A metagenome-wide association study of gut microbiota in type 2 diabetes.
Qin, J., Li, Y., Cai, Z., Li, S., Zhu, J., Zhang, F., Liang, S., Zhang, W., Guan, Y., Shen, D., Peng, Y., Zhang, D., Jie, Z., Wu, W., Qin, Y., Xue, W., Li, J., Han, L., Lu, D., Wu, P., Dai, Y., Sun, X., Li, Z., Tang, A., Zhong, S., Li, X., Chen, W., Xu, R., Wang, M., Feng, Q., Gong, M., Yu, J., Zhang, Y., Zhang, M., Hansen, T., Sanchez, G., Raes, J., Falony, G., Okuda, S., Almeida, M., LeChatelier, E., Renault, P., Pons, N., Batto, J. M., Zhang, Z., Chen, H., Yang, R., Zheng, W., Li, S., Yang, H., Wang, J., Ehrlich, S. D., Nielsen, R., Pedersen, O., Kristiansen, K., Wang, J. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490(7418):55-60 (2012).
In silico study on the substrate binding manner in human myo-inositol monophosphatase 2.
Fujita, S., Ohnishi, T., Okuda, S., Kobayashi, R., Fukuno, S., Furuta, D., Kikuchi, T., Yoshikawa, T., Fujita, N. In silico study on the substrate binding manner in human myo-inositol monophosphatase 2. J. Mol. Model. 17(10), 2559-67 (2011).
The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications.
Katayama, T., Wilkinson, M. D., Vos, R., Kawashima, T., Kawashima, S., Nakao, M., Yamamoto, Y., Chun, H. W., Yamaguchi, A., Kawano, S., Aerts, J., Aoki-Kinoshita, K. F., Arakawa, K., Aranda, B., Bonnal, R. J., Fernández, J. M., Fujisawa, T., Gordon, P. M., Goto, N., Haider, S., Harris, T., Hatakeyama, T., Ho, I., Itoh, M., Kasprzyk, A., Kido, N., Kim, Y. J., Kinjo, A. R., Konishi, F., Kovarskaya, Y., von, Kuster, G., Labarga, A., Limviphuvadh, V., McCarthy, L., Nakamura, Y., Nam, Y., Nishida, K., Nishimura, K., Nishizawa, T., Ogishima, S., Oinn, T., Okamoto, S., Okuda, S., Ono, K., Oshita, K., Park, K. J., Putnam, N., Senger, M., Severin, J., Shigemoto, Y., Sugawara, H., Taylor, J., Trelles, O., Yamasaki, C., Yamashita, R., Satoh, N., Takagi T. The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. J. Biomed. Semantics 2:4 (2011).
PubMed Journal of Biomedical Semantics
iPath2.0: interactive pathway explorer.
Yamada, T., Letunic, I., Okuda, S., Kanehisa, M., Bork, P. iPath2.0: interactive pathway explorer. Nucleic Acids Res. 39:W412-5 (2011).
ODB: a database for operon organizations, 2011 update.
Okuda, S., Yoshizawa, A. C. ODB: a database for operon organizations, 2011 update. Nucleic Acids Res. 39:D552-5 (2011).
Direct observation and analysis of bacterial growth on an antimicrobial surface.
Yamada, H., Takahashi, N., Okuda, S., Tsuchiya, Y., Morisaki, H. Direct observation and analysis of bacterial growth on an antimicrobial surface. Appl. Environ. Microbiol. 76(16):5409-14 (2010).
PubMed Applied and Environmental Microbiology
Comprehensive analysis of glycosyltransferases in eukaryotic genomes for structural and functional characterization of glycans.
Hashimoto, K., Tokimatsu, T., Kawano, S., Yoshizawa, A. C., Okuda, S., Goto, S., Kanehisa, M. Comprehensive analysis of glycosyltransferases in eukaryotic genomes for structural and functional characterization of glycans. Carbohydr. Res. 344(7):881-7 (2009).
Extraction and analysis of chemical modification patterns in drug development.
Shigemizu, D., Araki, M., Okuda, S., Goto, S., Kanehisa, M. Extraction and analysis of chemical modification patterns in drug development. J. Chem. Inf. Model. 49(4):1122-9 (2009).
Network analysis of adverse drug interactions.
Takarabe, M., Okuda, S., Itoh, M., Tokimatsu, T., Goto S., Kanehisa, M. Network analysis of adverse drug interactions. Genome Inform. 20:252-9 (2008).
KEGG Atlas mapping for global analysis of metabolic pathways.
Okuda, S., Yamada, T., Hamajima, M., Itoh, M., Katayama, T., Bork, P., Goto, S., Kanehisa, M. KEGG Atlas mapping for global analysis of metabolic pathways. Nucleic Acids Res. 36:W423-6 (2008).