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Ryan Bartelme

@microbialbart.bsky.social
652 followers 503 following 208 posts

Bioinformatician/Data Scientist in biotech. Occasional academic. Spending time with microbes, programming, maths, cats, & bicycles. Highly amateur analog photography. he/him

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Ryan Bartelme @microbialbart.bsky.social · 30/09/2026
Bitwise reproduction is hard, but at least the NVIDIA DGX Spark is fast at telling me when I'm wrong! New blogpost on my embedsing model ablation experiments: rbartelme.github.io/blog/tda-map...
rbartelme.github.io
Reproducing the Topology Bake-Off on a Second Machine
Cosine metrics reproduce to four decimals on a second machine. Mapper metrics don't, and can't be expected to. The first post's anchor ρ turns out to be a single draw resting on about eleven documents...
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Ryan Bartelme @microbialbart.bsky.social · 28/09/2026
I think about this post a lot on here: An Inconvenient Truth About AI rutgerbregman.substack.com/p/an-inconve...
rutgerbregman.substack.com
An Inconvenient Truth About AI
Twenty years ago, climate denial was a problem of the right. Today, AI denial is a problem of the left. And the consequences could be even more disastrous.
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Ryan Bartelme @microbialbart.bsky.social · 25/09/2026
This is one of the worst starts to a Packers season in a very long time...
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Ryan Bartelme @microbialbart.bsky.social · 22/09/2026
I genuinely dislike Discord as a platform. Eats memory in the browser, eats memory in the app.
static.klipy.com
Spirited Away: No-Face Eating Cake
ALT: Spirited Away: No-Face Eating Cake
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Ryan Bartelme @microbialbart.bsky.social · 21/09/2026
This is a wonderful opportunity for any marine microbiologists!!
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Ryan Bartelme @microbialbart.bsky.social · 19/09/2026
O’zapft is!
static.klipy.com
Homer Simpson Loves Oktoberfest
Alt: Homer Simpson Loves Oktoberfest
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Ryan Bartelme @microbialbart.bsky.social · 13/09/2026
On an academic AI slack group one person pointed out this sudden "cause for alarm" around LLM's from Anthropic, OpenAI, et al. amounts to "regulatory capture". I.e. the rule will be written to enshrine their business interests while they quietly nix their IPOs citing "problems". #AI #LLMs
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José Vargas-Muñiz @mycorican.bsky.social · 09/09/2026
That is a good question! The 2 drugs that we used are clinical immunosuppressants, so if they behave as they do in humans, I guess that they would also immunosuppress bats (but that is a huge assumption). Fungal & mammal calcineurin are a tad different; hopefully, it can be exploited to fight fungi
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Ryan Bartelme @microbialbart.bsky.social · 09/09/2026
Ok weirdly did an undergrad research project on Calcineurin pathway in Blastomyces...how does this not affect bats?! I thought calcineurin inhibition was bad for all Euks
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Ryan Bartelme @microbialbart.bsky.social · 04/09/2026
I think this is why I like using GFF3 to catch parallel annotations from multiple annotation tools
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Ryan Bartelme @microbialbart.bsky.social · 01/09/2026
static.klipy.com
Daniel Plainview in There Will Be Blood
ALT: Daniel Plainview in There Will Be Blood
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Noah Greifer @noahgreifer.bsky.social · 03/08/2026
Fascinating and clear paper by @corymccartan.com and @melodyyhuang.bsky.social, greatly enhancing our understanding of how Bayesian Additive Regression Trees (BART) works and why it is so effective. A must-read for my fellow BART enthusiasts. #statssky #causalinference
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Ryan Bartelme @microbialbart.bsky.social · 22/07/2026
imgs.xkcd.com/comics/calib...
