Enteropathway: the metabolic pathway database for the human gut microbiota.
Shiroma, H., Darzi, Y., Terajima, E., Nakagawa, Z., Tsuchikura, H., Tsukuda, N., Moriya, Y., Okuda, S., Goto, S., Yamada, T. Enteropathway: the metabolic pathway database for the human gut microbiota. Brief. Bioinform. 25(5):bbae419(2024).
Current progress and critical challenges to overcome in the bioinformatics of mass spectrometry-based metaproteomics.
Miura, N., Okuda, S. Current progress and critical challenges to overcome in the bioinformatics of mass spectrometry-based metaproteomics. Comput. Struct. Biotechnol. J. 21:1140-1150 (2023).
New method to construct a reference amino acid sequence database for metaproteome analysis.
Miura, N., Ishihama, Y., Okuda, S. New method to construct a reference amino acid sequence database for metaproteome analysis. HUPO2021, Stockholm/Hybrid (2021/11/18).
Construction of amino acid sequence database for metaproteome analysis using genomes of closely related species.
Miura, N., Ishihama, Y., Okuda, S. Construction of amino acid sequence database for metaproteome analysis using genomes of closely related species. ASMS2021, Philadelphia/Hybrid (2021/10/31).
The jPOST project promoting FAIR data principles in proteomics
AOHUPO2021, “The jPOST project promoting FAIR data principles in proteomics”, Online (2021/7/1).
The jPOST Repository as a Public Data Repository for Shotgun Proteomics.
Watanabe, Y., Yoshizawa, A. C., Ishihama, Y., Okuda, S. The jPOST Repository as a Public Data Repository for Shotgun Proteomics. Methods Mol. Biol. 2259:309-322(2021).
GlycoPOST realizes FAIR principles for glycomics mass spectrometry data.
Watanabe, Y., Aoki-Kinoshita, K. F., Ishihama, Y., Okuda, S. GlycoPOST realizes FAIR principles for glycomics mass spectrometry data. Nucleic Acids Res. 49(D1):D1523-D1528(2021).
The GlyCosmos portal as a partner in the GlySpace Alliance to provide access to integrated glycan-related data resources.
Yamada, I., Shiota, M., Shinmachi, D., Ono, T., Tsuchiya, S., Matsubara, M., Hosoda, M., Fujita, A., Aoki, N. P., Watanabe, Y., Fujita, N., Angata, K., Kaji, H., Narimatsu, H., Okuda, S., Aoki-Kinoshita, K. F. The GlyCosmos portal as a partner in the GlySpace Alliance to provide access to integrated glycan-related data resources. SFG2020, Virtual (2020/11/10).
The GlyCosmos Portal: a unified and comprehensive web resource for the glycosciences.
Yamada, I., Shiota, M., Shinmachi, D., Ono, T., Tsuchiya, S., Hosoda, M., Fujita, A., Aoki, N. P., Watanabe, Y., Fujita, N., Angata, K., Kaji, H., Narimatsu, H., Okuda, S., Aoki-Kinoshita, K. F. The GlyCosmos Portal: a unified and comprehensive web resource for the glycosciences. Nat. Methods 17(7):649-650(2020).
BioHackathon 2015: Semantics of data for life sciences and reproducible research.
Vos, R. A., Katayama, T., Mishima, H., Kawano, S., Kawashima, S., Kim, J-D., Moriya, Y., Tokimatsu, T., Yamaguchi, A., Yamamoto, Y., Wu, H., Amstutz, P., Antezana, E., Aoki, N. P., Arakawa, K., Bolleman, J. T., Bolton, E., Bonnal, R. J. P., Bono, H., Burger, K., Chiba, H., Cohen, K. B., Deutsch, E. W., Fernández-Breis, J. T., Fu, G., Fujisawa, T., Fukushima, A., García, A., Goto, N., Groza, T., Hercus, C., Hoehndorf, R., Itaya, K., Juty, N., Kawashima, T., Kim, J-H., Kinjo, A. R., Kotera, M., Kozaki, K., Kumagai, S., Kushida, T., Lütteke, T., Matsubara, M., Miyamoto, J., Mohsen, A., Mori, H., Naito, Y., Nakazato, T., Nguyen-Xuan, J., Nishida, K., Nishida, N., Nishide, H., Ogishima, S., Ohta, T., Okuda, S., Paten, B., Perret, J-L., Prathipati, P., Prins, P., Queralt-Rosinach, N., Shinmachi, D., Suzuki, S., Tabata, T., Takatsuki, T., Taylor, K., Thompson, M., Uchiyama, I., Vieira, B., Wei, C-H., Wilkinson, M., Yamada, I., Yamanaka, R., Yoshitake, K., Yoshizawa, A. C., Dumontier, M., Kosaki, K., Takagi, T. BioHackathon 2015: Semantics of data for life sciences and reproducible research. F1000Research 9:136 (2020).