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).
Innate Immune Responses in Serum and Cerebrospinal Fluid From Neonates and Infants Infected With Parechovirus-A3 or Enteroviruses.
Habuka, R., Aizawa, Y., Izumita, R., Domon, H., Terao, Y., Takihara, H., Okuda, S., Saitoh, A. Innate Immune Responses in Serum and Cerebrospinal Fluid From Neonates and Infants Infected With Parechovirus-A3 or Enteroviruses. J. Infect. Dis. 222(4):681-689(2020).
RNF43 mutation is associated with aggressive tumor biology along with BRAF V600E mutation in right-sided colorectal cancer.
Matsumoto, A., Shimada, Y., Nakano, M., Oyanagi, H., Tajima, Y., Nakano, M., Kameyama, H., Hirose, Y., Ichikawa, H., Nagahashi, M., Nogami, H., Maruyama, S., Takii, Y., Ling, Y., Okuda, S., Wakai, T. RNF43 mutation is associated with aggressive tumor biology along with BRAF V600E mutation in right-sided colorectal cancer. Oncol. Rep. 43(6):1853-1862(2020).
Phosphoproteomic and bioinformatic methods for analyzing signaling in vertebrate axon growth and regeneration.
Igarashi, M., Kawasaki, A., Ishikawa, Y., Honda, A., Okada, M., and 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., and Cohen, K. B. Open Agile text mining for bioinformatics: the PubAnnotation ecosystem. Bioinformatics 1;35(21): 4372-4380 (2019).