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...

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.

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”

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...

“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...

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.

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 👌

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...

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

Biology Department xkcd.com/3140/

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.

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...

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...

I LOVE that you can see pur Cocos Keeling voyage eDNA data on this figure. It's that straight line going north-west from Western Australia/Perth!

Save the date! #PEQG26 June 9-12 2026 in Asilomar, CA. Happens only every 2yrs, but is my favorite conference. Full website coming soon, and registration and abstract submission opens November 14, but I'm allowed to tease that keynotes will be @jnovembre.bsky.social @jennytung.bsky.social and me!

Omg nerd day made

I feel like there should be a "median rent in the area" based guidelines for conference registration fees. If your 3 day academic conference costs more than a median whole month's rent to live there, maybe something can be improved 🫠

Be like Fran www.abc.net.au/news/2025-08...

Fantastic new paper by @reeserichardson.bsky.social et al. An enormous amount of work showing the extent of coordinated scientific fraud and involvement of some editors. The number of fraudulent publications grows at a rate far outpacing that of legitimate science. www.pnas.org/doi/10.1073/...

SLiM 5: Eco-evolutionary simulations across multiple chromosomes and full genomes https://www.biorxiv.org/content/10.1101/2025.08.07.669155v1

Happy to be able to finally share our NLR pangenome paper, out now in CHM. "Pangenomic context reveals the extent of intraspecific plant NLR evolution" www.cell.com/cell-host-mi... #plantscience #plantimmunity #pangenomes #science #nlr

'And the need for grants long ago ceased to prioritize scientific questions, per se, supplanting them with a basic and insatiable institutional hunger for money as an end in itself (got to feed the beast!). This is both demoralizing and demotivating. ' 💔I feel this very much (and that's why I left)

This looks like an amazing tool www.biorxiv.org/content/10.1...

"With [some AI bullshit] you can go from a rough idea to a structured draft — in just 3 minutes" We're so cooked.

1/3 New preprint led by Shanshan Wang, in collaboration with the Timmermans lab. Several groups have presented sc/snRNA-seq analyses of Arabidopsis leaves after bacterial infection before. Is there anything left to discover? Turns out: Yes. #plantscience www.biorxiv.org/content/10.1...

WTF? I was quoted in this story but I have never spoken to the reporter nor would I have said those things. Is everything just generated by LLMs these days? cosmosmagazine.com/earth/oceans...

A lot of you had questions so I wrote about what I think happened here! Behold: wiczipedia.substack.com/p/i-got-trap...

Anyone who's visited the UK knows that the empty shells of monasteries destroyed by Henry VIII still dot the landscape. I've been seeing images of all the U.S. higher ed institutions being financially destroyed now & can't help thinking of what their empty shells might look like a century from now.

(1) This is of course absolute catnip for me; (2) I am SO disappointed in Washington state, do better, people; (3) You really can see the White-Tailed Deer Hegemony in the Northeast; (4) Fascinating that milkweed states are not also monarch butterfly states; (5) The green anole/brown anole line!!

1. From the FDA to the NSF’s new priorities to Chan-Zuckerberg’s recent pivot, there’s a massive push — particularly on they political right — to hand off as much of the scientific process as possible to AI. It’s not about competing with China in AI. Not while gutting the US research ecosystem.

This is a good time to remember that Moas, Emus, and the other ratites diverged so long ago, they FLEW to different continents, and then lost the ability to fly and became giants independently. You can't just sprinkle a few variants to make one into the other. www.science.org/doi/10.1126/...

K-mer-based ML method for estimating distances of reads to genomes enables genome-wide phylogenetic placement doi.org/10.1101/2025... Phylogenetic placement of Ceratophyllum submersum based on a complete plastome sequence derived from nanopore long read sequencing data doi.org/10.1101/2023...

I'm super happy to share this preprint on ‘Distribution of capsule and O types in #Klebsiella pneumoniae causing neonatal sepsis in Africa and South Asia: meta-analysis of genome-predicted serotype prevalence and potential vaccine coverage’ doi.org/10.1101/2025...