Arjun Raj

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

Yes. The one thing I truly can’t understand is why nobody even wants to try something new, even just a little bit. Witness the fracas over the relatively modest innovations proposed by eLife. You are so right—our insistence on consensus has created a situation where all innovation is snuffed out.

Scholarly Communication Is a Research Problem. This Means You. Scholarly Communication Is a Research Problem.

New Blog Post:
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.

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!

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

Various delays, hopefully out soon!

Very cool!

🤩

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...

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.

AP-1 Mediates Cellular Adaptation and Memory Formation During Therapy Resistance Cellular responses to environmental stimuli are typically thought to be governed by genetically encoded programs. We demonstrate that melanoma cells can form and maintain cellular memories during the ...

Entirely self-serving :), but here's one of my favorite papers from the lab, which I think you might enjoy: www.biorxiv.org/content/10.1...

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!

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/

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...

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)

Some proteins are primarily regulated by one mechanism: RNA abundance, translation, or clearance.

The regulation of most proteins is dominated by different regulatory mechanisms across cell types.

Gratifyingly, this complex regulation defines simple rules ⬇️

www.biorxiv.org/content/10.1...

Math often defines and redefines things in counterintuitive ways that reveal some deeper truth. Biology tends to define things based on intuition—I wonder if it could benefit from more counterintuitive definitions.

Only single cell sequencing of the all these post docs will reveal why

The older I get, the less likely it is that my birthday is a prime number. Sad.

My work email is a DDoS attack.

Manu Prakash, a bioengineer at Stanford University, interacts with students in a lab

Manu Prakash practices “recreational biology,” a scientific approach that explores life in the same playful way that puzzles probe math. “Basic science is not at the service of something, but the groundwork that is our entire society’s foundation.”
www.quantamagazine.org/how-paradoxi...

Ummm no comment :)

In principle, point 1 is also learnable; in practice it is pretty hard for people to change in this regard if it’s not a natural inclination. Point 3… feels pretty intrinsic.

Very true. In my experience, there are three aspects of “good hands”. 1. Be low entropy: when in doubt, do things in an orderly manner. 2. Make good micro decisions: observe what matters and what doesn’t in any given protocol. 3. Make fewer errors. Of these, I think 2 is the most learnable.

I'm all for well-reasoned critiques, but this piece is not one of them. 👎

My great pleasure to introduce DR. Aoife O’Farrell!! An incredible scientist and human being. @aofarrell.bsky.social not only produced an amazing thesis by her own sheer brilliance and will, but also provided tireless service to Penn Bioengineering. Will be sorely missed!

Scientists Found Sticky Goo Inside a 2,500-Year-Old Jar. Seventy Years Later, They Finally Know What It Is By studying the mysterious substance's chemical makeup, scientists determined the pot was once full of honey

It's reassuring to know that letting your beverages dry out in your workplace coffee mugs and turning them into disgusting gobs of sticky goo is an ancient and time-honored practice.

www.smithsonianmag.com/smart-news/s...

Dynamics of Ribosomal RNA Transcription and Abundance in Normal and Leukemic Hematopoiesis Transcription of ribosomal RNAs (rRNAs) from rDNA repeats is the first step of ribosome biogenesis, accounting for a major portion of all cellular transcription. Often regarded as a housekeeping proce...

📣 New preprint 📣

We present a detailed map of nascent and mature ribosomal RNAs in mouse hematopoiesis and AML (including absolute rRNA molecule numbers), and outline principles of rDNA regulation.

Work by Eleanor Sams (@eleanor44.bsky.social) & Victoria Feist (@victoriafeist.bsky.social). (1/x)

No, Gemini, I don’t want to consider the hybrid option. (Oh wait that’s actually pretty good.)

Was about to buy 100 stamps from Costco until I realized that’s a multi-lifetime supply.