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Alex Grigas

@agrigas.bsky.social
33 followers 39 following 20 posts

Postdoc, Manning Group, Syracuse University Personal website: agrigas115.github.io

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Reposted by Alex Grigas
Rajendra Singh Negi @dr-rajendra-s-negi.bsky.social · 28/04/2026
(1/n) Does basal stem cell division orientation regulate skin stratification and tissue mechanics? And can tissue mechanics feed back to control division orientation? In our new preprint, we use a 3D vertex model to explore this @manningresearch.bsky.social @somiealo.bsky.social
biorxiv.org
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Alex Grigas @agrigas.bsky.social · 01/04/2026
How much information does it take to fold a protein? Not much, if you use the right information! We find that residue burial, a binary label of core vs surface, encodes a protein's fold highly efficiently and even improves ESM2's structure representation. 1/8 www.biorxiv.org/content/10.6...
biorxiv.org
Residue burial encodes a protein's fold
Protein structure is controlled by a high-dimensional energy landscape, which is a function of all of the atomic coordinates of the protein. Can this landscape be accurately described by a low-dimensional representation? We find that residue core identity, a binary N-dimensional encoding indicating whether each of the N amino acids in a protein is buried in the core or not, can predict the protein's backbone conformation more efficiently than all other representations that we tested. Core identity is 4 times more efficient than previous estimates of the bits per residue needed to encode a protein's native fold, 2 times more efficient than the Cα contact map, and 1.5 times more efficient than the machine-learned embeddings from FoldSeek's 3Di. Even when the folded structure is unavailable, predicting each residue's burial from sequence yields a more accurate estimate of fold quality than predicting pairwise contacts from the same sequence information. Thus, this work emphasizes that the problem of determining a protein's native fold can be re-framed as predicting each residue's core identity. ### Competing Interest Statement The authors have declared no competing interest. Chan Zuckerberg Initiative (United States), 2023-329572 NIH, T32GM145452
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Reposted by Alex Grigas
Manning Research Group @manningresearch.bsky.social · 10/02/2026
Excited to highlight a new preprint about mechanical contributions to tissue homeostasis, from the Manning group in collaboration with the amazing Carien Niessen and Sara Wickstrom @sarawickstrom.bsky.social labs, spearheaded by Dr. Somiealo Azote: www.biorxiv.org/content/10.6...
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Alex Grigas @agrigas.bsky.social · 12/12/2025
How do sparse mesenchymal cells, with unique stellate arms spanning large gaps between cells, maintain their network while still flowing during development? In our new preprint we describe the avian PSM as a fluid under tension and develop new theory to explain it: www.biorxiv.org/content/10.6...
biorxiv.org
Sparse mesenchymal cell networks as a fluid under tension
Sparse mesenchymal cellular networks are ubiquitous across animals, shaping both embryonic and adult structures through dynamic interactions with epithelia. Yet, the physical principles underlying the...
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Alex Grigas @agrigas.bsky.social · 03/04/2025
Our new paper relating protein folding and jamming is out in PRX Life! All protein cores are densely packed irrespective of overall fold, and we show this arises from a jamming transition where amino acids reach a critical, incompressible density. journals.aps.org/prxlife/abst...
journals.aps.org
Protein Folding as a Jamming Transition
Densely packed protein cores have the same interior packing density irrespective of overall fold, arising from a jamming transition where amino acids reach a critical, incompressible density, as expla...
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