Applications and Challenges of Machine Learning to Enable Realistic Cellular Simulations

Autor: Ritvik Vasan, Meagan P. Rowan, Christopher T. Lee, Gregory R. Johnson, Padmini Rangamani, Michael Holst

Publikováno v: Frontiers in Physics, Vol 7 (2020)

In this perspective, we examine three key aspects of an end-to-end pipeline for realistic cellular simulations: reconstruction and segmentation of cellular structures; generation of cellular structures; and mesh generation, simulation, and data analy

Externí odkaz: https://doaj.org/article/d1064c7cb8614994af8e7032d5d6c53c

Integrated intracellular organization and its variations in human iPS cells

Autor: Matheus P. Viana, Jianxu Chen, Theo A. Knijnenburg, Ritvik Vasan, Calysta Yan, Joy E. Arakaki, Matte Bailey, Ben Berry, Antoine Borensztejn, Eva M. Brown, Sara Carlson, Julie A. Cass, Basudev Chaudhuri, Kimberly R. Cordes Metzler, Mackenzie E. Coston, Zach J. Crabtree, Steve Davidson, Colette M. DeLizo, Shailja Dhaka, Stephanie Q. Dinh, Thao P. Do, Justin Domingus, Rory M. Donovan-Maiye, Alexandra J. Ferrante, Tyler J. Foster, Christopher L. Frick, Griffin Fujioka, Margaret A. Fuqua, Jamie L. Gehring, Kaytlyn A. Gerbin, Tanya Grancharova, Benjamin W. Gregor, Lisa J. Harrylock, Amanda Haupt, Melissa C. Hendershott, Caroline Hookway, Alan R. Horwitz, H. Christopher Hughes, Eric J. Isaac, Gregory R. Johnson, Brian Kim, Andrew N. Leonard, Winnie W. Leung, Jordan J. Lucas, Susan A. Ludmann, Blair M. Lyons, Haseeb Malik, Ryan McGregor, Gabe E. Medrash, Sean L. Meharry, Kevin Mitcham, Irina A. Mueller, Timothy L. Murphy-Stevens, Aditya Nath, Angelique M. Nelson, Sandra A. Oluoch, Luana Paleologu, T. Alexander Popiel, Megan M. Riel-Mehan, Brock Roberts, Lisa M. Schaefbauer, Magdalena Schwarzl, Jamie Sherman, Sylvain Slaton, M. Filip Sluzewski, Jacqueline E. Smith, Youngmee Sul, Madison J. Swain-Bowden, W. Joyce Tang, Derek J. Thirstrup, Daniel M. Toloudis, Andrew P. Tucker, Veronica Valencia, Winfried Wiegraebe, Thushara Wijeratna, Ruian Yang, Rebecca J. Zaunbrecher, Ramon Lorenzo D. Labitigan, Adrian L. Sanborn, Graham T. Johnson, Ruwanthi N. Gunawardane, Nathalie Gaudreault, Julie A. Theriot, Susanne M. Rafelski

Publikováno v: Nature. 613:345-354

Understanding how a subset of expressed genes dictates cellular phenotype is a considerable challenge owing to the large numbers of molecules involved, their combinatorics and the plethora of cellular behaviours that they determine1,2. Here we reduce

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a684c7c821c5ce222400005b63258558
https://doi.org/10.1038/s41586-022-05563-7

Mechanistic insights into actin force generation during vesicle formation from cryo-electron tomography

Autor: Daniel Serwas, Matthew Akamatsu, Amir Moayed, Karthik Vegesna, Ritvik Vasan, Jennifer M. Hill, Johannes Schöneberg, Karen M. Davies, Padmini Rangamani, David G. Drubin

Publikováno v: Dev Cell
Developmental cell, vol 57, iss 9

Actin assembly provides force for a multitude of cellular processes. Compared to actin-assembly-based force production during cell migration, relatively little is understood about how actin assembly generates pulling forces for vesicle formation. Her

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::db072988ac9abee6a01d64227555008d
https://pubmed.ncbi.nlm.nih.gov/35504288

Principles of self-organization and load adaptation by the actin cytoskeleton during clathrin-mediated endocytosis

Autor: Michael Alexander Ferrin, Matthew Akamatsu, David G. Drubin, Padmini Rangamani, Ritvik Vasan, Daniel Serwas

Publikováno v: eLife, Vol 9 (2020)
eLife

Force generation by actin assembly shapes cellular membranes. An experimentally constrained multiscale model shows that a minimal branched actin network is sufficient to internalize endocytic pits against membrane tension. Around 200 activated Arp2/3

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b3c7494e0f1be1de285ededa0d36fa5e
https://elifesciences.org/articles/49840

DLITE: Dynamic Local Intercellular Tension Estimation

Autor: Mary M. Maleckar, Padmini Rangamani, C.D. Williams, Ritvik Vasan

Cell shapes and connectivities evolve over time as colony shapes change or embryos develop. Shapes of intercellular interfaces are closely coupled with the forces resulting from actomyosin interactions, membrane tension, or cell-cell adhesion. While

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::51fd04e0fdde922e50042861cbcaf66e
https://doi.org/10.1101/541144