Publication List | previous publications

2018

Ohashi, K., Fujii, M., Uda, S., Kubota, H., Komada, H., Sakaguchi, K., Ogawa, W. and Kuroda, S., (2018). Increase in hepatic and decrease in peripheral insulin clearance characterize abnormal temporal patterns of serum insulin in diabetic subjects. npj Systems Biology and Applications. 4:14. doi:10.1038/s41540-018-0051-6 [Full text] Yugi, K., Kuroda, S., (2018). Metabolism as a signal generator across trans-omic networks at distinct time scales. Current Opinions in Systems Biology. 8: 59-66. doi:10.1016/j.coisb.2017.12.002 [Abstract]

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2017

Tsuchiya, T., Fujii, M., Matsuda, N., Kunida., K, Uda, S., Kubota, H., Konishi, K. and Kuroda, S., (2017). System identification of signaling dependent gene expression with different time-scale data. PLoS Computational Biology. 13(12): e1005913. doi:10.1371/journal.pcbi.1005913 [Full text] Krycer, J.R., Yugi, K., Hirayama, A., Fazakerley, D.J., Quek, L.-E., Scalzo, R., Ohno, S., Hodson, M.P., Ikeda, S., Shoji, F., Suzuki, K., Domanova, W., Parker L.B., Nelson M.E., Humphrey, S.J., Turner, N., Hoehn, K.L., Cooney, GJ., Soga, T., Kuroda, S., and James, D.E., (2017). Dynamic Metabolomics Reveals that Insulin Primes the Adipocyte for Glucose Metabolism. Cell Reports. 21, 3536?354. doi:10.1016/j.celrep.2017.11.085 [Abstract] Fujii., M., Ohashi., K., Karasawa., Y., Hikichi., M., Kuroda., S., (2017) Small-Volume Effect Enables Robust, Sensitive, and Efficient Information Transfer in the Spine, Biophysical Journal 112(4): p813-826. doi:10.1016/j.bpj.2016.12.043 [Abstract] Yugi, K., Kuroda, S., (2017) Metabolism-Centric Trans-Omics, Cell Systems 4(1): 19-20. doi:10.1016/j.cels.2017.01.007 [Abstract]

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2016

Sano, T., Kawata, K., Ohno, S., Yugi, K., Kakuda, K., Kubota, H., Uda, S., Fujii, M., Kunida, K., Hoshino, D., Hatano, A., Ito, Y., Sato, M., Suzuki, Y., Kuroda, S., (2016) Selective control of up-regulated and down-regulated genes by temporal patterns and doses of insulin, Science Signaling 22(9): ra112. doi:10.1126/scisignal.aaf3739 [Abstract] Kudo, T., Uda, S., Tsuchiya, T., Wada, T., Karasawa, Y., Fujii, M., Saito, T. H., Kuroda, S., (2016) Laguerre Filter Analysis with Partial Least Square Regression Reveals a Priming Effect of ERK and CREB on c-FOS Induction, PLoS ONE 11(8): e0160548. doi:10.1371/journal.pone.0160548 [Full text] Filippi, S., Barnes, C. P., Kirk, P.D.W., Kudo, T., Kunida, K., McMahon, S. S., Tsuchiya, T., Wada, T., Kuroda, S., and Stumpf, M. P. H. (2016) Robustness of MEK-ERK Dynamics and Origins of Cell-to-Cell Variability in MAPK Signaling, Cell Reports 15, 1-12, doi:10.1016/j.celrep.2016.05.024 [Abstract] Yugi, K., Kubota, H., Hatano, A., Kuroda, S., (2016) Trans-Omics: How To Reconstruct Biochemical Networks Across Multiple ‘Omic?ELayers, Trends in Biotechnology. 34(4):276-290. doi:10.1016/j.tibtech.2015.12.013 [Abstract] Uda, S., Kuroda, S., (2016) Analysis of cellular signal transduction from an information theoretic approach, Seminars in Cell & Developmental Biology. 51, 24-31. doi:10.1016/j.semcdb.2015.12.011 [Abstract]

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2015

Ohashi, K., Komada, H., Uda, S., Kubota, H., Iwaki, T., Fukuzawa, H., Komori., Y, Fujii, M., Toyoshima, Y., Sakaguchi, K., Ogawa, W., Kuroda, S., (2015) Glucose Homeostatic Law: Insulin Clearance Predicts the Progression of Glucose Intolerance in Humans, PLoS One. 10(12), e0143880, doi:10.1371/journal.pone.0143880 [Full text] Katsura, Y., Kubota H., Kunida, K., Kanno A., Kuroda S., Ozawaa, T., (2015) An optogenetic system for interrogating the temporal dynamics of Akt, Sci. Rep. 5, 14589, 10.1038/srep14589 [Full text]

