K.D. Murray
A scientist, mostly
Naarm/Melbourne, AU & Tübingen, DE
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- Reposted by K.D. Murrayevery 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.
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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.- 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
- Reposted by K.D. Murray💾 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...
- Reposted by K.D. Murray“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
- Reposted by K.D. MurrayIn 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...
- 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...
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- Reposted by K.D. Murray📣 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.
- 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...
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- Reposted by K.D. MurrayLingua wanka is a hilarious moniker for scientific writing
- Fantastic editorial on #ScientificWriting. 👇
- Reposted by K.D. MurrayI wished I could have written something like this. Rude, fun and meaningful. static1.squarespace.com/static/686d9...
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- Reposted by K.D. MurrayThere’s a leak - and a conceptual artist - at the Max Planck 👌
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- Reposted by K.D. MurrayNew blog post – A quick look at Roche's SBX lh3.github.io/2025/09/11/a...
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- Reposted by K.D. MurrayBiology Department xkcd.com/3140/
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- Reposted by K.D. MurrayAbsolutely 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...
- Reposted by K.D. MurrayOk 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...
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- Reposted by K.D. MurraySave 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!
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- Reposted by K.D. MurrayFantastic 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/...
- Today, our article "The entities enabling scientific fraud at scale are large, resilient, and growing rapidly" is finally published in PNAS. I hope that it proves to be a wake-up-call for the whole scientific community. reeserichardson.blog/2025/08/04/a...
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- 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
- Long story short: we assemble 17 representative Arabidopsis thaliana genomes, exhaustively annotate NLRs with long read evidence & manual curation, and assay many measures of NLR diversity.
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- Reposted by K.D. MurrayThis looks like an amazing tool www.biorxiv.org/content/10.1...
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- Reposted by K.D. Murray1/3 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...
- Reposted by K.D. MurrayWTF? 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...
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- Reposted by K.D. MurrayI'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...
- Reposted by K.D. MurrayWe would love feedback on a new NCBI-BLAST service we are launching today: sky-blast.com Under the hood it's the same BLAST executable and databases provided by NCBI, with a replica of the NIH's interface - providing an alternative to the US gov service that's less congested, faster & more reliable
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- Reposted by K.D. Murray🧵 THREAD: Why the Cato Institute’s new paper on “misinformation panic” is dangerously wrong, and why it completely misunderstands the real crisis we face. www.cato.org/policy-analy...
- Reposted by K.D. MurrayYesterday, @carlbergstrom.com presented his course "Modern-day Oracles or BS Machines? How to thrive in a ChatGPT world". Neat way to make students aware of the capacities and limitations of LLMs👇🎰 Recording: www.youtube.com/watch?v=TZC0... Course: thebullshitmachines.com @unswbabs.bsky.social
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