A deep generative model of 3D single-cell organization.

Autor: Rory M Donovan-Maiye, Jackson M Brown, Caleb K Chan, Liya Ding, Calysta Yan, Nathalie Gaudreault, Julie A Theriot, Mary M Maleckar, Theo A Knijnenburg, Gregory R Johnson

Publikováno v: PLoS Computational Biology, Vol 18, Iss 1, p e1009155 (2022)

We introduce a framework for end-to-end integrative modeling of 3D single-cell multi-channel fluorescent image data of diverse subcellular structures. We employ stacked conditional β-variational autoencoders to first learn a latent representation of

Externí odkaz: https://doaj.org/article/01a428aaa62048a293fee6809efd8248

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

Advance Care Planning and Treatment Intensity Before Death Among Black, Hispanic, and White Patients Hospitalized with COVID-19

Autor: Amber E. Barnato, Gregory R. Johnson, John D. Birkmeyer, Jonathan S. Skinner, Allistair James O’Malley, Nancy J. O. Birkmeyer

Publikováno v: Journal of general internal medicine. 37(8)

Black and Hispanic people are more likely to contract COVID-19, require hospitalization, and die than White people due to differences in exposures, comorbidity risk, and healthcare access.To examine the association of race and ethnicity with treatmen

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::13dfa41aeaecfe4a24b8cf0e2c03607a
https://pubmed.ncbi.nlm.nih.gov/35412179

A deep generative model of 3D single-cell organization

Autor: Nathalie Gaudreault, Liya Ding, Jackson M. Brown, Caleb K. Chan, Calysta Yan, Mary M. Maleckar, Rory Donovan-Maiye, Gregory R. Johnson, Theo A. Knijnenburg, Julie A. Theriot

1AbstractWe introduce a framework for end-to-end integrative modeling of 3D single-cell multi-channel fluorescent image data of diverse subcellular structures. We employ stacked conditional β-variational autoencoders to first learn a latent represen

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::a086f0c69572d9370eadb452911bc2ec
https://doi.org/10.1101/2021.06.09.447725

Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes

Autor: Tanya Grancharova, Nathalie Gaudreault, Rebecca J. Zaunbrecher, M. Filip Sluzewski, Ruwanthi N. Gunawardane, Melissa C. Hendershott, Matheus P. Viana, HyeonWoo Lee, Jamie L. Gehring, Calysta Yan, Jianxu Chen, Rory Donovan-Maiye, Gregory R. Johnson, Jackson M. Brown, Kaytlyn A. Gerbin, Aditya Nath, Kimberly R. Cordes Metzler, Angelique M. Nelson, Susanne M. Rafelski, Julie A. Theriot, Stephanie Q. Dinh, Helen G. Anderson, Theo A. Knijnenburg

Publikováno v: Cell systems. 12(6)

Although some cell types may be defined anatomically or by physiological function, a rigorous definition of cell state remains elusive. Here, we develop a quantitative, imaging-based platform for the systematic and automated classification of subcell

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::38acfcd6fa500b96ee66a4ee9154b335
https://pubmed.ncbi.nlm.nih.gov/34043964