Really happy to see this preprint out on bioRxiv! An exciting project and results, a huge amount of work, and many people involved along the way. Thanks to everyone in Team PATHOCOM. Special thanks to Wei Yuan, Kevin Murray @kdm9.bsky.social, Ilja Bezrukov and Detlef @plantevolution.bsky.social!

1/11 🔥 New preprint alert 🔥
We wanted to know what plants in the wild really care about. So we asked them 🎤.
Here is what we learned: “Biotic-response networks are an important organizer of the transcriptome in wild Arabidopsis thaliana populations”
www.biorxiv.org/content/10.6...

rambaut/figtree Automatically exported from code.google.com/p/figtree - rambaut/figtree

The first version of FigTree was released nearly 20 years ago and it is still widely used (including by me). But there are currently 85 issues on the GitHub repo (github.com/rambaut/figt...) and some of them I don’t really like the look of.

Screening, sorting, and the feedback cycles that imperil peer review The process of peer review is vital to contemporary science, but is also under enormous strain. This study uses mathematical models to dissect the threats to the long-term viability of peer review, su...

1. Kevin Gross and I have a new paper out today PLOS Biology.

We used economic models based around screening games and the market for unpaid labor to highlight a meltdown cycle threatening peer review.

Lmer Fudd be like “it’s wandom effects season”

A tweet from Lior Pachter from July 26, 2024: "I think this paper is a Denial of Peer Review Attack (DOPRA). It's kind of like a DoS (denial of service) attack. There is so much data, so many methods, so much code, so many figures, so many panels, so much supplement, so much text, that it is overwhelming. 18/"

every big data paper with a bold story that is impossible to comprehend, evaluate, and independently verify reminds me of DOPRA. i've come to increasingly appreciate small, unassuming papers with humble conclusions that you can track word for word, data point by data point, assumption by assumption.

Now published in Algorithms for Molecular Biology: link.springer.com/article/10.1.... Key message: a tiny CNN model with 7k parameters can capture main splice signals across vertebrates+insect and halves the minimap2 & miniprot junction error rate. I always use this new feature now.

💾 Prokka 1.15.6 is released!

This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics

github.com/tseemann/pro...

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
🧵1/6

In case anyone is wondering if Watson was really THAT bad, @lpachter.bsky.social compiled a list of quotes that are absolutely not for the faint of heart.
liorpachter.wordpress.com/2018/05/18/j...

Revered and reviled, cats in the crosshairs on Christmas Island On a speck of land in the Indian Ocean, one of the world's most ambitious wars is being waged against feral cats. But not everyone is celebrating.

Brilliant story-telling and visuals, despite the tragic impacts of feral cats www.abc.net.au/news/2025-11...

This is how our customizable powder and seed dispenser for 2 ml tubes works.

Check it our here: custom-lab.de/products/48-...

When the Hapsburgs find out corn does inbreeding better they’re really gonna take it on the chin.

📣 Germany's close to reversing its opposition to mass surveillance & private message scanning, & backing the Chat Control bill. This could end private comms-& Signal-in the EU.

Time's short and they're counting on obscurity: please let German politicians know how horrifying their reversal would be.

Labor is close to a deal on environmental law reforms. There are troubling signs these will fall short Labor is close to a deal on its environmental law reforms. Will they strong enough to protect nature?

Australia's much loved wildlife and places sorely need greater care and legal protection.

Our latest for @aunz.theconversation.com.

theconversation.com/labor-is-clo... With good friends and colleagues, @drphilmccormack.bsky.social & @yungenchee.bsky.social.

Lingua wanka is a hilarious moniker for scientific writing

I wished I could have written something like this. Rude, fun and meaningful.
static1.squarespace.com/static/686d9...

'In Australia we are seeing the results of running universities like businesses without adequate governance: wage theft from staff, fee theft from students, and the academic equivalent of shrinkflation.'

Less than 2 weeks until our arboretum open days! Here's a few of the eucalypts flowering at the moment.

These free open days only occur biannually. Currency Creek Arboretum is about an hour's drive south of Adelaide in SA. Open details here: www.dn.com.au/Currency_Cre...

Left unchecked, openAI and other infotech providers will destroy any remnants of the American education system that manage to escape the Trump administration.

Read the full thread.

There’s a leak - and a conceptual artist - at the Max Planck 👌

Reti earmarks $70m of new agency's budget for AI commercialisation grants

new zealand government reaching new heights of stupidity

next year our public dollars will go more to AI grants ($70 million) than all investigator-initiated basic science combined ($56 million in the Marsden fund)

New blog post – A quick look at Roche's SBX
lh3.github.io/2025/09/11/a...

Kids are losing 'huge chunks' of their childhood to long COVID. Too many are being told it's 'all in their head' They're losing their formative years to this debilitating disease. But for too many children with long COVID, finding help is a frustrating and traumatic process that leaves them feeling isolated and ...

www.abc.net.au/news/2024-06...
@ashleydaltonmp.bsky.social

#Longcovidkids

Comic. [Building with large sign in front of it[ SIGN: Welcome to the *Biology Department* It has been [changeable sign: 3] days since we discovered something existentially horrifying about bugs that makes you question your whole reality

Biology Department

xkcd.com/3140/

If you haven't seen @shenwei356.bsky.social's other near-magical tools (csvtk, taxonkit, seqkit; all in go IIRC), absolutely check them out. Top stuff!

Must read, and not just for higher ed folks: anyone concerned about education and people’s ability to think rigorously and critically should read this manifesto.

Insurance in the Polycrisis | Kate Mackenzie & Tim Sahay The future is triage on an uninsurable earth.

Absolutely fantastic piece on the interfaces between climate risk and insurance in the Polycrisis newsletter today, by @70sbachchan.bsky.social and @katemac.bsky.social

Not a doom loop, but “communities of fate” and the moral economy of the welfare state.
www.phenomenalworld.org/analysis/ins...

One mother for two species via obligate cross-species cloning in ants - Nature In a case of obligate cross-species cloning, female ants of Messor ibericus need to clone males of Messor structor to obtain sperm for producing the worker caste, resulting in males from the same moth...

Ok this is mad
"...an ant that lays individuals from two distinct species. In this life cycle, females must clone males of another species because they require their sperm to produce the worker caste"

www.nature.com/articles/s41...