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K.D. Murray

@kdm9.bsky.social

A scientist, mostly Naarm/Melbourne, AU & Tübingen, DE

17 Posts299 Follower855 Folgt
@apaulalm.bsky.social · 5mo ago

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!

PlantEvolution 🌱🌾@plantevolution.bsky.social · 5mo ago

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...

Carl T. Bergstrom@carlbergstrom.com · 5mo ago

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.

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...

journals.plos.org

Berna Devezer@devezer.bsky.social · 7mo ago

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.

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/"
H
Heng Li@lh3lh3.bsky.social · 7mo ago

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.

HHeng Li@lh3lh3.bsky.social · last yr.

Preprint on "Improving spliced alignment by modeling splice sites with deep learning". It describes minisplice for modeling splice signals. Minimap2 and miniprot now optionally use the predicted scores to improve spliced alignment. arxiv.org/abs/2506.12986

Torsten Seemann@torstenseemann.bsky.social · 8mo ago

💾 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...

Release Heading into the sunset · tseemann/prokka

The future This is probably the last release of Prokka. I won't be making any code changes except bug fixes. I will update the databases occasionally. I strongly recommend you use Bakta by @oschwen...

github.com

Celeste Labedz@celestelabedz.bsky.social · 9mo ago

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...

James Watson in his own words

“Some anti-Semitism is justified” “Whenever you interview fat people, you feel bad, because you know you’re not going to hire them” “Japan should be bombed for d…

liorpachter.wordpress.com

Terry McGlynn@hormiga.bsky.social · 9mo ago

Hey folks, as news of Watson's demise spreads, please don't set aside his weighty legacy of misogyny and racism. He was truly among the worst of us. www.vox.com/2019/1/15/18...

Meredith Whittaker @meredithmeredith.bsky.social · 10mo ago

📣 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.

Signal@signal.org · 10mo ago

We are alarmed by reports that Germany is on the verge of a catastrophic about-face, reversing its longstanding and principled opposition to the EU’s Chat Control proposal which, if passed, could spell the end of the right to privacy in Europe. signal.org/blog/pdfs/ge...

Professor Euan Ritchie FAMS@euanritchie.bsky.social · 10mo ago

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.

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?

theconversation.com

Carl T. Bergstrom@carlbergstrom.com · 10mo ago

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.

Ben Williamson@benpatrickwill.bsky.social · 10mo ago

OpenAI's VP for education recently said the company wanted to become "core infrastructure" for schools and universities. Any infrastructure, though, always depends on habituating users to its technical affordances - so I've been trying to track how it's doing that 🧵 www.nytimes.com/2025/06/07/t...

samuel mehr@mehr.nz · 11mo ago

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)

Reti earmarks $70m of new agency's budget for AI commercialisation grants
M Hobart@mhobart.bsky.social · 11mo ago

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.

Olivia Guest · Ολίβια Γκεστ@olivia.science · 11mo ago

Finally! 🤩 Our position piece: Against the Uncritical Adoption of 'AI' Technologies in Academia: doi.org/10.5281/zeno... We unpick the tech industry’s marketing, hype, & harm; and we argue for safeguarding higher education, critical thinking, expertise, academic freedom, & scientific integrity. 1/n

Abstract: Under the banner of progress, products have been uncritically adopted or even imposed on users — in past centuries with tobacco and combustion engines, and in the 21st with social media. For these collective blunders, we now regret our involvement or apathy as scientists, and society struggles to put the genie back in the bottle. Currently, we are similarly entangled with artificial intelligence (AI) technology. For example, software updates are rolled out seamlessly and non-consensually, Microsoft Office is bundled with chatbots, and we, our students, and our employers have had no say, as it is not considered a valid position to reject AI technologies in our teaching and research. This is why in June 2025, we co-authored an Open Letter calling on our employers to reverse and rethink their stance on uncritically adopting AI technologies. In this position piece, we expound on why universities must take their role seriously toa) counter the technology industry’s marketing, hype, and harm; and to b) safeguard higher education, critical thinking, expertise, academic freedom, and scientific integrity. We include pointers to relevant work to further inform our colleagues.
Zamin Iqbal@zaminiqbal.bsky.social · 11mo ago

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...

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...

nature.com

Philipp Bayer@philippbayer.bsky.social · 11mo ago

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!

Rayan Chikhi@rayanchikhi.bsky.social · 11mo ago

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵 Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open. doi.org/10.1101/2024...