Genetic profiling for diffuse type and genomically stable subtypes in gastric cancer.
Ling, Y., Watanabe, Y., Nagahashi, M., Shimada, Y., Ichikawa, H., Wakai, T., Okuda, S. Genetic profiling for diffuse type and genomically stable subtypes in gastric cancer. Comput. Struct. Biotechnol. J. 18:3301-3308(2020).
Higher genome mutation rates of Beijing lineage of Mycobacterium tuberculosis during human infection.
Hakamata, M., Takihara, H., Iwamoto, T., Tamaru, A., Hashimoto, A., Tanaka, T., Kaboso, S. A., Gebretsadik, G., Ilinov, A., Yokoyama, A., Ozeki, Y., Nishiyama, A., Tateishi, Y., Moro, H., Kikuchi, T., Okuda, S., Matsumoto, S. Higher genome mutation rates of Beijing lineage of Mycobacterium tuberculosis during human infection. Sci. rep. 10(1):17997(2020).
Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics.
Yang, M., Petralia, F., Li, Z., Li, H., Ma, W., Song, X., Kim, S., Lee, H., Yu, H., Lee, B., Bae, S., Heo, E., Kaczmarczyk, J., Stępniak, P., Warchoł, M., Yu, T., Calinawan, A. P., Boutros, P. C., Payne, S. H., Reva, B.; NCI-CPTAC-DREAM Consortium, Boja, E., Rodriguez, H., Stolovitzky, G., Guan, Y., Kang, J., Wang, P., Fenyö, D., Saez-Rodriguez, J. Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics. Cell Systems 11(2):186-195.e9 (2020).
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).