Savoring little moments of calm in between shifts. Spring comes to early morning colors.

From Asgard to Earth: Tiny tubes may reveal the moment complex life began Stromatolites—and their close relatives, microbial mats—could be mistaken for what seems like a bunch of old dark rocks. But instead, they are dense, layered communities of microbes. Long before compl...

Our paper is out today! See this news article on it. Asgard archea have some cool proteins. If you are interested in protein evolution it’s a really exciting space. I’m lucky to be a structural biologist in the age of DL🧬🧶 @brendanburns999.bsky.social @iduggin.bsky.social @debnathghosal.bsky.social

@psy-fer.bsky.social dropped you a quick question over on 🐘!

Whenever I presented Phold, I was frequently asked "can you do the same beyond phages?" We ( @oschwengers.bsky.social @linsalrob.bsky.social @binomicalabs.org et al) finally did it with Baktfold github.com/gbouras13/ba... www.biorxiv.org/content/10.6...

Holy cow, I forgot about the world cup in Boston this summer. Hostel prices per night shot up 3x compared to the same time last year!

Extensive array of endogenous giant viral elements in a polar alga shows dynamic transcriptional response to abiotic stress Schultz et al. show that polar algae harbor extensive endogenous giant virus elements that are transcriptionally active, stress responsive, and integrated into host regulatory networks, highlighting v...

A good read on a large virus...

Extensive array of endogenous giant viral elements in a polar alga shows dynamic transcriptional response to abiotic stress: Current Biology www.cell.com/current-biol...

Holy cow. How is this even possible - or maybe we shouldn't even be surprised.

Man that's a lot of I's in a single skeet - should go out and get some coffee

Got registration scholarship to Boston Bacterial Meeting 2026, woot!

Will be reporting a pretty exciting (for me at least) observation from Haloarchaea sequencing project I've been running since 2024. Hopefully I can find some collaborators - I've been running into walls.

#BBM2026 #archaeasky 🦠🧫

Okay this is nonsense - I have two separate research university system email/library accounts and neither can access a nature microbiology letter from 2022. Apparently they're in the wrong subscription plan.

For profit journals is a plague on scientific research.

🧪

Thank you! I really didn't do much though haha

Happy to have made a small contribution for @gbouras13.bsky.social's study. Hope this is just one of many examples in independent researcher collaboration with academic scientists!

#archaeasky folks, this pipeline rules for global baseline annotation for archaea

doi.org/10.64898/202...

💻🧬🧫🦠

IMHO it's interesting that despite LLMs initially talking up replacing artists, real life benefits are pointing to coding aid for experienced developers & switching out junior devs.

What's coming out seems very impressive though.

Tonight in #NYC feels like a colder LA summer night. Wild.

#Archaeasky folks - I'm curious. How do you feel about the dorado polish bacteria mode for your archaeal ONT long read assembled genomes? I know it holds up well with bacteria, but archaea's always been a bit funny.

💻🧬

I feel the Subway these days serves a faded dream of a sandwich. That this could have been a real sandwich, and I could have been eating that sandwich in a better world. It is this idea that costs so darn much, not the limp bread thing in itself.

Lol I just set it up. SSHing to get sequencing work going while out at work still feels surreal

Do I dare run both the workstation's GPU at full and most of the CPU cores at the same time? With the mysterious power layout in the lab building this is more of an adventure than it ought to be.

Myloasm, our long-read metagenome assembler, is now published! w/ @mgmarin.bsky.social and @lh3lh3.bsky.social

Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers who gave very helpful feedback.

rdcu.be/famFj

Finally, AMD basecalling for ONT? I need to borrow some from hackerspace folks and test it out.

💻🧬

Oh man need to order more vegemite.

Marker gene phylogeny of ammonia oxidizing archaea genomes in the GlobDB annotated with their prevailing environmental categories

We now provide environmental metadata for the GlobDB genomes!
🖥️🧬🦠

More info here:
globdb.org/news

🧵

Transposable elements hitchhike on Starships across fungal genomes - Nature Communications Large mobile genetic elements known as Starships act as vehicles for transferring transposable elements (TEs) between fungi. Here, Griem-Krey et al. show that these ‘hitchhiking’ TEs can drive rapid e...

Now out!
We show that TEs can be horizontally transferred between fungal species via Starships. Once transferred, these TEs can become active, changing the genome organization and affecting the lifestyle of the recipient fungus.
www.nature.com/articles/s41...
@oggenfussursula.bsky.social #TEsky

Clustering the protein universe of life using DIAMOND DeepClust - Nature Methods DIAMOND DeepClust provides an ultra-fast clustering method for organizing the protein universe of life at low sequence identity, enabling large-scale dimensionality reduction and improving downstream ...

Clustering proteins using DIAMOND is out now @natmethods.nature.com www.nature.com/articles/s41...

Convergent extreme reductive evolution in ancient planthopper symbioses - Nature Communications Symbiotic bacteria can have exceedingly small genomes. This study finds that ancient bacterial symbionts of planthoppers have repeatedly evolved the smallest known genomes, losing most biosynthetic fu...

The smallest bacterial genome, further blurring the bacteria-organelle boundary!
Convergent extreme reductive evolution in ancient planthopper symbioses
www.nature.com/articles/s41...

Listening to Disney pulling out of the Sora generative video deal. Apparently the committed 1 billion USD?

It just hit me that's probably enough to hire 1000 animators for 10 years at a six figure salary... Imagine what they could have made with that!

Huh, if you're running Canu (yes, it's deprecated), latest conda installation of Canu doesn't play nice with java on linux. Solution is to just change the line 1078 at the lib/perl5/site_perl/canu/Defaults.pm to point toward working java installation, like:

$java="/your/java/bin";

Orchestrating podman containers is just a baseline skill in the brave new world of bio packages compiled against cutting edge glibc :-/

Maybe I should look into ansible too while I'm at this. Does anyone actually use it in #bioinformatics context out there?

Why is it when these fancy high-art circles envision a more worldly proactive mode of art, it's always in the shape of some 2010's era startup? I feel like I'm looking at some death of imagination here, more so than anything else.

Very fascinating (and brutal) take on the new New Museum opening exhibit. I have to say, I largely agree with the takes in the article. I'm even relieved that others think this way too.

hyperallergic.com/what-do-we-r...

#nyc