Absolutely. In the amplicon/microbiome sequencing space the chimeras and homopolymer errors with illumina were more easily recognizable. Particularly paired end chemistries, since you can throw away all the <100% completely overlapping reads.
FWIW, Roche 454 sequencing ruined our final microbial ecology undergrad capstone project in undergrad.
I think there's a generation of scientists that never really had to deal with homopolymer errors, since illumina short reads were the norm for a long time. While, now, in the long read era, we're back to homopolymer errors.
Interesting thread y'all. Hi-C makes sense with Euks where the structure is a lot more physically defined, seems like early days for protocols for anything not euk-structural variant related.
This is a cool use of Hi-C within microbiology.
Exposing Staph aureus to both low-dose antibiotics and a host drove rapid evolution of extreme virulence. Researchers passaged MRSA and MSSA through nematodes with sub-MIC oxacillin for 12 rounds, then tracked how virulence and resi...
https://www.biorxiv.org/content/10.1101/2024.08.31.610628
Most microbes don't live in shaking flasks; spatial structure shapes how microbes interact and evolve at every scale, as we discuss in our recent review @jeroenmeijer.bsky.social @simonvanvliet.bsky.social @bedutilh.bsky.social @bramvandijk.bsky.social and others
academic.oup.com/femsre/artic... 🧵👇
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
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!)
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!
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...
