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
Reposted by Arjun Raj
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)
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...
www.biorxiv.org
December 24, 2025 at 3:06 PM
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)
Reposted by Arjun Raj
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
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
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...
www.biorxiv.org
December 22, 2025 at 7:10 PM
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
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
Reposted by Arjun Raj
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...
December 19, 2025 at 7:26 PM
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...
Reposted by Arjun Raj
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!
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!
Excited to share SpaceBar - our new method for labeling and detecting clones with imaging-based spatial transcriptomics platforms! w/ Yael Heyman and @arjunraj.bsky.social www.biorxiv.org/content/10.1... 🧵
December 18, 2025 at 7:55 PM
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!
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!
Reposted by Arjun Raj
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...
www.nature.com/articles/s41...
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...
www.nature.com
December 17, 2025 at 3:57 PM
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...
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"?
December 17, 2025 at 5:57 PM
I just pinned a photo of a post-it to one of our lab Slack channels. Is this what they mean by "tech stack"?
Reposted by Arjun Raj
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...
December 16, 2025 at 4:06 PM
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...
Reposted by Arjun Raj
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...
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...
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...
www.cell.com
December 16, 2025 at 1:45 AM
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...
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...
Reposted by Arjun Raj
When your PI presents your work
December 15, 2025 at 12:00 PM
When your PI presents your work
Will I be the last person in my lab to ever run a Southern blot?
December 13, 2025 at 9:42 PM
Will I be the last person in my lab to ever run a Southern blot?
Reposted by 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
December 12, 2025 at 5:03 PM
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
Reposted by Arjun Raj
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...
podcasts.apple.com/us/podcast/n...
December 11, 2025 at 7:51 PM
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...
podcasts.apple.com/us/podcast/n...
Reposted by Arjun Raj
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🧵:
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
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.
www.nature.com
December 11, 2025 at 5:54 PM
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🧵:
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
Reposted by Arjun Raj
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...
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...
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...
www.biorxiv.org
December 10, 2025 at 3:18 PM
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...
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...
Reposted by Arjun Raj
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...
www.biorxiv.org/content/10.6...
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...
www.biorxiv.org
December 9, 2025 at 7:44 PM
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...
www.biorxiv.org/content/10.6...
Reposted by Arjun Raj
some people have security blankets
i have the 40 hidden slides in my presentation just in case i get asked specific obscure questions
i have the 40 hidden slides in my presentation just in case i get asked specific obscure questions
December 8, 2025 at 9:58 PM
some people have security blankets
i have the 40 hidden slides in my presentation just in case i get asked specific obscure questions
i have the 40 hidden slides in my presentation just in case i get asked specific obscure questions
Reposted by Arjun Raj
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
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
👋Meet Dr Srinivasan Rengachari (@rengachari-lab.bsky.social) our new Lecturer in Structural Biology.
In this interview, he discusses international research, his research interests and what excites him most about joining Imperial.
👉 blogs.imperial.ac.uk/doid-staff/2...
In this interview, he discusses international research, his research interests and what excites him most about joining Imperial.
👉 blogs.imperial.ac.uk/doid-staff/2...
December 5, 2025 at 6:05 PM
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
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
Reposted by Arjun Raj
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...
December 1, 2025 at 7:43 PM
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...
Reposted by Arjun Raj
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
1/n
Intro to Bedder – The Quinlan Lab
quinlanlab.org
December 2, 2025 at 2:28 AM
Reposted by Arjun Raj
Fig. 6: Mathematical model
November 29, 2025 at 8:13 AM
Fig. 6: Mathematical model
Reposted by Arjun Raj
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
@ehannezo.bsky.social @alleninstitute.org and James Sharpe @embl.org
#CellBio community, this one is for you! Applications are open for the #LakeConference on Modeling Life from Cells to Tissues – co-hosted with Circuit Neuroscience Basel!
📆 April 20-22, 2026
📍 Seattle, USA
🔬 All career stages welcomed.
Apply to attend by 12/12: alleninstitute.org/events/aics-...
📆 April 20-22, 2026
📍 Seattle, USA
🔬 All career stages welcomed.
Apply to attend by 12/12: alleninstitute.org/events/aics-...
2026 Lake Conference
Join the Allen Institute for Cell Science and Circuit Neuroscience Basel in Seattle, Washington, April 20–22, 2026, for a 3 day conference, Modeling...
alleninstitute.org
November 26, 2025 at 10:58 AM
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
@ehannezo.bsky.social @alleninstitute.org and James Sharpe @embl.org
Reposted by Arjun Raj
Image screening is going to fail. We need audit trails for data provenance.
I tried an even harder example on Gemini Pro image generation and this is quite scary/amazing. I asked for a microscopy image of around 20 HeLa cells, GFP tagged 20% nuclear, 10% membrane, +1 nuclear staining, + overlap. Image below and prompt in the following post.
November 22, 2025 at 4:21 PM
Image screening is going to fail. We need audit trails for data provenance.
Reposted by Arjun Raj
oh boy!
November 21, 2025 at 1:06 PM
oh boy!
Reposted by Arjun Raj
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
November 20, 2025 at 6:11 PM
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.
November 19, 2025 at 4:14 PM
Gemini 3 is the first model that I think might solve the “schedule a thesis committee meeting” problem.