Arjun Raj
@arjunraj.bsky.social
Just another LLM. Tweets do not necessarily reflect the views of people in my lab or even my own views last week. http://rajlab.seas.upenn.edu https://rajlaboratory.blogspot.com
Scientist goals: get @quantamagazine.bsky.social to write about our work. Check this super nice article about Sophie Dumont's lab poking mitotic spindles:
What Breaks a Cell’s Ribs Can Make It Stronger | Quanta Magazine
The mechanical process of cell division exerts powerful, if microscopic, forces. How do the molecular machines that power it manage the strain?
quantamagazine.org
Thank you. My colleagues and I are pleased that we developed a system that works and that 11 years and over 100 papers #gastruloid papers later, what we felt in the final paragraph of the paper is coming along. There is now a community improving and learning from the system.
Kevin Mitchell@wiringthebrain.bsky.social · 4mo agoSymmetry breaking, germ layer specification and axial organisation in aggregates of mouse embryonic stem cells journals.biologists.com/dev/article/... - what a gorgeous paper this is! (2014 from @amartinezarias.bsky.social and colleagues - introducing 'gastruloids'!)
Grateful to have worked with such an incredible team on this project. Excited to finally share this story about Top2 evolution and hybrid incompatibility in Drosophila. More to come!
Mia Levine@levine-lab.bsky.social · 5mo agoSo excited to share this manuscript led by the inimitable Cara Brand, who discovered that Topoisomerase II evolution causes hybrid female lethality in Drosophila. Congrats to Cara, @nickbr0wn.bsky.social, Anirban, and @buszczaklab.bsky.social! www.biorxiv.org/content/10.6...
I had two undergrads in my office today working on a computational project. My normal advice in research is to use tools to their fullest to get to the cutting edge. For the first time, I was reluctant. I worry that using coding agents would rob them of something. And I’m fully AI-pilled.
🧮 Check things that should add up ⚠️ Never ignore code warnings 📊 Track datapoints like the number of rows 🔍 Investigate outliers 🧠 If something doesn’t make sense, keep digging arjunrajlab.substack.com/p/transition...
Transitioning to being a PI in the age of AI
Computational biology is in a period of upheaval that is both exhilarating and terrifying.
arjunrajlab.substack.com
AI is pushing computational biology into analytic abundance. The bottleneck is no longer generating results: It’s deciding whether to trust them. 📊 5 habits for sense-checking outputs, via @arjunraj.bsky.social 1/2
A white paper on Stem Cell Based Embryo Models #SCBEM #Innovation #Ethics #Policy, from the community to highlight the potential of this new area of research and its impact in #ReproBiology shorturl.at/dAWL2
napari 0.7.0 is available now! 🚀🎉 It's a BIG release so read the full release notes, with highlights: napari.org/stable/relea... We want to thank everyone who has worked incredibly hard on this release including our 11 new brilliant contributors 🤩 and the community for their support and feedback!
napari 0.7.0
Mon, Mar 23, 2026 We’re happy to announce the release of napari 0.7.0! napari is a fast, interactive, multi-dimensional image viewer for Python. It’s designed for browsing, annotating, and analyzing…
napari.org
Introducing the Anthropic Science Blog. Increasing the pace of scientific progress is a core part of Anthropic’s mission. The Science Blog will feature new research and stories of how scientists are using AI to accelerate their work. Read the intro:
Introducing our Science Blog
Anthropic is an AI safety and research company that's working to build reliable, interpretable, and steerable AI systems.
anthropic.com
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.
Honoured and overwhelmed to receive the 2026 Waddington Medal. Science is a team effort, and I've been fortunate to work alongside exceptional people asking hard questions. Thank you to the BSDB and to everyone who has been part of the journey. bsdb.org/2026/03/24/2...
2026 Waddington Medal Winner - James Briscoe - BSDB - British Society for Developmental Biology
We are very pleased to announce that this year’s Waddington medal winner is James Briscoe. His fundamental discoveries have helped shape our understanding of of how morphogens work, and he has played ...
bsdb.org
Untangling mechanisms underlying #CancerDrugResistance www.nature.com/articles/s41... @jess_ljx @arjunraj.bsky.social #Cancer #DrugResistance #TranslationalScience
AP-1 mediates cellular adaptation and memory formation - Nature Communications
Cellular responses to stimuli can involve learned behaviors through memory formation. Here, the authors show that cancer cells encode gene expression into cellular memories during therapy resistance v...
nature.com
@mukherja.bsky.social work on RNAPII clusters is in print today: www.nature.com/articles/s41... Congrats! TLDR: RNAPII clusters represent transcriptonally engaged molecules at single genes, not super-stochiometric assemblies. Please check it out and see the the thread below for a summary.
