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
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...
Reposted by Ryan Bartelme
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...
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...
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...
doi.org
October 1, 2025 at 4:44 PM
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...
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...
Reposted by Ryan Bartelme
🚨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/...
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/...
RECLESS_Postdoc_single_cell_UniVie.pdf
u:cloud - Ihre Daten, auf Wolken gebettet.
ucloud.univie.ac.at
August 4, 2025 at 10:48 AM
🚨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/...
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/...
Reposted by Ryan Bartelme
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?
Do folks have recommendations for archaeal or bac-arch primer sets for PacBio 16S runs?
June 27, 2025 at 2:58 PM
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?
Do folks have recommendations for archaeal or bac-arch primer sets for PacBio 16S runs?
Reposted by Ryan Bartelme
How to delete your DNA from 23andMe www.bostonglobe.com/2025/03/25/b... via @bostonglobe.com
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.
www.bostonglobe.com
March 25, 2025 at 10:54 PM
How to delete your DNA from 23andMe www.bostonglobe.com/2025/03/25/b... via @bostonglobe.com
Reposted by Ryan Bartelme
We'll commit to a slice 🥧
Happy Pi Day!
Happy Pi Day!
March 14, 2025 at 5:27 PM
We'll commit to a slice 🥧
Happy Pi Day!
Happy Pi Day!
Reposted by Ryan Bartelme
@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
arxiv.org/abs/2501.13933
/Recurrence Plots for the Analysis of Complex Systems/
Norbert Marwan, Maria Carmen Romano, Marco Thiel, Jürgen Kurths
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...
arxiv.org
January 27, 2025 at 12:53 PM
@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
arxiv.org/abs/2501.13933
/Recurrence Plots for the Analysis of Complex Systems/
Norbert Marwan, Maria Carmen Romano, Marco Thiel, Jürgen Kurths
Reposted by Ryan Bartelme
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
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
Tears In Rain Ep4: Lev Tsypin
YouTube video by Sebastian Cocioba
youtu.be
January 6, 2025 at 12:35 AM
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
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
Reposted by Ryan Bartelme
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)
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)
Home
A tool for generating consensus long-read assemblies for bacterial genomes - rrwick/Autocycler
github.com
December 31, 2024 at 11:43 PM
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)
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)
Reposted by Ryan Bartelme
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
December 18, 2024 at 2:00 PM
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
This is a really cool read!
(1/5) Traditionally, antibiotic discovery has centered on bacteria and fungi—until now.
For the first time, we present a systematic exploration of Archaea—a major yet underexplored branch of the tree of life—as a source of novel antimicrobial compounds. www.biorxiv.org/content/10.1...
For the first time, we present a systematic exploration of Archaea—a major yet underexplored branch of the tree of life—as a source of novel antimicrobial compounds. www.biorxiv.org/content/10.1...
December 14, 2024 at 11:42 PM
This is a really cool read!
Well look at that... www.quantamagazine.org/mathematical...
November 21, 2024 at 4:58 PM
Well look at that... www.quantamagazine.org/mathematical...
Does it ever feel like biological fields are obsessive about memorization of facts and methods vs. heavily investing in broad quantitative skills?
I say this as a person who was the former and worked very hard post-PhD at bolstering the latter.
I say this as a person who was the former and worked very hard post-PhD at bolstering the latter.
November 20, 2024 at 6:07 PM
Does it ever feel like biological fields are obsessive about memorization of facts and methods vs. heavily investing in broad quantitative skills?
I say this as a person who was the former and worked very hard post-PhD at bolstering the latter.
I say this as a person who was the former and worked very hard post-PhD at bolstering the latter.
Reposted by Ryan Bartelme
We're hiring an undergraduate intern at the University of Arizona. This would be a good position for a sophomore or Junior at UofA looking to get into microbiology research (mostly soils and sediments).
Details: open.substack.com/pub/carinila...
Details: open.substack.com/pub/carinila...
We're hiring an undergraduate research intern
An opportunity for someone early in their scientific career
open.substack.com
November 19, 2024 at 5:25 PM
We're hiring an undergraduate intern at the University of Arizona. This would be a good position for a sophomore or Junior at UofA looking to get into microbiology research (mostly soils and sediments).
Details: open.substack.com/pub/carinila...
Details: open.substack.com/pub/carinila...
LAX makes O'Hare look awesome.
November 17, 2024 at 1:38 AM
LAX makes O'Hare look awesome.