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
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.
Reposted by Arjun Raj
#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.
@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.
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…
www.sciencedirect.com
November 16, 2025 at 5:42 AM
#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.
@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:
November 15, 2025 at 5:33 PM
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...
www.cell.com/cell/fulltex...
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...
www.cell.com
November 14, 2025 at 4:47 PM
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...
www.cell.com/cell/fulltex...
Reposted by Arjun Raj
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.
Check it out.
November 6, 2025 at 1:09 PM
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.
Check it out.
Reposted by Arjun Raj
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...
openrxiv.org/enabling-rev...
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...
openrxiv.org
November 6, 2025 at 2:32 PM
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...
openrxiv.org/enabling-rev...
Reposted by Arjun Raj
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!
November 5, 2025 at 10:41 AM
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!
Reposted by Arjun Raj
But @arjunraj.bsky.social showed similar results 10 yrs ago.
What's new in this paper?
www.cell.com/molecular-ce...
What's new in this paper?
www.cell.com/molecular-ce...
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...
www.cell.com
November 2, 2025 at 8:18 PM
But @arjunraj.bsky.social showed similar results 10 yrs ago.
What's new in this paper?
www.cell.com/molecular-ce...
What's new in this paper?
www.cell.com/molecular-ce...
Reposted by Arjun Raj
Cell size-dependent mRNA transcription drives proteome remodeling www.biorxiv.org/content/10.1...
Cell size-dependent mRNA transcription drives proteome remodeling
Increasing cell size drives proteomic changes that impact cell physiology. However, the molecular basis of size-dependent proteome remodeling has remained unclear. Here, we develop an inducible Cyclin...
www.biorxiv.org
November 1, 2025 at 10:31 PM
Reposted by Arjun Raj
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...
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...
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...
www.biorxiv.org
October 26, 2025 at 5:15 PM
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...
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!
October 26, 2025 at 6:33 PM
Super proud of Dr. @giannatbusch.bsky.social for successfully defending her thesis! Such a talented and wonderful human!
Reposted by Arjun Raj
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...
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...
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...
www.biorxiv.org
October 18, 2025 at 11:56 AM
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...
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...
Reposted by Arjun Raj
⚠️ 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
👉 We discover how sex and development signals are decoded at a single gene locus.
www.nature.com/articles/s41...
👇 Bluetorial
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.
www.nature.com
October 6, 2025 at 1:02 PM
⚠️ 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
👉 We discover how sex and development signals are decoded at a single gene locus.
www.nature.com/articles/s41...
👇 Bluetorial
Reposted by Arjun Raj
New Blog Post:
Scholarly Communication Is a Research Problem. This Means You.
pracheeac.substack.com/p/scholarly-...
Scholarly Communication Is a Research Problem. This Means You.
pracheeac.substack.com/p/scholarly-...
Scholarly Communication Is a Research Problem. This Means You.
Scholarly Communication Is a Research Problem.
pracheeac.substack.com
October 4, 2025 at 4:11 PM
New Blog Post:
Scholarly Communication Is a Research Problem. This Means You.
pracheeac.substack.com/p/scholarly-...
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.
September 30, 2025 at 2:10 PM
The bitter lesson of genomics: If you find yourself optimizing a targeted method, don't—betting against increased throughput is generally a bad idea.
Reposted by Arjun Raj
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!
September 29, 2025 at 2:31 AM
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!
Reposted by Arjun Raj
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
It's probably the deterioration of social media (I hope) but i'm exposed to a lot less cool science. It used to feel like a new cool study is being preprinted/published every week, and lately it's rare (at least so it seems). Share a recent study that's worth knowing!
September 27, 2025 at 1:29 PM
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
Reposted by Arjun Raj
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...
A Role for the Immediate Early Gene Product c-fos in Imprinting T Cells with Short-Term Memory for Signal Summation
T cells often make sequential contacts with multiple DCs in the lymph nodes and are likely to be equipped with mechanisms that allow them to sum up the successive signals received. We found that a per...
journals.plos.org
September 26, 2025 at 12:47 PM
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...
Of all the different metrics of scientific success, a kind word from a colleague you respect often means the most.
September 27, 2025 at 2:59 PM
Of all the different metrics of scientific success, a kind word from a colleague you respect often means the most.
Reposted by Arjun Raj
It's probably the deterioration of social media (I hope) but i'm exposed to a lot less cool science. It used to feel like a new cool study is being preprinted/published every week, and lately it's rare (at least so it seems). Share a recent study that's worth knowing!
September 26, 2025 at 10:26 AM
It's probably the deterioration of social media (I hope) but i'm exposed to a lot less cool science. It used to feel like a new cool study is being preprinted/published every week, and lately it's rare (at least so it seems). Share a recent study that's worth knowing!
Reposted by Arjun Raj
This is truly an incredible breakthrough IMO. Really exemplifies what you get when deep domain expertise (popgen/evolution/disease genetics in this case) fuses with cleverly crafted ML. What u get r sleek, well thought out architectures that absolutely destroy the behemoths. Wow!! 1/
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
September 22, 2025 at 8:34 AM
This is truly an incredible breakthrough IMO. Really exemplifies what you get when deep domain expertise (popgen/evolution/disease genetics in this case) fuses with cleverly crafted ML. What u get r sleek, well thought out architectures that absolutely destroy the behemoths. Wow!! 1/
Reposted by Arjun Raj
Some (+)ve news to lighten another heavy weekend: our latest preprint (c/o Mattiroli + Ramani labs) is up!
www.biorxiv.org/content/10.1...
A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)
www.biorxiv.org/content/10.1...
A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)
The eukaryotic replisome intrinsically generates asymmetric daughter chromatin fibers
DNA replication is molecularly asymmetric, due to distinct mechanisms for lagging and leading strand DNA synthesis. Whether chromatin assembly on newly replicated strands is also asymmetric remains un...
www.biorxiv.org
September 20, 2025 at 4:10 PM
Some (+)ve news to lighten another heavy weekend: our latest preprint (c/o Mattiroli + Ramani labs) is up!
www.biorxiv.org/content/10.1...
A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)
www.biorxiv.org/content/10.1...
A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)