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Metabolic Informatics Engineering Lab
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A lab that optimizes microbial metabolism through computation and experiments.
AboutAbout the lab
Driving innovation in bioengineering with both wet and dry approaches
The Metabolic Informatics Engineering Lab studies methods for improving cells into an optimal state for the production of substances by microorganisms.
Focusing on metabolic flux, the flow of cellular metabolism, the lab aims to design metabolic pathways that can produce target substances at high yield.
The lab combines computational metabolic design with metabolic flux analysis using stable isotope 13C-labeled compounds.
On the lab's website, it is introduced under the name "Shimizu Lab."
Key terms
- Metabolic flux
- The flow of metabolic reactions inside a cell. Metabolism is organized around this flow to consider how to optimize it.
- Stable isotope 13C labeling
- Cells take up compounds labeled with the stable isotope 13C, and mass spectrometry is used to determine which metabolites the label ends up in.
- Genome-scale metabolic model
- A model that represents the metabolic reactions of an entire cell. It is used to design metabolic states on a computer.
NewsLab news
A student won the Bio Division Excellent Poster Award at the 57th Autumn Meeting of the Society of Chemical Engineers, Japan
Research by Project Assistant Professor Imada was published in Bioscience, Biotechnology, and Biochemistry
Research by an alumnus was published in ACS Chemical Biology
A student received the Graduate School of Information Science Award
Research by an alumnus was published in Metabolic Engineering Communications
ResearchResearch themes
The lab views cellular metabolism as a multistep series of reactions, and aims to design metabolic pathways that can produce target substances at high yield and to determine the metabolic fluxes actually occurring inside cells. It evaluates the cells of various industrial microorganisms through metabolic design using genome-scale metabolic models and through analysis using stable isotope 13C-labeled compounds.
View More ↗MembersFaculty
The members of the Metabolic Informatics Engineering Lab consist of faculty, a project assistant professor, project researchers, PhD, master's, and undergraduate students, technical assistants, administrative assistants, and collaborators.As of 2026
- ProfessorHiroshi Shimizu
- Associate ProfessorYoshihiro Toya
- Assistant ProfessorTeppei Niide
- Project Assistant ProfessorTatsumi Imada
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Report an errorAbout the images
The top and research theme images are illustrative and were not taken at the lab. They are cropped from Wikimedia Commons images. Cropped CC BY-SA images are provided under the same CC BY-SA license as the original (version shown on each line).
- Top image: “Erlenmeyer TSB fermentation replicates” Luis Fernando Flores LAB / CC BY-SA 4.0 (cropped)
- Related lab (Bio-Information Measurement Lab): “Chromatography apparatus” Giac83 / CC BY-SA 2.5 (cropped)
- Related lab (Human Information Engineering Lab): “Virtuality 1000CS VR Headset” RetroEditor / CC BY 4.0 (cropped)
- Related lab (Applied Analysis Lab): “Lorenz yz x 0” German A. Chernykh & Irina A. Chernykh / CC BY-SA 4.0 (cropped)
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