Allen Institute for Cell Science publications

May 2023

Creating the gene-edited hiPSC lines in the Allen Cell collection 

Nelson, A et al (2021) in Maintenance of undifferentiated hiPSC cultures and differentiation to cardiomyocytes on glass surfaces

Roberts, B et al (2019) in Stem Cell Reports: Fluorescent Gene Tagging of Transcriptionally Silent Genes in hiPSCs 

Haupt, A et al (2018) in Jove: Endogenous Protein Tagging in Human Induced Pluripotent Stem Cells Using CRISPR/Cas9 

Roberts, B et al (2017) in Molecular Biology of the Cell: Systematic gene tagging using CRISPR/Cas9 in human stem cells to illuminate cell organization

Image Analysis and Automation tools created at the Allen Institute for Cell Science

Johnson, GT et al (2023) in Biophysical Journal: Building the next generation of virtual cells to understand cellular biology

Lyons, B et al (2022) in Nature Methods: The Simularium Viewer: an interactive online tool for sharing spatiotemporal biological models

Chen, J et al (2020) in bioRxiv: The Allen Cell and Structure Segmenter: a new open source toolkit for segmenting 3D intracellular structures in fluorescence microscopy images

Ounkomol, C et al (2018) in Nature Methods: Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy

Coston, ME et al (2020) in bioRxiv: Automated hiPSC culture and sample preparation for 3D live cell microscopy

Selected publications utilizing Allen Cell Collection gene-edited hiPSC lines (both Allen Institute and external authors)

Viana, MP et al (2023) in Nature: Integrated intracellular organization and its variations in human iPS cells

Wesley, CC and Levy DL (2023) in Molecular Biology of the Cell: Differentiation-dependent changes in Lamin B1 dynamics and Lamin B Receptor localization

Donovan-Maiye, R et al (2022) in PLoS Computational Biology: A deep generative model of 3D single-cell organization

Grancharova, T et al (2021) in Scientific Reports: A comprehensive analysis of gene expression changes in a high replicate and open-source dataset of differentiating hiPSC-derived cardiomyocytes

Hofbauer, P et al (2021) in Cell: Cardioids reveal self-organizing principles of human cardiogenesis

Gerbin, KA et al (2020) in BioRxiv: Cell states beyond transcriptomics: integrating structural organization and gene expression in hiPSC-derived cardiomyocytes

Chu, AJ et al (2020) in PLoS ONE: Co-culture of induced pluripotent stem cells with cardiomyocytes is sufficient to promote their differentiation into cardiomyocytes

Lee, J et al. (2020) in Nature: Hair-bearing human skin generated entirely from pluripotent stem cells

Hasselmann, J, et al. (2019) in NeuroResource: Development of a Chimeric Model to Study and Manipulate Human Microglia In Vivo.

Romero-Morales, AI, et al (2019) in bioRxiv: Spin∞ an improved miniaturized spinning bioreactor for the generation of human cerebral organoids from pluripotent stem cells

Viana, MP et al (2021) in bioRxiv: Robust integrated intracellular organization of the human iPS cell: where, how much, and how variable