Department of AI Technology Development

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Member

Satoru Miyano

Specially Appointed Professor (Acting Department Head)

Takashi Kamatani

Junior Associate Professor

Research Topics

Medical big-data analysis and evidence-based personalized medicine are crucial to settle on social issues that we face, such as the population decline and super-aging challenge. Our mission of Department of AI Technology Development is to develop the statistical and artificial intelligence methodologies that can be used in biomedical research and to identify evidence if precision medicine based on biomedical data analysis.
The main research areas of the Department of AI Technology Development include: 1. Development of the statistical and artificial intelligence methodologies that can be used in biomedical research; 2. Uncovering complex mechanism of diseases (e.g., cancer) based on biomedical data analysis.

Develop statistical and artificial methodologies for precision medicine

To improve efficiency of medical treatment and preventive care, genomic personalized medicine has been drawn a large amount of attention. One of our research topics is developing computational strategies for patient specific analysis and provide data-driven evidence to achieve effective precision medicine.

Network Biology

Gene regulatory network is crucial for understanding complex disease mechanisms because
the molecular mechanisms of diseases involve many genes intricately connected in a molecular network rather than the abnormality of a single gene. We conduct network biology studies, such as development of computational approaches for gene regulatory network estimation and network-based marker identification, especially we focus on interpretation of multilayer massive networks.

