Introducing glycomics data into the Semantic Web.
Aoki-Kinoshita, K. F., Bolleman, J., Campbell, M. P., Kawano, S., Kim, J. D., Lütteke, T., Matsubara, M., Okuda, S., Ranzinger, R., Sawaki, H., Shikanai, T., Shinmachi, D., Suzuki, Y., Toukach, P., Yamada, I., Packer, N. H., and Narimatsu, H. Introducing glycomics data into the Semantic Web. J. Biomed. Semantics 4(1):39 (2013).
PubMed Journal of Biomedical Semantics
Recent Efforts of Global Collaborations for Interconnecting Glycan-related Databases on the Semantic Web.
Sawaki, M., Kinoshita-Aoki, K., Yamada, I., Kawano, S., Okuda, S., Katoh, M., and Narimatsu, H. Recent Efforts of Global Collaborations for Interconnecting Glycan-related Databases on the Semantic Web. Glyco22, Dalian (2013/6).
Analysis of bacterial growth at various distances from an antimicrobial surface.
Nunose, S., Iwai, R., Okuda, S., Tsuchiya, Y., and Morisaki, H. Analysis of bacterial growth at various distances from an antimicrobial surface. Adv. Biosci. Biotechnol. 4:563-569 (2013).
Advances in Bioscience and Biotechnology
The Third ACGG-DB Meeting Report: Towards an international collaborative infrastructure for glycobioinformatics.
Aoki-Kinoshita, K. F., Sawaki, H., An, H. J., Cho, J. W., Hsu, D., Kato, M., Kawano, S., Kawasaki, T., Khoo, K. H., Kim, J., Kim, J. D., Li, X., Lütteke, T., Okuda, S., Packer, N. H., Paulson, J. C., Raman, R., Ranzinger, R., Shen, H., Shikanai, T., Yamada, I., Yang, P., Yamaguchi, Y., Ying, W., Yoo, J. S., Zhang, Y., and Narimatsu, H. The Third ACGG-DB Meeting Report: Towards an international collaborative infrastructure for glycobioinformatics. Glycobiology 23(2):144-6 (2013).
KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters.
Nakaya, A., Katayama, T., Itoh, M., Hiranuka, K., Kawashima, S., Moriya, Y., Okuda, S., Tanaka, M., Tokimatsu, T., Yamanishi, Y., Yoshizawa, A. C., Kanehisa, M., and Goto, S. KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters. Nucleic Acids Res. 41: D353-7 (2013).
Virtual metagenome reconstruction from 16S rRNA gene sequences.
Okuda, S., Tsuchiya, T., Kiriyama, C., Itoh, M., and Morisaki H. Virtual metagenome reconstruction from 16S rRNA gene sequences. Nat. Commun. 3:1203 (2012).
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., and Wang, J. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490(7418):55-60 (2012).
Meta-transcriptomic analysis of microbial community associated with a soda lake in Khovsgol, Mongolia.
Hamamura, N., Huang, H., Okuda, S., and Damdinsuren, N. Meta-transcriptomic analysis of microbial community associated with a soda lake in Khovsgol, Mongolia. ISME14, Copenhagen (2012/8).
Reconstruction of metagenomes from 16S rRNA gene sequence in biofilm formation process.
Okuda, S., Tsuchiya, Y., Kiriyama, C., Itoh, M., and Morisaki, H. Reconstruction of metagenomes from 16S rRNA gene sequence in biofilm formation process. ISME14, Copenhagen (2012/8).
Evolutionary analysis of the phosphorylation signaling reveals functionally conserved motifs.
Yoshizaki, H., and Okuda, S.; Evolutionary analysis of the phosphorylation signaling reveals functionally conserved motifs. ASCB annual meeting 2012, 2788, Denver (2011/12).