Calysta Yan
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View article: Integrated intracellular organization and its variations in human iPS cells
Integrated intracellular organization and its variations in human iPS cells Open
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 determine 1,2 . H…
View article: A deep generative model of 3D single-cell organization
A deep generative model of 3D single-cell organization Open
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 repres…
View article: A comprehensive analysis of gene expression changes in a high replicate and open-source dataset of differentiating hiPSC-derived cardiomyocytes
A comprehensive analysis of gene expression changes in a high replicate and open-source dataset of differentiating hiPSC-derived cardiomyocytes Open
We performed a comprehensive analysis of the transcriptional changes within and across cell populations during human induced pluripotent stem cell (hiPSC) differentiation to cardiomyocytes. Using the single cell RNA-seq combinatorial barco…
View article: Automated hiPSC culture and sample preparation for 3D live cell microscopy
Automated hiPSC culture and sample preparation for 3D live cell microscopy Open
Our goal is to identify and understand cellular behaviors using 3D live imaging of cell organization. To do this, we image human inducible pluripotent stem cell (hiPSC) lines expressing fluorescently tagged protein representing specific ce…
View article: Cell states beyond transcriptomics: integrating structural organization and gene expression in hiPSC-derived cardiomyocytes
Cell states beyond transcriptomics: integrating structural organization and gene expression in hiPSC-derived cardiomyocytes Open
Summary We present a quantitative co-analysis of RNA abundance and sarcomere organization in single cells and an integrated framework to predict subcellular organization states from gene expression. We used human induced pluripotent stem c…