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Laboratory for Gene-Expression Analysis • Okubo Group

Knowledge discovery through genome-wide measurements

Professor OKUBO, Kousaku kokubo
Assistant Professor OGASAWARA, Osamu oogasawa

1. Sharing and Integration of Data and Knowledge in Life Science
Science of 21 century is a discovery from digital observatory data of complex phenomena. Digital literature is also one of such data. For the fair competition of new knowledge from such data, data integration is inevitable. For data integration, we have to overcome semantic, syntactic, and pragmatic problems in science data. Being Involved in data sharing center for DNA sequence (DDBJ) and for literature and observatory data (DBCLS), we engineer technologies and resources which is necessary for sharing and integration of knowledge and data.

2. Theoretical studies of gene expression evolution
Gene expression evolution has long been hypothesized to serve as a bridge from molecular to phenotypic evolution. The advent of genomewide gene expression profiling techniques have prompted the studies of this field, but some conflicts have arisen in the interpretation of the observations.
Those are caused by the lack of definite theoretical models, and instead the use of inadequate analogies of molecular evolution. Therefore, we are constructing a theoretical model of gene expression evolution which provides consistent explanations of the pattern in the observations.

URL
http://lifesciencedb.jp/ddbj/
http://lifesciencedb.jp/cc/
http://lifesciencedb.jp/ag/

DNA database (DDBJ/EMBL/GenBank) overview and search. This enables that the DNA databases are browsed and searched in terms of research projects.

Kaminuma, E., Kosuge, T., Kodama, Y., Aono, H., Mashima, J., Gojobori, T., Sugawara, H., Ogasawara, O., Takagi, T., Okubo, K., and Nakamura, Y. (2011).
Nucleic Acids Res. 39(Database issue),D22-27.

Ogasawara, O., and Okubo, K. (2009). On theoretical models of gene expression evolution with random genetic drift and natural selection. PLoS One. 4, e7943.

Kaminuma, E., Mashima, J., Kodama, Y., Gojobori, T., Ogasawara, O., Okubo, K., Takagi, T., and Nakamura, Y. (2010). DDBJ launches a new archive database with analytical tools for next-generation sequence data. Nucleic Acids Res. 38(Database issue), D33-38.

Sugawara, H., Ogasawara, O., Okubo, K., Gojobori, T., and Tatetno, Y. (2008). DDBJ with new system and face. Nucleic Acids Res. 36(Database issue), D22-24.

Hoshino, H., Uchida, T., Otsuki, T., Kawamoto, S., Okubo, K., Takeichi, M., and Chisaka, O. (2007). Cornichon-like Protein Facilitates Secretion of HB-EGF and Regulates Proper Development of Cranial Nerves. Mol. Biol. Cell. 18, D1143-1152

Ogasawara, O., Otsuji, M., Watanabe, K., Iizuka, T., Tamura, T., Hishiki, T., Kawamoto, S., and Okubo, K. (2006). BodyMap-Xs: Anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression. Nucleic Acid Res. 34(Database issue), D628-D631.


Professor OKUBO, Kousaku kokubo	Assistant Professor OGASAWARA, Osamu oogasawa

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