Brent Pedersen, Mitchell Vollger and I have "posted" our preprint of the manuscript describing bedder, a complement to the functionality of bedtools. The "preprint server" we have chosen is google docs because it was rejected by biorxiv.
docs.google.com/document/d/1...
I've been through this before, and we decided to send our preprint to arxiv.org/archive/q-bio where it was posted rapidly
I kind of get why they made the rule (they don't want a new preprint for every version bump of every tool), but maintain that tools like this should have a place in bioRxiv
There is something darkly comical about vibe coding forcing a bunch of engineers who likely derided engineering management now managing a corral of AI agents that basically act like a mix between Amelia Bedelia and the guy from Memento
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
A line graph showing NSF grant awards made through 2/27/26 for fiscal year 2026 compared with grant awards for fiscal years 2021-2025.
NSF Update (Awards through 2/27/26)
Directorates to follow
1/10
How Colorectal Cancer rates among young folks are 📈 and what we can do about it:
www.hankgreen.com/crc
To his excellent list, I'd add one more actionable item:
Advocate for cancer research funding. Cancer is not insurmountable - we've cured many types! We just need dollars and brains working on it
We aren’t allowed to have coffee provided when working 9 hour day to review grants for NIH
“Taken together, these two policies create a structure in which dissent becomes professionally costly, alignment becomes professionally necessary, and the space for honest scientific judgment quietly contracts.”
open.substack.com/pub/elizabet...
There are 256 emails in my inbox, and I only have an 8-bit mind. Overflow imminent.
Back when SEPT1 was a gene name and it damn well stayed that way
We love The Week Jr too. A few years back, we realized that since our info comes from laptops/phones and not from newspaper/TV, our kids weren't getting any ambient exposure to news. This solved that problem, and has led to some great conversations that we wouldn't have otherwise had. Recommend.
Me looking at any analysis I've ever run my life
There’s a big story everyone is missing—but this article hits on it.
We aren’t just seeing public health dismantled bc we’ve been taken over by conspiracy theorists and lunatics.
What we’re really seeing is the giant, predatory, underegulated wellness industry come to Washington.
We all are guilty of it - that's why it lands! 😄
In more practical advice, I start with one simple message I want them to take home, and work backwards from there. Don't assume they are intrinsically motivated to understand - you have to explain to them why they should care throughout. (my 2¢)
The district court injunction that prevented NIH from capping indirects at 15% was upheld today on appeal!
www.reuters.com/world/trump-...
░░░░░░░░░░░░░░░░░░░░ 0.00%
Very cool
Since it's never explicitly stated in the post, ~10.5 is the number of basepairs it takes for "standard" B DNA to make one full rotation. I didn't know that number offhand, but I think I'm unlikely to forget it now!
$ file gemini
-bash: file: command not found
Aww - gonna make them find the compressed files the hard way, eh?
New blog post: Spiritual Bypass, but with GPUs. The "Machinal Bypass," when AI becomes a shortcut around the work that makes us human, and why some tasks should feel a little hard. blog.stephenturner.us/p/machinal-b...
How are people dealing with AI use in their grad programs, specifically for thesis proposal, qualifying exam, dissertation? Banned completely? Allowed, but have to recognize its use? No guardrails at all? We have to develop a policy and I’m totally at a loss.
SCOOP: American Academy of Pediatrics loses HHS funding after criticizing RFK Jr. Research included reducing sudden infant deaths and identifying autism early. Me and @Paigecunningham.Bsky.Social
www.washingtonpost.com/health/2025/...
I am once again struck by the unfair asymmetry between political philosophies here in the US. Tearing things down is easy. Building things is hard.
www.politico.com/news/2025/12...
Likewise. Video is useful to show how to reach in to replace a headlight bulb. But to transfer written information it’s an excruciating slow trickle. Just let me read it!
screenshot of a homework worksheet that includes the sentence: "Methyl groups, a type of chemical group, are present in the environment and may enter cells and attach to the DNA as a person ages, as shown in the diagram below"
absolutely losing it at my 14yo's biology homework
The devastation I feel about this attack on science in particular is hard to cope with. It’s like watching my dad die all over again. I would do anything to spare someone a death via pancreatic cancer.
Ungodly sums of money being spent on Workday -- hundreds of millions of $ per higher ed institution (!!). And everyone seems to hate it. What gives? This article has some answers. The summary: "Customer service is Workday's goal. It's just that the customer isn't you."
Reposting @stephenturner.us’s response to the article from Current Affairs on how AI is turning universities into businesses. As he points out, students expecting measurable returns on their investment in college are not the problems here. I couldn’t agree more.
