Thrilled that our paper "Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities" is out! ππ¦ π§¬
www.science.org/doi/10.1126/...
w/ @paulbrainey.bsky.social, Petros Skiadas, Paulien Hogeweg, @bedutilh.bsky.social
New blog post!
I analyse the new [email protected] basecalling model from @nanoporetech.com and discuss the conspicuous lack of a new sup model:
rrwick.github.io/2026/06/11/d...
Structural motif search across the protein universe with Folddisco - @martinsteinegger.bsky.social go.nature.com/4g8lCb0
Follow-up to my last blog post:
I now look at assembly polishing with Dorado v2 and the new [email protected] model from @nanoporetech.com.
rrwick.github.io/2026/06/19/d...
I'm happy to share the first pre-print of out Lab! π
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)
Folddisco is now published @natbiotech.nature.com. Itβs a fast motif search for similar 3D DISCOntinuous residues like catalytic sites or zinc fingers across the entire protein universe.
π www.nature.com/articles/s41...
πΎ folddisco.foldseek.comββββββββββββββββ
π https://search.foldseek.com/folddisco
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...
World-leading Aussie science fighting #AntimicrobialResistance!
PhD student George Bouras added 17M bacterial protein predictions to the #AlphaFold database.
This was made possible by a partnership between BioCommons & @pawseycentre.bsky.social to containerise #ColabFold on Setonix.
Read more π
Thrilled to share a major milestone from our long-running collaboration with Zuzanna Drulis-Kawa's lab in WrocΕaw β DepoCatalog, is now out in @natcomms.nature.com: 129 Klebsiella phage depolymerases, 75 capsule types, 5-class structural framework and public database.
www.nature.com/articles/s41...
A single bacteriophage can dominate microbial communities yet only evolves when migration changes its ecological context.
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
Australian researcher, George Bouras, has recently contributed an extraordinary 17 million protein predictions to the AlphaFold Protein Structure Database. This work was possible thanks to the availability of the ColabFold tool on Setonix AMD, the result of collaboration between BioCommons and the P
AbstractMotivation. Assembly graphs are a fundamental data structure used by genome and metagenome assemblers to represent sequences and their overlap info
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. 1/9π§Άπ§¬
π www.biorxiv.org/content/10.1...
π search.foldseek.com/folddisco
Martin Steinegger πΊπ¦
A standalone Streamlit app that collects community priority weights over fourassembly-QC metrics ...
