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RIKEN Center for Biosystems Dynamics Research Laboratory for Synthetic Biology

Team Leader: Hiroki Ueda (M.D., Ph.D.)

Research Summary

Hiroki  Ueda(M.D., Ph.D.)

A paradigm sift in biological research from reductionistic to synthetic approach has been undertaken in recent years. Even though the synthetic approach has been acknowledged as a central strategy of life science over the next few decades, basic technologies required in the synthetic approach, such like designing, controlling and manipulating biological molecules (DNAs, proteins and lipids) is remained to be established. The main tasks for laboratory for synthetic biology are to develop basic technologies for synthetic biology through close collaborative study within this center and to present pioneer studies in this new field.

Main Research Fields

  • Biological Sciences

Related Research Fields

  • Chemistry
  • Biology


  • Systems biology
  • Synthetic biology
  • Chronobiology
  • Sleep
  • Circadian clock

Selected Publications

  • 1.Susaki E.A., Ukai H., and Ueda H.R.;
    "Next-generation mammalian genetics toward organism-level systems biology"
    npj. Syst. Biol. Appl. 3, article number 15 (2017)
  • 2.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)
  • 3.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)
  • 4.Tatsuki, F., Sunagawa, G.A., Shi, S., et al.:
    "Involvement of Ca2+-Dependent Hyperpolarization in Sleep Duration in Mammals"
    Neuron 90, 1-16 (2016)
  • 5.Susaki E.A., and Ueda H.R.;
    "Whole-body and Whole-Organ Clearing and Imaging Techniques with Single-Cell Resolution: Toward Organism-Level Systems Biology in Mammals"
    Cell Chem. Biol. 23, 137-57 (2016)
  • 6.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)
  • 7.Susaki, E.A., Tainaka, K., Perrin, D., et al.:
    "Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging"
    Nat. prot. 10,1709-27 (2015)
  • 8.Tainaka, K., Kubota, S. I., Suyama, T. Q., Susaki, E. A., Perrin, D., et al.:
    "Whole-Body Imaging with Single-Cell Resolution by Tissue Decolorization"
    Cell 159, 911-924 (2014)
  • 9.Jolley, C. C., Ukai-Tadenuma, M., Perrin, D. & Ueda, H. R.:
    "A Mammalian Circadian Clock Model Incorporating Daytime Expression Elements"
    Biophys. J. 107, 1462-1473 (2014)
  • 10.Susaki, E. A., Tainaka, K., Perrin, D., Kishino, F., Tawara, T., et al.:
    "Whole-Brain Imaging with Single-Cell Resolution Using Chemical Cocktails and Computational Analysis"
    Cell 157, 726-739 (2014)

Recent Research Results

Related Links

Lab Members

Principal investigator

Hiroki Ueda
Team Leader

Core members

Rikuhiro Yamada
Senior Scientist
Hideki Ukai
Senior Scientist
Yohei Koyama
Research Scientist
Katsuhiko Matsumoto
Research Scientist
Genki Kanda
Special Postdoctoral Researcher
Hiroko Yukinaga
Special Postdoctoral Researcher
Arthur Robert Millius
Foreign Postdoctoral Researcher
Yuta Shinohara
Postdoctoral Researcher
Daisuke Tone
Postdoctoral Researcher
Maki Ukai
Technical Staff I
Hiroshi Fujishima
Technical Staff I
Chika Shimizu
Technical Staff I
Junko Garcon
Technical Staff I

Contact Information

Email: uedah-tky [at] umin.ac.jp