GlycoRDF: an ontology to standardize glycomics data in RDF.
Ranzinger, R., Aoki-Kinoshita, K. F., Campbell, M., P., Kawano, S., Lütteke, T., Okuda, S., Shinmachi, D., Shikanai, T., Sawaki, H., Toukach, P., Matsubara, M., Yamada, I., Narimatsu, H. GlycoRDF: an ontology to standardize glycomics data in RDF. Bioinformatics 31(6) 919-25 (2015).
Enhanced translocation and growth of Rhodococcus erythropolis PR4 in the alkane phase of aqueous-alkane two phase cultures were mediated by GroEL2 overexpression.
Takihara, H., Ogihara, J., Yoshida, T., Okuda, S., Nakajima, M., Iwabuchi, N., Sunairi, M. Enhanced translocation and growth of Rhodococcus erythropolis PR4 in the alkane phase of aqueous-alkane two phase cultures were mediated by GroEL2 over expression. Microbes Environ. 29(4):346-52 (2014).
Elucidation of the evolutionary expansion of phosphorylation signaling networks using comparative phosphomotif analysis.
Yoshizaki, H., Okuda S. Elucidation of the evolutionary expansion of phosphorylation signaling networks using comparative phosphomotif analysis. BMC Genomics 15:546 (2014).
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.
Katayama, T., Wilkinson M. D., Aoki-Kinoshita, K. F., Kawashima, S., Yamamoto, Y., Yamaguchi, A., Okamoto, S., Kawano, S., Kim, J. D., Wang, Y., Wu, H., Kano, Y., Ono, H., Bono, H., Kocbek, S., Aerts, J., Akune, Y., Antezana, E., Arakawa, K., Aranda, B., Baran, J., Bolleman, J., Bonnal, R. J., Buttigieg, P. L., Campbell, M. P., Chen, Y. A., Chiba, H., Cock, P. J., Cohen, K. B., Constantin, A., Duck, G., Dumontier, M., Fujisawa, T., Fujiwara, T., Goto, N., Hoehndorf, R., Igarashi, Y., Itaya, H., Ito, M., Iwasaki, W., Kalaš, M., Katoda, T., Kim, T., Kokubu, A., Komiyama, Y., Kotera, M., Laibe, C., Lapp, H., Lütteke, T., Marshall, M. S., Mori, T., Mori, H., Morita, M., Murakami, K., Nakao, M., Narimatsu, H., Nishide, H., Nishimura, Y., Nystrom-Persson, J., Ogishima, S., Okamura, Y., Okuda, S., Oshita, K., Packer, N. H., Prins, P., Ranzinger, R., Rocca-Serra, P., Sansone, S., Sawaki, H., Shin, S. H., Splendiani, A., Strozzi, F., Tadaka, S., Toukach, P., Uchiyama, I., Umezaki, M., Vos, R., Whetzel, P. L., Yamada, I., Yamasaki, C., Yamashita, R., York, W. S., Zmasek, C. M., Kawamoto, S., Takagi, T. BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. J. Biomed. Semantics 5(1):5 (2014).
The Fifth ACGG-DB Meeting Report: Towards an International Glycan Structure Repository.
Aoki-Kinoshita, K. F., Sawaki, H., An, H. J., Campbell, M., Cao, Q., Cummings, R., Hsu, D. K., Kato, M., Kawasaki, T., Khoo, K. H., Kim, J., Kolarich, D., Li, X., Liu, M., Matsubara, M., Okuda, S., Packer, N. H., Ranzinger, R., Shen, H., Shikanai, T., Shinmachi, D., Toukach, P., Yamada, I., Yamaguchi, Y., Yang, P., Ying, W., Yoo, J. S., Zhang, Y., Zhang, Y., Narimatsu, H. The Fifth ACGG-DB Meeting Report: Towards an International Glycan Structure Repository. Glycobiology 23(12): 1422-1424 (2013). Glycobiology
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., Narimatsu, H. Introducing glycomics data into the Semantic Web. J. Biomed. Semantics 4(1):39 (2013).
PubMed Journal of Biomedical Semantics
Analysis of bacterial growth at various distances from an antimicrobial surface.
Nunose, S., Iwai, R., Okuda, S., Tsuchiya, Y., 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., 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., 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., Morisaki H. Virtual metagenome reconstruction from 16S rRNA gene sequences. Nat. Commun. 3:1203 (2012).