• Ishihara lab at University of Pittsburgh


    Starting December 2022, I am joining the Department of Computational and Systems Biology at the University of Pittsburgh School of Medicine as Assistant Professor.


    The goal of my research is to develop new technologies (imaging, chemical, genetic, theory) to engineer the shape and function of brain and cardiac organoids.


    I will be hiring at all levels. Please get in touch if you are interested in building a new research group with me!


    This interview article interview article will give you a glimpse of my future group.

  • About

    I am interested in uncovering the guiding principles that help us engineer organs in the dish.


    As an ELBE postdoctoral fellow, I work among the groups of Jan Brugues (Max Planck Institute of Molecular Cell Biology and Genetics), Frank Jülicher (Max Planck Institute for the Physics of Complex Systems), and Elly Tanaka (Research Institute of Molecular Pathology) in Dresden and Vienna.


    I use stem cells to engineer organ-like structures, or organoids, and study how they change shape and become patterned. I combine quantitative 3D imaging with theoretical models to better understand and predict self-organization.


    Previously, I obtained a degree in Chemical Engineering with a certificate in Quantitative and Computational Biology at Princeton University. For my doctoral studies, I worked in Tim Mitchison's group at Harvard Medical School, studying how microtubule asters grow to fill millimeter-sized frog eggs.

  • Research

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    Topological morphogenesis of neuroepithelial organoids

    During development, sheets of cells bend, split, and fuse to generate the intricate shapes of various organs. While past studies have proposed how cell mechanics induce local shape changes, how the connectivity of epithelia emerges have not been addressed. By combining 3D tissue reconstitution, quantitative imaging, and theory, I discovered the that topological transitions, specifically the trans and cis modes of epithelial fusion govern the topology and shape of neuroepithelial organoids (Ishihara, Mukherjeet et al., bioRxiv 2021, and Nature Physics 2023, see Tweetorial).

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    Spontaneous emergence of a body axis

    How do the different body axes emerge from a fertilized egg to make an animal? Organ reconstitution is a powerful approach to study how a group of cells “pattern themselves” (Ishihara et al. 2018). Using stem cells, I grow neural tube organoids and study how the dorsal-ventral body axis is established in the absence external tissues (Meinhardt et al. 2014, Ishihara et al. 2017). By default, these organoids harbor dorsal identity, but treatment with retinoic acid initiates a self-organizing circuit that results in the localized expression of the ventral marker FoxA2. To study the dynamics of this spontaneous symmetry breaking at single cell resolution, I am applying light sheet microscopy on organoids made from FoxA2-Venus cells. In addition, I am investigating the molecular and physical basis of how FoxA2+ cells communicate with each other. (with Elena Gromberg and Teresa Krammer, Elly Tanaka group)

    How does the millimeter frog egg divide?

    Physical extremes in biology are interesting. The large cytoplasm of frog eggs is organized by radial arrays of microtubules called asters. Asters grow, interact and position themselves to help the frog egg find its division plane. As a graduate student in Tim Mitchison’s group, I asked how microtubule asters grow rapidly to one millimeter in diameter. By reconstituting asters in frog egg extract and imaging their growth, I found that new microtubules are nucleated at positions far from the centrosome (Ishihara et al., 2014). In collaboration with Kirill Korolev, I constructed a theoretical model of aster growth and tested its prediction by experiments (Ishihara et al., 2016). This led us to reconsider the textbook model and propose that large microtubule asters are a meshwork of short, interacting, self-amplifying microtubules.


    More recently, two additional projects have come out from my PhD research – one related to the theory of traveling waves (Ishihara et al., 2020 New J. of Phys.) and one report on the spatial regulation of microtubule depolymerization (Ishihara et al., 2021 Mol. Bio. Cell).

  • Selected Publications

    Please see PubMed or Google Scholar for a full list of publications.

    Topological morphogenesis of neuroepithelial organoids

    Ishihara, K.*, Mukherjee, A.*, Gromberg, E., Brugues, J., Tanaka, E., Jülicher, F. (2023) NaturePhysics, 10.1038/s41567-022-01822-6

    Spatial Variation of Microtubule Depolymerization in Large Asters

    Ishihara, K., Decker, F., Caldas, P., Pelletier, J., Loose, M., Brugues, J, Mitchison, T.J. (2021). Molecular Biology of the Cell. 10.1091/mbc.E20-11-0723

    Traveling fronts in self-replicating persistent random walks with multiple internal states

    Ishihara, K., George, AB., Cornelius, R., Kirill S. Korolev, KS, (2020). New J. Phys. 10.1088/1367-2630/aba219

    Reconstitution of a Patterned Neural Tube from Single Mouse Embryonic Stem Cells

    Ishihara, K., Ranga A., Lutolf, M.P., Tanaka, A.M., Meinhardt, A. (2017) Methods Mol. Biol. 10.1007/978-1-4939-6949-4_4

    Physical basis of large microtubule aster growth

    Ishihara, K., Korolev, K. S., Mitchison, T. J. (2016) eLife. 10.7554/eLife.19145.

    Science Sketches video abstract: https://youtu.be/jfjA2S-fE9U

  • Education

    Harvard University

    Doctor of Philosophy (Ph.D.) 2010 -2016

    Princeton University

    Bachelor of Science in Engineering (B.S.E.) 2006 -2010

  • Contact

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