Centers & Labs

RIKEN Quantitative Biology Center

Laboratory for Synthetic Biology

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

By current progresses in molecular biology and genome science, huge information about biological systems, such like constituent biological molecules and molecular network structures, has been dramatically accumulated, and 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.

Research Subjects

  • Design of chemicals controlling proteins and proteins with novel functions based on the dynamics
  • Design of molecular interactions in circadian clocks
  • Development of high-throughput genome engineering system
  • Gene synthesis for the design and construction of biological systems
  • Design and measurement of protein network dynamics at a single-cell level

Selected Publications

  1. 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)
  2. 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)
  3. 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)
  4. Ikeda, S., Tainaka, K., Matsumoto, K., Shinohara, Y., Ode, K. L., et al.:
    "Non-Enzymatic DNA Cleavage Reaction Induced by 5-Ethynyluracil in Methylamine Aqueous Solution and Application to DNA Concatenation"
    PLoS One 9 (2014)
  5. Adachi, K., Nikaido, I., Ohta, H., Ohtsuka, S., Ura, H., et al.:
    "Context-Dependent Wiring of Sox2 Regulatory Networks for Self-Renewal of Embryonic and Trophoblast Stem Cells"
    Molecular Cell 52, 380-392 (2013)
  6. Tsujino, K., Narumi, R., Masumoto, K., Susaki, E. A., Shinohara, Y., et al.:
    "Establishment of TSH beta real-time monitoring system in mammalian photoperiodism"
    Genes to Cells 18, 575-588 (2013)
  7. Sunagawa, G. A., Sei, H., Shimba, S., Urade, Y. & Ueda, H. R.:
    "FASTER: an unsupervised fully automated sleep staging method for mice"
    Genes to Cells 18, 502-518 (2013)
  8. Sasagawa, Y., Nikaido, I., Hayashi, T., Danno, H., Uno, K. D., et al.:
    "Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity"
    Genome Biol. 14 (2013)
  9. Jolley, C. C., Ode, K. L. & Ueda, H. R.:
    "A Design Principle for a Posttranslational Biochemical Oscillator"
    Cell Reports 2, 938-950 (2012)
  10. Kasukawa, T., Sugimoto, M., Hida, A., Minami, Y., Mori, M., et al.:
    "Human blood metabolite timetable indicates internal body time"
    Proc. Natl. Acad. Sci. U.S.A. 109, 15036-15041 (2012)

Lab Members

Principal Investigator

Hiroki Ueda
Group Director

Core Members

Rikuhiro Yamada
Senior Scientist
Hideki Ukai
Senior Scientist
Yohei Koyama
Research Scientist
Yasutaka Niwa
Special Postdoctoral Researcher
Genki Kanda
Special Postdoctoral Researcher
Hiroko Yukinaga
Special Postdoctoral Researcher
Arthur Robert Millius
Foreign Postdoctoral Researcher
Yuta Shinohara
Postdoctoral Researcher
Katsuhiko Matsumoto
Postdoctoral Researcher
Hitoshi Iuchi
Junior Research Associate
Maki Ukai
Technical Staff I
Hiroshi Fujishima
Technical Staff I
Chika Shimizu
Technical Staff I
Junko Garcon
Technical Staff I
Ryohei Narumi
Technical Staff I
Mayu Shiokawa
Technical Staff I
Yuki Fujiwara
Technical Staff I