論文・著書リスト

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Last update: Dec. 12, 2023

研究論文
著書等

2023
2022
2021
2020
2019
2018
2017
2016
2015
2014
2013
2012
~2011

Ito Y., Uda S., Kokaji T., Hirayama A., Soga T., Suzuki Y., Kuroda S., and Kubota H.

Comparison of hepatic responses to glucose perturbation between healthy and obese mice based on the edge type of network structures.

Sci. Rep., 13(1): 4758, 2023.

Maehara H., Kokaji T., Hatano A., Suzuki Y., Matsumoto M., Nakayama I. K., Egami R., Tsuchiya T., Ozaki H., Morita K., Shirai M., Li D., Terakawa A., Uematsu S., Hironaka K., Ohno S., Kubota H., Araki H., Miura F., Ito T., Kuroda S.

DNA hypomethylation characterizes genes encoding tissue-dominant functional proteins in liver and skeletal muscle.

Sci Rep., 19118, 2023.

Fujita S., Karasawa Y., Fujii M., Hironaka K. I., Uda S., Kubota H., Inoue H., Sumitomo Y., Hirayama A., Soga T. and Kuroda S.

Four features of temporal patterns characterize similarity among individuals and molecules by glucose ingestion in humans.

NPJ Syst. Biol. Appl., 8(1): 6, 2022.

Uematsu S., Ohno S., Tanaka K., Hatano A., Kokaji T., Ito Y., Kubota H., Hironaka K., Suzuki Y., Matsumoto M., Nakayama K., Hirayama A., Soga T., Kuroda S.

Multi-omics-based label-free metabolic flux inference reveals obesity-associated dysregulatory mechanisms in liver glucose metabolism.

iScience, 103787, 2022.

Kokaji T., Eto M., Hatano A., Yugi K., Morita K., Ohno S., Fujii M., Hironaka K., Ito Y., Egami R., Uematsu S., Terakawa A., Pan Y., Maehara H., Li D., Bai Y., Tsuchiya T., Ozaki H., Inoue H., Kubota H., Suzuki Y., Hirayama A., Soga T., Kuroda S.

In vivo transomic analyses of glucose-responsive metabolism in skeletal muscle reveal core differences between the healthy and obese states.

Sci. Rep., 13719, 2022.

Matshzaki F, Uda S, Yamauchi Y, Matsumoto M, Soga T, Maehara K, Ohkawa Y, Nakayama K, Kuroda S. and Kubota H,

An extensive and dynamic trans-omic network illustrating prominent regulatory mechanisms in response to insulin in the liver.

Cell Rep., 36(8): 109569, 2021.

　　　　　　　　　　　　プレスリリース（日本語）

Kubota H.

Selective Regulation of the Insulin-Akt Pathway by Simultaneous Processing of Blood Insulin Pattern in the Liver.

Methods of Mathematical Oncology (proceedings), 203-213, 2021.

Egami R, Kokaji T, Hatano A, Yugi K, Eto M, Morita K, Ohno S, Fujii M, Hironaka K, Uematsu S, Terakawa A, Bai Y, Pan Y, Tsuchiya T, Ozaki H, Inoue H, Uda S, Kubota H, Suzuki Y, Matsumoto M, Nakayama KI, Akiyoshi Hirayama A, Soga T, and Kuroda S.

Trans-omic analysis reveals obesity-associated dysregulation of inter-organ metabolic cycles between the liver and skeletal muscle.

iScience, 24(3): 102217, 2021.

Kokaji T, Hatano A, Ito Y, Yugi K, Eto M, Morita K, Ohno S, Fujii M, Hironaka K, Egami R, Terakawa A, Tsuchiya T, Ozaki H, Inoue H, Uda S, Kubota H, Suzuki Y, Ikeda K, Arita M, Matsumoto M, Nakayama KI, Hirayama A, Soga T, and Kuroda S.

Transomics analysis reveals allosteric and gene regulation axes for altered hepatic glucose-responsive metabolism in obesity.

Sci. Signal., 13(660): eaaz1236, 2020.

Wada T, Hironaka K, Wataya M, Fujii M, Eto M, Uda S, Hoshino D, Kunida K, Inoue H, Kubota H, Takizawa T, Karasawa Y, Nakatomi H, Saito N, Hamaguchi H, Furuichi Y, Manabe Y, Fujii NL, and Kuroda S.

