If you are looking for web-based phage annotation, phage-annotation.org is live. Upload a genome to run Pharokka, Phold and Phynteny sequentially (see our recent protocols paper doi.org/10.1002/cpz1...). If you have feedback, please reach out Thanks to @ardc.edu.au for making this possible!

If you are looking for web-based phage annotation, phage-annotation.org is live. Upload a genome to run Pharokka, Phold and Phynteny sequentially (see our recent protocols paper doi.org/10.1002/cpz1...). If you have feedback, please reach out Thanks to @ardc.edu.au for making this possible!

I am excited to share that our manuscript titled 'Defining the ESKAPE pathogen prophage repertoire with PHORAGER' is now available online as a preprint in BioRxiv! 🤩 (doi.org/10.64898/202...) Here we present PHORAGER, a Nextflow pipeline for the identification and quality assessment of prophages 🧬

Riboseek is a fast RNA/DNA search. More sensitive than nhmmer at 250x speed. Structure-aware realignment produces MSAs approaching rMSA quality. Plus 1.7M precomputed RNA MSAs, and an API to search your own 📄 www.biorxiv.org/content/10.6... 💾 github.com/steineggerla... 🌐 search.foldseek.com/riboseek

We are hosting the 2026 @abacbs.bsky.social conference at RMIT University City Campus Melbourne on 16-20 Nov 2026. Hope to see you there.

Polypolish v0.7.1 is out! github.com/rrwick/Polyp... Main new feature is better handling of read name suffixes, which makes it easier to use Polypolish with aligners other than BWA-MEM. I've been using it with minibwa, which seems pretty great: github.com/lh3/minibwa

GitHub - rrwick/Polypolish: a short-read polishing tool for long-read assemblies

a short-read polishing tool for long-read assemblies - rrwick/Polypolish

github.com

New blog post! I reran the Autocycler paper benchmarks on some new tools/versions/pipelines: rrwick.github.io/2026/07/24/b... (1/3)

It's out! Excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂 www.nature.com/articles/s41...

The planktonic microbiome of the Great Barrier Reef - Nature

The Great Barrier Reef Microbial Genomes Database compiles prokaryotic, viral and eukaryotic genomes from seawater collected from the Great Barrier Reef, providing a rich resource for the study of mar...

nature.com

🚨 JOB ALERT🚨 We are very excited to be hiring the lab's ✨very first postdoc✨! Work on new AI technologies for decoding antigen protein evolution in a fresh research environment, at the heart of Paris 🇫🇷 Details & link to apply: research.pasteur.fr/en/job/postd... Deadline: Sep 1st

Happy to share the first preprint out of the Nomburg lab! Many aspects of cellular immunity are shared across the tree of life. Here, we show that some of these conserved aspects of cellular immunity are mirrored by conserved effectors of immune antagonism. Thread below! 1/15

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 4w ago

Conserved folds enable immune antagonism across the tree of life https://www.biorxiv.org/content/10.64898/2026.07.21.739742v1

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

Results of the first ICTV Computational Virus Taxonomy Challenge are out! Metabuli was among the most accurate and fastest classifiers evaluated. doi.org/10.64898/202... Try Metabuli App, a desktop GUI for DB curation, read QC, classification, and visualization: jaebeom-kim.github.io/metabuli-doc/

First community challenge for automated virus taxonomy

The rapid rate of virus discovery renders manual curation by taxonomy experts increasingly impractical, creating a need for reliable software that can reproducibly assign viral contigs to taxa at all ...

doi.org

Significant update to the AllTheBacteria paper, including discovering new antimicrobial peptides and testing in vitro and vivo. This has grown into a fantastic collaboration!

César de la Fuente@delafuentelab.bsky.social · 4w ago

Biology has plenty of data—the challenge is making it usable. AllTheBacteria transforms 2.44 million public bacterial and archaeal genomes into an open, uniformly processed, searchable, AI-ready resource. www.biorxiv.org/content/10.1...

@wheelerlab.org is talking about his effort to build a resource for protein dynamics (PDB for MD). MDRepo is a repository to store simulation data. This is really needed to push the needle in design, function and more. Please help make it successful by sharing your MD data. #ismb2026 🌐 mdrepo.org

And this is how it all began: communities.springernature.com/posts/from-s...

From small talk to big science

How a casual conversation and a satchel-dependent courier service for honey bees led to a reasearch project that employed three PhD students – so far.

communities.springernature.com

At last, available in its final form: www.nature.com/articles/s41...

The honey bee triad: a comprehensive catalogue of phages in the Apis mellifera gut microbiome - Nature Communications

The gut microbiome of the honey bee is relatively simple, but its phages are not well studied. Here, Basler et al. use metagenomics to provide a comprehensive catalogue of honey bee gut phag...

nature.com

First paper with the lab's affiliation!! ✨✨ summarising some of the cool concepts that the Antigen Evolution & Design Lab will be working on! Together with amazing collaborators @mghafari.bsky.social and @grovearmada.bsky.social www.annualreviews.org/content/jour...