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2014

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.I., Kashikura, K., Endo, K., Ikeda, K., Soga, T., Kuroda, S., (2014) Reconstruction of insulin signal flow from phosphoproteome and metabolome data, Cell Rep. 8(4):1171-1183, doi:10.1016/j.celrep.2014.07.021 [abstract], [Full text], [pdf], [3D network file] Koumura, T., Urakubo, H., Ohashi, K., Fujii, M., Kuroda, S., (2014) Stochasticity in Ca2+ Increase in Spines Enables Robust and Sensitive Information Coding, PLoS ONE 9(6), e99040, doi:10.1371/journal.pone.0099040 [Full text] Urakubo, H., Sato, M., Ishii, S., Kuroda, S., (2014) In Vitro Reconstitution of a CaMKII Memory Switch by an NMDA Receptor-Derived Peptide, Biophysical Journal 106(6), 1414-1420 [abstract]

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2013

Akimoto, Y., Yugi, K., Uda, S., Kudo, T., Komori, Y., Kubota, H., Kuroda, S., (2013) The Extraction of Simple Relationships in Growth Factor-Specific Multiple-Input and Multiple-Output Systems in Cell-Fate Decisions by Backward Elimination PLS Regression, PLoS ONE 8(9), e72780, doi:10.1371/journal.pone.0072780 [Full text] Uda, S., Saito, T., H., Kudo, T., Kokaji, T., Tsuchiya, T., Kubota, H., Komori, Y., Ozaki, Y., Kuroda, S., (2013) Robustness and Compensation of Information Transmission of Signaling Pathways, Science 341, 558-561 [abstract], [reprint], [Full text], [experimental data] Noguchi, R.., Kubota, H., Yugi, K., Toyoshima, Y., Komori, Y., Soga, T., and Kuroda, S., (2013) The selective control of glycolysis, gluconeogenesis and glycogenesis by temporal insulin patterns, Molecular Systems Biology 9:664 [Full text], [experimental data] Honda, M., Urakubo, H., Koumura, T., and Kuroda, S., (2013) A Common Framework of Signal Processing in the Induction of Cerebellar LTD and Cortical STDP, Neural Networks 43, 114-124 [abstract] Saito, T. H., Uda, S., Tsuchiya, T., Ozaki, Y., and Kuroda, S., (2013) Temporal Decoding of MAP Kinase and CREB Phosphorylation by Selective Immediate Early Gene Expression, PLoS ONE 8(3), e57037. doi:10.1371/journal.pone.0057037 [Full text], [experimental data]

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2012

Yamamoto, Y., Lee, D., Kim, Y., Lee, B., Seo, C., Kawasaki, H., Kuroda, S., Tanaka-Yamamoto, K. (2012) Raf Kinase Inhibitory Protein is Required for Cerebellar Long-Term Synaptic Depression by Mediating PKC-Dependent MAPK Activation, J. Neurosci. 32 (41), 14254-14264, doi:10.1523/JNEUROSCI.2812-12.2012 [abstract] Kubota, H., Noguchi, R., Toyoshima, Y., Ozaki, Y., Uda, S., Watanabe, K., Ogawa, W. and Kuroda, S., (2012) Temporal Coding of Insulin Action through Multiplexing of the AKT Pathway, Mol. Cell, 46(6), 1-13 [abstract] Toyoshima, Y., Kakuda, H., Fujita, K., Uda, S. and Kuroda, S.(2012) Sensitivity control through attenuation of signal transfer efficiency by negative regulation of cellular signalling. Nat. Commun. 3,743 [pdf,S1,S2,S3] Watanabe,K., Akimoto, Y., Yugi, K., Uda, S., Chung, J., Nakamuta, S., Kaibuchi, K. and Kuroda, S.(2012) Latent process genes for cell differentiation are common decoders of neurite extension length. Journal of Cell Science. 125(Pt9), 2198-2211 [in press] Toni, T., Ozaki, Y., Kirk, P., Kuroda, S. and Stumpf, M. P. (2012) Elucidating the in vivo phosphorylation dynamics of the ERK MAP kinase using quantitative proteomics data and Bayesian model selection. Mol. BioSyst. 8 (7), 1921-1929, doi:10.1039/C2MB05493K [in press]

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2011

Honda, M., Urakubo, H., Tanaka, K. and Kuroda, S.(2011) Analysis of Development of Direction Selectivity in Retinotectum by a Neural Circuit Model with Spike Timing-Dependent Plasticity. J. Neurosci., 31 (4),1516-1527 [pdf]

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2010

Otsuji, M., Terashima, Y., Ishihara, S., Kuroda, S. and Matsushima, K. (2010) A Conceptual Molecular Network for Chemotactic Behaviors Characterized by Feedback of Molecules Cycling Between the Membrance and the Cytosol. Science Signaling,3(152),ra89 Fujita, K. A., Toyoshima, Y., Uda, S., Ozaki, Y., Kubota, H., Kuroda, S. (2010) Decoupling of Receptor and Downstream Signals in the Akt Pathway by Its Low-Pass Filter Characteristics. Science Signaling,3(132),ra56. [Full text], [pdf] Ozaki, U., Uda, S., Saito, T. H., Chung, J., Kubota, H. and Kuroda, S. (2010) A quantitative image cytometry technique for time series or population analyses of signaling networks. PLoS ONE, 5(4), e9955 Chung, J., Kubota, H., Ozaki, Y., Uda, S. and Kuroda, S. (2010) Timing-Dependent Actions of NGF Required for Cell Differentiation. PLoS ONE, 5(2), e9011

