How can we hope to understand organismal development when it is controlled by huge, complex networks of interacting genes?
One option is to move away from molecular details and focus on learning representations and rules.
Check out the new perspective from me and @jamesbriscoe.bsky.social
How can we hope to understand organismal development when it is controlled by huge, complex networks of interacting genes?
One option is to move away from molecular details and focus on learning representations and rules.
Check out the new perspective from me and @jamesbriscoe.bsky.social
Genomes? Pah, who needs them... let's delete them!
actually courtesy of @arjunraj.bsky.social!
a cow painted with stripes to look like a zebra
Heroic winner of the IgNobel prize for biology: paint zebra stripes on cows to stop them getting bitten
journals.plos.org/plosone/arti...
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sjablonen 11
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The failures of language in biology -- and the most apt description of biology I know:
it is difficult to find a black cat in a dark room, especially if there is no cat.
www.sciencedirect.com/science/arti...
'It’s not the destination, it’s the journey.'
As true for stem cells as for humans!
I said some things about my PhD, and now they've appeared here. How fun!
ALT text: A UMAP representation of a single cell RNAseq dataset from the Drosophila ventral nerve cord as well as images of the Drosophila nerve cord connectome and different stages of fly development.
Neuronal diversity is written in transcriptional codes 🧬. But what is the logic of these codes that define cell types and wiring patterns?
To find out we built a #scRNAseq developmental atlas of the Drosophila nerve cord and linked it to the #connectome 🪰🧠
#preprint thread ⬇️1/8
Excited to share our paper on deciphering the design & control principles of tissue scaling w/ Luisa Arispe! Amazing work by co-first authors Danielle Pi and Jonas Braun. We show *differentiated* endothelial cell proliferate in waves with ultrafast cell cycle time of ~5h
www.cell.com/cell-systems...
Just published: The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube
A global temporal chromatin program, operating across the CNS, directs binding of specific spatial TFs & hence when/where neurons & glia are born
authors.elsevier.com/sd/article/S...
No new genes needed to fly - just rewire what you have! 🦇🧬
Great new paper from the labs of @fany-real.bsky.social @stemundi.bsky.social @dariloops.bsky.social
doi.org/10.1038/s415...
#EvoDevo #SingleCell #BatWings
Patterning of cell identities in the posterior E8.5 mouse embryo. Co-expression of mesoderm marker TBXT (blue) and neural marker SOX2 (green) identifies cells in the neuromesodermal (NMP) progenitor region at the intersection of their respective gene expression gradients. TBX6 (red) marks paraxial mesoderm and also marks sporadic mesoderm-committed cells emerging within the NMP region. LAMINB1 (white) marks the nuclear envelope of all cells. Credit: Matthew French.
Measuring properties of individual cells in relation to their neighbors in 3D tissues is challenging. @cellysally.bsky.social &co develop a computational toolkit to facilitate this, analyzing developmental patterning in mouse, chick & #Drosophila #embryo @plosbiology.org 🧪 plos.io/4lQMeNu
genomebiology.biomedcentral.com/articles/10....
Quite an indictment of some of the current single cell "virtual cell" foundation models. Even for the relatively mundane applications, cell labeling, batch correction etc, they are poor compared to much simpler & cheaper methods.
Our latest "Dynamic Landscape Analysis of Cell Fate Decisions: Predictive Models of Neural Development From Single-Cell Data"
A rigorous mathematical foundation for Waddington's landscape to study cell fate decision making
Applied to ventral neural tube development
www.biorxiv.org/content/10.1...
Congratulations to Tiago Rito @ritolab.bsky.social starting his own research group at Hong Kong U
