Philipp Bayer
Bioinformatics / tech / books
'It is required that one man should goof gloriously for the people.'
- While the Summer Olympics are your normal sports, running and whatnot, the Winter Olympics are drunken bets, professionalised
- Reposted by Philipp BayerI used to love computer it was my friend. Now I have hate in my heart
- Reposted by Philipp BayerNew 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
- 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
- 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
- Reposted by Philipp BayerBlog post on the new OpenAI Codex app doi.org/10.59350/b6e... #Rstats
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- 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
- Reposted by Philipp BayerWe 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...
- 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?"
- 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'
- Reposted by Philipp BayerMen, 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.
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- "Observers have noted that the agents on Moltbook display complex and often bizarre emergent behaviors that were not explicitly programmed" Of course it's bizarre! It's meaningless!
- Re last RT: after three years of working in very-rich-peopleland, you won't believe how fast, willingly, happily people debase themselves for the powerful and wealthy. Even if there's no power or money to be had directly - just to be in the orbit. It's so, so depressing
- Reposted by Philipp BayerAcademics vying for a spot in Epstein‘s world. There are so many. I feel the need to make a thread, so I don’t keep confusing them. 1/
- Went digging through the epstein files a bit and among the horrors it's always so frustrating how plain stupid these messages are. You found alzheimers in plants in Monsanto data?!? Sure, man. Sure
- Reposted by Philipp BayerThis is Nathan Wolfe. Nathan is a virus hunter. Nathan has a bit of a reputation. Through the years, I've told multiple journalists stories I've heard, like "Nathan thanks Jeffrey Epstein in his book." Somehow no one ever wrote anything up. Want to see what Nathan was up to in today's Epstein files?
- Reposted by Philipp BayerA new study from Anthropic finds that gains in coding efficiency when relying on AI assistance did did not meet statistical significance; AI use noticeably degraded programmers’ understanding of what they were doing. Incredible.
- Reposted by Philipp BayerFoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social. 📄 www.science.org/doi/10.1126/... 🌐 search.foldseek.com/foldmason 💾 github.com/steineggerla...
- Me looking at any analysis I've ever run my life
- Good luck to anyone applying for a DECRA!!!!
- Reposted by Philipp BayerCalling all OrthoFinder users! We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny. GLADE runs directly on OrthoFinder results. www.biorxiv.org/content/10.6... github.com/lauriebelch/... (1/10)
- this is a beautiful album and you're all missing out
- Wooo level 8 on wanikani (I've always refused to learn kanji and focused on vocabulary, but wow does it help to retain new Japaanese words when you know the underlying kanji meaning - 'well of course mortality means shibou. just look at the kanji's readings!')
- The new position is a bit more corpo/stiff than I'm used to, so now I'm putting ❤️-reacts onto most thing I'm sent. i'm carving out my niche
- Please Don’t Say Mean Things About The AI That I Just Invested a Billion Dollars In www.mcsweeneys.net/articles/ple...
- Reposted by Philipp BayerAnnouncing a new tool for "denoising" long-read amplicon sequences: savont. Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay. 1/4 github.com/bluenote-157...
- My wish for 2026 is for people to stop dunking on screenshots from Twitter on bluesky/reddit/wherever. I'm not going to Nazi bars to gawk at the Nazis either. So why drag them to me?
- Yeaaaah stepped away from a way-too-long-running collaboration. Cleaning up my life
- Brassicaceae at it again
- Rational improvement of pennycress using CRISPR. #PlantScience From: www.nature.com/articles/s41...
- This is *chef's kiss* www.jampa.dev/p/lessons-le...
- People have been screaming from the rooftops for decades that the incentives in academia are all wrong - a career to make your publication number go up - AI overreliance is the latest symptom of a broken evaluation system those in charge cannot be bothered to fix
- I have social media so I can needlessly feel like garbage about events completely outside my sphere of influence
- In a world of darkness, a bright light shines
- Reposted by Philipp Bayer🎯 Marine sites wanted! Join eDNA Expeditions, an OBIS-led project mobilizing environmental DNA to support local marine biodiversity monitoring and increase global ocean knowledge. ☑️ Kits, training & support provided ✅ Don't miss the opportunity! ➡️ ednaexpeditions.org
- Which country, outside of a China, has seen this as an opportunity to bolster their own scientific work-force? It looks like only China has taken up the opportunity (at scale) of becoming the new scientific leader. Other countries just crickets
- This is the most astonishing graph of what the Trump regime has done to US science. They have destroyed the federal science workforce across the board. The negative impacts on Americans will be felt for generations, and the US might never be the same again. www.nature.com/immersive/d4...
- Reposted by Philipp BayerThis is the most astonishing graph of what the Trump regime has done to US science. They have destroyed the federal science workforce across the board. The negative impacts on Americans will be felt for generations, and the US might never be the same again. www.nature.com/immersive/d4...
- Reposted by Philipp BayerMy time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring! mirdita.org
- Reposted by Philipp Bayer1,000 PacBio genomes in a prospectively designed clinical utility study. This was the biggest and most important study that made us go live in diagnostics. Long-read genomes as a genetic first tier test across many rare diseases! www.medrxiv.org/content/10.6...
- Spent the entire afternoon getting a company-internal Quarto theme to work. It's just a regular Quarto extension, loaded via the yaml. But Quarto render completely ignores the header. tried every possible thing. I think I'm going insane
- It has finally happened: qs was removed from CRAN. I only realised because I tried to build my fancy-pants targets pipeline from start (the solution is to use qs2, but it seems like targets does not yet support qs2?) #rstats
- Oh seems like targets supports qs2 and will autoswitch, it's just that my previous runs were all in qs format.
- Reposted by Philipp BayerWeekend thoughts on Gas Town, Beads, slop AI browsers, and AI-generated PRs flooding overwhelmed maintainers. I don't think we're ready for our new powers we're wielding. lucumr.pocoo.org/2026/1/18/ag...
- Reposted by Philipp BayerWe mourn the passing of Peer Bork, EMBO Member since 2000: embl.org/news/embl-announcem…
- But whyyyyyyy
- Belated Christmas miracle in my house: the can of WD40 was where it was supposed to be! I thought by now the WD40 gremlins had whisked it away, never to be found again
- Found a weird way of working with ML: - have LLM write image processing Python that calls on classic, local CNNs via preprocessing - upload the preprocessed images and the boundary box images to the LLM - have LLM adjust the Python for the CNN - repeat until results good