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2009

Urakubo, H., Honda, M., Tanaka, K. and Kuroda, S. (2009) Experimental and computational aspects of signaling mechanisms of spike-timing-dependent plasticity. HFSP J. 3(4):240-254, doi:10.2976/1.3137602

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2008

Urakubo, H., Honda, M., Froemke, R.C. and Kuroda, S. (2008) Requirement of an allosteric kinetics of NMDA receptors for spike-timing-dependent plasticity. J. Neurosci., 28 (13), 3310-3323

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2007

Otsuji, M. Ishihara, S. Co C. Kaibuchi, K. Mochizuki, A. and Kuroda,S. (2007) A Mass Conserved Reaction-Diffusion System Captures Properties of Cell Polarity. PLoS. Comput. Biol., 3 (6), e108

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2006

Maeda, A., Ozaki, Y., Sivakumaran, S., Akiyama, T., Urakubo, H., Usami, A., Sato, M., Kaibuchi, K. and Kuroda, S. (2006) Ca2+-independent phospholipase A2-dependent sustained Rho-kinase activation exhibits all-or-none response. Genes Cells, 11 (9), 1071-1083 Fujioka, A., Terai, K., Itoh, R.E., Aoki, K., Nakamura, T., Kuroda, S., Nishida, E. and Matsuda, M. (2006) Dynamics of the Ras/ERK MAP kinase casacade as monitored by fluorescence probes. J. Biol. Chem., 281 (13), 8917-8926

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2005

Ozaki, Y., Sasagawa, S. and Kuroda, S. (2005) Dynamic characteristics of transient responses. J. Biochem., review, 137 (6), 659-663 Sasagawa, S., Ozaki, Y. Fujita, K. and Kuroda, S. (2005) Prediction and validation of the distinct dynamics of transient and sustained ERK activation. Nat. Cell Biol, 7 (4), 365-373 Doi, T., Kuroda, S., Michikawa, T., and Kawato, M. (2005) Spike-Timing Detection by Calcium Signaling Pathways of Cerebellar Purkinje Cells in Different Forms of Long-Term Depression. J. Neurosci., 25 (4), 950-961.

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2004

Nakaya, Y., Kuroda, S., Kaibuchi K. and Takahashi, Y (2004) Mesenchymal-epithelial transition during somitic segmentation is regulated by differential roles of Cdc42 and Rac1. Dev. Cell, 7 (3), 425-438. Urakubo, H., Aihara, T., Kuroda, S., Watanabe, M., and Kondo, S. (2004) Spatial localization of synapses required for supralinear summation of action potentials and EPSPs. Journal of Computational Neuroscience, 16 (3), 251-256. Schweighofer, N., Doya, K., and Kuroda, S. (2004) Cerebellar Aminergic Neuromodulation: towards a functional understanding. Brain Research Reviews, 44, (2-3), 103-116

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2002

Fukata, M., Nakagawa, M., Kuroda, S., and Kaibuchi, K. (2002) Effects of Rho family GTPases on cell-cell adhesion. In Methods in Molecular Biology 189, 121-128 Fukata, M., Watanabe, T., Noritake, J., Nakagawa, M., Yamaga, M., Kuroda, S., Matsuura, Y., Iwamatsu, A., Perez, F., and Kaibuchi, K. (2002) Rac1 and Cdc42 capture microtubules through IQGAP1 and CLIP-170. Cell, 109, (7), 873-885

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2001

Kuroda, S.*, Schweighofer, N., Amano, M., Kaibuchi, K., and Kawato, M. (2001) Distinct roles of Rho-kinase pathway and myosin light chain kinase pathway in phosphorylation of myosin light chain: kinetic simulation study. In Foundations of Systems Biology, MIT press, 279-294 Kuroda, S.*, Schweighofer, N., and Kawato, M. (2001) Exploration of signal transduction pathways in cerebellar long-term depression by kinetic simulation. J. Neurosci., 21, (15), 5693-5702 Fukata, M., Nakagawa, M., Itoh, N., Kawajiri, A., Yamaga, M., Kuroda, S., and Kaibuchi, K. (2001) Dynamic localization of a-catenin during cell scattering: Involvement of Cdc42, Rac1, and IQGAP1 in its regulation. Mol. Cell. Biol., 21, (6), 2165-2183 Kuroda, S., Yamamoto, K., Miyamoto, H., Doya, K., and Kawato, M. (2001) Statistical characteristics of climbing fiber spikes necessary for efficient cerebellar learning. Biol. Cybern., 84, (3), 183-192

Publication List | previous publications

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