This article is a homecoming for me. As a PhD student, I focused on the growth-rate transcriptional regulation in yeast. Now, ~ 20 years later, we report protein regulation scaling with the growth rates of single cells in mammalian tissues. www.biorxiv.org/content/10.1...

⚠️ Paper alert: Using a novel CRISPR screening approach, we mapped the entire regulatory network controlling Xist—key for X-chromosome inactivation. 👉 We discover how sex and development signals are decoded at a single gene locus. www.nature.com/articles/s41... 👇 Bluetorial

New Blog Post: Scholarly Communication Is a Research Problem. This Means You. pracheeac.substack.com/p/scholarly-...

The bitter lesson of genomics: If you find yourself optimizing a targeted method, don't—betting against increased throughput is generally a bad idea.

What are people using for calling m6A from pacbio revio data? This is for analysis of fiberseq library. Any suggestions appreciated, we are newbies with m6A analysis!

Amazing recommendations, thanks everybody! ❤️ In the old days I used different tricks to get papers updates, but OldTwitter worked so well that I got lazy and too dependent on it. I wish the algorithms still worked and we could reliably hear about exciting science on social media

sounds interesting and i look forward to reading it! from the abstract it reminds me of an old paper P. Bousso's group had on T cells; I always thought the finding was fascinating: journals.plos.org/plosone/arti...

Of all the different metrics of scientific success, a kind word from a colleague you respect often means the most.

It's probably the deterioration of social media (I hope) but i'm exposed to a lot less cool science. It used to feel like a new cool study is being preprinted/published every week, and lately it's rare (at least so it seems). Share a recent study that's worth knowing!

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