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Ryan Bartelme @microbialbart.bsky.social · 03/07/2026
@cbo.bsky.social doing the heavy lifting for biologists here 🏋️
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A. Murat Eren (Meren) @merenbey.bsky.social · 28/06/2026
@hifmb.de advertised 5 post-doc positions to work on social science / basic science interface, and here is a blog post to tell you why I care about this, and what it looks like: merenlab.org/blog/HIPP-on... Please spread the word if you can.
merenlab.org
Five Postdocs, Five Questions: An Experiment in Transdisciplinary Thinking at HIFMB
Some personal notes on what we are trying to achieve, and how we are planning to achieve that
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Ryan Bartelme @microbialbart.bsky.social · 24/06/2026
Whoa...
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Torsten Seemann @torstenseemann.bsky.social · 24/06/2026
"Genome sequence data underwent quality control using FastQC [13]" means "We ran FastQC on all our data, but we didn't really look at, or understand the reports, and we certainly didn't remove any samples from our study." #bioinformatiocsr #humour #reality
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Ryan Bartelme @microbialbart.bsky.social · 23/06/2026
#Bioinformatics people. I know we're all enamored with Rust at the moment, but I've been pondering Zig for extending bioinformatics software from C/C++. It's great htslib has rust bindings or you can use noodles as a pure rust alternative. Is the lack of a Zig 1.0 release the issue here?
static.klipy.com
Batman Deep in Thought
ALT: Batman Deep in Thought
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Ryan Bartelme @microbialbart.bsky.social · 21/06/2026
static.klipy.com
Call Data Comrades CDC Meme
ALT: Call Data Comrades CDC Meme
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Ryan Bartelme @microbialbart.bsky.social · 15/06/2026
Telemundo coverage of the World Cup is impeccable.
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Ryan Bartelme @microbialbart.bsky.social · 12/05/2026
"The metadata quality on SRA is genuinely awful for environmental amplicon studies." -AI Agent. Klanker's got a point here.
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Ryan Bartelme @microbialbart.bsky.social · 30/04/2026
"Running an Academic Lab is Not Running A Small Business" rbartelme.github.io/blog/running...
rbartelme.github.io
Running an Academic Lab is Not Running a Small Business
The PI-as-entrepreneur analogy flatters both sides but obscures where the real risks, incentives, and accountability actually live.
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Laura Helmuth @laurahelmuth.bsky.social · 22/03/2026
This is a great list of techniques for getting real information out of a Google search and avoiding AI slop and paid results. (One thing not included is that if you add "-ai" to a search, you block the AI summary) cardcatalogforlife.substack.com/p/google-has...
cardcatalogforlife.substack.com
Google Has a Secret Reference Desk. Here's How to Use It.
40 Google features to find exactly what you need, the alternative search engines that do things Google won't, and the reference desk framework underneath all of it.
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Ryan Bartelme @microbialbart.bsky.social · 04/03/2026
FWIW, Roche 454 sequencing ruined our final microbial ecology undergrad capstone project in undergrad.
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Ryan Bartelme @microbialbart.bsky.social · 04/03/2026
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.
media.tenor.com
a man in a gray shirt is holding a can of soda and says `` time is a flat circle . ''
ALT: a man in a gray shirt is holding a can of soda and says `` time is a flat circle . ''
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Ryan Bartelme @microbialbart.bsky.social · 27/02/2026
This is a cool use of Hi-C within microbiology.
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🧬Jacob L Steenwyk @jlsteenwyk.bsky.social · 13/02/2026
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... www.biorxiv.org/content/10.1101/202…
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Marcel Bäcker @marcelbaecker.bsky.social · 12/02/2026
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... 🧵👇
academic.oup.com
Spatial structure: shaping the ecology and evolution of microbial communities
Spatial structure naturally emerges in microbial communities, shaping growth, interactions, and evolution, and revealing how microscale processes scale up
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Ryan Bartelme @microbialbart.bsky.social · 31/01/2026
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
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Ryan Bartelme @microbialbart.bsky.social · 29/01/2026
R is effectively C++/FORTRAN-lite. I said what I said.
