IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models academic.oup.com/mbe/article/...

It took years after my masters to publish BaGPipe, now it's out! It's a Nextflow pipeline to run end-to-end bacterial GWAS, heavily tested and benchmarked on different datasets, and now in good hands of the Sanger's Pathogen Informatics Team. link.springer.com/article/10.1...

Looking good on Day 3 of #Shigella2026 ☀️🇫🇷🧫

@hughcottingham.bsky.social did a fantastic job on this benchmarking work, especially with the constant shifting of ONT tech!

Join my campaign to properly fund medical research in Australia 🔬 www.moniqueryan.com.au/medical_rese...

Some background to this, and an example I think of Phil's attitudes towards fostering students and encouraging others. I never got a chance to meet Phil in person, but will share his act of generosity that helped myself and @hdashnow.bsky.social and I think had in indelible mark on our careers. 1/8

Courtesy of @martibartfast.bsky.social , we have a new release of AllTheBacteria which adds another 322,920 assemblies, covering all ENA (illumina, isolate) prokaryotes to May 2025. allthebacteria.readthedocs.io/en/latest/ov...

It's a bit last minute, but we have an RA/junior postdoc position available in my lab (closing Sunday). Please reach out if you're interested in developing and applying methods to analyse microbial genomes and metagenomes! careers.petermac.org/job/MELBOURN...

To make sure the whole Shigella community will be gathered at this inaugural meeting, we have re-opened abstract submission for poster presentation until the end of the month. Please RT! www.shigella2026.conferences-pasteur.org/registration...

Spotted on the Chappell Roan merch store. I don’t think they know what Shigella is… what am I missing???

Our new paper on Insertion Sequences (IS) in #Klebsiella - Lineages have vastly different IS loads and profiles - An inverse relationship between IS load and metabolic capacity, in particular phosphorus use, consistent with early reductive evolution. www.microbiologyresearch.org/content/jour...

Finally got my #triplej #hottest100 votes in! Thought I heard no new music this year but that was a lie, my short list was huge. Ur A Rat and Keith I can never get out of my head

(1/7) Really pleased to have this published in @natcomms.nature.com We looked at all public genomes encoding blaIMP (carbapenem #AMR ) 🦠🧫🧬💊. We show 5 IMP variants achieved global endemicity while 2 are regionally endemic. www.nature.com/articles/s41... #MicroSky #microbiology #IDSky #EpiSky 🧪

Absolutely stoked to have this published in @plosbiology.org We looked at the metabolism of #Klebsiella pneumoniae 🦠🧫. We not only demonstrated lineage-specific #metabolism, but that lineages can cross-feed and support each other. journals.plos.org/plosbiology/... #MicroSky #microbiology 🧬 🧪 💊

The GTDB website now has an ANI calculator based on skani that supports uploading of user genomes. Try it at gtdb.ecogenomic.org/tools/skani. Find more information about @jimshaw.bsky.social fantastic tool at www.nature.com/articles/s41....

A new tool we’ve developed to identify AMR-associated SNPs in short- and long-read metagenome data….allows a greater understanding of the total resistome of a sample

I can’t explain why but reading the news feels like this at the moment

Very interesting to see what amendments were pushed by different parties for this bit of legislation. The One Nation amendment to remove a focus on public health issues caused by climate change (thankfully voted down) was typically 🙄

New online! Microbial genomics for antimicrobial resistance ecology and action

Are you hungry for some Shigella news? Why not come to the 1st International Shigella meeting www.shigella2026.conferences-pasteur.org/home 20-24 April 2026 Paris

There are millions of openly available microbial genomes, but searching them can be slow. Until now 🥁 Introducing LexicMap, a new alignment tool that lets scientists search these data in minutes, helping track antibiotic resistance, trace outbreaks, and more. www.ebi.ac.uk/about/news/r... 🦠

Happy to share that the paper describing Autocycler is now 100% up: doi.org/10.1093/bioi... (1/3)

To summarise our recent pre-print: Autocycler, the automated consensus assembler, when used with Nanopore long-read only Enterobacterales assemblies, produces more complete chromosomes and plasmids, with an accuracy comparable to hybrid assemblies.

A great opportunity to attend the #Shigella meeting April 20-24, 2026! Abstract submissions are open! @shigellameeting.bsky.social #Microsky

Come and join us at @shigellameeting.bsky.social in Paris 2026. Registrations are now open! www.shigella2026.conferences-pasteur.org/home and follow the Shigella starter pack go.bsky.app/6Vbwhjc (message to be added)! 215 days to go!

I am beyond excited to announce that ggplot2 4.0.0 has just landed on CRAN. It's not every day we have a new major #ggplot2 release but it is a fitting 18 year birthday present for the package. Get an overview of the release in this blog post and be on the lookout for more in-depth posts #rstats

Academia may not give you job security, flexibility, or wealth, but it will let you unexpectedly connect to eduroam in foreign cities

Really liked the explanation about human understanding, and what we miss when we use black box models. This has always been my gripe with prediction models for eg AMR - I want to know why that feature is associated with resistance!

