Escherichia coli-derived outer-membrane vesicles induce immune activation and progression of cirrhosis in mice and humans.
Natsui, K., Tsuchiya, A., Imamiya, R., Osada-Oka, M., Ishii, Y., Koseki,Y., Takeda, N., Tomiyoshi, K., Yamazaki, F., Yoshida, Y., Ohashi, R., Ling, Y., Ueda, K., Moritoki, N., Sato, K., Nakajima, T., Hasegawa, Y., Okuda, S., Shibata, S., Terai, S. Escherichia coli-derived outer-membrane vesicles induce immune activation and progression of cirrhosis in mice and humans. Liver Int. 43(5):1126-1140(2023).
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).
The ProteomeXchange consortium at 10 years: 2023 update.
Deutsch, E. W., Bandeira, N., Perez-Riverol, Y., Sharma, V., Carver, J. J., Mendoza, L., Kundu, D. J., Wang, S., Bandla, C., Kamatchinathan, S., Hewapathirana, S., Pullman, B. S., Wertz, J., Sun, Z., Kawano, S., Okuda, S., Watanabe, Y., MacLearn B., MacCoss, M. J., Zhu, Y., Ishihama, Y.,Vizcaíno, J. A. The ProteomeXchange consortium at 10 years: 2023 update. Nucleic Acids Res. 51(D1):D1539-D1548(2022).
Elucidating the multiple genetic alterations involved in the malignant transformation of a KRAS mutant neurenteric cyst. A case report.
Saito, S., Natsumeda, M., Sainouchi, M., Takino, T., Shibuya, K., On, J., Kanemaru, Y., Ogura, R., Okada, M., Oishi, M., Shimada, Y., Wakai, T., Okuda, S., Ajioka,Y., kakita, A., Fujii, Y. Elucidating the multiple genetic alterations involved in the malignant transformation of a KRAS mutant neurenteric cyst. A case report. Neuropathology 42(6):519-525 (2022).
Deep learning classification of urinary sediment crystals with optimal parameter tuning.
Nagai, T., Onodera, O., Okuda, S. Deep learning classification of urinary sediment crystals with optimal parameter tuning. Sci. Rep. 12(1):21178(2022).
Copy number alteration is an independent prognostic biomarker in triple-negative breast cancer patients.
Nagahashi, M., Ling, Y., Toshikawa, C., Hayashida, T., Kitagawa, Y., Futamura, M., Kuwayama, T., Nakamura, S., Yamauchi, H., Yamauchi, T., Kaneko, K., Kanbayashi, C., Sato, N., Tsuchida, J., Moro, K., Nakajima, M., Shimada, Y., Ichikawa, H., Lyle, S., Miyoshi, Y., Takabe, K., Okuda, S., Wakai, T. Copy number alteration is an independent prognostic biomarker in triple-negative breast cancer patients. SABCS2022, San Antonio (2022/12/6).
A Novel Approach to Construct Variant Protein Sequences for Precision Medical Proteogenomics.
Yiwei, Ling., Okuda, S. A Novel Approach to Construct Variant Protein Sequences for Precision Medical Proteogenomics. HUPO2022, Cancun (2022/12/5).
NKp44-based chimeric antigen receptor effectively redirects primary T cells against synovial sarcoma.
Murayama,Y., Kasahara, Y., Kubo, N., Shin, C., Imamura,M., Oike, N., Ariizumi, T., Saitoh, A., Baba, M., Miyazaki, T., Suzuki, Y., Ling, Y., Okuda, S., Mihara, K., Ogose, A., Kawashima, H., Imai, C. NKp44-based chimeric antigen receptor effectively redirects primary T cells against synovial sarcoma. Transl. Oncol. 25:101521(2022).
Elevated bile acid metabolism and microbiome are associated with suppressed cell proliferation and better survival in breast cancer.
Wu, R., Yu, I., Tokumaru, Y., Asaoka, M., Oshi, M., Yan, L., Okuda, S., Ishikawa, T., Takabe, K. Elevated bile acid metabolism and microbiome are associated with suppressed cell proliferation and better survival in breast cancer. Am. J. Cancer Res. 12(11):5271-5285(2022).
Differential analysis of microbiomes in mucus and tissues obtained from colorectal cancer patients.
Tajima, Y., Okuda, S., Hanai, T., Hiro, J., Masumori, K., Koide, Y., Kamiya, T., Cheong, Y., Inaguma, G., Shimada, Y., Wakai, T., Takihara, H., Akimoto, S., Matsuoka, H., Uyama, I., Suda, K. Differential analysis of microbiomes in mucus and tissues obtained from colorectal cancer patients. Sci. Rep. 12(1)18193(2022).