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Arjun Raj

@arjunraj.bsky.social
6.7K followers 1K following 411 posts

Just another LLM. Tweets do not necessarily reflect the views of people in my lab or even my own views last week. rajlab.seas.upenn.edu rajlaboratory.blogspot.com

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Reposted by Arjun Raj
Itai Yanai @itaiyanai.bsky.social · 17/07/2026
Maybe creativity is just how big a bag of tricks you have; how many different tricks you've seen, applied in different contexts. And perhaps some people have a little bit more skill remembering all those tricks or applying them in different situations. - Arjun Raj, @arjunraj.bsky.social
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Ted Pavlic (he/him/his) @tedpavlic.bsky.social · 13/08/2026
Side note: If students are using LLMs to help them choose statistical processing pipelines, these skills/plugins may help to synthesize more rigorous choices (via @arjunraj.bsky.social). arjunrajlab.substack.com/p/keeping-yo...
arjunrajlab.substack.com
Keeping your analysis correct: mycelium and scilintr
Coding agents have made data analysis far easier to produce. The hard part now is verifying what comes out. Here’s the scaffolding I built to help.
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Ted Pavlic (he/him/his) @tedpavlic.bsky.social · 12/08/2026
Updated my guide on using LLMs with #Rstats (including #Rstudio, #Positron, and #VSCode options) to be more BYOK friendly and reflect changes in both VS Code Chat and Posit Assistant. github.com/tpavlic/docs...
github.com
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Christophe 🔬 Leterrier @christlet.bsky.social · 30/06/2026
Scientist goals: get @quantamagazine.bsky.social to write about our work. Check this super nice article about Sophie Dumont's lab poking mitotic spindles:
quantamagazine.org
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?
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Richard Sever @richardsever.bsky.social · 01/04/2026
Why bioRxiv
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Alfonso Martinez Arias @amartinezarias.bsky.social · 31/03/2026
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.
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Cara Brand @carabrand.bsky.social · 24/02/2026
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!
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Arjun Raj @arjunraj.bsky.social · 27/03/2026
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.
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Paperpile @paperpile.com · 26/03/2026
🧮 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...
arjunrajlab.substack.com
Transitioning to being a PI in the age of AI
Computational biology is in a period of upheaval that is both exhilarating and terrifying.
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Paperpile @paperpile.com · 26/03/2026
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
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Alfonso Martinez Arias @amartinezarias.bsky.social · 25/03/2026
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
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napari @napari.org · 24/03/2026
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.org
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…
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Anthropic {bot} @anthropicai.xmirror.bot · 23/03/2026
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:
anthropic.com
Introducing our Science Blog
Anthropic is an AI safety and research company that's working to build reliable, interpretable, and steerable AI systems.
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Dmitri Petrov @petrovadmitri.bsky.social · 24/03/2026
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.
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James Briscoe @jamesbriscoe.bsky.social · 25/03/2026
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...
bsdb.org
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 ...
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UPENN_ITMAT @itmat.bsky.social · 24/03/2026
Untangling mechanisms underlying #CancerDrugResistance www.nature.com/articles/s41... @jess_ljx @arjunraj.bsky.social #Cancer #DrugResistance #TranslationalScience
nature.com
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...
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Mir Lab @mirlab.bsky.social · 20/03/2026
@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.
nature.com
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...
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Steve Fleming @smfleming.bsky.social · 22/03/2026
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...
elifesciences.org
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...
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Zebrafish Rock! @zebrafishrock.bsky.social · 22/03/2026
Live imaging of macrophages and neutrophils in a transgenic zebrafish larva. Credit to Prof. Anna Huttenlocher Lab @uwmadisonmmi.bsky.social. #ZebrafishZunday 🧪
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Arjun Raj @arjunraj.bsky.social · 21/03/2026
Blog post: transitioning to being a PI in the age of AI open.substack.com/pub/arjunraj...
open.substack.com
Transitioning to being a PI in the age of AI
Computational biology is in a period of upheaval that is both exhilarating and terrifying.
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Arjun Raj @arjunraj.bsky.social · 21/03/2026
One of my very favorite papers from the lab! Shows that individual cells can learn by forming memories. Amazing work by Jess Li!
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Arjun Raj @arjunraj.bsky.social · 08/02/2026
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"
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Arjun Raj @arjunraj.bsky.social · 31/01/2026
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.
