Phosphoproteomic and bioinformatic methods for analyzing signaling in vertebrate axon growth and regeneration.
Igarashi, M., Kawasaki, A., Ishikawa, Y., Honda, A., Okada, M., Okuda, S. Phosphoproteomic and bioinformatic methods for analyzing signaling in vertebrate axon growth and regeneration. J. Neurosci. Methods 339:108723(2020).
Phenological shifts and genetic differentiation between sympatric populations of Sargassum horneri (Fucales, Phaeophyceae) in Japan.
Homma, Y., Okuda, S., Kasahara, M., Takahashi, F., Yoshikawa, S., Uwai, S. Phenological shifts and genetic differentiation between sympatric populations of Sargassum horneri (Fucales, Phaeophyceae) in Japan. Mar. Ecol. Prog. Ser. 642:103-116 (2020)
Marine Ecology Progress Series
XCL1 expression correlates with CD8-positive T cells infiltration and PD-L1 expression in squamous cell carcinoma arising from mature cystic teratoma of the ovary.
Tamura, R., Yoshihara, K., Nakaoka, H., Yachida, N., Yamaguchi, M., Suda, K., Ishiguro, T., Nishino, K., Ichikawa, H., Homma, K., Kikuchi, A., Ueda, Y., Takei, Y., Fujiwara, H., Motoyama, T., Okuda, S., Wakai, T., Inoue, I., Enomoto, T. XCL1 expression correlates with CD8-positive T cells infiltration and PD-L1 expression in squamous cell carcinoma arising from mature cystic teratoma of the ovary. Oncogene 39(17):3541-3554(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).
The ProteomeXchange consortium in 2020: enabling ‘big data’ approaches in proteomics.
Deutsch, E. W., Bandeira, N., Sharma, V., Perez-Riverol, Y., Carver, J. J., Kundu, D. J., García-Seisdedos, D., Jarnuczak, A. F., Hewapathirana, S., Pullman, B. S., Wertz, J., Sun, Z., Kawano, S., Okuda, S., Watanabe, Y., Hermjakob, H., MacLean, B., MacCoss, M. J., Zhu, Y., Ishihama, Y., Vizcaíno, J. A. The ProteomeXchange consortium in 2020: enabling ‘big data’ approaches in proteomics. Nucleic Acids Res. 48(D1):D1145-D1152 (2020).
Rice Endosperm Protein Administration to Juvenile Mice Regulates Gut Microbiota and Suppresses the Development of High-Fat Diet-Induced Obesity and Related Disorders in Adulthood.
Higuchi, Y., Hosojima, M., Kabasawa, H., Kuwahara, S., Goto, S., Toba, K., Kaseda, R., Tanaka, T., Kitamura, N., Takihara, H., Okuda, S., Taniguchi, M., Arao, H., Narita, I., Saito, A. Rice Endosperm Protein Administration to Juvenile Mice Regulates Gut Microbiota and Suppresses the Development of High-Fat Diet-Induced Obesity and Related Disorders in Adulthood. Nutrients 11(12): 2919 (2019).
Open Agile text mining for bioinformatics: the PubAnnotation ecosystem.
Kim, J. D., Wang, Y., Fujiwara, T., Okuda, S., Callahan, T. J., Cohen, K. B. Open Agile text mining for bioinformatics: the PubAnnotation ecosystem. Bioinformatics 1;35(21): 4372-4380 (2019).
BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services.
Katayama, T., Kawashima, S., Micklem, S., Kawano, S., Kim, J-D., Kocbek, S., Okamoto, S., Wang, Y., Wu, H., Yamaguchi, A., Yamamoto, Y., Antezana, E., Aoki-Kinoshita, K. F., Arakawa, K., Banno, M., Baran, J., Bolleman, J. T., Bonnal, R. J. P., Bono, H., Fernández-Breis, J. T., Buels, R., Campbell, M. P., Chiba, H., Cock, P. J. A., Cohen, K. B., Dumontier, M., Fujisawa, T., Fujiwara, T., Garcia, L., Gaudet, P., Hattori, E., Hoehndorf, R., Itaya, K., Ito, M., Jamieson, D., Jupp, S., Juty, N., Kalderimis, A., Kato, F., Kawaji, H., Kawashima, T., Kinjo, A. R., Komiyama, Y., Kotera, M., Kushida, T., Malone, J., Matsubara, M., Mizuno, S., Mizutani, S., Mori, H., Moriya, Y., Murakami, K., Nakazato, T., Nishide, H., Nishimura, Y., Ogishima, S., Ohta, T., Okuda, S., Ono, H., Perez-Riverol, Y., Shinmachi, D., Splendiani, A., Strozzi, F., Suzuki, S., Takehara, J., Thompson, M., Tokimatsu, T., Uchiyama, I., Verspoor, K., Wilkinson, M. D., Wimalaratne, S., Yamada, I., Yamamoto, N., Yarimizu, M., Kawamoto, S., Takagi, T. BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services. F1000Research 8:1677 (2019).
The Human Gut Microbiome is Structured to Optimize Molecular Interaction Networks.
Ling, Y., Watanabe, Y., Okuda, S. The Human Gut Microbiome is Structured to Optimize Molecular Interaction Networks. Comput. Struct. Biotechnol. J. 17:1040-1046 (2019).
PubMed Computational and Structural Biotechnology Journal
Towards a standardized bioinformatics infrastructure for N- and O- glycomics.
Rojas-Macias, M. A., Mariethoz, J., Andersson, P., Jin, C., Venkatakrishnan, V., Aoki, N. P., Shinmachi, D., Ashwood, C., Madunic, K., Zhang, T., Miller, R. L., Horlacher, O., Struwe, W. B., Watanabe, Y., Okuda, S., Levander, F., Kolarich, D., Rudd, P. M., Wuhrer, M., Kettner, C., Packer, N. H., Aoki-Kinoshita, K. F., Lisacek, F., Karlsson, N. G. Towards a standardized bioinformatics infrastructure for N- and O- glycomics. Nat. commun. 10(1):3275 (2019).