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Gennady Gorin @goringennady.bsky.social · 12h

Amazing! None of the answers are even in the same ballpark as the physics usage (neutral net+symbolic regression) or my usage (neutral net parametrizing some physical model)

Reposted by Gennady Gorin

The Ass is the father of the legs @internethippo.bsky.social · 5d

"We're going to create superintelligence" How about making outlook search work first. How about that

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Gennady Gorin @goringennady.bsky.social · 7d

The optimistic point of view, then 🙃

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Gennady Gorin @goringennady.bsky.social · 7d

Very excited to see it! You may also be interested in the preprint v2: lots of detailed reanalysis of the unfortunately few nonhuman heart datasets.

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Gennady Gorin @goringennady.bsky.social · 7d

It is also—again and again, in various contexts—associated with heart disease.

Gennady Gorin @goringennady.bsky.social · 7d

Any updates on this? I have been doing a great deal of pseudoalignment across species, and it would be great to have some aligned data to draw on.

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Gennady Gorin @goringennady.bsky.social · 7d

A new revision is out! Lots of interesting cross-species data analysis, all of it pointing to the same conclusion: male XIST expression in the heart really is only detectable in humans!

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Gennady Gorin @goringennady.bsky.social · 9d

ASL: like BSL, but a nested acronym, conflicts with two other acronyms in common use, and carries no regulatory meaning. Terrific

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Reposted by Gennady Gorin

Waggoner Lab @labwaggoner.bsky.social · 11d

scFLUENT-seq reveals that individual cells—lymphocytes to stem cells—transcribe only ∼0.02%–3.1% of the genome, versus >80% in bulk, revealing limited genome engagement and profound cell-type and cell-to-cell heterogeneity @cellcellpress.bsky.social
www.cell.com/cell/fulltex...

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Gennady Gorin @goringennady.bsky.social · 11d

I have never seen them, and I will not seek them out, but perhaps there are! It is always possible to find a toxic niche community. But what they're not doing is setting up thousands of ChatGPT wrappers to comment on the post of every scientist with >1000 followers, and that's enough data for me.

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Gennady Gorin @goringennady.bsky.social · 11d

That how you feel about the platforms is your prerogative, but they are not the same, and the bot saturation in particular is not even in the same ballpark.
The original post got a bot response, and it was not here.

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Gennady Gorin @goringennady.bsky.social · 11d

Best I can tell, it is!

Gennady Gorin @goringennady.bsky.social · 12d

We just put out v2 of this preprint! Biology has some weird exceptions
www.biorxiv.org/content/10.1...

Male XIST expression in cardiac pseudo-glia does not induce X chromosome inactivation

XIST is a long non-coding RNA that mediates the process of X chromosome inactivation in females, and has not been previously observed in males outside of developmental, pathological, and ectopic conte...

www.biorxiv.org

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Gennady Gorin @goringennady.bsky.social · 12d

And yet. x.com/boolman37230...

x.com

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Gennady Gorin @goringennady.bsky.social · 13d

This is, on one hand, a somewhat cynical joke, and on the other the recognition that the tech industry runs on the move fast where it's unwarranted/break things in a user-hostile way/fix them never strategy even in their core commercial products. What's it like for noncore proofs of concept I wonder

Gennady Gorin @goringennady.bsky.social · 13d

the lengths Apple will go to to avoid making consumer software are amazing. hope we get some good scientific software out of it

Jase Gehring @skyjase.bsky.social · 13d

a performant model without protein specific architecture.

One comment: they trained on 9M structures, >95% generated by deep learning models that DO use protein specific architecture.

I’d call this knowledge distillation and challenge the core claim of the paper. Will read more deeply

Stephen Turner @stephenturner.us · 14d

Apple is entering the protein folding arena.
SimpleFold: Folding Proteins is Simpler than You Think arxiv.org/abs/2509.18480 🧬🖥️🧪 github.com/apple/ml-sim...

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Gennady Gorin @goringennady.bsky.social · 13d

sperm is stored in the female visceral fat, of course, everybody knows this

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Gennady Gorin @goringennady.bsky.social · 14d

gaming is when you press circle

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Reposted by Gennady Gorin

Jase Gehring @skyjase.bsky.social · 17d

don't release preprints without a Methods section
don't release preprints with a Supplementary Materials section
don't release preprints without data
don't release preprints without code

use preprint servers to share your science, not advertisements

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Reposted by Gennady Gorin

Slavov Laboratory @slavovlab.bsky.social · 18d

We quantified mRNA abundance, translation, protein abundance, protein degradation and cell growth across thousands of single cells from a mammalian tissue.

The results revealed 𝐜𝐨𝐦𝐩𝐥𝐞𝐱 regulation & 𝐬𝐢𝐦𝐩𝐥𝐞 organizing principles:

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

🧵

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Gennady Gorin @goringennady.bsky.social · 18d

Don Quixote: the Spanish Ogniem i mieczem

Reposted by Gennady Gorin

Reese Richardson @reeserichardson.bsky.social · 19d

There's been a recent explosion in shoddy, cookie-cutter analysis of large, widely-available public health datasets (think NHANES, the UK Biobank, FAERS, etc). Matt Spick and I offer some advice in our new Viewpoint in European Science Editing:

doi.org/10.3897/ese....

More reading material below!

Figure 1 of the commentary with caption:

igure 1. Artificial intelligence–assisted workflows enable rapid acceleration in publications.
(A) Illustrative workflow schematic. (B) PubMed search using the following search string:
“nhanes[tiab] OR uk biobank[tiab] OR finngen[tiab] OR global burden of disease study[tiab] OR
faers[tiab].” The estimate for the publication count in the remainder of 2025 is derived by
applying the same ratio of H2 2024 / H1 2024 publication count to the H1 2025 publication count
and assumes a similar seasonal pattern of higher publication rates in the first 6 months of the year.

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Gennady Gorin @goringennady.bsky.social · 19d

no

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Gennady Gorin @goringennady.bsky.social · 19d

It's a limitation of communication; people come at the question with different priorities and values, and see that these cases do not exist in isolation. But insisting that people must be both pedantic and unreasonably charitable to appear honest and be taken seriously is something else entirely

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Reposted by Gennady Gorin

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 26d

Fundamental Limits of Inferring Dynamical Gene Regulatory Models from Single-Cell Data https://www.biorxiv.org/content/10.1101/2025.09.12.674509v1

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