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Research Output 2004 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

Matrix rank minimization approach to signal recovery and nonlinear function estimation for nonlinear ARX model with input nonlinearity

Konishi, K., Fujii, M., Kunida, K., Uda, S. & Kuroda, S., Feb 8 2018, Control Conference (ASCC), 2017 11th Asian. IEEE

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

Recovery
Signal transduction
Systems Biology

Matrix rank minimization approach to signal recovery and nonlinear function estimation for nonlinear ARX model with input nonlinearity

Konishi, K., Fujii, M., Kunida, K., Uda, S. & Kuroda, S., Feb 7 2018, 2017 Asian Control Conference, ASCC 2017. Institute of Electrical and Electronics Engineers Inc., p. 1428-1431 4 p. (2017 Asian Control Conference, ASCC 2017; vol. 2018-January).

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

Nonlinear Estimation
Function Estimation
Autoregressive Model
Nonlinear Function
Nonlinear Model

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 : Food Science and Human Wellness. 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

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

Kawata, K., Hatano, A., Yugi, K., 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., 2018, In : iScience. 7, p. 212-229

Research output: Contribution to journalArticle

Gene Regulatory Networks
Metabolic Networks and Pathways
Insulin
Immediate-Early Genes
Metabolomics
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
10 Citations (Scopus)

Analysis of cellular signal transduction from an information theoretic approach

Uda, S. & Kuroda, S., Mar 1 2016, In : Seminars in Cell and Developmental Biology. 51, p. 24-31 8 p.

Research output: Contribution to journalReview article

Signal Transduction
Information Theory
Cell Differentiation
Cell Death
Cell Proliferation
1 Citation (Scopus)

Laguerre filter analysis with partial least square regression reveals a priming effect of ERK and CREB on c-FOS induction

Kudo, T., Uda, S., Tsuchiya, T., Wada, T., Karasawa, Y., Fujii, M., Saito, T. H. & Kuroda, S., Aug 1 2016, In : PloS one. 11, 8, e0160548.

Research output: Contribution to journalArticle

Least-Squares Analysis
mitogen-activated protein kinase
least squares
Molecules
Immediate-Early Genes
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
2015
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
2014
36 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
51 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
15 Citations (Scopus)

Temporal Decoding of MAP Kinase and CREB Phosphorylation by Selective Immediate Early Gene Expression

Saito, T. H., Uda, S., Tsuchiya, T., Ozaki, Y. I. & Kuroda, S., Mar 4 2013, In : PloS one. 8, 3, e57037.

Research output: Contribution to journalArticle

Phosphorylation
Immediate-Early Genes
mitogen-activated protein kinase
Gene expression
Decoding
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
2012
17 Citations (Scopus)

Latent process genes for cell differentiation are common decoders of neurite extension length

Watanabe, K., Akimoto, Y., Yugi, K., Uda, S., Chung, J., Nakamuta, S., Kaibuchi, K. & Kuroda, S., May 1 2012, In : Journal of Cell Science. 125, 9, p. 2198-2211 14 p.

Research output: Contribution to journalArticle

Neurites
Cell Differentiation
Genes
Nerve Growth Factors
Nerve Growth Factor
14 Citations (Scopus)

Sensitivity control through attenuation of signal transfer efficiency by negative regulation of cellular signalling

Toyoshima, Y., Kakuda, H., Fujita, K. A., Uda, S. & Kuroda, S., Apr 4 2012, In : Nature communications. 3, 1745.

Research output: Contribution to journalArticle

Cell signaling
S 6
MAP Kinase Signaling System
Epidermal Growth Factor Receptor
attenuation
60 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
37 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
2009

Specific features of transient Ras and sustained Rap1 activation

Ozaki, Y., Uda, S. & Kuroda, S., 2009, Systems Biology: the Challenge of Complexity Springer . p. 121-127

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

2006
41 Citations (Scopus)

Analysis of CDMA systems that are characterized by eigenvalue spectrum

Takeda, K., Uda, S. & Kabashima, Y., 2006, In : Europhysics Letters. 76, p. 1193-1199

Research output: Contribution to journalArticle

2005
11 Citations (Scopus)

Statistical mechanical development of a sparse Bayesian classifier

Uda, S. & Kabashima, Y., 2005, In : Journal of the Physical Society of Japan. 74, p. 2233-2242

Research output: Contribution to journalArticle

2004
6 Citations (Scopus)

A BP-Based Algorithm for Performing Bayesian Inference in Large Perceptron-Type Networks

Kabashima, Y. & Uda, S., 2004, International Conference on Algorithmic Learning Theory. p. 479-493

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

6 Citations (Scopus)

Minimizing the Cross Validation Error to Mix Kernel Matrices of Heterogeneous Biological Data

Tsuda, K., Uda, S., Kin, T. & Asai, K., 2004, In : Neural Processing Letters. 19, p. 63-72

Research output: Contribution to journalArticle