Laboratory for Systems Biology
Research Areas
| A paradigm shift is occurring in all field of life science, from the molecular level to the system level. 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, and their application for identification of the genetic network underlying dynamic and complex biological processes such as mammalian circadian rhythm and somite formation. The characteristic of this research team is seamless integration of computational and experimental technologies utilizing genome-wide information, technologies and resources toward system identification of complex and dynamic biological processes. |  Team Leader Hiroki R. UEDA (M.D., Ph.D.)  |
Research Subjects
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List of Selected Publications
| (1) | Ukai-Tadenuma, M., Kasukawa, T., and Ueda, H.R.: "Proof-by-Synthesis of the Transcriptional Logic of Mammalian Circadian Clocks." nature cell Biology, 10, 1154-1163 (2008) |
| (2) | Kumaki, Y., Ukai-Tadenuma, M., Uno, K.D., Nishio, J., Masumoto, K., Nagano, M., Komori, T., Shigeyoshi, Y., Hogenesch, J.B., and Ueda, H.R.: "Analysis and Synthesis of High-amplitude Cis-elements in the Mammalian Circadian Clock." PNAS, 105 (39), 14946-14951 (2008) |
| (3) | Nakao, N., Ono, H., Yamamura, T., Anraku, T., Takagi, T., Higashi, K., Yasuo, S., Katou, Y., Kageyama, S., Uno, Y., Kasukawa, T., Iigo, M., Sharp, P.J., Iwasawa, A., Suzuki, Y., Sugano, S., Niimi, T., Mizutani, M., Namikawa, T., Ebihara, S., Ueda, H.R. and Yoshimura, T.: "Thyrotrophin in the pars tuberalis triggers photoperiodic response." Nature, 452, 317-322 (2008) |
| (4) | Ukai, H., Kobayashi, T.J., Nagano, M., Masumoto, K., Sujino, M., Kondo, T., Yagita, K., Shigeyoshi, Y., and Ueda, H.R.: "Melanopsin-dependent photo-perturbation reveals desynchronization underlying the singularity of mammalian circadian clocks." Nature Cell Biology, 9, 1327 - 1334 (2007). |
| (5) | Matsumoto, A., Ukai-Tadenuma, M., Yamada, R.G., Houl, J., Uno, K.D., Kasukawa, T., Dauwalder, B., Itoh, T.Q., Takahashi, K., Ueda, R., Hardin, P.E., Tanimura, T., and Ueda, H.R.:( corresponding authors) "A functional genomics strategy reveals clockwork orange as a transcriptional regulator in the Drosophila circadian clock." Genes and Development, 21, 1687-1700 (2007) |
| (6) | Trey, K., Sato, Yamada, R.G., Ukai, H., Baggs, J.E., Miraglia, L.J., Kobayashi, T.J., Welsh, D.K., Kay, S.A., Ueda, H.R., and Hogenesch, J.B.: "Feedback repression is required formammalian circadian clock function." Nature Genetics, 38, 312-319 (2006). |
| (7) | Ueda, H.R., Hayashi, S., Chen, W., Sano, M., Machida, M., Shigeyoshi, Y., Iino, M., and Hashimoto, S.: "System-level Identification of Transcriptional Circuits Underlying Mammalian Circadian Clocks." Nature Genetics, 37, 187-192 (2005). |
| (8) | Ueda, H.R., Chen, W., Minami, Y., Honma, S., Honma, K., Iino, M., and Hashimoto, S.: "Molecular-Timetable Methods for Detection of Body Time and Rhythm Disorders from Single-time-point Genome-wide Expression Profiles." PNAS, 101, 11227-11232 (2004). |
| (9) | Ueda, H.R., Hayashi, S., Matsuyama, S., Yomo, T., Hashimoto, S., Kay, S.A., Hogenesch, J.B., and Iino, M.: "Universality and flexibility in gene expression from bacteria to human." PNAS, 101, 3765-3769 (2004). |
| (10) | Ueda, H.R., Chen, W., Adachi, A., Wakamatsu, H., Hayashi, S., Takasugi, T., Nagano, M., Nakahama, K., Suzuki, Y., Sugano, S., Iino, M., Shigeyoshi, Y., and Hashimoto, S.: "A transcription factor response element for gene expression during circadian night." Nature, 418, 534-539 (2002). |