Generative Modeling with Conditional Autoencoders: Building an Integrated Cell

Authors: Johnson, Gregory R., Donovan-Maiye, Rory M., Maleckar, Mary M.

Subject Terms: Statistics - Machine Learning, Quantitative Biology - Cell Behavior, Quantitative Biology - Subcellular Processes

Access URL: http://arxiv.org/abs/1705.00092

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

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

Source: In Cell Systems 16 June 2021 12(6):670-687

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

Authors: Donovan-Maiye, Rory M.¹ (AUTHOR), Brown, Jackson M.¹ (AUTHOR), Chan, Caleb K.¹ (AUTHOR), Ding, Liya¹ (AUTHOR), Yan, Calysta¹ (AUTHOR), Gaudreault, Nathalie¹ (AUTHOR), Theriot, Julie A.^1,2 (AUTHOR), Maleckar, Mary M.¹ (AUTHOR), Knijnenburg, Theo A.¹ (AUTHOR) theo.knijnenburg@alleninstitute.org, Johnson, Gregory R.¹ (AUTHOR)

Source: PLoS Computational Biology. 1/18/2022, Vol. 18 Issue 1, p1-24. 24p. 1 Color Photograph, 1 Diagram, 4 Charts, 4 Graphs.

Subject Terms: *CELL morphology, *CELL anatomy, *CELL imaging, *NUCLEAR shapes, *NUCLEAR models

A comprehensive analysis of gene expression changes in a high replicate and open-source dataset of differentiating hiPSC-derived cardiomyocytes.

Authors: Grancharova, Tanya, Gerbin, Kaytlyn A., Rosenberg, Alexander B., Roco, Charles M., Arakaki, Joy E., DeLizo, Colette M., Dinh, Stephanie Q., Donovan-Maiye, Rory M., Hirano, Matthew, Nelson, Angelique M., Tang, Joyce, Theriot, Julie A., Yan, Calysta, Menon, Vilas, Palecek, Sean P., Seelig, Georg, Gunawardane, Ruwanthi N.

Source: Scientific Reports; 8/4/2021, Vol. 11 Issue 1, p1-21, 21p

Subject Terms: RNA sequencing, HEART cells, CELL differentiation, GENE expression, PLURIPOTENT stem cells

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