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Reposted by David Angeles

Harold Pimentel @hjp.bsky.social · 9d

Super excited to get this out. This collab started a few years ago and is the first paper from it. Here, with experimental and computational approaches we:

1. establish that cell villages can be just as accurate (one might argue more accurate!) than arrayed-based designs

bsky.app/profile/bior...

bioRxiv Genetics @biorxiv-genetic.bsky.social · 9d

Cell villages and Dirichlet modeling map human cell fitness genetics https://www.biorxiv.org/content/10.1101/2025.09.26.678880v1

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Reposted by David Angeles

Matthew Hodson @matthewhodson.bsky.social · Aug 13

27 years ago, two years after the introduction of effective HIV treatment, the Bay Area Reporter, San Francisco’s lesbian and gay community newspaper, ran ‘No Obits’ as its headline.
It was the first edition not to report an AIDS death in almost 15 years.

The Bay Area Reporter front page, 13 August 1998.
The headline ‘No obits’ is written in red above the lead story.

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Reposted by David Angeles

Buster Jiggs @kdxkawboy.bsky.social · Aug 1

🗃️
A history mystery solved: where do potatoes come from?

Nine million years ago, as the Andes were rising, a tomato cross pollinated a plant from the S. etuberosum lineage. Each plant contributed a gene, that together enabled underground stems to form tubers.

www.sciencenews.org/article/pota...

Potatoes have their roots in ancient tomatoes

Knowing potatoes’ origin story could help future-proof the crucial crop against climate threats.

www.sciencenews.org

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David Angeles @davidangeles.bsky.social · Jul 15

huh.

Vinay Ayyappan @vayyappan.bsky.social · Jul 15

[0/8] Stoked to share our work with @arjunraj.bsky.social on tissue organization in the gastruloid. We use lineage tracing and spatial transcriptomics to show that diversity among stem cell clones promotes, rather than hinders, gastruloid development: www.biorxiv.org/content/10.1...

Gastruloid patterning reflects division of labor among biased stem cell clones

Embryonic development typically requires precise coordination among cells to achieve reproducible outcomes, leading to the assumption that cellular heterogeneity must be minimized or buffered against....

www.biorxiv.org

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David Angeles @davidangeles.bsky.social · Jun 23

What does it say if you see circles at the bottom and rectangles at the top? Asking for a friend...

Christie Wilcox @nerdychristie.bsky.social · Jun 23

What you see when you look at this image depends on the culture you grew up in. The question is: Are you shocked to hear that some people see rectangles or circles? That and more of the best from @science.org and science in this edition of #ScienceAdviser: www.science.org/content/arti...

These lines either make rectangles or circles to you. Anthony Norcia/Smith-Kettlewell Eye Research Institute

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Reposted by David Angeles

Anshul Kundaje @anshulkundaje.bsky.social · Jun 19

@saramostafavi.bsky.social (@Genentech) & I (@Stanford) r excited to announce co-advised postdoc positions for candidates with deep expertise in ML for bio (especially sequence to function models, causal perturbational models & single cell models). See details below. Pls RT 1/

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David Angeles @davidangeles.bsky.social · Jun 13

My biggest question: he showed a regeneration suppression program that is AP polarized. How does this work when injuries happen at the P end? What about lateral injuries? Is there a lateral program?

David Angeles @davidangeles.bsky.social · Jun 13

He shows that in planarian species that cannot regenerate, knocking down these “regeneration suppressors” restores their ability to regenerate. Awesome.

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David Angeles @davidangeles.bsky.social · Jun 13

Next he did a screen and found genes that mediate this suppression in the tail allegedly. claims they are working through regulating differentiated tissue turnover
rates.

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David Angeles @davidangeles.bsky.social · Jun 13

ok. what does this systemic response do and why is it needed?

He performed a smart series of cutting experiments to show an inhibitory program of regeneration is likely encoded in the posterior segment and is erk mediated.

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David Angeles @davidangeles.bsky.social · Jun 13

how does the injury passage through the body? in cases of Anterior wounds, it’s through Erk signaling using the longitudinal muscles. unclear how he showed that. I was pretty far away and the talk went by fast.

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David Angeles @davidangeles.bsky.social · Jun 13

planarians have stem cells known as neoblasts. really cool cells. bo is talking about planarians regeneration. however, only proximal neoblasts to the wound activate initially. later, the rest of the body activates a secondary response. I missed what "activation" entails.

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David Angeles @davidangeles.bsky.social · Jun 13

BO WANG, Stanford

Identifying and understanding regeneration suppressors

#isscr2025

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David Angeles @davidangeles.bsky.social · Jun 13

She said humans dont have a recognizable blastema. I am not sure why she is saying that… blastema to me means regenerative, proliferative tissue, i don't know if blastemas have a molecular/cellular definition (missing in humans).

Fascinating study of human regeneration.

#isscr2025

David Angeles @davidangeles.bsky.social · Jun 13

mass spec of exudate shows different proteins secreted at different stages

an important point is that is that re-epithelialization happens at the end of regeneration. in axolots, it happens earlier, after coagulation.

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David Angeles @davidangeles.bsky.social · Jun 13

coagulation is early and closes wound. next, fingers grow a granular tissue that looks raw, blistery. in proliferation we see more normal growth but the shape and texture is all wrong. the final stage reconfigures the finger to form the correct structures and final cell types.

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David Angeles @davidangeles.bsky.social · Jun 13

They identified four different stages of regrowth: coagulation, hypergranulation, proliferation and epithelialization.

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David Angeles @davidangeles.bsky.social · Jun 13

Note: she pointed out antibiotics are unnecessary because the regenerative program involves a lot of immune mobilization, highly antibacterial!

A leading hypothesis for the limits of regeneration has been immunity--this throws a bit of a wrench in that.

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David Angeles @davidangeles.bsky.social · Jun 13

wow. they set up a program to recruit injured folks to a trial where they collected exudate, encased the finger in a transparent casing, and where the injury was neither disinfected nor antibiotic treated. 2 sets of xrays for fingertips.

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David Angeles @davidangeles.bsky.social · Jun 13

salamanders can regrow limbs in 40 days. upon amputation, the wound closes quickly. then it forms an apical epithelial cap, under which is a proliferative tissue, this tissue forms the blastema, and the regeneration program is on.

Note: human fingertips can regenerate even in older folks.

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David Angeles @davidangeles.bsky.social · Jun 13

up next @tatianasg.bsky.social

shared and distinct mechanisms in salamander limb and human fingertip regeneration.

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David Angeles @davidangeles.bsky.social · Jun 13

now… do they proliferate in injury settings? EdU pulse! And yea! these cells proliferate post injury especially at 28D post injury. Beautiful work and ongoing.

David Angeles @davidangeles.bsky.social · Jun 13

They found some tiny muscle cells stain for pax7, right morphology for stem cells, developed tools to study them (found an ab). now isolating them they have proliferative and stem cell characteristics

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David Angeles @davidangeles.bsky.social · Jun 13

ALBERT ERNESTO ALMADA Quiescent preexisting cells in skeletal muscle heal tail injuries in anole lizards 🦎

after tail amputation you see a thing called a blastema forming, muscle only starts to reappear after ~28 days of growth though.

#isscr2025

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David Angeles @davidangeles.bsky.social · Jun 13

now can we reprogram human astrocytes into glial bridge cells? She says yes. Four factors reprogram astrocytes into bridge cells. She didn't disclose the factors. In vitro characterization looks like cells are behaving as expected. Preliminary in vivo looks good.