Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data.
The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k...
Figure 1 shows they key result
Yesterday, five-year-old Liam and his dad Adrian were released from Dilley detention center. I picked them up last night and escorted them back to Minnesota this morning.
Liam is now home. With his hat and his backpack.
You’ve opened Pandora’s box. We’ve been spending our weekends taking our kid to cubing competitions.
I really think the net benefit for society is greater if we banned social media for those over 16.
💾 Prokka 1.15.6 is released!
This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics
github.com/tseemann/pro...
Big news!
🧬 Come check out my poster on agtools, an open-source Python framework for analysing and manipulating assembly graphs at #ABACBS2025 Poster #106
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💻 Github: github.com/Vini2/agtools
📄 Preprint: biorxiv.org/content/10.110…
End qualified immunity.
PubMed is running on autopilot during shutdown, but key independent committee has been abolished www.bmj.com/content/391/... 🧪
Graduate seminar did a deep dive on Thomas Paine’s Common Sense yesterday. At the line, “in America the law is king,” they (14 students from 6 countries) burst out laughing. I've been doing this for 35 years and this is the first time that was a laugh line.
You know you work for a software company when the description of meeting room names in your new office comes with regex that they will all follow.
Our new preprint is up! This is the main postdoc work of @wiesner-t.bsky.social focusing on exocytosis along the axon shaft and its regulation by the sub membrane actin-spectrin scaffold: www.biorxiv.org/content/10.1...
Read the thread below for a summary of our findings 🧵1/11
New blog post – A quick look at Roche's SBX
lh3.github.io/2025/09/11/a...
Now published in GigaScience with minor improvements: academic.oup.com/gigascience/...
* Download: zenodo.org/records/1490...
* More info: github.com/lh3/panmask
"Did you know the mighty redwood is actually the same species as brocoli and kale ? it's just a different cultivar" "Every year or two, botanists add another plant to Brassica oleracea and see if anyone calls them on it"
Plants phylogeny is a mess anyway
Credit : @xkcd.com
A picture of William Adams, from the TV show Battlestar Galactica, with the quote: "There's a reason you separate military and the police. One fights the enemies of the state, the other serves and protects the people. When the military becomes both, then the enemies of the state tend to become the people."
Always relevant.
My 6th grader is doing a survey for ethics class on the concepts of happiness and luck (or Glück for the German speakers). If you have a few minutes to submit your thoughts she’d appreciate it. docs.google.com/forms/d/1y2b...
Plot of life expectancy after Type 1 diabetes diagnosis, 1850-2025. After the discovery of insulin in 1921, life expectancies go gradually from zero to seventy years.
These are VERY rough estimates, but here's life expectancy after diagnosis of type-I diabetes over the past 150 years.
It was Banting and Best's discovery of how to isolate insulin in 1921 — not some fucking cooking class — that gave people including my daughter a new lease on life.
I’m overwhelmed by the expressions of sympathy and support.
And still this pales in comparison to what they are doing to immigrants and to undermine the Bill of Rights.
If you could do one thing for me, call your representatives and demand accountability for their white supremacist terrorism.
This seems like a good thing. Are we aloud to have good things? I feel like this is going to turn into a Charlie Brown and Lucy with the football sort of situation.
Were you able to screenshot that? All I see is „blocked“.
Anyone want to go in on an industry collab to fund this?
I've seen enough. Donald Trump is not abiding by a lawful Supreme Court ruling. As a member of Congress, I fully support impeaching him. NOW.
How is this Python package real pypi.org/project/tari...
Cruel Fate, 1525: Our cow died during the night. We will surely perish.
Cruel Fate, 2025: Our Keurig stopped working during the night. We will surely perish.
That’s a wild backdoor…
Burn
I have yet to see a boring thread from you…
