@wytamma.bsky.social 's WASM tools have transformed my experience of teaching Python to first year undergraduate biologists this year. Since last year, I've been teaching ~400 undergrads how to code (functions, lists, dictionaries, loops) over (one hour intro lecture +) two 2-hour practicals. 1/n
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...
At long last, my final PhD chapter is out: we developed a novel evolutionary simulator of bacterial pangenomes, Pansim, fitting it to data from >600K genomes using a likelihood-free framework, PopPUNK-mod, to explore neutral and adaptive pangenome dynamics www.biorxiv.org/content/10.6...
Proud to announce SimPhyNI, a new tool for bacterial GWAS with higher precision and scalability than existing tools. Try it out and let us know what you think!!
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 🧬 🧪 💊
Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years
#phagesky
www.nature.com/articles/s41...
🧬 Come check out my poster on agtools, an open-source Python framework for analysing and manipulating assembly graphs at #ABACBS2025 Poster #106
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💻 Github: github.com/Vini2/agtools
📄 Preprint: biorxiv.org/content/10.110…
PeterMac @petermaccc.bsky.social representing at #abacbs2025 What a community 😍
Great talk from Michael Payne at #ABACBS2025 on DAMPA - tool for designing probe panels for targeted metagenomics using pangenome graphs! Captures all diversity efficiently, uses fewer probes than competitors. Critical for syndromic surveillance! 🧬🔬 #Metagenomics
Happy to share our new AMR resource which has phenotypic AMR (usually MIC data) collected from publications and databases. This is paired with assemblies and annotations
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
📣 Join us for the 2025 @isbscience.org Virtual Microbiome Symposium, focused on "Gut Microbial Metabolites and Their Impact on Host Systems".
co-director - @flash-point.bsky.social 🦠💥
It's free, & we have an amazing line-up of speakers!
Dec. 12th. Please share!
isbscience.org/2025-isb-vir...
Logo of Bin Chicken (Australian white ibis) on a rubbish bin, pulling out a strand of DNA
“Bin Chicken” is now published in Nature Methods! It substantially improves genome recovery through rational coassembly 🧬🖥️. Applied to public 🌍 metagenomes, we recovered 24,000 novel species 🦠, including 6 new phyla.
doi.org/10.1038/s415...
@benjwoodcroft.bsky.social @rhysnewell.bsky.social
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We're very happy to release our new database Metalog metalog.embl.de ! It offers manually curated and harmonised contextual data for 110k metagenomics samples across the globe, incl. precomputed taxonomic profiles, for interactive browsing and for download 🧵 1/7
#microsky
Happy to share that the paper describing Autocycler is now 100% up:
doi.org/10.1093/bioi...
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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
Happy to see that Spacedust is now published on Nature Methods!
It combines sensitive Foldseek structure search and conserved neighborhood detection to discover functionally-associated gene clusters in prokaryotic & viral genomes.
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Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
Large AI models are reported to achieve high accuracy (AUROC) predicting pathogenic variants across the genome.
A preprint reports that the predictions are based on splice variants. Using only this info (no sequences, no AI) achieves AUROC=0.944 across noncoding variants.
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🌎👩🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
What was antibiotic resistance like before we ever used antibiotics? How did we change what antibiotic resistance genes looked like over 100 years?
Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen:
www.microbiologyresearch.org/content/jour...
The view of the Adelaide Oval, site of the 2025 Australian Biology and Computational Biology Society (ABACBS) conference, from across the River Torrens. The conference will be held in Adelaide from 24 to 28 November and celebrates 10 years of ABACBS.
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
Logo for the Sandpiper website
Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵
The day is finally here! 🎉 We’re releasing the invited speaker line-up, key dates, and lots more info for ABACBS 2025.
Check it out and share widely: www.abacbs.org/abacbs2025
Registrations and abstract submissions open next week, with abstracts due in August!
Are you a recent PhD (or soon to be PhD) from outside Canada looking to do a postdoc in Quebec?
Get in touch if you are excited about microbes, evolution, ecology, genomics (or all of the above!) and I'd be happy to help develop a project together!
www.mcgill.ca/gps/funding/...
www.bath.ac.uk/jobs/Vacancy...
Post doc available to work on Candida genomics with me at the Milner Centre for Evolution (U Bath, UK) as part of the JPIAMR funded project Fugaci www.jpiamr.eu/projects/fug...
For queries, email me!
Delighted our study (7+ years in the making) is out today in Nature. In a nutshell, 48 hours of antibiotics in week 1 led to impaired vaccine responses up to 15 months later in infants. We show (in-vivo) a probiotic can fix it #microbiome #science #immunology
www.nature.com/articles/s41...
Being able to data plasmid acquisition, and to see the diversity of plasmids being gained and lost from lineages, was really eye opening! It was a pleasure to contribute my tiny bit to this huge paper and the data has so much more to give! @arredondo.bsky.social @gerrythill.bsky.social et al.
We are recruiting a group leader in laboratory research at Peter Mac Cancer Centre in
Melbourne, Australia 🔬🦘💥
Work in a cutting edge research environment in a vibrant world city!
We value research excellence, creativity and diversity.
Join us!
careers.petermac.org/job/MELBOURN...
Interested in predicting AMR in bacteria? We show ignoring phylogenetic structure in genome collections leads to overly optimistic evaluations of machine learning methods for AMR prediction. With @nwheeler443.bsky.social and former PhD student Yanying Yu. 🦠🧫🧬🖥️🧪
www.biorxiv.org/content/10.1...
New year, new assemblies!
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
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