I want to spell this out in case the implications aren't clear:

This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited.

The file allowed this. Cut that - cut off all tools the public & others were using.

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.
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We're looking for highly motivated candidates for PhD positions in the physics of living systems.

Our group uses theoretical physics to understand how cells collectively self-organize.

If you're interested, get in touch & check out the Biozentrum PhD Fellowship program, deadline October 12th!

Willing to join us @pasteur.fr for a PhD for a project on how interactions between mobile genetic elements shape bacterial adaptation? Subject to be tailored to candidates with keen interest in evolution, genomics, computational biology, microbiology. Check www.pasteur.fr/en/education...

It was a great pleasure to contribute to this work by Jemma Fendley, @mmolari.bsky.social, and Boris Shraiman on pan-genomes, linkage, and recombination in phage genomes.

We analyzed data collected by the fantastic SEA-PHAGES program in phagesdb.org.

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www.biorxiv.org/content/10.1...

📢New job posting!📢
Are you excited by the idea of building global infrastructure to make pathogen sequencing more accessible, interpretable, and equitable? 🧑🏻‍💻🧬

My group at @swisstph.ch has an opening working with ARTIC2, @pathoplexus.org, & Loculus - read on!

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Bonsai is out! Finally, we can visually explore high-dimensional data in a distortion-free way. Try it out! It works from scRNA-seq data (bonsai.unibas.ch/bonsai-scout...) up to football statistics (bonsai.unibas.ch/bonsai-scout...). 
Ever wondered why low-dimensional embeddings like t-SNE

Agencies within the Trump administration have flagged hundreds of words to limit or avoid, according to a compilation of government documents. These terms appeared in government memos, in official and unofficial agency guidance and in other documents. www.nytimes.com/interactive/...

The contribution of natural transformation for the acquisition of novel genes has been notoriously difficult to quantify because it relies on recombination (which is affected by other processes). Here's a first estimate : doi.org/10.1101/2025... (for the very busy: 1-6% of gene gains) #MicroSky

Building on the UShER tree of millions of SARS-CoV-2 genomes maintained by Angie Hinrichs, Hugh Haddox and Georg Angehrn (and others in @matsen.bsky.social lab and @jbloomlab.bsky.social) have looked into how the neutral mutation rate varies along the genome:

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www.biorxiv.org/content/10.1...

Thrilled to announce that our work (w. with fantastic @neher.io and Liam Shaw) has been published on Molecular Biology and Evolution! 🎉

academic.oup.com/mbe/advance-...

Are you curious about how fast the genome of E.coli evolves structurally (gains, rearrangements...) ? 🧬

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It's a huge honour to have been named by Nature as "One to Watch" in 2025 for
@pathoplexus.org ! 🙏

I'm proud to see Pathoplexus continuing to draw attention - but this is truly a team effort and only possible thanks to all the amazing people involved! 🙌

swisstph.ch/en/news/news...

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It's an incredible honour to have received this #OpenData prize from Swiss Academies of Arts & Sciences for @pathoplexus.org!

Though not everyone in Pathoplexus could be there in person, it was a fantastic & thought-provoking event, & I'm so glad were part of it! #OpenScience #OpenSource