Ryan Bartelme

You could run the reads through kraken2??

It does somewhat turbocharge search and retrieval for what you describe. Much closer to semantic search than say Google or brute force search character encoding in the PubMed search bar.

I kind of love all the fraking out about Claude for Life Sciences. It's just a really cheap intern with some spellcheck/grammar/autoformatting baked in.

Being bad at statistics and modeling is highly correlated with some MD's

In my personal experience, "integrates with Benchling", likely involves taming five dragons, a descent into madness, and maybe a working MVP at the end of your quest.

Rust's memory safety?

As an alumn of this department, I'm super jealous of this mug!

This is really interesting...

I promised myself I'd start blogging on my personal site. So here's my more nuanced take on that old R vs Python "debate". How, reinventing functionality in your preferred language is a big time sink vs treating other languages and tools as learning opportunities: rbartelme.github.io/blog/the-par...

ChatGPT is pretty terrible for these sorts of tasks. Claude 4.2+ does a much better job. At least Anthropic is a PBC too...

Megaplasmids associate with Escherichia coli and other Enterobacteriaceae Humans and animals are ubiquitously colonized by Enterobacteriaceae , a bacterial family that contains both commensals and clinically significant pathogens. Here, we report Enterobacteriaceae megaplas...

New pre-print from the Banfield lab, highlighting an interesting case of 1.5Mb megaplasmids found in human gut.

Plasmid genomes were resolved using #PacBio HiFi sequencing with hifiasm-meta for #metagenome assembly. Host association was detected using epigenetic signals.

doi.org/10.1101/2025...

How much of NCBI is mirrored on EMBL? I don't remember.

🚨3-yr Postdoc Position on #SingleCell Activities in #Marine #N-Cycling🦠🧪👩‍🎓🔬

Join me @univie.ac.at @dome-vienna.bsky.social
Part of our ERC Synergy #RECLESS looking at microbes in marine oxygen minimum zones

Apply by Oct 15, start March 2026!

-> ucloud.univie.ac.at/index.php/s/...

Maybe the rub here is if reviewers request more work...those reviewers probably need to reject the manuscript.

We just got our 1st full-length 16S rRNA PacBio dataset back and it's a game changer (in the context of bacterial isolates)!

Do folks have recommendations for archaeal or bac-arch primer sets for PacBio 16S runs?

How to delete your DNA from 23andMe - The Boston Globe If you’re one of the 15 million people who shared your DNA with 23andMe, it might be time to delete your genetic data.

How to delete your DNA from 23andMe www.bostonglobe.com/2025/03/25/b... via @bostonglobe.com

I don't, but I wish I had these

We'll commit to a slice 🥧

Happy Pi Day!

Same thing happened when I paid off my student loans...because I "closed a line of credit"

If this doesn't get resolved feel free to ask me on Sunday's ride 😎

With enough time or money, anything can scale, but point taken. It's far more useful for clade level comparisons.

Well major evolutionary event will do that 🙃

It could, you'd need to setup a means of downloading the GenBank files and then run anvio.org/help/main/pr... The nice part is this parses annotations so it saves some compute time. Curious what broad questions would require all NCBI genomes?

anvio.org/learn/pangen... This plus the visualizer will allow you to physically explore a javascript/html file with protein clusters across strains, color them by clade, group them by phylogeny, etc.

Idk seems like anvio with extra steps...

Recurrence Plots for the Analysis of Complex Systems Recurrence is a fundamental property of dynamical systems, which can be exploited to characterise the system's behaviour in phase space. A powerful tool for their visualisation and analysis called rec...

@bifurcations.bsky.social :

arxiv.org/abs/2501.13933

/Recurrence Plots for the Analysis of Complex Systems/

Norbert Marwan, Maria Carmen Romano, Marco Thiel, Jürgen Kurths

a cartoon character is standing in front of a purple monitor ALT: a cartoon character is standing in front of a purple monitor

Using LLM's is like... #AI #ML #LLM

YouTube video by Sebastian Cocioba Tears In Rain Ep4: Lev Tsypin

Episode 4 of Tears In Rain is live!!!

In this episode I hung out with Lev Tsypin (@ltsyp.in) and we talked about his adventures in microbiology during the pandemic and all the struggles that came with it. A nice dive into his project and lots of wisdom shared. Enjoy!
youtu.be/ucSORPmTrl0

Home A tool for generating consensus long-read assemblies for bacterial genomes - rrwick/Autocycler

New year, new assemblies!
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
(1/5)

The most depressing thing about this public access policy discussion is the low agency about what journals will do/permit. They literally work for us & take money for services (existing only by overselling gatekeeping as truth IMO). We act like we aren’t every single aspect of what gives them power