Philipp Bayer
@philippbayer.bsky.social
Bioinformatics / tech / books
'It is required that one man should goof gloriously for the people.'
'It is required that one man should goof gloriously for the people.'
Reposted by Philipp Bayer
Happy birthday to one of my favourite haters, Charles Darwin
February 12, 2026 at 4:31 PM
Happy birthday to one of my favourite haters, Charles Darwin
when the README on github looks like this you KNOW the pipeline hasn't been updated in >2 years
February 13, 2026 at 7:02 AM
when the README on github looks like this you KNOW the pipeline hasn't been updated in >2 years
the most annoying (of many) things of this AI/copilot integration in Positron is when the AI integration is faster than the file-system integration, so you get an AI-hallucinated file path (always wrong) far faster than the real file on your filesystem
February 12, 2026 at 2:50 AM
the most annoying (of many) things of this AI/copilot integration in Positron is when the AI integration is faster than the file-system integration, so you get an AI-hallucinated file path (always wrong) far faster than the real file on your filesystem
we invented literate programming so you don't write English text around your code blocks
February 11, 2026 at 1:18 AM
we invented literate programming so you don't write English text around your code blocks
Love having this kind of brain-brokenness where I spend 20 minutes looking for my phone, not remembering where I put it, only remembering thinking "haha what an unusual place to put the phone"
(It was on top of the children's clothes drawer)
(It was on top of the children's clothes drawer)
February 10, 2026 at 11:59 PM
Love having this kind of brain-brokenness where I spend 20 minutes looking for my phone, not remembering where I put it, only remembering thinking "haha what an unusual place to put the phone"
(It was on top of the children's clothes drawer)
(It was on top of the children's clothes drawer)
They know when I'm getting too relaxed. That's why they send these at 6:33pm
February 10, 2026 at 10:40 AM
They know when I'm getting too relaxed. That's why they send these at 6:33pm
Haven't seen a plant pangenome in Science for a while!
www.science.org/doi/abs/10.1...
Eleven T2T genomes + 1720 accessions sequenced
www.science.org/doi/abs/10.1...
Eleven T2T genomes + 1720 accessions sequenced
Gapless pangenome analyses reveal fast Brassica rapa subspeciation
Brassica rapa (Br) encompasses many morphotypes and subspecies, so it is a good model with which to investigate plant diversification and subspeciation. Here, we resequenced the genomes of 1720 Br acc...
www.science.org
February 10, 2026 at 12:09 AM
Haven't seen a plant pangenome in Science for a while!
www.science.org/doi/abs/10.1...
Eleven T2T genomes + 1720 accessions sequenced
www.science.org/doi/abs/10.1...
Eleven T2T genomes + 1720 accessions sequenced
Recently finished reading Capek's War With The Newts; funniest and smartest book I've read in ages.
www.goodreads.com/review/show/...
Now reading Nabokov's Speak, Memory and it's just unfair how good it is. Every sentence beautiful, takes time to savour, all while being hilarious
#booksky
www.goodreads.com/review/show/...
Now reading Nabokov's Speak, Memory and it's just unfair how good it is. Every sentence beautiful, takes time to savour, all while being hilarious
#booksky
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www.goodreads.com
February 10, 2026 at 12:03 AM
Recently finished reading Capek's War With The Newts; funniest and smartest book I've read in ages.
www.goodreads.com/review/show/...
Now reading Nabokov's Speak, Memory and it's just unfair how good it is. Every sentence beautiful, takes time to savour, all while being hilarious
#booksky
www.goodreads.com/review/show/...
Now reading Nabokov's Speak, Memory and it's just unfair how good it is. Every sentence beautiful, takes time to savour, all while being hilarious
#booksky
I'm not slacking off, my agent is stuck in a deep, deep rabbit hole and I have to slavishly watch it
February 9, 2026 at 1:34 AM
I'm not slacking off, my agent is stuck in a deep, deep rabbit hole and I have to slavishly watch it
You couldn't write London Calling these days, nobody can afford to live by the river
February 8, 2026 at 5:09 AM
You couldn't write London Calling these days, nobody can afford to live by the river
Reposted by Philipp Bayer
This is an especially good article about why the Epstein files matter so much.
