Arjun Raj

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...

Causal modelling of gene effects from regulators to programs to traits - Nature Approaches combining genetic association and Perturb-seq data that link genetic variants to functional programs to traits are described.

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🧵:

Programmatic design and editing of cis-regulatory elements The development of modern genome editing and DNA synthesis has enabled researchers to edit DNA sequences with high precision but has left unsolved the problem of designing these edits. We introduce Le...

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...

The fitness costs of reproductive specialization scale inversely with organismal size The evolution of reproductive specialization represents a fundamental innovation in multicellular life, yet the conditions favoring its evolution remain poorly understood. Here, we develop a populatio...

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...

I think my ratio of used to unused hidden slides is like 1:100 or more.

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

That all depends on the relative power of the reviewers vs. authors :).

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.

Single-cell susceptibility to viral infection is driven by variable cell states 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 typ…

#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:

Single-cell susceptibility to viral infection is driven by variable cell states Not all cells that can be infected by a virus become infected with that virus. Single-cell clone tracing reveals intrinsic cell states with variable expression patterns that increase susceptibility to...

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.

Enabling options for review: from training and transparency to author-centered AI tools - openRxiv Peer review is widely viewed as a critical aspect of biomedical communication. Ideally, it provides authors with feedback so they can improve manuscripts and gives readers, particularly nonspecialists...

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!

Single Mammalian Cells Compensate for Differences in Cellular Volume and DNA Copy Number through Independent Global Transcriptional Mechanisms Padovan-Merhar et al. combine single-molecule transcript counting with computational measurement of cellular volume, showing that single cells maintain transcript abundance despite variability in cell...

But @arjunraj.bsky.social showed similar results 10 yrs ago.
What's new in this paper?

www.cell.com/molecular-ce...

#RNAsky

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!

Hierarchical lineage architecture of human and avian spinal cord revealed by single-cell genomic barcoding The formation of neural circuits depends on the precise spatial and temporal organisation of neuronal populations during development. In the vertebrate spinal cord, progenitors are patterned into mole...

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!

Principles of protein abundance regulation across single cells in a mammalian tissue Protein synthesis and clearance are major regulatory steps of gene expression, but their in vivo regulatory roles across the cells comprising complex tissues remains unexplored. Here, we systematicall...

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...

Reporter CRISPR screens decipher cis-regulatory and trans-regulatory principles at the Xist locus - Nature Structural & Molecular Biology Here Schwämmle et al. develop CRISPR reporter screens to map transcription-factor-regulatory element interactions at the Xist locus, revealing a two-step mechanism integrating developmental and X-dosage signals to initiate X-chromosome inactivation.

⚠️ 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