Centers & Labs

RIKEN Quantitative Biology Center

Cell Design Research Core

Core Director: Hiroki Ueda (M.D., Ph.D.)
Hiroki  Ueda(M.D., Ph.D.)

By observing how they respond to small perturbations, we are designing artificial systems that act like biological ones to understand how complex and dynamical networks function within systems. Using experimental and theoretical data, we are building large-scale models for the study of molecular complexes, and gene and cellular networks. Of particular interest will be the understanding of how various spatial and temporal properties like polarity and periodicity emerge from these networks. Along with identifying the operating principles used to determine the cell state, we aim to manipulate a cell’s response into a desired effect.

Main Research Field

Biological Sciences

Related Research Fields

Chemistry / Engineering / Biology / Medicine, dentistry, and pharmacy


  • Systems biology
  • Synthetic biology
  • Cell-free protein synthesis
  • Genome editing
  • Biodevice

Selected Publications

  1. Ode K.L., Ukai H., Susaki E.A., et al.:
    "Knockout-rescue embryonic stem cell-derived mouse reveals circadian-period control by quality and quantity of CRY1"
    Mol. Cell 65, 176-190 (2017)
  2. Narumi, R., Shimizu, Y., Ukai-Tadenuma, M., et al.:
    "Mass spectrometry-based absolute quantification reveals rhythmic variation of mouse circadian clock proteins"
    PNAS 113, E3461-7 (2016)
  3. Tatsuki, F., Sunagawa, G.A., Shi, S., et al.:
    "Involvement of Ca2+-Dependent Hyperpolarization in Sleep Duration in Mammals"
    Neuron 90, 1-16 (2016)
  4. Sunagawa, G.A., Sumiyama, K., Ukai-Tadenuma, M., et al.:
    "Mammalian Reverse Genetics without Crossing Reveals Nr3a as a Short-Sleeper Gene"
    Cell Reports 14, 662-77 (2016)
  5. Matsuura, T., Tanimura, N., Hosoda, K., et al.:
    "Reaction dynamics analysis of a reconstituted Escherichia coli protein translation system by computational modeling."
    Proc. Natl. Acad. Sci. U. S. A. 114: E1336-E1344 (2017)
  6. Tanaka, Y. and Shimizu, Y.
    "Integration of a reconstituted cell-free protein-synthesis system on a glass microchip."
    Anal. Sci. 31: 67-71. (2015)
  7. Shimizu, Y.
    "Biochemical aspects of bacterial strategies for handling the incomplete translation processes."
    Front. Microbiol. 5: 170. (2014)
  8. Yalikun, Y., and Tanaka, Y.
    "Ultra-thin glass sheet integrated transparent diaphragm pressure transducer"
    Sensors and Actuators A: Physical, 263, 102-112 (2017)
  9. Tanaka, N., Yamashita, T., Sato, A., et al.:
    "Simple agarose micro-confinement array and machine-learning-based classification for analyzing the patterned differentiation of mesenchymal stem cells."
    PLoS ONE, 12, e0173647 (2017)
  10. Funano, S., Tanaka, N., and Tanaka, Y.
    "Analysis of long-term morphological changes of micro patterned molecules and cells on PDMS and glass surfaces."
    Analytical Sciences, 33(6), 723-725 (2017)