February 6, 2026 at 9:54 PM
This is an especially good article about why the Epstein files matter so much.
While the Summer Olympics are your normal sports, running and whatnot, the Winter Olympics are drunken bets, professionalised
The Winter Olympics are a lot more about almost dying than the summer ones, tbh
February 7, 2026 at 1:19 AM
While the Summer Olympics are your normal sports, running and whatnot, the Winter Olympics are drunken bets, professionalised
Reposted by Philipp Bayer
I used to love computer it was my friend. Now I have hate in my heart
February 5, 2026 at 9:17 PM
I used to love computer it was my friend. Now I have hate in my heart
Reposted by Philipp Bayer
New paper! From Sam Snodgrass and @genomeofforrest.bsky.social, w/ @druncie.bsky.social, @gcbias.bsky.social, and a collaboration with Andres Moreno and @santiagogmm.bsky.social. Can we quantify the impact of humans on maize dispersal?
Plant yourself in a comfy chair and lend me your ear:
1/10
Plant yourself in a comfy chair and lend me your ear:
1/10
www.biorxiv.org
February 6, 2026 at 5:49 AM
New paper! From Sam Snodgrass and @genomeofforrest.bsky.social, w/ @druncie.bsky.social, @gcbias.bsky.social, and a collaboration with Andres Moreno and @santiagogmm.bsky.social. Can we quantify the impact of humans on maize dispersal?
Plant yourself in a comfy chair and lend me your ear:
1/10
Plant yourself in a comfy chair and lend me your ear:
1/10
so glad I got rid of a whole bunch of 'geek arrogance' from my life. Use excel for your work? sure, go for it. Powerpoint? ok! Python? Also good. whatever gets the job done
there have been 0 LaTeX-caused overful vboxes in my life these past years and I'm a better person for it
there have been 0 LaTeX-caused overful vboxes in my life these past years and I'm a better person for it
February 6, 2026 at 6:31 AM
so glad I got rid of a whole bunch of 'geek arrogance' from my life. Use excel for your work? sure, go for it. Powerpoint? ok! Python? Also good. whatever gets the job done
there have been 0 LaTeX-caused overful vboxes in my life these past years and I'm a better person for it
there have been 0 LaTeX-caused overful vboxes in my life these past years and I'm a better person for it
I remember when I was young, supposedly 'negative' hobbies were sold as to be good down the track. Harry Potter obsessed will bring back literature once they move on! World of Warcraft addicts will become great managers!
Loosk like neither happened
Loosk like neither happened
February 5, 2026 at 11:58 PM
I remember when I was young, supposedly 'negative' hobbies were sold as to be good down the track. Harry Potter obsessed will bring back literature once they move on! World of Warcraft addicts will become great managers!
Loosk like neither happened
Loosk like neither happened
Reposted by Philipp Bayer
Blog post on the new OpenAI Codex app doi.org/10.59350/b6e... #Rstats
OpenAI Codex App
Vibe-updating my old qqman R package to ggplot2 with plan+execute.
