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K.D. Murray

@kdm9.bsky.social
306 followers 855 following 17 posts

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

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Reposted by K.D. Murray
apaulalm.bsky.social @apaulalm.bsky.social · 16/03/2026
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!
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PlantEvolution 🌱🌾 @plantevolution.bsky.social · 14/03/2026
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...
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 28/02/2026
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.
github.com
rambaut/figtree
Automatically exported from code.google.com/p/figtree - rambaut/figtree
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Carl T. Bergstrom @carlbergstrom.com · 24/02/2026
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.
journals.plos.org
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...
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Kevin Bird @stairwaytokevin.bsky.social · 16/01/2026
Lmer Fudd be like “it’s wandom effects season”
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Berna Devezer @devezer.bsky.social · 15/01/2026
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/"
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Heng Li @lh3lh3.bsky.social · 06/01/2026
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.
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Torsten Seemann @torstenseemann.bsky.social · 15/12/2025
💾 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...
github.com
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...
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Samuel Aroney @aroneys.bsky.social · 13/11/2025
“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
Logo of Bin Chicken (Australian white ibis) on a rubbish bin, pulling out a strand of DNA
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Celeste Labedz @celestelabedz.bsky.social · 07/11/2025
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...
liorpachter.wordpress.com
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…
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Professor Euan Ritchie FAMS @euanritchie.bsky.social · 07/11/2025
Brilliant story-telling and visuals, despite the tragic impacts of feral cats www.abc.net.au/news/2025-11...
abc.net.au
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.
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The Custom-Lab Institute @custom-lab.bsky.social · 18/10/2025
This is how our customizable powder and seed dispenser for 2 ml tubes works. Check it our here: custom-lab.de/products/48-...
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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 18/10/2025
When the Hapsburgs find out corn does inbreeding better they’re really gonna take it on the chin.
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Meredith Whittaker @meredithmeredith.bsky.social · 06/10/2025
📣 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.
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Professor Euan Ritchie FAMS @euanritchie.bsky.social · 10/10/2025
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.
theconversation.com
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?
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Stuart McDaniel @stuartmcdaniel.bsky.social · 09/10/2025
Lingua wanka is a hilarious moniker for scientific writing
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Malick Mbengue @malick-mbengue.bsky.social · 09/10/2025
I wished I could have written something like this. Rude, fun and meaningful. static1.squarespace.com/static/686d9...
static1.squarespace.com
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Philipp Bayer @philippbayer.bsky.social · 01/10/2025
'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.'
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Dean Nicolle @deannicolle1.bsky.social · 30/09/2025
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...
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Carl T. Bergstrom @carlbergstrom.com · 27/09/2025
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.
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Honour McCann @honour.bsky.social · 18/09/2025
There’s a leak - and a conceptual artist - at the Max Planck 👌
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samuel mehr @mehr.nz · 18/09/2025
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
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Heng Li @lh3lh3.bsky.social · 12/09/2025
New blog post – A quick look at Roche's SBX lh3.github.io/2025/09/11/a...
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Esther @elhopkins.bsky.social · 11/09/2025
www.abc.net.au/news/2024-06... @ashleydaltonmp.bsky.social #Longcovidkids
abc.net.au
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 ...
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Randall Munroe @xkcd.com · 11/09/2025
Biology Department xkcd.com/3140/
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
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M Hobart @mhobart.bsky.social · 11/09/2025
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.
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Ben Abraham @afterclimate.com.au · 11/09/2025
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...
phenomenalworld.org
Insurance in the Polycrisis | Kate Mackenzie & Tim Sahay
The future is triage on an uninsurable earth.
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Zamin Iqbal @zaminiqbal.bsky.social · 05/09/2025
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...
nature.com
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...
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Philipp Bayer @philippbayer.bsky.social · 04/09/2025
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!
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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 03/09/2025
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!
genetics-gsa.org
Homepage - Population, Evolutionary, and Quantitative Genetics Conference
Visit our website to learn more.
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Julie Blommaert @drjulieb.bsky.social · 02/09/2025
Omg nerd day made
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naturepoker @binomicalabs.org · 26/08/2025
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 🫠
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Professor Euan Ritchie FAMS @euanritchie.bsky.social · 25/08/2025
Be like Fran www.abc.net.au/news/2025-08...
abc.net.au
Retired doctor takes on rare fungi finding 'work of a lifetime'
Fran Guard turned to fungi research after finding a species that had not yet been scientifically described while weeding her rainforest property.
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Elisabeth Bik @elisabethbik.bsky.social · 04/08/2025
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/...
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 11/08/2025
SLiM 5: Eco-evolutionary simulations across multiple chromosomes and full genomes www.biorxiv.org/content/10.1101/202…
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K.D. Murray @kdm9.bsky.social · 14/08/2025
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
cell.com
Pangenomic context reveals the extent of intraspecific plant NLR evolution
Individual- and population-level diversity is required for pathogen defense by nucleotide-binding site leucine-rich repeat (NLR) proteins. Teasdale et al. leverage annotated, divergent A. thaliana gen...
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Philipp Bayer @philippbayer.bsky.social · 14/08/2025
'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)
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Matthew Hahn @3rdreviewer.bsky.social · 06/08/2025
This looks like an amazing tool www.biorxiv.org/content/10.1...
biorxiv.org
Phyling: phylogenetic inference from annotated genomes
Phyling is a fast, scalable, and user-friendly tool supporting phylogenomic reconstruction of species phylogenies directly from protein-encoded genomic data. It identifies orthologous genes by searchi...
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Carl T. Bergstrom @carlbergstrom.com · 05/08/2025
"With [some AI bullshit] you can go from a rough idea to a structured draft — in just 3 minutes" We're so cooked.