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Ryan Bartelme @microbialbart.bsky.social · 29/01/2026
Has anyone explored using MCP with Juicer for de novo assembly chromosomal rearrangement? #bioinformatics #AI
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Ryan Bartelme @microbialbart.bsky.social · 28/01/2026
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...
Artist rendering of Sagittarius A* Supermassive Black Hole
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Ryan Bartelme @microbialbart.bsky.social · 16/01/2026
Working on a self-hosting code/data blogpost. Pretty excited about this one.
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Ryan Bartelme @microbialbart.bsky.social · 29/12/2025
Plant genomes are so weird!
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Tiffany Lowe-Power stands with Minnesota @tlowepower.bsky.social · 23/12/2025
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!)
academic.oup.com
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
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Ryan Bartelme @microbialbart.bsky.social · 11/12/2025
Add this to the list of things no one asked for!
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Ryan Bartelme @microbialbart.bsky.social · 10/12/2025
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?
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Ryan Bartelme @microbialbart.bsky.social · 06/12/2025
St. Jude's bioinformatics team is putting out some very high quality work lately!
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Ryan Bartelme @microbialbart.bsky.social · 05/12/2025
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
rbartelme.github.io
Bioinformatics Code Rot: Do We Have an Abandonware Problem?
Graduate students need novel tools to publish. Labs lack funding for maintenance. How can we build sustainable bioinformatics software without fixing the incentive structure?
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Ryan Bartelme @microbialbart.bsky.social · 05/12/2025
GSC and ISME are in New Zealand next year?? Might need to budget that in for 2026.
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Ryan Bartelme @microbialbart.bsky.social · 05/12/2025
Krampusnacht!
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Pablo Laborda @pablolaborda.bsky.social · 05/12/2025
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...
biorxiv.org
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...
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Virginia Gewin @virginiagewin.bsky.social · 26/11/2025
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.
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Ryan Bartelme @microbialbart.bsky.social · 21/11/2025
This is really exciting!!
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DSMZ Digital Diversity @dsmzd3.bsky.social · 19/11/2025
🧬🖥️SILVA in 2026: a global core biodata resource for rRNA within the DSMZ digital diversity 📑The new publication about the #SILVA database for the #NAR database issue is now online. 👉 academic.oup.com/nar/article/...
academic.oup.com
SILVA in 2026: a global core biodata resource for rRNA within the DSMZ digital diversity
Abstract. Since 2007, the SILVA database (https://www.arb-silva.de/) has served as a comprehensive resource providing quality-checked, aligned, and classif
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Ryan Bartelme @microbialbart.bsky.social · 19/11/2025
All of Jurassic Park's conflict could have been avoided if the eccentric billionaire just paid his IT guy more.
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Daniel Probst @skepteis.bsky.social · 18/11/2025
Interesting...
phoronix.com
Python Developers Looking At Introducing The Rust Programming Language In CPython
A proposal has been raised by two CPython core developers to introduce the Rust programming language to CPython
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Laura Hug @lhug.bsky.social · 11/11/2025
New paper from our group - megaphages, compact CRISPR-Cas effectors, and more from landfill phage, led by the talented Dr. Nikhil George (not on bsky). rdcu.be/ePo8o
link.springer.com
Discarded diversity: novel megaphages, auxiliary metabolic genes, and virally encoded CRISPR-Cas systems in landfills
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Ryan Bartelme @microbialbart.bsky.social · 11/11/2025
The Cost of 'Waiting for Data': Why Curiosity Without Guardrails Undermines Research. Arbitrary experimental choices disguised as data-driven discovery lead to p-hacking, waste, and irreproducible results. My thoughts on the matter: rbartelme.github.io/blog/is-wait...
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Ryan Bartelme @microbialbart.bsky.social · 10/11/2025
The "fun" part about self hosting a blog is finding minor formatting errors after the post is published.
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