhizobium meliloti. jobs.apply.vt.edu/jobs/postdoc...
jobs.apply.vt.edu
Postdoctoral Associate - Blacksburg, Virginia, United States
Job Description A full-time postdoctoral researcher position is available in the Scharf lab in the Department of Biological Sciences at Virginia Tech to study motility and chemotaxis in the symbioti...
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Paul Turner Lab @paulturnerlab.bsky.social · 04/04/2026
Our perspective on measuring individual virus traits, led by staff scientist @antanij.bsky.social #phagesky #microsky
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