Lightnews — Scholar-powered news

Reposted by Arjun Raj

Edda Schulz @eddaschulz.bsky.social · 2d

⚠️ 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

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

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Arjun Raj @arjunraj.bsky.social · 2d

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.

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Reposted by Arjun Raj

Prachee Avasthi @pracheeac.bsky.social · 4d

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.

Scholarly Communication Is a Research Problem.

pracheeac.substack.com

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Arjun Raj @arjunraj.bsky.social · 8d

The bitter lesson of genomics: If you find yourself optimizing a targeted method, don't—betting against increased throughput is generally a bad idea.

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Reposted by Arjun Raj

Molly Schumer @mollyschumer.bsky.social · 9d

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!

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Reposted by Arjun Raj

Oded Rechavi @odedrechavi.bsky.social · 11d

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

Oded Rechavi @odedrechavi.bsky.social · 12d

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!

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Arjun Raj @arjunraj.bsky.social · 11d

Various delays, hopefully out soon!

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Arjun Raj @arjunraj.bsky.social · 11d

Very cool!

Arjun Raj @arjunraj.bsky.social · 11d

🤩

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Reposted by Arjun Raj

Carolyn King @immunologyking.bsky.social · 12d

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

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Arjun Raj @arjunraj.bsky.social · 11d

Of all the different metrics of scientific success, a kind word from a colleague you respect often means the most.

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Arjun Raj @arjunraj.bsky.social · 12d

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...

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 ...

www.biorxiv.org

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Reposted by Arjun Raj

Oded Rechavi @odedrechavi.bsky.social · 12d

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!

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Reposted by Arjun Raj

Anshul Kundaje @anshulkundaje.bsky.social · 16d

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/

Yun S. Song @yun-s-song.bsky.social · 16d

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)

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Vijay Ramani @vram142.bsky.social · 18d

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)

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

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Reposted by Arjun Raj

Nikolai Slavov @slavov-n.bsky.social · 16d

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...

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Arjun Raj @arjunraj.bsky.social · 18d

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.

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Reposted by Arjun Raj

Oded Rechavi @odedrechavi.bsky.social · 19d

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

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Arjun Raj @arjunraj.bsky.social · 23d

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

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Wolfgang Huber @wkhuber.bsky.social · 23d

My work email is a DDoS attack.

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Reposted by Arjun Raj

Quanta Magazine @quantamagazine.bsky.social · Jun 1

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...

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

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Arjun Raj @arjunraj.bsky.social · Sep 6

Ummm no comment :)

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Arjun Raj @arjunraj.bsky.social · Sep 6

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.

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Arjun Raj @arjunraj.bsky.social · Sep 6

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.

Michael Baym @baym.lol · Sep 1

Every few months the "good lab hands" thing comes up and it misses a key point: you can learn to have good hands. Training matters.

Good hands aren't some magic gift from the PCR gods, you have to develop them through directed repetitive practice, like any other skill

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Arjun Raj @arjunraj.bsky.social · Sep 6

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

Olivia Guest · Ολίβια Γκεστ @olivia.science · Sep 6

Finally! 🤩 Our position piece: Against the Uncritical Adoption of 'AI' Technologies in Academia:
doi.org/10.5281/zeno...

We unpick the tech industry’s marketing, hype, & harm; and we argue for safeguarding higher education, critical
thinking, expertise, academic freedom, & scientific integrity.
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Abstract: Under the banner of progress, products have been uncritically adopted or
even imposed on users — in past centuries with tobacco and combustion engines, and in
the 21st with social media. For these collective blunders, we now regret our involvement or
apathy as scientists, and society struggles to put the genie back in the bottle. Currently, we
are similarly entangled with artificial intelligence (AI) technology. For example, software updates are rolled out seamlessly and non-consensually, Microsoft Office is bundled with chatbots, and we, our students, and our employers have had no say, as it is not
considered a valid position to reject AI technologies in our teaching and research. This
is why in June 2025, we co-authored an Open Letter calling on our employers to reverse
and rethink their stance on uncritically adopting AI technologies. In this position piece,
we expound on why universities must take their role seriously toa) counter the technology
industry’s marketing, hype, and harm; and to b) safeguard higher education, critical
thinking, expertise, academic freedom, and scientific integrity. We include pointers to
relevant work to further inform our colleagues.

Figure 1. A cartoon set theoretic view on various terms (see Table 1) used when discussing the superset AI
(black outline, hatched background): LLMs are in orange; ANNs are in magenta; generative models are
in blue; and finally, chatbots are in green. Where these intersect, the colours reflect that, e.g. generative adversarial network (GAN) and Boltzmann machine (BM) models are in the purple subset because they are
both generative and ANNs. In the case of proprietary closed source models, e.g. OpenAI’s ChatGPT and
Apple’s Siri, we cannot verify their implementation and so academics can only make educated guesses (cf.
Dingemanse 2025). Undefined terms used above: BERT (Devlin et al. 2019); AlexNet (Krizhevsky et al.
2017); A.L.I.C.E. (Wallace 2009); ELIZA (Weizenbaum 1966); Jabberwacky (Twist 2003); linear discriminant analysis (LDA); quadratic discriminant analysis (QDA).

Table 1. Below some of the typical terminological disarray is untangled. Importantly, none of these terms
are orthogonal nor do they exclusively pick out the types of products we may wish to critique or proscribe.

Protecting the Ecosystem of Human Knowledge: Five Principles

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