doi.org
February 4, 2026 at 10:01 PM
Blog post on the new OpenAI Codex app doi.org/10.59350/b6e... #Rstats
Reposted by Philipp Bayer
Preprint from @lpachter.bsky.social lab argues journals should treat results as machine-readable objects, not just PDFs. Narratives stay for humans, but claims, evidence, and evaluations should ship in structured form so machines can index and verify. www.biorxiv.org/content/10.6... 1/ 🧵
February 4, 2026 at 9:27 AM
Preprint from @lpachter.bsky.social lab argues journals should treat results as machine-readable objects, not just PDFs. Narratives stay for humans, but claims, evidence, and evaluations should ship in structured form so machines can index and verify. www.biorxiv.org/content/10.6... 1/ 🧵
Finally arriving at the good vocabulary
February 4, 2026 at 12:50 AM
Finally arriving at the good vocabulary
I finally caught an Excel-doing-dates in the wild!! Opened an SRA metadata sheet in Excel where the experiments were named 6-1, 6-2, 6-3, 8-1, 10-4 etc. and Excel did its thing
February 3, 2026 at 1:00 PM
I finally caught an Excel-doing-dates in the wild!! Opened an SRA metadata sheet in Excel where the experiments were named 6-1, 6-2, 6-3, 8-1, 10-4 etc. and Excel did its thing
Reposted by Philipp Bayer
We can start by asserting that these so-called great men are not, that we need to stop listening to them, that they are morally bankrupt and corrupt and that their impoverished visions driven by their most base and vile indulgences have gotten us here. Fuck those guys. All of ‘em.
I read thousands of pages of Epstein files this weekend trying to understand what he wanted out of his meeting with 4chan's Christopher Poole. Here's everything we know about Epstein's plans to dismantle the internet and, eventually, democracy.
www.garbageday.email/p/here-s-how...
www.garbageday.email/p/here-s-how...
February 3, 2026 at 8:15 AM
We can start by asserting that these so-called great men are not, that we need to stop listening to them, that they are morally bankrupt and corrupt and that their impoverished visions driven by their most base and vile indulgences have gotten us here. Fuck those guys. All of ‘em.
was banging my head against a bug (VEP classifying my in-exon variants as 'downstream') that Claude Sonnet 4.5 fixed in about 5 minutes. I can understand the scepticism on LLMs being jammed into every corner of life, but there's merit in these tools
February 3, 2026 at 1:46 AM
was banging my head against a bug (VEP classifying my in-exon variants as 'downstream') that Claude Sonnet 4.5 fixed in about 5 minutes. I can understand the scepticism on LLMs being jammed into every corner of life, but there's merit in these tools
This sentence from my biology undergrad botany key is forever burned into my memory
"Sind die Grannen bespelzt oder unbespelzt?"
"Sind die Grannen bespelzt oder unbespelzt?"
reading about organisms that aren’t your specialty is like
margins of the quorbus eplungulate, ploobular processes bent posteriorly towards the foobulum
define term “eplungulate”
- lacking plungae. synonym: thubulous
margins of the quorbus eplungulate, ploobular processes bent posteriorly towards the foobulum
define term “eplungulate”
- lacking plungae. synonym: thubulous
February 2, 2026 at 11:29 PM
This sentence from my biology undergrad botany key is forever burned into my memory
"Sind die Grannen bespelzt oder unbespelzt?"
"Sind die Grannen bespelzt oder unbespelzt?"
me, coming from plants, working with human genomes: 'wow! you have VERSIONS of your assemblies?? and I can look anything up I like in most versions?!?'
me, four weeks later: 'great, I've assumed the wrong version again, and now I have to rerun everything'
me, four weeks later: 'great, I've assumed the wrong version again, and now I have to rerun everything'
February 2, 2026 at 6:51 AM
me, coming from plants, working with human genomes: 'wow! you have VERSIONS of your assemblies?? and I can look anything up I like in most versions?!?'
me, four weeks later: 'great, I've assumed the wrong version again, and now I have to rerun everything'
me, four weeks later: 'great, I've assumed the wrong version again, and now I have to rerun everything'
Reposted by Philipp Bayer
Men, it's worth pondering that these academic men are the same ones that teach young women straight out of school. These are the men given academic authority over young women's careers.
It's really challenging for young women to negotiate the minefield of creepiness these men create for them.
It's really challenging for young women to negotiate the minefield of creepiness these men create for them.
February 1, 2026 at 7:29 AM
Men, it's worth pondering that these academic men are the same ones that teach young women straight out of school. These are the men given academic authority over young women's careers.
It's really challenging for young women to negotiate the minefield of creepiness these men create for them.
It's really challenging for young women to negotiate the minefield of creepiness these men create for them.