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Research Output 2000 2019

2019

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

Kawata, K., Yugi, K., Hatano, A., Kokaji, T., Tomizawa, Y., Fujii, M., Uda, S., Kubota, H., Matsumoto, M., Nakayama, K. & Kuroda, S., Jan 1 2019, In : Genes to Cells. 24, 1, p. 82-93 12 p.

Research output: Contribution to journalArticle

Insulin
Phosphorylation
Proteins
Protein Kinases
Hepatocellular Carcinoma
2018
1 Citation (Scopus)
Western Blotting
Insulin
Liver
1 Citation (Scopus)

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

Ohashi, K., Fujii, M., Uda, S., Kubota, H., Komada, H., Sakaguchi, K., Ogawa, W. & Kuroda, S., Dec 1 2018, In : npj Systems Biology and Applications. 4, 1, 14.

Research output: Contribution to journalArticle

Insulin
Clearance
Decrease
Diabetes Mellitus
Liver

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

Ohashi, K., Fujii, M., Uda, S., Kubota, H., Komada, H., Sakaguchi, K., Ogawa, W. & Kuroda, S., 2018, In : npj Systems Biology and Applications. 4, 14.

Research output: Contribution to journalArticle

Open Access
Insulin
Liver
Serum
Type 2 Diabetes Mellitus
Glucose
2 Citations (Scopus)

In Vivo Decoding Mechanisms of the Temporal Patterns of Blood Insulin by the Insulin-AKT Pathway in the Liver

Kubota, H., Uda, S., Matsuzaki, F., Yamauchi, Y. & Kuroda, S., Jul 25 2018, In : Cell Systems. 7, 1, p. 118-128.e3

Research output: Contribution to journalArticle

Insulin
Liver
Hormones
Homeostasis
Glucose Clamp Technique

Sparse Gaussian graphical model with missing values

Uda, S. & Kubota, H., Jan 8 2018, Proceedings of the 21st Conference of Open Innovations Association, FRUCT 2017. IEEE Computer Society, p. 336-343 8 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Signal transduction
Molecular interactions
Factorization
Genes
Proteins
5 Citations (Scopus)

Trans-omic Analysis Reveals Selective Responses to Induced and Basal Insulin across Signaling, Transcriptional, and Metabolic Networks

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., Saitoh, K., Kato, K., Ueno, A., Ohishi, M., Hirayama, A., Soga, T. & Kuroda, S., Sep 28 2018, In : iScience. 7, p. 212-229 18 p.

Research output: Contribution to journalArticle

Open Access
Gene Regulatory Networks
Metabolic Networks and Pathways
insulin
Insulin
Immediate-Early Genes
2017
1 Citation (Scopus)

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

Tsuchiya, T., Fujii, M., Matsuda, N., Kunida, K., Uda, S., Kubota, H., Konishi, K. & Kuroda, S., Dec 1 2017, In : PLoS Computational Biology. 13, 12, e1005913.

Research output: Contribution to journalArticle

System Identification
Gene expression
Gene Expression
gene expression
Identification (control systems)
2016
4 Citations (Scopus)

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

Fukuda, S., Nishida-Fukuda, H., Nanba, D., Nakashiro, K. I., Nakayama, H., Kubota, H. & Higashiyama, S., Feb 2 2016, In : Scientific reports. 6, 20209.

Research output: Contribution to journalArticle

Epidermal Growth Factor Receptor
Breast
Epithelial Cells
Maintenance
Epidermal Growth Factor
5 Citations (Scopus)

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

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. & Kuroda, S., Nov 22 2016, In : Science Signaling. 9, 455, ra112.

Research output: Contribution to journalArticle

Genes
Insulin
Transcription
RNA Stability
Medical problems
67 Citations (Scopus)

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

Yugi, K., Kubota, H., Hatano, A. & Kuroda, S., Apr 1 2016, In : Trends in Biotechnology. 34, 4, p. 276-290 15 p.

Research output: Contribution to journalReview article

Data integration
Metabolism
Life Style
Technology
Phenotype
2015
22 Citations (Scopus)

An optogenetic system for interrogating the temporal dynamics of Akt

Katsura, Y., Kubota, H., Kunida, K., Kanno, A., Kuroda, S. & Ozawa, T., Oct 1 2015, In : Scientific reports. 5, 14589.

Research output: Contribution to journalArticle

Optogenetics
Light
Muscular Atrophy
Protein-Serine-Threonine Kinases
Lighting
8 Citations (Scopus)

Glucose homeostatic law: Insulin clearance predicts the progression of glucose intolerance in humans

Ohashi, K., Komada, H., Uda, S., Kubota, H., Iwaki, T., Fukuzawa, H., Komori, Y., Fujii, M., Toyoshima, Y., Sakaguchi, K., Ogawa, W. & Kuroda, S., Dec 1 2015, In : PLoS One. 10, 12, A38.

Research output: Contribution to journalArticle

Glucose Intolerance
glucose tolerance
insulin
Insulin
Glucose

Temporal coding of insulin signaling

Kubota, H. & Kuroda, S., Sep 2 2015, Protein Modifications in Pathogenic Dysregulation of Signaling. Springer Japan, p. 95-109 15 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Insulin
Cell signaling
Molecules
Biological systems
Medical problems
2014
37 Citations (Scopus)

Reconstruction of insulin signal flow from phosphoproteome and metabolome data

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, K., Kashikura, K., Endo, K., Ikeda, K., Soga, T. & Kuroda, S., Aug 21 2014, In : Cell Reports. 8, 4, p. 1171-1183 13 p.