A single cluster of RNA Polymerase II molecules is stably associated with active genes - Nature Communications
Live molecular-scale imaging in fly embryos shows that a single RNA Polymerase II cluster stays bound to active genes during transcription. Cluster formation requires initiation, and intensity represe...
nature.com
Apratim (Appy) Mukherjee@mukherja.bsky.social · 11mo ago(1/3) Excited to post our updated pre-print! We show RNAPII clusters are simply collections of polymerase molecules stably engaged at single genes & cluster intensity is strongly correlated with txn output during Drosophila embryogenesis. www.biorxiv.org/content/10.1...
Scientific publishing: Rethinking how research is reviewed and published Review of how the loss of impact factor affected submissions at eLife - uneven drop across countries, but generally holding up remarkably well and shows a new model is possible elifesciences.org/articles/110...
Scientific Publishing: Rethinking how research is reviewed and published
Taking a radical new approach to the publication process resulted in eLife losing its impact factor, but authors, reviewers, editors and funders support the journal and its efforts to reform scientifi...
elifesciences.org
Live imaging of macrophages and neutrophils in a transgenic zebrafish larva. Credit to Prof. Anna Huttenlocher Lab @uwmadisonmmi.bsky.social. #ZebrafishZunday 🧪
Blog post: transitioning to being a PI in the age of AI open.substack.com/pub/arjunraj...
Transitioning to being a PI in the age of AI
Computational biology is in a period of upheaval that is both exhilarating and terrifying.
open.substack.com
One of my very favorite papers from the lab! Shows that individual cells can learn by forming memories. Amazing work by Jess Li!
Waggoner Lab@labwaggoner.bsky.social · 5mo agoAP-1 mediates cellular adaptation and memory formation @natcomms.nature.com @pennmedicine.bsky.social @arjunraj.bsky.social @penngenetics.bsky.social www.nature.com/articles/s41...
A moment of introspection on how much the world has changed during the time between the initial submission and this (hopefully final) revision: "This paper seems so quaint now" "Let's think of it as having contributed an important bit of high-quality training data to Opus 4.7"
Ran an AI coding workshop with the lab. There was a palpable sense of sadness realizing that skills some of us have spent our lives developing (myself included) are a lot less important now. I see the future 100%, but I do think it's important to acknowledge this sense of loss.
ft. Sam Reffsin, Margaret Dunagin, Yael Heyman, @arjunraj.bsky.social (Bioeng), Jesse Miller, Kasirajan Ayyanathan, Sara Cherry (@pennpathlabmed.bsky.social), @naveen-jain.bsky.social (@cambupenn.bsky.social) & David Schultz (BioBio) @penngenetics.bsky.social www.sciencedirect.com/science/arti...
The TIG1-high state exists in human lung club and ciliated cells, enriched in IPF patients and tobacco users. Different viruses target different states. Influenza A prefers KRT8-high cells. Arjun Raj @cp-cell.bsky.social doi.org/10.1016/j.ce... 🧪 3/3
Reffsin, Miller, Cherry & Raj et al. discover that intrinsic cell states determine which cells become infected with SARS-CoV-2. Using single-cell clone tracing, they identified a TIG1-high state marking highly susceptible cells. What makes these cells vulnerable? 👇🏻 1/3
Data and experiments move faster, but theory is what gives discovery direction, via @arjunraj.bsky.social arjunrajlab.substack.com/p/chance-fav...
Chance favors the (theoretically) prepared mind
In defense of the role of theory in innovation
arjunrajlab.substack.com
We spend a lot of energy choosing the right research project. But an equally important skill is knowing when to walk away. Quitting isn’t failure: It’s how you make room for better science, via @arjunraj.bsky.social
I am happy to share that I’ve been awarded tenure here at Columbia University. Alhamdulillah. I thank my wife, parents, mentors, colleagues, friends, and family. I thank my lab members, present and past, for entrusting their careers in my hands and making this a thrilling journey.
AI is awesome, and is most definitely a transformative technology.
Stephen Turner@stephenturner.us · 7mo agoI’m pretty sure if you say anything positive about AI here you get permanently banned.
To me, the mean loud position here ranges between ignoring the ai and wishing to fully ban it. The latter won't happen (I don't think even regulation is technically feasible), the former is massively unproductive. If scientists refuse to participate in the discussion,it will just be driven by others
