About the Lab
The Ishihara Lab is part of the Department of Computational & Systems Biology at the University of Pittsburgh. We study synthetic morphogenesis: how living tissues self-organize into complex three-dimensional forms.
We build and analyze organoids (miniature tissue models grown from stem cells) as experimental systems to probe the physical and molecular principles that govern morphogenesis. By engineering organoids with defined composition and geometry, we can ask how form, fate, and function emerge from the collective behavior of cells.
Our Approach
Organoid Biology
We engineer cardiac and brain organoids from human and mouse stem cells, controlling matrix composition, geometry, and signaling inputs to dissect morphogenetic mechanisms.
Quantitative Imaging
Light-sheet and confocal microscopy provide 3D snapshots and live time-lapses of morphogenesis. We develop analysis pipelines to extract quantitative shape and motion descriptors.
Physical Theory
We build minimal physical models (continuum mechanics, reaction-diffusion, and active matter) to identify the organizing principles behind the patterns we observe.
Computation
We develop interpretable machine learning tools for biological imaging and physiological recordings, grounded in physical intuition and designed to be open and shareable.
Lab Values
- Curiosity-driven science
- We ask fundamental questions about how living tissues acquire their shape. Our projects are motivated by biological puzzles, not just technical opportunity.
- Quantitative rigor
- Every experiment is designed to yield numbers. We combine imaging, physical theory, and data analysis to move beyond qualitative description.
- Collaborative culture
- We work across disciplines and institutions. Biologists, physicists, and computational scientists all have a home in the lab.
- Open and reproducible
- We share code, data, and protocols. Building on each other's work, inside and outside the lab, makes science better.
Teaching & Outreach
Graduate Course
Cellular, Systems, and Molecular Modeling
Keisuke teaches a graduate-level course covering quantitative and computational approaches in modern biology, including dynamical systems, image analysis, and data-driven modeling. The course is designed for students from biology, physics, and computational backgrounds.
High School Outreach
UPMC Hillman Cancer Center Academy: Computational Biology Site
Keisuke co-directs the Computational Biology site of the UPMC Hillman Academy, a competitive summer research program that brings exceptional high school students to the University of Pittsburgh for immersive research experiences. Students in the computational biology track gain hands-on exposure to quantitative approaches in biomedical research.
Affiliations
- Department of Computational & Systems Biology, University of Pittsburgh
- UPMC Hillman Cancer Center