Ryan Bartelme
@microbialbart.bsky.social
Bioinformatician/Data Scientist in biotech. Occasional academic. Spending time with microbes, programming, maths, cats, & bicycles. Highly amateur analog photography. he/him
Pinned
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?
rbartelme.github.io
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
Plant genomes are so weird!
The modern-day potato came to be from the natural interbreeding between wild tomatoes and a potato-like species from South America about 9 million years ago. www.cell.com/news-do/pr-p...
@cp-cell.bsky.social
@cp-cell.bsky.social
December 29, 2025 at 10:40 PM
Plant genomes are so weird!
Reposted by Ryan Bartelme
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!)
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!)
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
December 23, 2025 at 5:14 PM
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!)
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!
December 11, 2025 at 7:06 PM
Add this to the list of things no one asked for!
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?
December 10, 2025 at 3:34 PM
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!
From @genomeweb.bsky.social early adopters of Spatial Biology developing standards, resources and QC tools.
December 6, 2025 at 4:34 PM
St. Jude's bioinformatics team is putting out some very high quality work lately!
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
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?
rbartelme.github.io
December 5, 2025 at 5:25 PM
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.
Might need to budget that in for 2026.
December 5, 2025 at 4:23 PM
GSC and ISME are in New Zealand next year??
Might need to budget that in for 2026.
Might need to budget that in for 2026.
Krampusnacht!
Were you naughty or nice this year? Cause it’s Krampusnacht, the night Santa’s fearsome counterpart comes to collect the bad kids! #ArtAdventCalendar bonus post!
My #linocut print shows Krampus, the scary horned creature of Alpine folklore, complete with birch rods, and naughty child in a basket. 🧵
My #linocut print shows Krampus, the scary horned creature of Alpine folklore, complete with birch rods, and naughty child in a basket. 🧵
December 5, 2025 at 3:05 PM
Krampusnacht!
Reposted by Ryan Bartelme
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...
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...
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...
www.biorxiv.org
December 5, 2025 at 10:38 AM
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...
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...
Reposted by Ryan Bartelme
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.
RTs appreciated.
November 26, 2025 at 12:18 AM
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.
RTs appreciated.
This is really exciting!!
Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social
doi.org/10.1093/bioa...
The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠
doi.org/10.1093/bioa...
The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠
GlobDB: a comprehensive species-dereplicated microbial genome resource
AbstractMotivation. Over the past years, substantial numbers of microbial species’ genomes have been deposited outside of conventional INSDC databases.Resu
doi.org
November 21, 2025 at 4:29 PM
This is really exciting!!
Reposted by Ryan Bartelme
🧬🖥️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/...
📑The new publication about the #SILVA database for the #NAR database issue is now online.
👉 academic.oup.com/nar/article/...
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
academic.oup.com
November 19, 2025 at 10:36 AM
🧬🖥️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/...
📑The new publication about the #SILVA database for the #NAR database issue is now online.
👉 academic.oup.com/nar/article/...
All of Jurassic Park's conflict could have been avoided if the eccentric billionaire just paid his IT guy more.
November 19, 2025 at 1:30 PM
All of Jurassic Park's conflict could have been avoided if the eccentric billionaire just paid his IT guy more.
Reposted by Ryan Bartelme
Interesting...
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
www.phoronix.com
November 18, 2025 at 11:35 PM
Interesting...
Reposted by Ryan Bartelme
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
Discarded diversity: novel megaphages, auxiliary metabolic genes, and virally encoded CRISPR-Cas systems in landfills
link.springer.com
November 11, 2025 at 6:38 PM
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
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...
rbartelme.github.io/blog/is-wait...
November 11, 2025 at 4:52 PM
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...
rbartelme.github.io/blog/is-wait...
The "fun" part about self hosting a blog is finding minor formatting errors after the post is published.
November 10, 2025 at 11:43 PM
The "fun" part about self hosting a blog is finding minor formatting errors after the post is published.
Reposted by Ryan Bartelme
The next video in the Laplace Transform sequence is up!
youtu.be/FE-hM1kRK4Y
Here, we dig into a concrete example, the forced oscillator. Some of you may remember that this was relevant for studying why light slows down in a medium.
youtu.be/FE-hM1kRK4Y
Here, we dig into a concrete example, the forced oscillator. Some of you may remember that this was relevant for studying why light slows down in a medium.
November 5, 2025 at 1:37 PM
The next video in the Laplace Transform sequence is up!
youtu.be/FE-hM1kRK4Y
Here, we dig into a concrete example, the forced oscillator. Some of you may remember that this was relevant for studying why light slows down in a medium.
youtu.be/FE-hM1kRK4Y
Here, we dig into a concrete example, the forced oscillator. Some of you may remember that this was relevant for studying why light slows down in a medium.
Reposted by Ryan Bartelme
So many Academic/Honor Societies try to broaden their membership base but are out of touch in how to tell the average student how membership will benefit them.
October 30, 2025 at 6:15 PM
So many Academic/Honor Societies try to broaden their membership base but are out of touch in how to tell the average student how membership will benefit them.
Maybe a start would be avoiding the word "promulgation"...just a thought.
Do you teach microbiology and constantly seek ways of raising interest and excitement in your students? This might be worth a glance 👇
enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...
enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...
October 29, 2025 at 9:35 PM
Maybe a start would be avoiding the word "promulgation"...just a thought.
Fish microbiomes will always be close to my ❤️
I am so proud of @spasqualetti.bsky.social and this BioRxiv paper! I have to prep for class, but later today I'll highlight some of her findings about a stickleback gut isolate that can degrade plastic and other microbes that inhibit it's ability. 🦠🔬
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Cold-water gut isolate from threespine stickleback (Gasterosteus aculeatus) reveals polypropylene surface oxidation and co-culture inhibition
Polyethylene terephthalate (PET) and polypropylene (PP), two of the most widely produced plastics in the United States, persist in cold-water environments where plastic-degrading microbes have been po...
www.biorxiv.org
October 23, 2025 at 3:34 PM
Fish microbiomes will always be close to my ❤️
Reposted by Ryan Bartelme
Sharing for conference organizers: I’ve been part of many Indigenous science sessions at the major science organizations— Ecological Society of America, American Geophysical Union, Soil Science Society of America, and now Living Data. I’m so appreciative to be part of these communities.
October 23, 2025 at 2:27 PM
Sharing for conference organizers: I’ve been part of many Indigenous science sessions at the major science organizations— Ecological Society of America, American Geophysical Union, Soil Science Society of America, and now Living Data. I’m so appreciative to be part of these communities.
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.
October 21, 2025 at 5:29 PM
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.
This is really interesting...
Prolonged Starvation Drives Epigenetic Remodeling: Insights from DNA Methylation Profiling in the Aquatic Pathogen Flavobacterium columnare https://www.biorxiv.org/content/10.1101/2025.10.01.679924v1
October 3, 2025 at 4:48 AM
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...
Beyond Programming Language Maximalism in Data Science and Bioinformatics: The Case for Polyglot Programming
Why choosing the right tool for each job beats forcing everything through your favorite programming language
rbartelme.github.io
October 2, 2025 at 8:02 PM
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...