Studying the Deep Evolution of Viruses in the Era of Artificial Intelligence Structure Prediction

High mutation rates erode viral sequence similarity, obscuring deep evolutionary history. While protein structure is far more conserved than sequence, its use in evolutionary studies has historically ...

annualreviews.org

In some recent blog posts, I had a Klebsiella genome with a mysteriously higher ONT error rate. But Michael Biggel (University of Zurich) emailed me with the likely explanation: 7-deazaguanine mods. Thanks, Michael! Here's his preprint about this: www.biorxiv.org/content/10.6...

Standalone nanopore sequencing for foodborne pathogen surveillance: a large-scale evaluation and quality control framework

Whole-genome sequencing (WGS) is central to foodborne pathogen surveillance and cross-border outbreak detection. Long-read sequencing using Oxford Nanopore Technologies (ONT) promises rapid, complete,...

biorxiv.org

Follow-up to my last two blog posts: I now look at methylation calling with Dorado v2 and the new hac@v6.0.0 model from @nanoporetech.com. rrwick.github.io/2026/07/08/d...

Humans and bacteria share strategies to defend against viruses. We wondered: could they use each other's genes? Yes, both can! Bacteria can use human immune genes to defend against phages AND Human cells can use bacterial genes for viral defense. www.biorxiv.org/content/10.6...

Bacterial and human exonucleases mediate interkingdom antiviral immunity

All kingdoms of life have developed strategies to limit viral infection. In humans, interferons induce a suite of antiviral factors that collectively provide immunity. Some human immune genes are homo...

biorxiv.org

Happy to share the latest work from Zunair Khurram, a PhD student in our lab! Zunair has developed a new method, MxSure, to infer within-host substitution rates and transmission thresholds from longitudinal isolate and metagenomic sequencing data. www.biorxiv.org/content/10.6...

MxSure: a mixture model for inferring within-host substitution rates and transmission SNP thresholds

Quantifying short-term evolutionary rates of microbial genomes is essential for understanding the processes that shape within-host evolution and for establishing thresholds needed to track transmissio...

biorxiv.org

Microbes that have the greatest genomic potential for secondary metabolism tend to be multicellular. Here, we show that signatures of ancestral BGC expansions within 3 bacterial phyla and 2 fungal lineages coincide with origins of complex multicellularity [1/12] 🧵 www.nature.com/articles/s41...

Complex multicellularity is linked with expanded specialized metabolite production in microorganisms - Nature Microbiology

The evolutionary emergence of complex multicellularity in bacteria and fungi, such as the ability for mycelial growth, is strongly associated with increased genomic carriage of biosynthetic machinery ...

nature.com

For #bbm2026 folks - come check out my poster on 3FL, #21! It's part of the data going out on my soon-to-be published preprint, some aspects can definitely use feedback. 🧫🦠

Follow-up to my last blog post: I now look at assembly polishing with Dorado v2 and the new hac@v6.0.0 model from @nanoporetech.com. rrwick.github.io/2026/06/19/d...

For anyone doing ONT Microbial Genomics, please take 1 minute (less?) to tell us which assembly metrics you care most about when evaluating whether an assembly is "good". We are doing a benchmark of different QC tools (barcode/adapter trimming and QC filtering). microbial-qc-survey.streamlit.app

Microbial QC Survey

A standalone Streamlit app that collects community priority weights over fourassembly-QC metrics ...

microbial-qc-survey.streamlit.app

New blog post! I analyse the new hac@v6.0.0 basecalling model from @nanoporetech.com and discuss the conspicuous lack of a new sup model: rrwick.github.io/2026/06/11/d...

Folddisco is now published @natbiotech.nature.com. It’s a fast motif search for similar 3D DISCOntinuous residues like catalytic sites or zinc fingers across the entire protein universe. 📄 www.nature.com/articles/s41... 💾 folddisco.foldseek.com​​​​​​​​​​​​​​​​ 🌐 https://search.foldseek.com/folddisco

Structural motif search across the protein universe with Folddisco - Nature Biotechnology

Folddisco enables protein structural motif search in million scale databases.

nature.com

Martin Steinegger 🇺🇦@martinsteinegger.bsky.social · last yr.

Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬 📄 www.biorxiv.org/content/10.1... 🌐 search.foldseek.com/folddisco

I'm happy to share the first pre-print of out Lab! 🎉 Introducing ArchaeaHQ www.biorxiv.org/content/10.6... We curated 21,644 genomes across all 4 archaeal kingdoms to bridge the gap in public datasets for computational biology What is inside ArchaeaHQ... (1/2)

Structural motif search across the protein universe with Folddisco - @martinsteinegger.bsky.social go.nature.com/4g8lCb0

Structural motif search across the protein universe with Folddisco - Nature Biotechnology

Folddisco enables protein structural motif search in million scale databases.

go.nature.com

Thrilled that our paper "Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities" is out! 🎉🦠🧬 www.science.org/doi/10.1126/... w/ @paulbrainey.bsky.social, Petros Skiadas, Paulien Hogeweg, @bedutilh.bsky.social

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