Publications

Paper & Review

Ikeda N, Kubota H, Suzuki R, Morita M, Yoshimura A, Osada Y, Kishida K, Kitamura D, Iwata A, Yotsumoto S, Kurotaki D, Nishimura K, Tamura T, Kamatani T, Tsunoda T, Murakawa Miyako, Asahina Y, Hayashi Y, Harada H, Harada Y, Yokota A, Hirai H, Seki T, Kuwahara M, Yamashita M, Shichino S, Tanaka M, Asano K. The early neutrophil-committed progenitors aberrantly differentiate into immunoregulatory monocytes during emergency myelopoiesis. Cell Reports (2023 Accepted.).
H. Park, S. Imoto and S. Miyano.GRN-classifier: Gene regulatory network-based classifier and its applications to gastric cancer drug (5-FU) marker identification.Journal of Computational Biology, In press.
H. Park, S. Imoto and S. Miyano.PredictiveNetwork: predictive gene network estimation with application to gastric cancer drug response-predictive network analysis. BMC Bioinformatics, 23(1):342. (2022)
H. Park, R. Yamaguchi, S. Imoto and S. Miyano.Xprediction: Explainable EGFR-TKIs response prediction based on drug sensitivity specific gene networks.PLoS One, 17(5):e0261630. (2022)
H. Park, R. Yamaguchi, S. Imoto and S. Miyano.Uncovering Molecular Mechanisms of Drug Resistance via Network-Constrained Common Structure Identification. Journal of Computational Biology, 29(3):257-275. (2022)
Kameyama N, Sato T, Arai D, Fujisawa D, Takeuchi M, Nakachi I, Kawada I, Yasuda H, Ikemura S, Terai H, Nukaga S, Nakano Y, Hirano T, Minematsu N, Asakura T, Kamatani T, Tanaka K, Suzuki S, Miyawaki M, Naoki K, Fukunaga K, Soejima K. Most important things and associated factors with prioritizing ‘daily life’ in patients with advanced lung cancer. JCO Oncology Practice, 18, e1977-86 (2022).
Baba R, Kabata H, Shirasaki Y, Kamatani T, Yamagishi M, Irie M, Watanabe R, Matsusaka M, Masaki K, Miyata J, Moro K, Uemura S, Fukunaga K. Upregulation of IL-4 receptor signaling pathway in circulating ILC2s from asthma patients. The Journal of Allergy and Clinical Immunology: Global, 1, 299-304 (2022).
Matsuo H, Kamatani T, Hamba Y, Boroevich KA, Tsunoda T. Association between high immune activity and worse prognosis in uveal melanoma and low-grade glioma in TCGA transcriptomic data. BMC Genomics, 23, 351 (2022).
Sugawara T, Miya F, Ishikawa T, Lysenko A, Nishino J, Kamatani T, Takemoto A, Boroevich KA, Kakimi K, Kinugasa Y, Tanabe M, Tsunoda T. Immune subtypes and neoantigen-related immune evasion in advanced colorectal cancer. iScience, 25, 103740 (2022)
Hakozaki K, Tanaka N*, Takamatsu K, Takahashi R, Yasumizu Y, Mikami S, Shinojima T, Kakimi K, Kamatani T, Miya F, Tsunoda T, Aimono E, Nishihara H, Mizuno R & Oya M. Landscape of prognostic signatures and immunogenomics of the AXL/GAS6 axis in renal cell carcinoma. BR. J. Cancer, 125, 1533-43 (2021)
Takamatsu K, Tanaka N*, Hakozaki K, Takahashi R, Teranishi Y, Murakami T, Kufukihara R, Niwa N, Mikami S, Shinojima T, Sasaki T, Sato Y, Kume H, Ogawa S, Kakimi K, Kamatani T, Miya F, Tsunoda T, Aimono E, Nishihara H, Sawada K, Imamura T, Mizuno R, and Oya M. Profiling the inhibitory receptors LAG-3, TIM-3, and TIGIT in renal cell carcinoma reveals malignancy. Nat. Commun., 12, 5547 (2021).
Ishioka K, Yasuda H, Hamamoto J, Terai H, Emoto K, Kim TJ, Hirose S, Kamatani T, Mimaki S, Arai D, Ohgino K, Tani T, Masuzawa K, Manabe T, Shinozaki T, Mitsuishi A, Ebisudani T, Fukushima T, Ozaki M, Ikemura S, Kawada I, Naoki K, Nakamura M, Ohtsuka T, Asamura H, Tsuchihara K, Hayashi Y, Hegab AE, Kobayashi SS, Kohno T, Watanabe H, Ornitz DM, Betsuyaku T, Soejima K, Fukunaga K. Upregulation of FGF9 in Lung Adenocarcinoma Transdifferentiation to Small Cell Lung Cancer. Cancer Res., 81, 3916-29 (2021)
DU R, Xie S, Fang Y, Igarashi-Yokoi T, Moriyama M, Ogata S, Tsunoda T, Kamatani T, Yamamoto S, Cheng CY, Saw SM, Ting D, Wong TY, Ohno-Matsui K. Deep Learning Approach for Automated Detection of Myopic Maculopathy and Pathologic Myopia in Fundus Images. Ophthalmol. Retinal., S2468-6530 (2021).
Nishiguchi KM*, Miya F* (equal contribution), Fujita K, Akiyama M, Takigawa T, Kamatani T, Koyanagi Y, Ueno S, Tsugita M, Kunikata H, Cisarova K, Nishino J, Murakami A, Abe T, Momozawa Y, Terasaki H, Wada Y, Sonoda K, Rivolta C, Ishibashi T, Tsunoda T, Tsujikawa M, Ikeda Y, Nakazawa T. A hypomorphic variant in EYS detected by genome-wide association study contributes toward retinitis pigmentosa. Commun. Biol., 29, 140 (2021).
H. Park, K. Maruhashi, R. Yamaguchi, S. Imoto and S. Miyano.Global gene network exploration based on explainable artificial intelligence approach. PLoS One, 15(11):e0241508. (2020)
H. Park, R. Yamaguchi, S. Imoto and S. Miyano.Automatic sparse principal component analysis.Canadian Journal of Statistics, 49(3):678-697. (2020)
Sato Y, Wada I, Odaira K, Kobayashi Y, Hosoi A, Nagaoka K, Karasaki T, Matsushita H, Yagi K, Yamashita H, Fujita M, Watanabe S, Kamatani T, Miya F, Mineno J, Nakagawa H, Tsunoda T, Takahashi S, Seto Y, Kakimi K. Integrative immunogenomic analysis of gastric cancer dictates novel immunological classification and the functional status of tumor-infiltrating cells. Clin. Transl. Immunology 9, e1194 (2020).
Masaki K, Miyata J, Kamatani T, Tanosaki T, Mochimaru T, Kabata H, Suzuki Y, Asano K, Betsuyaku T, Fukunaga K. Risk factors for poor adherence to inhaled corticosteroid therapy in patients with moderate to severe asthma. Asian Pac J Allergy Immunol. 2020
Nishino J, Watanabe S, Miya F, Kamatani T, Sugawara T, Boroevich KA, Tsunoda T. Quantification of multicellular colonization in tumor metastasis using exome sequencing data. Int. J. Cancer, 146, 2488-2497 (2020).