This is truly an incredible breakthrough IMO. Really exemplifies what you get when deep domain expertise (popgen/evolution/disease genetics in this case) fuses with cleverly crafted ML. What u get r sleek, well thought out architectures that absolutely destroy the behemoths. Wow!! 1/

Some (+)ve news to lighten another heavy weekend: our latest preprint (c/o Mattiroli + Ramani labs) is up! www.biorxiv.org/content/10.1... A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)

Some proteins are primarily regulated by one mechanism: RNA abundance, translation, or clearance. The regulation of most proteins is dominated by different regulatory mechanisms across cell types. Gratifyingly, this complex regulation defines simple rules ⬇️ www.biorxiv.org/content/10.1...

Math often defines and redefines things in counterintuitive ways that reveal some deeper truth. Biology tends to define things based on intuition—I wonder if it could benefit from more counterintuitive definitions.

Only single cell sequencing of the all these post docs will reveal why

The older I get, the less likely it is that my birthday is a prime number. Sad.

My work email is a DDoS attack.

Manu Prakash practices “recreational biology,” a scientific approach that explores life in the same playful way that puzzles probe math. “Basic science is not at the service of something, but the groundwork that is our entire society’s foundation.” www.quantamagazine.org/how-paradoxi...

Very true. In my experience, there are three aspects of “good hands”. 1. Be low entropy: when in doubt, do things in an orderly manner. 2. Make good micro decisions: observe what matters and what doesn’t in any given protocol. 3. Make fewer errors. Of these, I think 2 is the most learnable.

I'm all for well-reasoned critiques, but this piece is not one of them. 👎

My great pleasure to introduce DR. Aoife O’Farrell!! An incredible scientist and human being. @aofarrell.bsky.social not only produced an amazing thesis by her own sheer brilliance and will, but also provided tireless service to Penn Bioengineering. Will be sorely missed!

It's reassuring to know that letting your beverages dry out in your workplace coffee mugs and turning them into disgusting gobs of sticky goo is an ancient and time-honored practice. www.smithsonianmag.com/smart-news/s...

📣 New preprint 📣 We present a detailed map of nascent and mature ribosomal RNAs in mouse hematopoiesis and AML (including absolute rRNA molecule numbers), and outline principles of rDNA regulation. Work by Eleanor Sams (@eleanor44.bsky.social) & Victoria Feist (@victoriafeist.bsky.social). (1/x)

No, Gemini, I don’t want to consider the hybrid option. (Oh wait that’s actually pretty good.)

Was about to buy 100 stamps from Costco until I realized that’s a multi-lifetime supply.

This is such a cool paper and dataset from lab of @arjunraj.bsky.social. There are [ahem] a lot of spatial transcriptomics papers out there. Here's a [rare?] example of one from which we can truly learn some interesting things... www.biorxiv.org/content/10.1...

Why do the youth not use commas?

In 1958, the ecologist Charles Elton posited that an ecosystem with more species should be more resilient against invasive species. Recently, in a series of microbial experiments, the physicist Jeff Gore found that the opposite is true. www.quantamagazine.org/the-ecosyste...

Check out this awesome work from @vayyappan.bsky.social… Embryo Economics! :)

[0/8] Stoked to share our work with @arjunraj.bsky.social on tissue organization in the gastruloid. We use lineage tracing and spatial transcriptomics to show that diversity among stem cell clones promotes, rather than hinders, gastruloid development: www.biorxiv.org/content/10.1...

Very excited to share our new work on gastruloids by the incredible Cat Triandafillou! We mapped gene expression across 26 individual gastruloids at single-cell resolution and discovered some pretty amazing patterns about how these "mini-embryos" organize themselves. www.biorxiv.org/content/10.1...

Excellent work indeed, but I feel in this context @adrianobolondi.bsky.social fantastic work should also be mentioned www.cell.com/developmenta...

Two new preprints from the @arjunraj.bsky.social‬ on #gastruloids. Both excellent. Exploring the relationship between macroscopic reproducibility v microscopic heterogeneity. Stunning experiments and much to think about biorxiv.org/content/earl... biorxiv.org/content/earl...

