主要論文

1. Kawaguchi S, Iida K, Harada E, Hanada K, Matsui A, Okamoto M, Shinozaki K Seki M, Toyoda T.:
   "Positional correlation analysis improves reconstruction of full-length transcripts and alternative isoforms from noisy array signals or short reads.’"
   Bioinformatics (2012)
2. Kobayashi, N., Ishii, M., Takahashi, S., Mochizuki, Y., Matsushima, A., Toyoda, T.:
   "Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases.'"
   Nucleic Acids Res 39(Web Server issue): W533-40(2011)
3. 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)
4. 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)
5. 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)
6. 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)
7. 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)
8. 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)
9. Kobayashi N, Toyoda T.:
   "Statistical Search on the Semantic Web."
   Bioinformatics. 24(7), 1002-1010 (2008)
10. 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)

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