Register today for the 14th International Meeting on Microbial Epidemiological Markers (IMMEM XIV)! Topics range from how genomics inform resistance profiling to pathogen surveillance in a #OneHealth framework. 🧬 ✍️ Register: ow.ly/gjOZ50WpOXX 👀 Programme: ow.ly/Whj850WpOXY#OneHealth #IDSky

This surprisingly relaxing footage is from SIX MILES under the ocean – and it’s the deepest ecosystem yet discovered

Huge amount of work in this paper, very proud of Hugh getting through all these benchmarking tests. We’re much more confident now using ONT-only data for our clinical questions

New preprint where we analysed IS loads in 🦠 #Klebsiella pneumoniae lineages and found they're inversely associated with nutrient usage. We propose an insertional tolerance model, whereby IS can only insert into metabolically-tolerable sites. #IDSky #MicroSky 🧪 www.biorxiv.org/content/10.1...

Fold first, ask later: structure-informed function annotation of Pseudomonas phage proteins Structural predictions to improve #phage genome annotation! @hannelorelongin.bsky.social @gbouras13.bsky.social y.social @susiegriggo.bsky.social @veravannoort.bsky.social www.biorxiv.org/content/10.1...

🚨Abstract submission & registration for #MicroSeq2025 is OPEN! 🚨Get in quick! The first 50 registrations are FREE for PhD students and ECRs who are current ASM members, thanks to @aussocmic.bsky.social. Head to our website to register now 👇 www.microseqconference.com/registration...

A periodic table of bacteria?: Mapping bacterial diversity in trait space https://www.biorxiv.org/content/10.1101/2025.07.11.664459v1

The 10th anniversary #ABACBS conference will be held in Adelaide from Nov 24-28. If you're thinking of coming, get in quick, as it's going to be a big week: A fantastic #bioinformatics conference with outstanding national and international speakers, and we're wrapping up the ABACBS week an AC/DC gig

Doesn’t destroy the planet if you use solar energy to power it - in summer our house regularly produces way more solar than we can use, our AC runs entirely off solar during the day with energy to spare

🦋Hello BlueSky!🦋 Let's get right into it. MicroSeq is back September 3-4, 2025! Stay tuned for more details on registration and abstract submission coming soon here and at www.microseqconference.com. 🌟Save the date!🌟 #MicroSeq2025

🚨Plasmid ALERT – new @eurosurveillance.org rapid comms! @ecdc.europa.eu-led study finds mosaic IncHI1B(pNDM-MAR) plasmid with blaOXA-48 + aerobactin in 492 K. pneumoniae isolates across 8 EU countries (2019–2024). First ESGMAP-backed paper: tinyurl.com/4acezh92 #AMR #plasmids #OneHealth #ESGMAP

Israel: silencing dissent everywhere theshot.net.au/uncategorize...

🚨🚨New paper out in @natcomms.nature.com!! Come for the first large-scale analysis of plasmid copy number across species, stay for one of the most intriguing results of my lab: universal scaling laws in plasmid biology! 📈🧬 👉 www.nature.com/articles/s41...

So excited that this is now online. It's been a huge collaborative effort to estimate the prevalence of capsule and O antigens associated with #klebsiella neonatal sepsis in Africa and South Asia. The first step to prioritising antigens for a vaccine to protect 1000s of newborns. #MicroSky #AMR

Explore the important role of #genomics and data-driven technologies for accelerating advances in #AMRresearch, at our Antimicrobial Resistance meeting! #AMR2026 Discover the latest developments informing a dynamic global response to controlling this crisis. 🗓️ 23–25 March 2026 📎 bit.ly/3SWzJUm

Excited to share this preprint focused on the genomic taxonomy of C. diphtheriae #diphtheria ➡️ www.biorxiv.org/content/10.1... Hope it helps advance research and surveillance of this relevant bacterial pathogen. Thanks to @sylvainbrisse.bsky.social and BEBP and BIGSdb teams for making it possible!

Main character energy is OUT, this summer we’re bringing NPC energy. We’re posted up at the bar dropping lore and suggesting side quests. We’re leaning casually near a locked door and saying “I don’t think you have the key for that” when someone tries the handle. We’re staring at a tree.

New blog post! In it, I benchmark the new version of Dorado from @nanoporetech.com, which comes with new DNA basecalling models. Short version: big accuracy gains for hac, small improvements for sup. Check it out for the full results: rrwick.github.io/2025/05/27/d...

immem hackthon registration closes 31st May. https://www.escmid.org/congress-events/immem-xiv/12th-microbial-bioinformatics-hackathon/

Sexually transmissible shigellosis has gone from an obscure cause of sporadic outbreaks to a sustained endemic AMR priority in only two decades! 🧫💊 Check out our latest preprint to understand how this happened 1/11 www.medrxiv.org/content/10.1...

Happy to share this resource of 568 closed Klebsiella pneumoniae species complex hybrid assemblies, including 1416 plasmids! ⭕️🦠 We hope this will be useful - short reads, long reads, hybrid assembly or all combined - for your own tools/validations 🥳 #Microsky journals.asm.org/doi/10.1128/...