Laboratories

Computational Biology

Assoc Prof. Sakumura
Associate Professor
Yuichi SAKUMURA
Assistant Professor
Katsuyuki KUNIDA

Outline of Research and Education

Our laboratory aims to extract the principle between biological molecules and target biological function and phenotype by computationally analyzing experimental data. We quantitatively associate molecules with function and phenotype to elucidate the underlying mechanism as a set of interactions among various physical quantities. Biological molecules and biochemical interactions actually play an important role in the regulation of biological function and phenotype. Many of functions and phenotypes are expressed in quantities different from molecular concentration, and some of them actively interacting with molecules. In other words, biological system functions as the interactions of multimodal quantities beyond the biochemistry! We aim to understand biological functions and phenotypes as aspects of the multimodal system. To achieve this goal, we collaborate with experimental researchers and analyze experimental data using mathematics and computer programs.

Major Research Topics

Systems biology on cell morphogenesis and migration (Fig.1)

  • System between morphogenesis and molecules regulating cytoskeleton formation and mechanical force
  • Cell taxis depending on substratum stiffness
  • Neuronal axon guidance depending on membrane potential

Systems biology on tissue formation (Fig. 2)

  • Cell communication and synchronization for development of vertebrates
  • Angiogenesis based on cell morphogenesis and migration

Estimation of essential components by machine learning and control theory(Fig. 3)

  • Molecular system identification using membrane potential time series and single-cell time series of nutrition response
  • Computer-assisted diagnosis using human breath gas
  • Estimation of essential kinases using inhibitor compounds
  • Frequency response analysis of single-cell response data with system identification method

References

  1. Inoue et al., Cell Struct Funct., 2018, in press
  2. Okimura et al., Phys. Rev. E., 97:052104, 2018.
  3. Yamada et al., Sci Rep., 8, 4559, 2018.
  4. Tsuchiya et al., PLoS Comput. Biol., 13, 2017.
  5. Sakumura et al., Sensors, 17, 2017
  6. Okimura et al., Cell Adhesion & Migration, 10, 331-341, 2016
  7. Katsuno et al., Cell Reports, 12, 1–13, 2015
  8. Fujimuro et al., Scientific Reports, 4, 6462, 2014
  9. Pham et al., Mol. Microbiol., 90, 584-596, 2013
  10. Toriyama et al., Curr. Biol., 23, 529–534, 2013
  11. Kunida et al., J Cell Sci, 125, 2381-2392, 2012
  12. Kim et al., Mol. Biol. Cell, 22, 3541-3549, 2011
Fig.1
Fig.1 Examples of system consisting of membrane potential and molecules, and system consisting of neurite length, mechanical force, and molecules. Signal transduction between various quantities are derived from experimental data. System can be reconstructed by integrating these signal transductions.
Fig.2
Fig.2 Tissue formation can be regarded as the system consisting of cell, cell communication, and tissue itself. We aim to understand tissue formation as an aspect of this system.
Fig.3
Fig.3 Identification of molecular system from membrane potential time series. Measuring membrane potential is relatively easier than observing cell-cell interaction. Computation enables us to estimate intracellular molecular system from membrane potential.
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