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).
Mutational signatures and clinicopathological relationship extracted from clinical sequence data of 201 caseswith colorectal cancer.
Takeuchi, S., Ling, Y., Watanabe, Y., Shimada, Y., Wakai, T., Okuda, S. Mutational signatures and clinicopathological relationship extracted from clinical sequence data of 201 caseswith colorectal cancer. ASHG2019, Houston (2019/10/16).
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).
Network analysis of proteogenomics data in lung cancer cell lines.
Watanabe, Y., Ling, Y., Uemura, H., Yoshizawa, A. C., Ishihama, Y., Okuda, S. Network analysis of proteogenomics data in lung cancer cell lines. HUPO2019, Adelaide (2019/9/17).
Promotion of proteomic data sharing through a specialized data journal.
Kawano, S., Okuda, S., Matsumoto, M., Ishihama, Y. Promotion of proteomic data sharing through a specialized data journal. HUPO2019, Adelaide (2019/9/16).
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
Genome-wide analysis of mutational impact on post translational modification.
Ling, Y., Yoshizaki, H., Okuda, S. Genome-wide analysis of mutational impact on post translational modification. ISMB2019, Bazel (2019/7/23).
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).