a soft looking and somewhat worn felt swan with a big beak and trailing feathers

thinking about this 1500 year old plush swan made of reindeer wool

Last week I successfully passed my viva 🎓! It was a pleasure to discuss the work with @aidarodrigo.bsky.social, @bayraktarlab.bsky.social and @willmacnair.bsky.social, and to celebrate with the lab @annawilliamslab.bsky.social (thanks for this amazing single-cell hat!)

Pancreatic cancer mRNA vaccine shows lasting results in an early trial Scientists caution that more research is needed, but nearly all of the patients who responded to the personalized vaccine are still alive six years later.

"Pancreatic cancer mRNA vaccine shows lasting results in an early trial: Scientists caution that more research is needed, but nearly all of the patients who responded to the personalized vaccine are still alive six years later."

I want a "conference" where every academic cooks a dish for everyone and we all talk about our work casually while cooking. People can sous chef for each other. We eat and talk about our work in progress. You submit an abstract and a recipe.

We are excited to share our latest preprint on spatialFDA, a method for the statistical analysis of spatial omics data.

bioconductor.org/packages/3.2...

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🧬 Happy to share our new preprint on modeling cis-regulatory variation in human brain enhancers across a large Parkinson’s disease cohort: www.biorxiv.org/content/10.6...
Details in the thread below:

"The real threat is a slow, comfortable drift toward not understanding what you're doing."

This is very interesting I think:
ergosphere.blog/posts/the-ma...
"What he actually demonstrated, if you read carefully, is that the supervision is the physics."
i.e. if we outsource our thinking to LLMs, how do we learn to think, and where does the next generation of thinkers come from?

Our April issue is now live!

www.nature.com/neuro/volume...

Agents for comp bio are advancing rapidly, but evals are lagging. Current benchmarks can be overly prescriptive. Full analysis vignettes are hard to verify. We introduce CompBioBench: 100 diverse, challenging, verifiable tasks. We benchmark Codex and Claude Code.

biorxiv.org/content/10.6...

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Cell-Type-Resolved Pseudobulk Classification Across Independent Cohorts Identifies Microglial PTPRG as a Transcriptional Hub in Alzheimer's Disease #NeuroDegeneration 🧪🧠
www.biorxiv.org/content/10.64898/2026.04...

We're looking for a publicly available 10x Flex v2 gene expression dataset to test out our simpleaf pipeline on (we need raw FASTQ data and, ideally, CellRanger count matrices). Unfortunately, 10x only has Flex v1 data available on their website, and the v2 chemistry is different. Any ideas?

this type of person is so annoying to deal with and mastodon is full of them

cover of the book "Bayesian Workflow" by Gelman, Vehtari, et al. Coming out later this year, in the summer probably.

I would have preferred to have the "draw the rest of the owl" meme on the cover, but this will do. Seems like it is on schedule, and we'll leave some typos so you know we didn't write it with AI.

rewrites.bio - A manifesto for bioinformatics Principles for responsible AI-assisted rewriting of bioinformatics tools.

I'm both excited and a little terrified. It feels like a wave of AI-assisted tool rewrites is coming to bioinformatics whether we like it or not.

We figured that the best we can do is to try to get ahead of it, so we wrote down some principles for doing it responsibly: rewrites.bio

Extremely niche gripe:

There are a lot of books where the author rejects the idea of the brain as a computer, saying it's a metaphor and imperfect. That's a tenable case, but it's almost always poorly made, and based on two things. One little, one small.

Flexible ensheathment of axons enables myelination of complex CNS networks - Nature The rate of axon ensheathment varies within individual myelinating processes, resulting in chains of myelin sheaths connected by bridges consisting of thin cytoplasmic processes that provide&nbsp...

Latest offering. How myelin ensheathes axons!

Born from chat with Dwight Bergles on "weird things" we saw oligodendrocytes do, like making "bridges" between sheaths.

Driven forward by Cody Call, Kelly Monk, and myelin folks @edinburgh-uni.bsky.social

Enjoy!
www.nature.com/articles/s41...

Delighted to have been involved in this too!!

Yeah insisting that people with a lot of followers aren’t allowed to have feelings seems a great way to ensure that the only people who seek high profile roles are sociopaths

Why do schizophrenia GWAS signals look so flat across the genome?

In our recent preprint, we explored why psychiatric disorders — and, more broadly, brain-related traits involving the central nervous system — appear to have unusual genetic architectures.

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Delighted to share our latest preprint: Julie Zhu identifies a surprising reason why the genetic architecture of brain-related traits is so different than other traits. Check it out!

When Your Brain's Immune System Burns Out: A New Way to Think About Alzheimer's Disease What if Alzheimer's isn't just about the buildup of toxic proteins — but about the immune cells that were supposed to clean them up, and why they eventually stop doing their job?

When Your Brain's Immune System Burns Out: A New Way to Think About Alzheimer's Disease
open.substack.com/pub/hyassine...

A question for biologists: we often talk about evolutionary novelty. What does “novelty” mean for you? What’s your favorite definition if any? Or just a rule of thumb for what is and isn’t novel.

SIB Training organizes ~60 courses per year in the computational life sciences in Switzerland and online, which are open to attend for all researchers. We have launched a training needs survey. It takes 5-10 minutes to complete.
forms.office.com/e/WmSxcBeMYX
@sib.swiss

a strong moral principle to prevent me from deliberately stepping into the street, and methodically knocking people’s hats off

De-slop the text you shouldn't be writing anyway. A Claude skill to remove all the AI patterns from AI-generated text. blog.stephenturner.us/p/deslop

Some before/after:

10x Flex Gene expression support is now part of the piscem -> alevin-fry workflow, and also has a nice, low-friction command in simpleaf! Check out the tutorial here (combine-lab.github.io/alevin-fry-t...). This was a major feature upgrade, so we're looking for testers and feedback :).

Anna's hummingbird hovering. Facing to the right. With a small ant on the tip of its bill.

Sometimes you just get that shot. Anna's hummingbird with a little friend, in my yard. Davis, CA. #birds #ants

oh interesting. maybe worth dropping a line to the authors?

I've only skimmed the paper but this looks pretty impressive!