Bioinformatics And Systems Engineering division
| We are developing methods to link phenome to genome, using the mutants generated in our project. Establishing a high-speed phenotype mapping system and a method for efficient extraction of candidate genes from critical chromosomal regions is essential to our work, and integration informatics plays a central role. We are developing a high-throughput gene identification system (PosMed) to elucidate the genes responsible for phenotypes of interest by integrating all available information on gene expression profiling and in research literature. We also integrate the data published by GSC and other institutes. We are responsible for global servicing of the integrated database system, the fruit of our genomic sciences activities. In the GSC's second stage (from April 2005), we are expected to provide a global-standard database capable of representing the dynamics of higher-order systems (i.e., their life strategies) based on the vast amount of accumulated knowledge in the omic space (i.e., multiple omic-level relationships and networks from genome through to phenome). |  Director Tetsuro TOYODA (Ph.D.) 
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Research Subjects
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List of Selected Publications
| (1) | Kaminuma, E., Masuya, H., Miura, I., Motegi, H., Takahashi, K.R., Nakazawa, M., Matsui, M., Gondo, Y., Noda, T., Shiroishi, T., Wakana, S., and Toyoda, T.: "Objective evaluation measures of genetic marker selection in large-scale SNP genotyping." J Bioinform Comput Biol. 6 (5), 905-917 (2008) |
| (2) | Kaminuma, E., Yoshizumi, T., Wada, T., Matsui, M., and Toyoda, T.: "Quantitative analysis of heterogeneous spatial distribution of Arabidopsis leaf trichomes using micro X-ray computed tomography." The Plant Journal 56 (3), 470-482 (2008) |
| (3) | Kobayashi, N. and Toyoda, T.: "Statistical Search on the Semantic Web." Bioinformatics. 24 (7), 1002-1010 (2008) |
| (4) | Toyoda, T., Mochizuki, Y., Player, K., Heida, N., and Sakaki, Y.: "OmicBrowse: a browser of multidimensional omics annotations." Bioinformatics 23, 524-526 (2006) |
| (5) | Kaminuma, E., Heida, N., Yoshizumi, T., Nakazawa, M., Matsui, M., and Toyoda, T.: "In silico phenotypic screening method of mutants based on statistical modeling of genetically mixed samples." J Bioinform Comput Biol. 3 (6), 1281-93 (2005) |
| (6) | Toyoda, T. and Shinozaki, K.: "Tiling-array-driven elucidation of transcriptional structures based on maximum-likelihood and Markov models." The Plant Journal, 43 (3), 611-621 (2005) |
| (7) | Kaminuma, E., Heida, N., Tsumoto, Y., Nakazawa, M., Goto, N., Konagaya, A., Matsui, M., and Toyoda, T.: "Three-dimensional definition of leaf morphological traits of Arabidopsis in silico phenotypic analysis." J Bioinform Comput Biol, 3 (2), 401-414 (2005) |
| (8) | Toyoda, T. and Wada, A.: "Omic space: coordinate-based integration and analysis of genomic phenomic interactions." Bioinformatics 20 (11), 1759-1765 (2004) |
| (9) | Heida, N., Hasegawa, Y., Mochizuki, Y., Hirosawa, K., Konagaya, A., and Toyoda, T.: "TraitMap: an XML-based genetic-map database combining multigenic loci and biomolecular networks." Bioinformatics 20, i152-i160 (2004) |
| (10) | Kaminuma, E., Heida, N., Tsumoto, Y., Yamamoto, N., Goto, N., Okamoto, N., Konagaya, A., Matsui, M., and Toyoda, T.: "Automatic quantification of morphological traits via three-dimensional measurement of Arabidopsis." Plant J 38(2), 358-365 (2004) |