We observed this in a small, engineered plasmid in B. velezensis that contained a copy of a gene that was also chromosomally present to overexpress it for enzyme production. Probably homologous recombination.
For all their ignorance, I really think that they’re not implying directly staring into the sun.
Preprint out for myloasm, our new nanopore / HiFi metagenome assembler!
Nanopore's getting accurate, but
1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?
with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
🌎👩🔬 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...
Very exciting work here from Sanjana Kulkarni, Maha Farhat and team. CNN prediction of MIC, v thoroughwork!!
OpenAlex (openalex.org)
Joe Rogan might call this a brutal KO, if it wasn't him getting knocked the F out.
A supremely delightful takedown by @climatetown.bsky.social of Rogan's confident, ignorant, and dangerous climate denial.
Didn't realise this nonsensical government advice about deleting emails was now all over the news as top advice. Madness.
www.thetimes.com/uk/environme...
www.telegraph.co.uk/news/2025/08...
www.independent.co.uk/news/delete-...
metro.co.uk/2025/08/12/d...
Grateful to @marionkoopmans.bsky.social for writing this thoughtful piece in Nature Rev Micro. We can’t push back against anti-science movements without taking the threat seriously, proactively address our limitations, and engage with the public clearly & candidly.
www.nature.com/articles/s41...
What a sentence: “One pharma company "is banking on a continuing decline in vaccination rates to fuel [investment]”
What a world.
This is like saying you’re banking on seat belt use declining so you can make money on head injury treatment. It’s logical sure, but what are we even doing here?
If I could change one thing about #ScientificPublishing I'd ask funding bodies to stipulate all work they fund be published in non-profit journals.
The knock-on effects would alleviate most of the strain on #AcademicSky.
This isn't hard. It's big, but actually, it's pretty easy.
1/n
Proud to share my second paper!
Metagenomics could be a powerful tool to study antibiotic resistance in entire microbial communities.
Here we tested several new nanopore-enabled methods such as detecting DNA methylation, or strain-haplotyping.
www.frontiersin.org/journals/mic...
Logo for the Sandpiper website
Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵
Now on YouTube too! youtu.be/mCQLTfEHiS8?...
Hello Bluesky! Our lab is very excited to be here. This is post is a little older but is a really lovely article by the @washingtonpost.com and @shannonosaka.bsky.social about some of the work we are doing on microbiomes to combat climate change!
www.washingtonpost.com/climate-solu...
#microbiome
Frank Stahl died today at 95. He and his colleague Matt Meselson found a way to demonstrate how DNA replicated. Their lab experiment has been called the "most beautiful experiment". Here's a video of them describing how they did it. Video h/t NYT. #science
www.youtube.com/watch?v=7-tn...
Springer Nature book on machine learning is full of made-up citations Would you pay $169 for an introductory ebook on machine learning with citations that appear to be made up? If not, you might want to pass on purchasing Mastering Machine Learning: From Basics to Advanced, published by Springer Nature in April. Based on a tip from a reader, we checked 18 of the 46 citations in the book. Two-thirds of them either did not exist or had substantial errors. And three researchers cited in the book confirmed the works they supposedly authored were fake or the citation contained substantial errors. https://retractionwatch.com/2025/06/30/springer-nature-book-on-machine-learning-is-full-of-made-up-citations/#more-132235
Springer Nature--pioneering the new world of science where facts can be made up and citations generated to support them
Interesting paper on precisely detecting species of interest in metagenomes. I thought this was a thoughtful investigation for a problem that most folks don't discuss much, but implicitly think about often.
www.biorxiv.org/content/10.1...
Just for clarity: Fortunate Son is an anti-Vietnam song specifically about those who dodge the draft.
Beautiful work from my friend @kiranrpatil.bsky.social . Gut bacteria can accumulate Forever chemicals and help us get rid of them! Happy we could contribute! www.nature.com/articles/s41...
A new paper in The Lancet, one of the world’s foremost peer reviewed medical journals, estimates that USAID prevented 91 million deaths across 133 countries over 20 years.
The paper estimates that Elon Musk’s DOGE funding cuts to USAID will lead to 14 million deaths by 2030 (4.5 million children).
Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social).
myloasm-docs.github.io
Amazing @nytimes project on NIH cuts and grant freezes to cancer, alzheimer's, diabetes and other research:
“I would like to cure brain cancer,” Dr. Tanner said. “I think that's not particularly controversial.”
GIFT: www.nytimes.com/interactive/...
Extract from scientific paper that describes humans as “a recent and relatively inbred species” when compared to bacteria
www.biorxiv.org/content/10.1...
Gotta love this excerpt from @shenwei356.bsky.social and @zaminiqbal.bsky.social’s lexicmap preprint
Ardem Patapoutian's story is not just the American dream, it is the dream of American science. He arrived in Los Angeles in 1986 at age 18 after fleeing war-torn Lebanon. He spent a year writing for an Armenian newspaper and delivering Domino's at night to become eligible for the University of California, where he earned his undergraduate degree and a postdoctoral fellowship in neuroscience. He started a lab at Scripps Research in San Diego with a grant from the National Institutes of Health, discovered the way humans sense touch, and in 2021 won the Nobel Prize. But with the Trump administration slashing spending on science, Dr. Patapoutian's federal grant to develop new approaches to treating pain has been frozen. In late February, he posted on Bluesky that such cuts would damage biomedical research and prompt an exodus of talent from the United States. Within hours, he had an email from China, offering to move his lab to "any city, any university I want," he said, with a guarantee of funding for the next 20 years.
Man comes to the US from Lebanon. Starts out delivering pizzas, becomes a Nobel winning neuroscientist. Trump freezes his funding, he gets an email from China offering to move his lab “any city, any university I want" with guaranteed funding for 20 years.
What are we doing?
Unicore is now published on GBE 🚀
Unicore rapidly identifies structural single-copy core genes from input species proteomes for phylogenetic analysis. Powered by Foldseek and ProstT5, Unicore enables linear-scale structure-based phylogeny of any given set of taxa. 🧵1/n
📃 doi.org/10.1093/gbe/evaf109
Bigger not necessarily better. The right small (<150) person conference can produce more networking opportunities than a big one, particularly for students just getting started
For example, in the Klebsiella assemblies, there was often an error in the GAGCT motif (or its rev-comp AGCTC). I suspected this could be methylation, but I ran @acritschristoph.bsky.social's MicrobeMod and couldn't find anything at those sites. So a mystery to me 🤷
Corporate administrators who have only experienced jobs whose main benefit was pay cannot fathom that the very best find intrinsic value in excellence and are best left to do it without undue interference or burden