• 2020年
    • Quek, L.-E., Krycer, J.R., Ohno, S., Yugi, K., Fazakerley, D., Scalzo, R., Elkington, S.D., Dai, Z., Hirayama, A., Ikeda, S., Shoji, F., Suzuki, K., Locasale, J.W., Soga, T., James, D.E., & Kuroda, S. (2019). Dynamic 13C Flux Analysis Captures the Reorganization of Adipocyte Glucose Metabolism in Response to Insulin. iScience, 23(2), 21. doi: 10.1016/j.isci.2020.100855
  • 2019年
    • Tottori, T., Fujii, M., & Kuroda, S. (2019). Robustness against additional noise in cellular information transmission. Physical Review E, 100(4), 042403. doi: 10.1103/PhysRevE.100.042403
    • Fujii, M., Murakami, Y., Karasawa, Y., Sumitomo, Y., Fujita, S., Koyama, M., Uda, S., Kubota, H., Inoue, H., Konishi, K., Oba, S., Ishii, S., Kuroda, S. (2019). Logical design of oral glucose ingestion pattern minimizing blood glucose in humans. Npj Systems Biology and Applications, 5(1), 31. doi: 10.1038/s41540-019-0108-1
    • 伊藤 翔, 唐沢 康暉, 星野 太佑, 藤井 雅史, 衛藤 樹, 鶴 純也, 柏戸 千絵子, 黒田 真也. (2019) 低糖質食事法およびレジスタンス運動が身体組成と血中代謝物・ホルモン濃度に与える影響. 体力科学 第68巻 第3号 223-227(2019)DOI:10.7600/jspfsm.68.223
    • Yugi, K., Ohno, S., Krycer, J.R., James, D.E., Kuroda, S., (2019) Rate-oriented trans-omics: integration of multiple omic data on the basis of reaction kinetics. Current Opinion in Systems Biology. (in press) doi:https://doi.org/10.1016/j.coisb.2019.04.005
    • Tottori, T., Fujii, M., Kuroda, S., (2019). NMDAR-Mediated Ca2+ Increase Shows Robust Information Transfer in Dendritic Spines. Biophysical Journal. 116:1748-1758. doi:10.1016/j.bpj.2019.03.030
  • 2018年
    • Kawata, K., Yugi, K., Hatano, A., Kokaji, T., Tomizawa, Y., Fujii, M., Uda, S., Kubota, H., Matsumoto, M., Nakayama, K. I., Kuroda, S., (2018). Reconstruction of global regulatory network from signaling to cellular functions using phosphoproteomic data. Genes to Cells. 2018:1-12. doi:10.1111/gtc.12655
    • 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., (2018). Trans-omic Analysis Reveals Selective Responses to Induced and Basal Insulin across Signaling, Transcriptional, and Metabolic Networks. iScience. 7:212-229. doi:10.1016/j.isci.2018.07.022
    • Inoue, H., Kunida, K., Matsuda, N., Hoshino, N., Wada, T., Imamura, H., Noji, H. and Kuroda, S., (2018). Automatic Quantitative Segmentation of Myotubes Reveals Single-cell Dynamics of S6 Kinase Activation. Cell Structure and Function. 43: 153–169. doi: 10.1247/csf.18012.
    • Kubota, H., Uda, S., Matsuzaki, F., Yamauchi, Y. and Kuroda, S., (2018). In Vivo Decoding Mechanisms of the Temporal Patterns of Blood Insulin by the Insulin-AKT Pathway in the Liver. Cell Systems. 7, 1–11. doi:10.1016/j.cels.2018.05.013
    • 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
    • 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
  • 2017年
    • 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
    • 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
    • Fujii., M., Ohashi., O., Karasawa., Y., Hikichi., M., Kuroda., S., (2017) Small-Volume Effect Enables Robust, Sensitive, and Efficient Information Transfer in the Spine, Biophysical Journal. 112(4): 813–826. doi:10.1016/j.bpj.2016.12.043
    • Yugi, K., Kuroda, S., (2017) Metabolism-Centric Trans-Omics, Cell Systems. 4(1): 19-20. doi:10.1016/j.cels.2017.01.007
  • 2016年
    • 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
    • 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
    • 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 Rep. 15, 1-12, doi:10.1016/j.celrep.2016.05.024
    • Yugi, K., Kubota, H., Hatano, A., Kuroda, S., (2016) Trans-Omics: How To Reconstruct Biochemical Networks Across Multiple ‘Omic’ Layers, Trends in Biotechnology. 34(4):276-290. doi:10.1016/j.tibtech.2015.12.013
    • 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
  • 2015年
    • 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
    • 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
  • 2014年
    • 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
    • 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
    • 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
  • 2013年
    • 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
    • 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, 558-5614
    • 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
    • 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
    • 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
  • 2012年
    • 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
    • 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
    • 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
    • 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
    • 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
  • 2011年
    • 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
  • 2010年
    • 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
      プレスリリース(1, 2)
    • 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
  • 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
  • 2008年
    • 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
  • 2007年
    • 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
  • 2006年
    • 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
  • 2005年
    • 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.
  • 2004年
    • 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
  • 2002年
    • 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
  • 2001年
    • 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


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