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Adlung Lab @adlunglab.com · 20/01/2026
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
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Adlung Lab @adlunglab.com · 20/01/2026
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
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Paperpile @paperpile.com · 19/01/2026
Data and experiments move faster, but theory is what gives discovery direction, via @arjunraj.bsky.social arjunrajlab.substack.com/p/chance-fav...
arjunrajlab.substack.com
Chance favors the (theoretically) prepared mind
In defense of the role of theory in innovation
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Paperpile @paperpile.com · 12/01/2026
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
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Mark @mkeller7.bsky.social · 10/01/2026
libertypuzzles.com these are very nice
libertypuzzles.com
Liberty Puzzles | Wooden Jigsaw Puzzles
The original wooden jigsaw puzzle maker. Established in 2005, all of our 1000+ puzzles are handmade in Boulder, CO with exquisite quality & craftsmanship. Full of odd-shaped "whimsy" pieces, our woode...
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Blitzy 🩺 ⚡️🏁 @blitz-y.bsky.social · 10/01/2026
Anyone have a thought about this weird mol on my hand?
My left hand with Avagadro’s Constant
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Ishmail Abdus-Saboor @ishmailsaboor.bsky.social · 02/07/2025
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.
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Arjun Raj @arjunraj.bsky.social · 07/01/2026
AI is awesome, and is most definitely a transformative technology.
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Anton Goloborodko @golobor.bsky.social · 07/01/2026
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
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Arjun Raj @arjunraj.bsky.social · 07/01/2026
So… Bluesky for science and X for Claude Code?
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Arjun Raj @arjunraj.bsky.social · 04/01/2026
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...
open.substack.com
Chance favors the (theoretically) prepared mind
In defense of the role of theory in innovation
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Nicole Rust @nicolecrust.bsky.social · 04/01/2026
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!
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Jase Gehring @skyjase.bsky.social · 02/01/2026
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
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Daniel Gorelick @danielgorelick.bsky.social · 31/12/2025
2025 was the year we stopped debating whether paying peer reviewers might work and started showing that it does.
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Dmitri Petrov @petrovadmitri.bsky.social · 30/12/2025
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
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Maureen Barr @barrlab.bsky.social · 30/12/2025
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.
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Arjun Raj @arjunraj.bsky.social · 30/12/2025
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.
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Arjun Raj @arjunraj.bsky.social · 30/12/2025
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...
open.substack.com
Just quit
Quitting projects in science is hard, but we should be doing a lot more of it.
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Alex Stark @alex-stark.bsky.social · 24/12/2025
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)
biorxiv.org
Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo
Enhancers control tissue-specific gene expression across metazoans. Although deep learning has enabled enhancer prediction and design in mammalian cell lines and invertebrate systems, it remains uncle...
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junhyongkim.bsky.social @junhyongkim.bsky.social · 22/12/2025
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
biorxiv.org
AlphaGenome: advancing regulatory variant effect prediction with a unified DNA sequence model
Deep learning models that predict functional genomic measurements from DNA sequence are powerful tools for deciphering the genetic regulatory code. Existing methods trade off between input sequence le...
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Grant Kinsler @grantkinsler.bsky.social · 18/12/2025
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!
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Rottinger Lab @rottingerlab.bsky.social · 17/12/2025
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...
nature.com
Whole body regeneration deploys a rewired embryonic gene regulatory network logic - Nature Communications
To what extent regeneration recapitulates embryonic development is a longstanding question. Here, they show that embryonic gene modules are re-used, rewired, and interconnected to specific injury-indu...
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Arjun Raj @arjunraj.bsky.social · 17/12/2025
I just pinned a photo of a post-it to one of our lab Slack channels. Is this what they mean by "tech stack"?
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Glennis Logsdon @glennislogsdon.bsky.social · 16/12/2025
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...
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James Briscoe @jamesbriscoe.bsky.social · 16/12/2025
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...
cell.com
Investigating morphogen and patterning dynamics with optogenetic control of morphogen production
Benzinger et al. develop a chemo-optogenetic system for precise spatiotemporal control of morphogen production in vitro. Using light-controlled Sonic hedgehog expression, they recapitulate neural tube...
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