🖥️ New design for #SILVA #SILVA 🧬 joined @leibniz-dsmz.bsky.social 🧫 and the @dsmzd3.bsky.social in 2023. This is now also visible on the redesigned website 🖌️, which has been restructured reorganized in a first step towards an improved and modernized #SILVA! Try it out at www.arb-silva.de

Finally, the results of my postdoc at the @bigdatabiology.bsky.social lab in Shanghai see the light! The work includes my three favorite things research-wise: 🦠 microbiome, 🧬 long-reads, and 🐶 dogs. See our new preprint: www.biorxiv.org/content/10.1...

Signed up for bunch of EMBL webinars on pangenomics coming up this October. Hoping to get a crash course on the topic in preparation for a paper I'm writing on Archaeal data of last year or so. Can never be too sure when working as an independent researcher! www.ebi.ac.uk/training/eve...

It's been a while since I've been out in Manhattan during day time and... Holy cow what's with the SUVs? More than 2/3 of the cars on the street were SUVs - fully decked out Lincolns and Cadillacs. Also I've never seen so many luxury sedans around at the same time growing up here. #nyc

Fascinating!

One of the more striking sights I've seen on the Southwest Chief journey was how widely spread and extensive wind farms are in the US. And that's with reduced scales compared to the original plans. Banks and banks of GE marked wind farm blades out there too. Didn't realize they're carbon fiber.

#SymbioSky must read 👇 (not the "chloroplast route" as in 𝘗𝘢𝘶𝘭𝘪𝘯𝘦𝘭𝘭𝘢, but the "nitroplast route of UCYN-A in 𝘉𝘳𝘢𝘢𝘳𝘶𝘥𝘰𝘴𝘱𝘩𝘢𝘦𝘳𝘢 ?)

Hmm that could be interesting. Will the core linux tool chain really end up moving on to rust, at least eventually? Git Developers Debate Making Rust Mandatory - Phoronix www.phoronix.com/news/Git-Wei...

Given the job market, looks like I'll be working as a part time personal nurse soon. My list of random jobs grows - adjunct researcher at a uni, dock worker, welder, translator, and did I mention when I worked as a porter in Cairo and ended up in a pyramid out yonder? And then there was Hong Kong...

#NYC weather today is like the great one I've seen in LA during ASM. Try not to stay inside today folks!

Caulophiles take note 👇 #MicroSky

#BWAC (Brooklyn Waterfront Artists Coalition) burned down overnight. That's probably hundreds of artists losing out on life's worth of work. Not a good news going into the colder season and #nyc real estate being what it is now.

The famous bears of Alaska's Katmai National Park are enjoying an abundance of salmon, and even some playtime, as they pack on pounds to prepare for the winter.

I wanted to get a video of this ghost crab but every time I got close to their hole they scuttled back in, so I tried getting clever with it. I made a little sandcastle and shoved my phone into it, hit record, and walked away. Crab was VERY suspicious of this addition to their environment.

Can vouch for quality, communication, and timeliness. A pro.

New preprint from the lab: we show that the ability to switch mating type was lost at least 13 times independently in the evolution of S. cerevisiae. At least 27% of isolates are heterothallic with a strong association with polyploidy and heterozygosity www.biorxiv.org/content/10.1...

🧪

So, fellas, when do you think these commercial sequencing companies will stop pretending sample blind unicycler pipeline is some sort of value added bioinformatics/assembly service? I always get better output from re-basecalling and doing long-reads first assembly myself. Smh. 🧬💻

gotta bump this back up on my TL again because it’s 40% near its goal… If you like culture crit, backrooms, liminal spaces, and horror… this is up your alley! it’s a wonderful collection of essays on the topic. I wrote the chapter about games!

GPU-accelerated homology search with MMseqs2 | Nature Methods https://www.nature.com/articles/s41592-025-02819-8

The paper: the genetic program that enables digit formation in limbs is derived from the system that drives cformation of the cloaca. Me, the headline writer:

We just released v1.1.0 of our #eDNA amplicon nextflow pipeline! We replaced the way LCAs are calculated - we now rely on Fishbase taxonomy first, then WoRMS and NCBI - and have added FAIRe-standard-aligned output files github.com/MinderooFoun...

This is very important to the #eDNA community: The Darwin Core Maintenance Group is inviting comments to the proposed extensions to Darwin Core format, which make the format much more malleable/easier to work with eDNA data gbif.github.io/dwc-dp/

Interested in doing a PhD in environmental research at Oxford? We offer fully-funded positions through ILESLA, now open for applications at iles.web.ox.ac.uk! Happy to discuss applications with students whose interests align with modelling marine dispersal or oceanic forcing of coral reefs.