Using barcodes 📊 to track cancer 💊 resistance evolution: is it clonal selection or plasticity? @fwhiting.bsky.social‬ knows! His new "Evolutionary Informed Resistance Assays" (EIRAs) framework infers resistance evolution dynamics from barcode diversity data. www.nature.com/articles/s41... @icr.ac.uk

Very cool story and especially useful mathematical models for everyone to use! Check it out!!!

The equivocation of age comes both with the worry of a creeping relativism and the hopefulness of compassion.

The sounds of ancient computers from my past conjure up a surprisingly powerful form of nostalgia.

NimbusImage is great for spot analysis using the Piscis model from Will Niu; give it a try! www.nimbusimage.com www.loom.com/share/49d795...

Awesome work from @atishayjay.bsky.social!

You can just take academic papers and paste them into Gemini 2.5/ChatGPT o3/Claude 4 with the prompt "build me a game based on this paper, make it interesting and thematic but still conveying key findings" and get a tiny working educational game. (In this case, I used Gemini)

I wonder if it would be worth doing the exercise of asking, assuming we could measure absolutely everything, what should we *not* bother measuring?

Today, I hooded a PhD student who is about to begin an exciting new chapter of their life. Later in the day, I called my PhD advisor to catch up after a few years. A good day, all in all.

Just like most drivers think they are above average at driving, most scientists think they are above average at writing.

Are you interested in synthetic and systems biology approaches to study #spatiotemporal processes in cancer? Join NCI for virtual workshops on May 13, 15, & 20 (next week!) from 12:00–4:30 PM ET: registration: events.cancer.gov/nci/syntheti... #SynSysBio4SpatialCancerResearch

It is somewhat jarring to think that it is reasonable to ask which will happen first: achieving AGI or getting the second round of reviews back on our paper.

This is the best place in Paris to buy reagents to quench your crosslinking experiment

Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social. I'm so excited about this! www.biorxiv.org/content/10.1...

Is it bad that my favorite gene is EEF2 because it gives really good RNA FISH signal?

Thanks! Here's more info on cellpose-SAM for anyone interested bsky.app/profile/mari...

Wow, just implemented the new Cellpose-SAM from @computingnature.bsky.social in NimbusImage and it's *awesome*! Give it a try! nimbusimage.com

🚀🔬🦠 Releasing 🤖Cellpose-SAM🤖, a cellular segmentation algorithm with superhuman generalization 🦸‍♀️. Try it now on 🤗 huggingface.co/spaces/mouse... paper: www.biorxiv.org/content/10.1... w/ @computingnature.bsky.social 1/n

While I understand the sentiment, I must disagree. We are already required to do too many different things at a high level. Communicating with the public is not an easy skill and requiring that students be good at it is in some ways another barrier. Instead, make a podcast with NotebookLM!

Friends. This is the first orchid ever I have not killed, and that has come back to life underneath my very not green thumbs. Please clap.

New podcast episode about @aofarrell.bsky.social's latest prepeint! creators.spotify.com/pod/show/arj...

Check out our latest preprint, led by Dr. Siyu Chen, that brings together an amazing team of scientists from several labs ( @vram142.bsky.social, Tavazoie, and Navickas) to tackle a fundamental problem in biology: how do cells regulate expression of their tRNAs? www.biorxiv.org/content/10.1...

very few things make me as happy as data replication by different hands.

Honored and humbled. I have been very fortunate to have worked with amazing, inspirational colleagues in my lab, at Penn and in the broader community. Science matters www.nasonline.org/news/2025-na...

🚀 Excited to share that our work on BiaPy has been published today in Nature Methods! BiaPy makes deep learning accessible for bioimage analysis, from small datasets to terabyte-scale 3D images. 👇 (1/7) 🔗 www.nature.com/articles/s41... #DeepLearning #BioimageAnalysis #OpenSource #BiaPy

Pull apart a bronze trilobite (Cryptolithus bellulus) and put it back together. #TrilobiteTuesday #InverteFest (sound on for satisfying clicks)