Research output: Contribution to journalArticle

Metabolome
Phosphorylation
Homeostasis
Liver Type Phosphofructokinase-1
Insulin
2013
54 Citations (Scopus)

Robustness and compensation of information transmission of signaling pathways

Uda, S., Saito, T. H., Kudo, T., Kokaji, T., Tsuchiya, T., Kubota, H., Komori, Y., Ozaki, Y. I. & Kuroda, S., Jan 1 2013, In : Science. 341, 6145, p. 558-561 4 p.

Research output: Contribution to journalArticle

Intercellular Signaling Peptides and Proteins
Entropy
Neurites
Pharmacology
Gene Expression
3 Citations (Scopus)

The Extraction of Simple Relationships in Growth Factor-Specific Multiple-Input and Multiple-Output Systems in Cell-Fate Decisions by Backward Elimination PLS Regression

Akimoto, Y., Yugi, K., Uda, S., Kudo, T., Komori, Y., Kubota, H. & Kuroda, S., Sep 9 2013, In : PloS one. 8, 9, e72780.

Research output: Contribution to journalArticle

Least-Squares Analysis
mitogen-activated protein kinase
growth factors
least squares
Intercellular Signaling Peptides and Proteins
26 Citations (Scopus)

The selective control of glycolysis, gluconeogenesis and glycogenesis by temporal insulin patterns

Noguchi, R., Kubota, H., Yugi, K., Toyoshima, Y., Komori, Y., Soga, T. & Kuroda, S., Jan 1 2013, In : Molecular Systems Biology. 9, 1, 664.

Research output: Contribution to journalArticle

glycogenesis
Glycolysis
Gluconeogenesis
gluconeogenesis
Insulin
2012
61 Citations (Scopus)

Temporal Coding of Insulin Action through Multiplexing of the AKT Pathway

Kubota, H., Noguchi, R., Toyoshima, Y., Ozaki, Y. I., Uda, S., Watanabe, K., Ogawa, W. & Kuroda, S., Jun 29 2012, In : Molecular Cell. 46, 6, p. 820-832 13 p.

Research output: Contribution to journalArticle

Insulin
Phosphorylation
Ribosomal Protein S6 Kinases
Glycogen Synthase Kinase 3
Glucose-6-Phosphatase
2010
23 Citations (Scopus)

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

Ozaki, Y. I., Uda, S., Saito, T. H., Chung, J., Kubota, H. & Kuroda, S., Sep 10 2010, In : PloS one. 5, 4, e9955.

Research output: Contribution to journalArticle

Image Cytometry
Cell signaling
Time series
time series analysis
Systems Biology
39 Citations (Scopus)

Decoupling of receptor and downstream signals in the Akt pathway by its low-pass filter characteristics

Fujita, K. A., Toyoshima, Y., Uda, S., Ozaki, Y. I., Kubota, H. & Kuroda, S., Jul 27 2010, In : Science Signaling. 3, 132

Research output: Contribution to journalArticle

Phosphorylation
Low pass filters
Epidermal Growth Factor Receptor
Molecules
Ribosomal Protein S6
33 Citations (Scopus)

Timing-dependent actions of NGF required for cell differentiation

Chung, J., Kubota, H., Ozaki, Y. I., Uda, S. & Kuroda, S., Feb 2 2010, In : PLoS One. 5, 2, e9011.

Research output: Contribution to journalArticle

Nerve Growth Factor
cell differentiation
neurites
Cell Differentiation
phosphatidylinositol 3-kinase
2005
15 Citations (Scopus)

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

matsuo, R., Kubota, H., Obata, T., Kito, K., Ota, K., Kitazono, T., Ibayashi, S., Sasaki, T., Iida, M. & Ito, T., Apr 25 2005, In : FEBS Letters. 579, 11, p. 2433-2438 6 p.

Research output: Contribution to journalArticle

Sirolimus
Yeast
Yeasts
Proteins
Amino Acids
2004
32 Citations (Scopus)

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

Ichimura, T., Kubota, H., Goma, T., Mizushima, N., Ohsumi, Y., Iwago, M., Kakiuchi, K., Shekhar, H. U., Shinkawa, T., Taoka, M., Ito, T. & Isobe, T., May 25 2004, In : Biochemistry. 43, 20, p. 6149-6158 10 p.

Research output: Contribution to journalArticle

Proteomics
Yeast
Genes
Yeasts
Saccharomyces cerevisiae
2003
80 Citations (Scopus)

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

Kubota, H., Obata, T., Ota, K., Sasaki, T. & Ito, T., Jun 6 2003, In : Journal of Biological Chemistry. 278, 23, p. 20457-20460 4 p.

Research output: Contribution to journalArticle

Sirolimus
Transfer RNA
Phosphotransferases
Chemical activation
Messenger RNA
2002
96 Citations (Scopus)

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

Ito, T., Ota, K., Kubota, H., Yamaguchi, Y., Chiba, T., Sakuraba, K. & Yoshida, M., Jan 1 2002, In : Molecular & cellular proteomics : MCP. 1, 8, p. 561-566 6 p.

Research output: Contribution to journalReview article

Fungal Proteins
Hybrid systems
Two-Hybrid System Techniques
Proteins
Yeast
2001
37 Citations (Scopus)

Budding Yeast GCN1 Binds the GI Domain to Activate the eIF2α Kinase GCN2

Kubota, H., Ota, K., Sakaki, Y. & Ito, T., May 18 2001, In : Journal of Biological Chemistry. 276, 20, p. 17591-17596 6 p.

Research output: Contribution to journalArticle

Eukaryotic Initiation Factor-2
Saccharomycetales
Yeast
Phosphotransferases
Bearings (structural)
2000
40 Citations (Scopus)
Eukaryotic Initiation Factor-2
Saccharomycetales
Yeast
Phosphotransferases
Association reactions