Integrated Database Unit

Our objective is to deepen our overall understanding of life by analyzing the vast quantities of data produced in the life sciences so as to promote information technology research strategically directed at making higher-order scientific discoveries. We will also work to pioneer the important future science of genome design, and build the bioinformatics infrastructure that is needed to resolve so many of humanity's problems. A comprehensive analysis of the huge volume of newly produced data together with existing data will be essential for future life science research. The Bioinformatics And Systems Engineering division will organize existing and new data into a database which will be made available to the public for greater convenience of use and continuity. At the same time, we will carry out large-scale analysis of this vast data resource to elucidate biological functions, and pursue informatics research for genome design.

Research Subjects

• Research and develop new bioinformatics methods
• Promote bioinformatics collaborations
• Develop an information platform for RIKEN-wide researchers to create, release and collaborate on databases efficiently
• Promote database cooperation and publication within RIKEN

Publications

1. Hanada, K, Higuchi-Takeuchi, M, Okamoto, M, Yoshizumi, T, Shimizu, M, Nakaminami, K, Nishi, R, Ohashi, C, Iida, K, Tanaka, M, Horii, Y, Kawashima, M, Matsui, K, Toyoda, T, Shinozaki, K, Seki, M, Matsui, M (2013). 'Small open reading frames associated with morphogenesis are hidden in plant genomes.', Proc. Natl. Acad. Sci. U.S.A., 110, 2395-2400.
2. Ogata, Y, Chikayama, E, Morioka, Y, Everroad, RC, Shino, A, Matsushima, A, Haruna, H, Moriya, S, Toyoda, T, Kikuchi, J (2012). 'ECOMICS: a web-based toolkit for investigating the biomolecular web in ecosystems using a trans-omics approach.', PLoS ONE, 7, e30263.
3. Itoh, Y, Moriyama, Y, Hasegawa, T, Endo, TA, Toyoda, T, Gotoh, Y (2013). 'Scratch regulates neuronal migration onset via an epithelial-mesenchymal transition-like mechanism.', Nat. Neurosci., doi:10.1038/nn.3336.
4. Nakajima-Takagi, Y, Osawa, M, Oshima, M, Takagi, H, Miyagi, S, Endoh, M, Endo, TA, Takayama, N, Eto, K, Toyoda, T, Koseki, H, Nakauchi, H, Iwama, A (2013). 'Role of SOX17 in hematopoietic development from human embryonic stem cells.', Blood, 121, 447-58.
5. Endoh, M, Endo, TA, Endoh, T, Isono, K, Sharif, J, Ohara, O, Toyoda, T, Ito, T, Eskeland, R, Bickmore, WA, Vidal, M, Bernstein, BE, Koseki, H (2012). 'Histone H2A mono-ubiquitination is a crucial step to mediate PRC1-dependent repression of developmental genes to maintain ES cell identity.', PLoS Genet., 8, e1002774.
6. Kurihara, Y, Schmitz, RJ, Nery, JR, Schultz, MD, Okubo-Kurihara, E, Morosawa, T, Tanaka, M, Toyoda, T, Seki, M, Ecker, JR (2012). 'Surveillance of 3' Noncoding Transcripts Requires FIERY1 and XRN3 in Arabidopsis.', G3 (Bethesda), 2, 487-498.
7. Kawaguchi, S, Iida, K, Harada, E, Hanada, K, Matsui, A, Okamoto, M, Shinozaki, K, Seki, M, Toyoda, T (2012). 'Positional correlation analysis improves reconstruction of full-length transcripts and alternative isoforms from noisy array signals or short reads.', Bioinformatics, 28, 929-937.
8. Endo, A, Tatematsu, K, Hanada, K, Duermeyer, L, Okamoto, M, Yonekura-Sakakibara, K, Saito, K, Toyoda, T, Kawakami, N, Kamiya, Y, Seki, M, Nambara, E (2012). 'Tissue-specific transcriptome analysis reveals cell wall metabolism, flavonol biosynthesis and defense responses are activated in the endosperm of germinating Arabidopsis thaliana seeds.', Plant Cell Physiol., 53, 16-27.
9. Baerenfaller K, Bastow R, Beynon J, Brady S, Brendel V, Donaldson S, Forster M, Gifford D, Grotewold E, Gutierrez R, Huala E, Jaiswal P, Joshi H, Kersey P, Liu L, Loraine A, Lyons E, May S, Mayer K, MacLean D, Meyers B, Mueller L, Muller R, Muller H.M, Ouellette F, Pires J.C, Provart N, Staiger D, Stanzione D, Taylor J, Taylor C, Town, C.J. Toyoda T, Vaughn M, Walsh S, Ware D, Weckwerth W. 'Taking the Next Step: Building an Arabidopsis Information Portal' Plant Cell 24: 2248-56(2012)