Blog post: Chance favors the (theoretically) prepared mind Data is big, machines are learning, so what good is theory anyway? Isn't most discovery driven by serendipity anyway, with theory mostly a "post-mortem"? I argue that this view discounts the value of theory. open.substack.com/pub/arjunraj...

Beautiful - recommended! Here, @sasolla.bsky.social recaps her decades-long journey from physics to neural networks (working with LeCun & Hopfield) to motor cortex, & and from industry (including Bell Labs) to academia, all driven by curiosity and awe (which flows from her voice). Inspiring!

i've re-implemented PoPE from scratch as part of a model overhaul (w/ Claude Code). i don't have clean ablations yet but it's working. took about two hours to re-write my entire model i think the PoPE idea is really cool and a great fit for scientific data

2025 was the year we stopped debating whether paying peer reviewers might work and started showing that it does.

Agreed. The sunken cost fallacy is real. What I tend to do is to put projects on the shelf and once in a while look at them again wondering whether new technology or data would allow us to make progress. Emotionally it feels less like quitting and more as postponement

Great advice received as a postdoc: Do the easiest thing. I was 3 years into my postdoc and juggling projects w/nothing concrete = career crisis I went to my advisor Paul Sternberg for help. He asked what was going on & what mutant had the strongest phenotype. "Clone the easiest one." It worked.

Bad antibodies are such a huge problem. It’s not just the money wasted on buying them. It’s the amount of time spent trying to validate them.

Blog post: Just quit Quitting projects in science is hard, but we should be doing a lot more of it. open.substack.com/pub/arjunraj...

Our preprint "Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo" is on bioRxiv: www.biorxiv.org/content/10.6... . Amazing collaboration by @shenzhichen1999.bsky.social, Vincent Loubiere (@impvienna.bsky.social,@viennabiocenter.bsky.social),... (1/2)

I just finished my 28th yr of teaching grad compbio. Following the inevitable trend, a 3rd of the course is now Deep Learning (DL). One activity we did was a deep dive into the AlphaGenome pre-print (www.biorxiv.org/content/10.1...). Question is, how do we evaluate it as a science paper? 1/n

A new paper out in @natmethods.nature.com introduces NimbusImage, a cloud-computing platform for image analysis ft. William Niu (SAS), Jingxin Li (@cambupenn.bsky.social), @aofarrell.bsky.social (Bioengineering) & @arjunraj.bsky.social (@penngenetics.bsky.social) www.nature.com/articles/s41...

We designed SpaceBar to be as easy to use as possible: Cells are labeled via lentivirus transduction, and barcode detection works with any standard imaging-based spatial transcriptomics workflow. w/ Yael Heyman and @arjunraj.bsky.social Check out the thread from the preprint for more info!

Stoked that this paper, summarizing a vast series of experiments from past and present members of the team is out. A great way to end this year. www.nature.com/articles/s41...

I just pinned a photo of a post-it to one of our lab Slack channels. Is this what they mean by "tech stack"?

Absolutely thrilled to share the latest work from my lab focused on the variation and evolution of human centromeres among global populations! We assembled 2,110 human centromeres, identifying 226 new major haplotypes and 1,870 α-satellite HOR variants. www.biorxiv.org/content/10.6...

Good to see the peer reviewed version of this published A chemo-optogenetic system for spatiotemporal control of gene expression We use it to: - Reconstruct SHH mediated neural tube patterning in vitro - Measure extracellular half-life of Shh www.cell.com/developmenta...

When your PI presents your work

Will I be the last person in my lab to ever run a Southern blot?

Myths can be helpful ways to metaphorically view our science journeys! Jennifer Oyler-Yaniv (Assistant Prof. at Harvard) delivered a masterful lecture on her science by framing it as a “Hero’s Journey" on the Night Science Seminar Series. cassyni.com/events/ZYQow... @night-science-inst.bsky.social

Have you heard about the Night Science Podcast, where we talk about the creative process of doing science? We explore this with discussions with brilliant scientists & philosophers and artists, to figure out the tricks of the creative scientific trade. podcasts.apple.com/us/podcast/n...

GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult. Our latest work on causal models for this is out yesterday: www.nature.com/articles/s41... A short🧵:

After a huge amount of work w/ @alex-stark.bsky.social's group, a new version of our Ledidi preprint is now out! In an era of AI-designed proteins, the next leap will be controlling when, where, and how much of these proteins are expressed in living cells. www.biorxiv.org/content/10.1...

1/28 New preprint up, which I think is the best theoretical idea I've ever had. We asked a simple question: what are the costs of investment into non-reproductive somatic cells? Turns out these costs decrease with the *logarithm* of organism size! www.biorxiv.org/content/10.6...

some people have security blankets i have the 40 hidden slides in my presentation just in case i get asked specific obscure questions

I’m pleased to finally share that I’ve joined Imperial College London as Lecturer in Structural Biology. I am most grateful to my mentors. Over the past seven years, Patrick @patrick-cramer.maxplanck.de provided me with unconditional freedom, support and the space to grow and succeed. 🧵 1/3

ft. Sam Reffsin, Margaret Dunagin, Yael Heyman, @arjunraj.bsky.social (@pennengineering.bsky.social), Jesse Miller, Kasirajan Ayyanathan, Sara Cherry (@pennpathlabmed.bsky.social), @naveen-jain.bsky.social (@cambupenn.bsky.social) & David Schultz (BioBio) www.sciencedirect.com/science/arti...

We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen. 1/n

Fig. 6: Mathematical model

Emergence and Self-organisation across biological scales! I hope you are ready for next year conference! It will be an incredible event April 20-22 2026. The first of many #LakeConference organised by @ehannezo.bsky.social @alleninstitute.org and James Sharpe @embl.org

Image screening is going to fail. We need audit trails for data provenance.

oh boy!

The lab’s first pre-print! We investigated how growth-inducing Erk activity waves are regulated in regenerating zebrafish scales. We discovered that Erk waves are followed by waves of expression of their own inhibitors, as predicted by excitable waves theory. tinyurl.com/26r2cmpj

Gemini 3 is the first model that I think might solve the “schedule a thesis committee meeting” problem.

#Medsky🧪 #IDsky #immunosky #publichealth @cellpress.bsky.social The ability of a virus to infect a cell is partly determined by host factors required for the viral life cycle. However, not every cell of a given type is equally susceptible to infection.

Also, here’s an accessible video intro:

So awesome to have this great paper from Sam Reffsin and Sara Cherry out! In it, we use retrospective clone tracing to show that there are particular single cell states that are more susceptible to viral infection (both SARS-CoV-2 and flu)! www.cell.com/cell/fulltex...

The Lab of Stephan Grill at MPI-CBG has finally made it to Bluesky and we also have a brand new homepage: grill-lab.org Check it out.

Excited to launch an openRxiv partnership with the scientist-run AI review service qed (@qedscience.bsky.social), the brainchild of @odedrechavi.bsky.social 1/n openrxiv.org/enabling-rev...

Huh, that new paper looks cool! Although in our paper, we found that it was transcriptional burst size that changed with volume, not burst fraction. Here, they seem to find burst fraction. Admittedly, their technique is probably better suited to make the distinction. Interesting!

But @arjunraj.bsky.social showed similar results 10 yrs ago. What's new in this paper? www.cell.com/molecular-ce...

Thrilled to share my main postdoc work with @jamesbriscoe.bsky.social We used genomic barcoding + scRNAseq in chick & human embryos to reveal a lineage architecture that reshapes how we understand neural tube development & cell fate decisions 🧵👇 www.biorxiv.org/content/10.1...

Super proud of Dr. @giannatbusch.bsky.social for successfully defending her thesis! Such a talented and wonderful human!

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...