Naiavirus: an enveloped giant virus with a pleomorphic, flexible tail nature.com/articles/s41467-025-63463-6

Happy to share that our story on the bacterial archaellum was published today in @natmicrobiol.nature.com www.nature.com/articles/s41... Congrats to the authors: @sshamphavi.bsky.social @loumollat.bsky.social @mariejoest.bsky.social Najwa Taib and @sgribaldo.bsky.social

“I fear not the man who has transferred 10,000 cultures one time, I fear the man who has transferred one culture 10,000 times” — @relenski.bsky.social, probably

We're shortstaffed on RPS and need some rad PC-minded freelancers for urgent review work. Specifically: - Borderlands 4 (yes I know it's out already) - Dying Light: The Beast - Silent Hill f Standard rate is £200 GBP per review, make yourselves known at [email protected]

I'm curious about the state of the art circa 2025 as well. My impression (working with rabbit neurons about a year ago) was just masurca/flye and then additional polishing with short reads. I heard of mixed results from wengan, not sure if it's still true. 🧬💻

Microbes may be small, but the discoveries they drive are huge! 🦠 This #InternationalMicroorganismDay, see how #PacBio HiFi sequencing is uncovering microbial mysteries, from mapping hidden HIV-1 reservoirs to revealing novel AMR pathways. Details here: bit.ly/4mSgPeL

The Onion again being better news commentary than actual news publishers with world-leadingly expensive legal teams.

Free Atlantic subscription to all public US high schools! Please tell your local teacher While I don't necessarily agree with everything they publish, it's a historic venue that published age defining pieces from people like Frederick Douglass and Vannevar Bush www.theatlantic.com/press-releas...

🚨🚨🚨 ProPublica reporting job alert 🚨🚨🚨 Where: The Midwest (Illinois, Michigan, Missouri, Wisconsin, Ohio, Indiana, Minnesota). What: Accountability reporting! Salary: $90K-$125K job-boards.greenhouse.io/propublica/j...

Yikes, GNU sort might or might not take character case into account depending on the locale. Something to take into account for minor scripts & pseudo pipelines we have around. superuser.com/questions/17...

Please check out our updated version of this preprint - now with even more transposable elements! 🧬🦠 No really, we added in a few more analyses about TEs and further compared Mycetohabitans to related bacteria, plus other treats. @bhuwanabbot.bsky.social www.biorxiv.org/content/10.1...

이건 귀엽지 않냐구

Lovely to see David Stephens highlighted in 100 years of cell biologists at J. Cell Sci., alongside Linda Amos, Peter Medawar, Juan Bonifacino, and others journals.biologists.com/jcs/article/...

When cave science emerged in the early 20th century, early speleological communities became entangled in right-wing nationalism. Cave explorers became nationalist symbols, as "conquerors" of an underground world. #histsci 🗃️ daily.jstor.org/underground-...

🆕 Event! We are hosting the Functional Multi-omics Symposium this autumn. Supported by the @microbiologysociety.org , @norwichmicro.bsky.social and @aibio-uk.bsky.social 🗓️ 17 October Register now ⤵️

The critiques of academic publishing are valid. But in seeking a solution, we should not discard the baby with the bathwater. Journals, in particular non-profit society journals, still provide many useful functions for scientists. journals.asm.org/doi/full/10....

Excellent editorial by my friend and colleague @pracheeac.bsky.social: "Academic Publishing Has Become a Racket" www.wsj.com/opinion/acad...

Oh wow. I've seen those half-moon bears in Korea look curiously people like, but this is on another level.

NGL I think Julia and python handles creating separate environment situation so much better than R.

Take a sneak peak at The Paradox of the Organism at Google books books.google.com/books?hl=sv&... Don’t forget to pre-order!

Using experimental evolution in host-mimicking media, researchers show that inflammation-like environments limit the loss of quorum sensing—a common adaptation during chronic infections—in Pseudomonas aeruginosa. Learn more in #mSystems: asm.social/2vd

Reminds me of other guy who 'founded' diybio - got a nice @wired.com article out of the shtick. His twitter bio was just a google link to his own name for a few years. Alas, another person with same name was a victim of a serial killer and ended up ranking higher on google algo than him. Life, huh?

Oh jeez dude. I don't know about describing yourself as a 'founder and a visionary' in your SNS bio page.

Writing up a quick python Archaeal genome rotator that doesn't rely on origin of replication - some of these buggers have too many of those for the usual bacterial approach to work. IMHO this might be so much easier in just shell & awk.