Single-Cell Information Analysis Reveals That Skeletal Muscles Incorporate Cell-to-Cell Variability as Information Not Noise.

Cell Rep., 32(9): 108051, 2020.

Fujii M., Murakami Y., Karasawa Y., Sumitomo Y., Fujita S., Koyama M., Uda S., Kubota H., Inoue H., Konishi K., Oba S., Ishii S., and Kuroda S.

Logical design of oral glucose ingestion pattern minimizing blood glucose in humans.

NPJ Syst Biol Appl., 5: 31, 2019.

Ohigashi I., Tanaka Y., Kondo K., Fujimori S., Kondo H., Palin AC., Hoffmann V., Kozai M., Matsushita Y., Uda S., Motosugi R., Hamazaki J., Kubota H., Murata S., Tanaka K., Katagiri T., Kosako H., and Takahama Y.

Trans-omics Impact of Thymoproteasome in Cortical Thymic Epithelial Cells.

Cell Rep., 29(9): 2901-2916, 2019.

Uda S., and Kubota H.

Sparse Gaussian graphical model with missing values.

Proceedings of the 21st Conference of Open Innovations Association, FRUCT 2017, Vol. Part F134240: 336-343, 2018.

Kawata K., Yugi K., Hatano A., Kokaji T., Tomizawa Y., Fujii M., Uda S., Kubota H., Matsumoto M., Nakayama K. I., and Kuroda S.

Reconstruction of global regulatory network from signaling to cellular functions using phosphoproteomic data.

Genes to Cells., 00: 1-12, 2018.

Kawata K., Hatano A., Yugi K., Kubota H., Sano T., Fujii M., Tomizawa Y., Kokaji T., Tanaka K. Y., Uda S., Suzuki Y., Matsumoto M., Nakayama K. I., Saitoh K., Kato K., Ueno A., Ohishi M., Hirayama A., Soga T., and Kuroda S.

Trans-omic analysis reveals selective responses to induced and basal insulin across signaling, transcriptional, and metabolic networks.

iScience, 7: 212-229, 2018.

Kubota H., Uda S., Matsuzaki F., Yamauchi Y., and Kuroda S.

In vivo

decoding mechanisms of the temporal patterns of blood insulin by the insulin-AKT pathway in the liver.

Cell Syst., 7: 1-11, 2018.

　　　　　　　　　　　　プレスリリース（日本語）

Ohashi K., Fujii M., Uda S., Kubota H., Komada H., Sakaguchi K., Ogawa W., and Kuroda S.

Increase in hepatic and decrease in peripheral insulin clearance characterize abnormal temporal patterns of serum insulin in diabetic subjects.

NPJ Syst Biol Appl., 4: 14, 2018.

Tsuchiya T., Fujii M., Matsuda N., Kunida K., Uda S., Kubota H., Konishi K., and Kuroda S.

System identification of signaling dependent gene expression with different time-scale data.

PLoS Comput. Biol., 13(12): e1005913, 2017.

Sano T., Kawata K., Ohno S., Yugi K., Kakuda H., Kubota H., Uda S., Fujii M., Kunida K., Hoshino D., Hatano A., Ito Y., Sato M., Suzuki Y., and Kuroda S.

Selective control of up-regulated and down-regulated genes by temporal patterns and doses of insulin.

Sci. Signal., 9(455): ra112, 2016.

Yugi K., Kubota H., Hatano A., and Kuroda S.

Trans-Omics: How To Reconstruct Biochemical Networks Across Multiple 'Omic' Layers.

Trends Biotechnol., 34(4): 276-290, 2016.

Fukuda S., Nishida-Fukuda H., Nanba D., Nakashiro K., Nakayama H., Kubota H., and Higashiyama S.

Reversible interconversion and maintenance of mammary epithelial cell characteristics by the ligand-regulated EGFR system.

Sci. Rep., 6: 20209, 2016.

Katsura Y., Kubota H., Kunida K., Kuroda S., and Ozawa T.

An optogenetic system for interrogating the temporal dynamics of Akt.

Sci. Rep., 5: 14589, 2015.

Ohashi K., Komada H., Uda S., Kubota H., Iwaki T., Fukuzawa H., Komori Y., Fujii M., Toyoshima Y., Sakaguchi K., Ogawa W., and Kuroda S.

