Ryan Bartelme

Nevermind the jobs you had, tell me five classes you took at university

International Relations
History of the Scientific Revolution
Vampires in Literature & Film
Microbial Ecology
Microeconomics

Congratulations!!

R is effectively C++/FORTRAN-lite. I said what I said.

Has anyone explored using MCP with Juicer for de novo assembly chromosomal rearrangement? #bioinformatics #AI

Artist rendering of Sagittarius A* Supermassive Black Hole

New Blog Post, Self-Hosting is a Beautiful Black Hole: Self-hosting—running your own services on hardware you control—offers a DIY path to digital autonomy. Whether you want to fight platform enshittification, own your data, or just tinker with hardware for fun... rbartelme.github.io/blog/selfhos...

Working on a self-hosting code/data blogpost. Pretty excited about this one.

For some reason oatmeal + peanut butter + maple syrup gets me through morning eating troubles. Call it a deconstructed cookie.

Plant genomes are so weird!

Still far better than having to buy options for a privately held company. That makes even less sense IMHO.

🤣😂🤣😂

AFAIK, this is due to Delta Dental's ADA association

Genome Reduction Is Associated with Bacterial Pathogenicity across Different Scales of Temporal and Ecological Divergence Abstract. Emerging bacterial pathogens threaten global health and food security, and so it is important to ask whether these transitions to pathogenicity h

academic.oup.com/mbe/article/...

Question for the #microsky nerds -- Would you expect to see the same trends for environmentally transmitted plant pathogens?
(Also if you have any papers on this topic, please share!)

a man with a beard is wearing a black and white sweater and making a face . ALT: a man with a beard is wearing a black and white sweater and making a face .

So fundamental they paywalled the article.

Add this to the list of things no one asked for!

www.rdocumentation.org/packages/Rbi...

I've had my oldest cat for ~13 of his 14 years on Earth. He's still a little stinker, but also an elderly baby?

St. Jude's bioinformatics team is putting out some very high quality work lately!

I think the tech changing quickly is why I'm very pro-single purpose software so it's easily swapped out.

Does bioinformatics have an abandonware problem? My thoughts after reflecting on the Tucson Genomic Standards Consortium Meeting for a while: rbartelme.github.io/blog/the-aba... #bioinformatics #computationalbiology #FAIRdata #HPC #datascience

GSC and ISME are in New Zealand next year??
Might need to budget that in for 2026.

Krampusnacht!

Immune protection and disease tolerance in Pseudomonas aeruginosa infections by pyruvate cross-feeding Chronic infections by Pseudomonas aeruginosa in people with cystic fibrosis are characterized by persistent inflammation and oxidative stress, yet the mechanisms enabling bacterial persistence are not...

New preprint!👇
Pyruvate secreted by P. aeruginosa acts as a signaling molecule during infection, reducing oxidative stress, dampening immune activation and promoting persistence
Bacterial metabolism isn’t just a background process but an active player in infection🦠🧫
www.biorxiv.org/content/10.6...

My guess would be databricks?

Maybe the NFL needs to start subsidizing college football programs, since it's their farm system.

Same here. Regardless of field. I also really wish journals would stick to intro -> methods -> results -> discussion.

Scientists: have you been the target of an online harassment campaign, doxxing, or weaponized FOIA requests? I'd like to talk to you about steps you had to take to protect your digital security for an upcoming Nature story. (You can be anonymous if necessary.)

RTs appreciated.

A nice-to-have could be popular cloud provider object storage service mirrors of the downloads? This might allow cloud users to create their own persistent storage objects from the versioned object storage service. Ex. AWS S3 (end-user AWS Lambda) -> AWS EBS (end-user analysis) -> AWS EC2 + EBS vol.

This is really exciting!!

Oh this is super useful! Thank you to all the authors for this!