No more endless academic paper searches!

Writing a research paper used to take weeks. With tlooto AI, you can go from a rough idea to a structure draft -- in just 3 minutes.
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PlantEvolution 🌱🌾 @plantevolution.bsky.social · 02/08/2025
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...
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David Ho @davidho.bsky.social · 29/07/2025
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...
To whom it may concern, and it should concern the editor:

I was quoted in your publication:

https://cosmosmagazine.com/earth/oceans/can-we-engineer-our-way-out-of-ocean-acidification/

Still, others aren't convinced that good intentions are enough. Dr. David Ho, Professor of Oceanography at University of Hawaii at Manoa, a cofounder and the Chief Science Officer of |C|Worthy, a non-profit that works on verifying ocean-based carbon dioxide removal, believes carbon removal efforts like ocean alkalinity enhancement shouldn't be left solely in the hands of private companies.

"They have no way to prove that what they're doing is effective - that's a big problem," Dr Ho said.

The crux of the dilemma, he explains, is that we are fighting a planetary-scale problem, but are doing it with tools that are still being built and tested. Geoengineering is not inherently good or bad, but it is inherently powerful. And power, especially when exercised in ecosystems as complex and fragile as the ocean, must be handled with caution.
However, I have never spoken to your reporter, nor would I have said those things. I would like you to remove my quote from your story, and issue a public correction and apology. Furthermore, you should look into whether the other parts of the article are also factually correct. Thanks.

d.
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Nina Jankowicz @ninajankowicz.com · 23/07/2025
A lot of you had questions so I wrote about what I think happened here! Behold: wiczipedia.substack.com/p/i-got-trap...
wiczipedia.substack.com
I Got Trapped in the AI Ouroboros
A foreign news outlet fabricated a quote from me. LLMs have already picked it up.
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Monica H Green @monicamedhist.bsky.social · 25/07/2025
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.
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Jeremy Yoder says no war @jbyoder.org · 22/07/2025
(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!!
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Carl T. Bergstrom @carlbergstrom.com · 21/07/2025
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.
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Fernando Villanea @fervillanea.bsky.social · 09/07/2025
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/...
Maps of continents breaking apart does not match the order in which flightless birds speciate, which indicates they flew over water rather than walk across a mega continent.
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plantgenomics.bsky.social @plantgenomics.bsky.social · 02/07/2025
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...
doi.org
A k-mer-based maximum likelihood method for estimating distances of reads to genomes enables genome-wide phylogenetic placement.
Comparing each sequencing read in a sample to large databases of known genomes has become a fundamental tool with wide-ranging applications, including metagenomics. These comparisons can be based on r...
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Kat Holt @katholt.bsky.social · 01/07/2025
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...
doi.org
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
Background: Klebsiella pneumoniae causes ~20% of sepsis in neonates, with ~40% crude mortality. A vaccine administered to pregnant women, protecting against 70% of K. pneumoniae infections, could aver...
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