RIKEN Bioinformatics And Systems Engineering division
Director
Tetsuro TOYODA (Ph.D.)
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 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
- July 13,2009
- Gene research streamlined using information retrieval system simulating human brain mechanisms
- Iida K, Kawaguchi S, Kobayashi N, Yoshida Y, Ishii M, Harada E, Hanada K, Matsui A, Okamoto M, Ishida J, Tanaka M, Morosawa T, Seki M, Toyoda T.:
"ARTADE2DB: Improved Statistical Inferences for Arabidopsis Gene Functions and Structure Predictions by Dynamic Structure-Based Dynamic Expression (DSDE) Analyses."
Plant and Cell Physiology 52(2), 254-264 (2011) - Masuya H, Makita Y, Kobayashi N, Nishikata K, Yoshida Y, Mochizuki Y, Doi K, Takatsuki T, Waki K, Tanaka N, Ishii M, Matsushima A, Takahashi S, Hijikata A, Kozaki K, Furuichi T, Kawaji H, Wakana S, Nakamura Y, Yoshiki A, Murata T, Fukami-Kobayashi K, Mohan S, Ohara O, Hayashizaki Y, Mizoguchi R, Obata Y, Toyoda T.:
" The RIKEN integrated database of mammals."
Nucleic Acids Research 39 (Database issue), D861-870 (2011) - Makita Y, Kobayashi N, Mochizuki Y, Yoshida Y, Asano(Matsushita) S, Heida N, Muinalini D, Rinki B, Matsushima A, Ishii M, Kawaguchi S, Iida K, Hanada K, Kuromori T, Seki M, Shinozaki K, Toyoda T.:
" An Intelligent Search Engine that Inferentially Integrates Cross-species Information Resources for Molecular Breeding of Plants"
Plant and Cell Physiology 50(7), 1249-59 (2009) - Matsushima A, Kobayashi N, Mochizuki Y, Ishii M, Kawaguchi S, Endo T, Umetsu R, Makita Y, Toyoda T.:
" OmicBrowse: a Flash-based high-performance graphics interface for genomic resources"
Nucleic Acids Research 37(Web Server issue), W57-62 (2009) - Yoshida Y, Makita Y, Heida N, Asano(Matsushita) S, Matsushima A, Ishii M, Mochizuki Y, Masuya H, Wakana S, Kobayashi N, Toyoda T
" Prioritizing genes with an artificial neural network comprising medical documents to accelerate positional cloning"
Nucleic Acids Research 37(Web Server issue), W147-52 (2009) - Kaminuma E, Masuya H, Miura I, Motegi H, Takahashi K R, Nakazawa M, Matsui M, Gondo Y, Noda T, Shiroishi T, Wakana S, Toyoda T.:
" Objective evaluation measures of genetic marker selection in large-scale SNP genotyping."
J Bioinform Comput Biol. 6(5), 905-917 (2008) - Kaminuma E, Yoshizumi T, Wada T, Matsui M, 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) - Kobayashi N, Toyoda T.:
" Statistical Search on the Semantic Web."
Bioinformatics. 24(7), 1002-1010 (2008) - Toyoda T, Mochizuki Y, Player K, Heida N, Sakaki Y.:
" OmicBrowse: a browser of multidimensional omics annotations."
Bioinformatics 23, 524-526 (2006) - Toyoda T, Shinozaki K.:
" Tiling-array-driven elucidation of transcriptional structures based on maximum-likelihood and Markov models."
The Plant Journal, 43(3), 611-621 (2005)