Laboratory for Systems Biology

One of the major challenges in current biology is system-level understanding of dynamic and complex biological phenomena. The laboratory for systems biology has specific aims at development of the systems-biological technologies to dissect dynamic and complex biological systems, that covering atomic-level to molecular-level, cellular/tissue-level and organism-level, and their application for system-level understanding of the dynamic and complex organism-level biological processes such as mammalian circadian rhythm and early embryogenesis.

Research Subjects

• Robustness of biological clock from the atomic level
• The season-detection mechanism of biological calendar from the molecular level.
• The hourglass mechanism of sleep from the cellular level
• Development of the systems-biological technologies to dissect dynamic and complex organism-level biological systems

Publications

1. Hogenesch JB, Ueda HR.:
   "Understanding systems-level properties: timely stories from the study of clocks."
   Nat Rev Genet. 2011 Jun;12(6):407-16.
2. Kasukawa T, Masumoto KH, Nikaido I, Nagano M, Uno KD, Tsujino K, Hanashima C, Shigeyoshi Y, Ueda HR.:
   "Quantitative expression profile of distinct functional regions in the adult mouse brain."
   PLoS One. 2011;6(8):e23228.
3. Koyama YM, Kobayashi TJ, Ueda HR.:
   "Perturbation analyses of intermolecular interactions."
   Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Aug;84(2 Pt 2):026704.
4. Khan SK, Xu H, Ukai-Tadenuma M, Burton B, Wang Y, Ueda HR, Liu AC.:
   "Identification of a novel cryptochrome differentiating domain required for feedback repression in circadian clock function."
   J Biol Chem. 2012 Jul 27;287(31):25917-26.
5. Kasukawa T, Sugimoto M, Hida A, Minami Y, Mori M, Honma S, Honma K, Mishima K, Soga T, Ueda HR.:
   " Human blood metabolite timetable indicates internal body time."
   Proc Natl Acad Sci U S A. 2012 Sep 11;109(37):15036-41.
6. Okamura-Oho Y, Shimokawa K, Takemoto S, Hirakiyama A, Nakamura S, Tsujimura Y, Nishimura M, Kasukawa T, Masumoto KH, Nikaido I, Shigeyoshi Y, Ueda HR, Song G, Gee J, Himeno R, Yokota H.:
   "Transcriptome tomography for brain analysis in the web-accessible anatomical space."
   PLoS One. 2012;7(9):e45373.
7. Jolley CC, Ode KL, Ueda HR.:
   "A design principle for a posttranslational biochemical oscillator."
   Cell Rep. 2012 Oct 25;2(4):938-50.
8. Yoshimoto N, Kida A, Jie X, Kurokawa M, Iijima M, Niimi T, Maturana AD, Nikaido I, Ueda HR, Tatematsu K, Tanizawa K, Kondo A, Fujii I, Kuroda S.:
   "An automated system for high-throughput single cell-based breeding."
   Sci Rep. 2013;3:1191.