Medical AI center, Niigata University School of Medicine/Niigata University Graduate School of Medical and Dental Sciences - Medical AI Center/Bioinformatics laboratory

About us

Bioinformatics laboratory focuses on the following topics.

Functional genomics/metagenomics

Human gut microbiomes
Comparative metagenomics
Evolution of phosphorylation
Cancer genomics
Artificial intelligence (machine learning)

Database construction

HEMM: Human - Earth Microbes and Microbiomes
ODB: Operon DataBase
GlycoEpitope
jPOST: Japan ProteOme STandard repository/database.

Latest publications

Hsiao, Y.T., Yoshida, Y., Okuda, S., Abe, M., Mizuno, S., Takahashi, S., Nakagami, H., Morishita, R., Kamimura, K., Terai, S., Aung, T.M., Li, J., Furihata, T., Tang, J.Y., Walsh, K., Ishigami, A., Minamino, T., Shimizu, I. PCPE-1, a brown adipose tissue-derived cytokine, promotes obesity-induced liver fibrosis. EMBO J. 43(21):4846-4869(2024). PubMed The EMBO Journal
Paper
Ichikawa, H., Aizawa, M., Kano, Y., Hanyu, T., Muneoka, Y., Hiroi, S., Ueki, H., Moro, K., Hirose, Y., Miura, K., Shimada, Y., Sakata, J., Yabusaki, H., Nakagawa, S., Kawasaki, T., Okuda, S., Wakai, T. Landscape of homologous recombination deficiency in gastric cancer and clinical implications for first-line chemotherapy. Gastric Cancer 27(6):1273-1286(2024). PubMed Gastric Cancer
Paper
Katsumi, T., Hayashi, R., Takei, S., Ansai, O., Takatsuka,S., Takenouchi, T., Saito, K., Suda, K., Yoshihara, K., Nagai, T., Okuda, S., Fukumoto, T., Ansai, S. I., Nakamura, A., Katsuumi, K., Ariizumi, T., Ogose, A., Kawashima, H., Abe, R. Reevaluating hybrid neurofibroma/schwannoma: Predominance of schwannoma features despite CD34 positivity and initial neurofibroma diagnosis. J. Dermatol. 51(11):1461-1469(2024). …
Paper
Liu, Y., Yoshizawa, A.C., Ling, Y., Okuda, S. Insights into predicting small molecule retention times in liquid chromatography using deep learning. J. Cheminform. 16(1):113(2024) PubMed Journal of Cheminformatics
Paper
Mitsui, A., Iioka, H., Ling, Y., Okuda, S., Kurose, A., Schopperle, M., Kondo, T., Sakaguchi, M., Saito, K., Kondo, E. Pathological and Biological Significance of the Specific Glycan, TRA-1-60, on Aggressive Gastric Adenocarcinoma. Lab Invest. 104(7):102073(2024). PubMed Laboratory Investigation .
Paper
Shiroma, H., Darzi, Y., Terajima, E., Nakagawa, Z., Tsuchikura, H., Tsukuda, N., Moriya, Y., Okuda, S., Goto, S., Yamada, T. Enteropathway: the metabolic pathway database for the human gut microbiota. Brief. Bioinform. 25(5):bbae419(2024). PubMed Briefings in Bioinformatics
Paper

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