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Bio-Information Measurement Lab [Graduate School of Information Science and Technology]
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The lab measures, interprets, and simulates the metabolism of cells.
AboutAbout the lab
Exploring the operating principles of metabolism through biology, informatics, and measurement
The Bio-Information Measurement Lab conducts research aimed at clarifying why biological metabolism works so well and applying that knowledge to biotechnology and information technology.
The lab develops measurement technologies to determine how metabolism operates, and finds simple operating principles in complex measurement data.
It aims to apply the principles it discovers to biomanufacturing and new drug discovery.
Key terms
- Central metabolism
- The core metabolism of life, which breaks down sugars and other substances to extract energy and also produces materials for building new cells
- Metabolic flux
- The flow of compounds through a metabolic pathway
- Warburg effect
- Cancer-specific metabolism in which cancer cells convert most of the glucose they take up into lactate and excrete it
- Ensemble modeling
- A method of building multiple mathematical models with similar predictive power and regarding the predictions they share as reliable
ResearchResearch themes
Living organisms break down sugars and other substances through central metabolism in their cells to extract energy, and also produce the materials needed to build new cells. The lab develops technologies to quantify the behavior of this central metabolism, technologies to find key points in data, and technologies to reproduce metabolism inside a computer.
*Illustrative imageDeveloping Technologies to Measure Metabolism
The lab develops technologies to measure metabolite concentrations, the expression levels of enzyme proteins, and metabolic flux, which is the flow of metabolism. Concentrations are measured with mass spectrometers, enzyme amounts with quantitative proteomics by LC-MS, and flux with 13C metabolic flux analysis.
*Illustrative imageTechnologies to Decipher Operating Principles from Data
The lab develops data interpretation technologies that find clues in data and build hypotheses, based on statistical analysis and existing knowledge. In mevalonate-producing E. coli, it identified effective points for metabolic modification from changes in Gibbs free energy.
*Illustrative imageData-Based Metabolic Simulation
A mathematical metabolic model, which combines many equations, faces the obstacle that most of its parameters are unknown. The lab therefore uses its own measurement technologies to develop data-driven metabolic simulation techniques. Together with Prof. James Liao of UCLA and colleagues, it also developed an ensemble modeling method.
*Illustrative imageElucidating Cancer-Specific Metabolism
Cancer cells convert most of the glucose they take up into lactate and excrete it. The lab aims to re-examine the significance of this Warburg effect, known as cancer-specific metabolism, and it is expected to lead to the discovery of new drug targets.
MembersFaculty
The Bio-Information Measurement Lab consists of faculty members, secretaries, dispatched staff, and doctoral, master's, and undergraduate students.
- ProfessorFumio Matsuda
- Associate ProfessorNobuyuki Okahashi
- Assistant ProfessorTakeo Taniguchi
VoicesStudent voices
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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: “Thermo - Finnigan LCQ Mass Spectrometer ( )” Kitmondo Marketplace / CC BY 2.0 (cropped)
- Developing Technologies to Measure Metabolism: “Biological Mass Spectrometry ( )” Oak Ridge National Laboratory / CC BY 2.0 (cropped)
- Technologies to Decipher Operating Principles from Data: “Network graph visualization showing bibliography and keywords” Ecpp / CC BY-SA 4.0 (cropped)
- Data-Based Metabolic Simulation: “MetabolicNetworkBLCK” J3D3 / CC BY-SA 4.0 (cropped)
- Elucidating Cancer-Specific Metabolism: “Glucose metabolism in triple-negative breast cancer cells (Homo sapiens)” Andrawaag / CC BY-SA 4.0 (cropped)
- Related lab (代謝情報工学講座［情報科学研究科］
): “Yeast culture plate” BMC bildes / CC BY-SA 3.0 (cropped) - Related lab (細胞工学領域): “Plant tissue culture sample” Syed Sajidul Islam / CC BY-SA 4.0 (cropped)
- Related lab (分子微生物学領域
[生物工学国際交流センター] ): “Hot spring in Yellowstone” Jon Sullivan / Public domain (cropped) - Related lab (高分子バイオテクノロジー領域): “TOF mass spectrometer June2007” Mwillett4000 / Public domain (cropped)
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