New paper out! We discovered a tiny archaeon with the smallest known archaeal genome — only 238 kbp! Candidatus Sukunaarchaeum mirabile has almost no recognizable metabolic pathways and may rely heavily on a host to survive. doi.org/10.1101/2025.0…

Just casually doing some SUP basecalling on an AMD 7900XTX GPU 😅 with ROCm in a workstation at home. A work in progress by Hasindu and Bonson in the lab.

Published in Microbiology Society tinyurl.com/4248jyuv highlighting: - Contribution of #prophage dynamics in the #pangenome evolution - Pangenome data structure to trace orthologous prophages - Generalist & specialist prophages in the Pectobacterium genus

9th de.NBI / ELIXIR-DE "Microbial Genomics training course" now open for registration! 3 sessions full of microbial bioinformatics at JLU Giessen: I: QC & QA, assembly II: regional & functional annotation III: comparative genomics Info & registration: denbi.de/training-cours…

Out now in Molecular Cell: Cyanobacterial Argonautes and Cas4 family nucleases cooperate to interfere with invading DNA cell.com/molecular-cell… Most long-A pAgos interfere with invading DNA solo. Why then are cyanobacterial pAgos co-encoded with a Cas4-like protein? A 🧵

Hunting extreme microbes that redefine the limits of life book by Karen Lloyd USC Earth Science USC Marine & Environmental Biology nature.com/articles/d4158…

Expanding the cultivable human archaeome: Methanobrevibacter intestini sp. nov. and strain Methanobrevibacter smithii ‘GRAZ-2’ from human faeces. Available to read in #IJSEM: doi.org/10.1099/ijsem.…

Very proud to announce that the Windows Subsystem for Linux is now open source! blogs.windows.com/windowsdevelop…

Functional prediction of proteins from the human gut archaeome #microbiology #microbiota #archaea ISME Communications ISME - International Society for Microbial Ecology academic.oup.com/ismecommun/art…

Congratulations! :)

A genomic catalog of Earth's bacterial and archaeal symbionts biorxiv.org/content/10.110…

Our new article “Advancing general ecosystem models (GEMs): Towards a mechanistic understanding of the biosphere in the light of the Anthropocene” let by Joachim Paul Töpper just out at Ecological Solutions and Evidence besjournals.onlinelibrary.wiley.com/doi/10.1002/26…

For many of those who were asking on BLOW5 vs POD5 for nanopore signal data, here is a finally detailed benchmark we did: biorxiv.org/content/10.110… Summary: performance of BLOW5 is >= POD5 (from ~= to 100X, see below), with benefit of having ~3 dependencies instead of >50.

It has been a while… but an updated, faster & more accurate version of OrthoFinder is now out! Scales to thousands of species on conventional compute resources with higher accuracy than ever before and the same data rich fully phylogenetic outputs 👉biorxiv.org/content/10.110…

this is crazy (spectrogram of training data vs reproduced) now you think about it, birds probably also feel "this is crazy" when they hear us talking to each other

McCullough Foundation No, it did not. At best, it found that people with cancer or other diseases have different expression profiles. But it absolutely does not show any relationship with mRNA vaccines. It is a severely flawed study. Read my review here: scienceintegritydigest.com/2025/07/25/pre…

Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation

skani v0.3.0 is released. github.com/bluenote-1577/… * 30-40% potential reduction in memory * Breaking changes to indexing and searching databases Calculate ANI for contigs, genomes. Search vs > 140k genomes: pre-indexed GTDB-R226 available for download.

Our magnetic beads separate DNA based on its size. You can isolate the fraction, for example, of 200-700 bp, removing shorter and longer DNA strands. The DNA molecules stick to the carboxylated surface, and the strength of sticking depends on the size of the DNA. For some

New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!