Glucose Homeostatic Law: Insulin Clearance Predicts the Progression of Glucose Intolerance in Humans.

PLoS ONE, 10(12): e0143880, 2015.

Yugi K., Kubota H., Toyoshima Y., Noguchi R., Kawata K., Komori Y., Uda S., Kunida K., Tomizawa Y., Funato Y., Miki H., Matsumoto M., Nakayama KI., Kashikura K., Endo K., Ikeda K., Soga T., and Kuroda S.

Reconstruction of insulin signal flow from phosphoproteome and metabolome data.

Cell Rep., 8: 1171-1183, 2014.

Noguchi R., Kubota H., Yugi K., Toyoshima Y., Komori Y., Soga T., and Kuroda S.

The Selective Control of Glycolysis, Gluconeogenesis and Glycogenesis by Temporal Insulin Patterns.

Mol. Syst. Biol., 9: 664, 2013.

Uda S., Saito T., Kudo T., Kokaji T., Tsuchiya T., Kubota, H., Komori Y., Ozaki Y., and Kuroda, S.

Robustness and compensation of information transmission of signaling pathways.

Science, 34(6145): 558-561, 2013.

Akimoto Y., Yugi K., Uda S., Komori Y., Kubota H., and Kuroda S.

The extraction of simple relationships in growth factor-specific multiple-input and multipleoutput systems in cell-fate decisions by backward elimination PLS regression.

PLoS ONE, 8(9): e72780, 2013.

Kubota H., and Kuroda S.

シグナル伝達機構による時間情報コード

生物物理, 53(4): 184-189, 2013.

Kubota H., Noguchi R., Toyoshima Y., Ozaki Y., Uda S., Watanabe K., Ogawa W., and Kuroda S.

Temporal Coding of Insulin Action through Multiplexing of the AKT Pathway.

Mol. Cell, 46: 820-832, 2012.

Fujita K., Toyoshima Y., Uda S., Ozaki Y., Kubota H., and Kuroda S.

Decoupling of Receptor and Downstream Signals in the Akt Pathway by Its Low-Pass Filter Characteristics.

Sci. Signal., 3(132): ra56, 2010.

Ozaki Y., Uda S., Saito T., Chung J., Kubota H., and Kuroda S.

A quantitative image cytometry technique for time series or population analyses of signaling networks.

PLoS ONE, 5(4): e9955, 2010.

Chung J., Kubota H., Ozaki Y., Uda S., and Kuroda, S.

Timing-Dependent Actions of NGF Required for Cell Differentiation.

PLoS ONE, 5(2): e9011, 2010.

Matsuo R., Kubota H., Obata T., Kito K., Ota K., Kitazono T., Ibayashi S., Sasaki T., Iida M., and Ito T.

The yeast eIF4E-associated protein Eap1p attenuates GCN4 translation upon TOR inactivation.

FEBS Lett., 579: 2433-2438, 2005.

Ichimura T., Kubota H., Goma T., Mizushima N., Ohsumi Y., Iwago M., Kakiuchi K., Shekhar H. U., Shinkawa T., Taoka M, Ito T., and Isobe T.

Transcriptomic and proteomic analysis of a 14-3-3 gene-deficient yeast.

Biochemistry, 43: 6149-6158, 2004.

Kubota H., Obata T., Ota K., Sasaki T., and Ito T.

Rapamycin-induced translational derepression of GCN4 mRNA involves a novel mechanism for activation of the eIF2α kinase GCN2.

J. Biol. Chem., 278: 20457-20460, 2003.

Ito T., Ota K., Kubota H., Yamaguchi Y., Chiba T., Sakuraba K., and Yoshida M.

Roles for the two-hybrid system in exploration of the yeast protein interactome.

Mol. Cell. Proteomics, 1: 561-566, 2002.

Kubota H., Ota K., Sakaki Y., and Ito T.

Budding yeast GCN1 binds the GI domain to activate the eIF2α kinase GCN2.

J. Biol. Chem., 276: 217591-217596, 2001.

Kubota H., Sakaki Y., and Ito T.

GI domain-mediated association of the eukaryotic initiation factor 2α kinase GCN2 with its activator GCN1 is required for general amino acid control in budding yeast.

J. Biol. Chem., 275: 20243-20246, 2000.