• Ohshima, D., et al., “Potential Roles of Spatial Parameters in the Regulation of NF-κB Oscillations, as Revealed by Computer Simulations”, pp63, ”Protein Modifications in Pathogenic Dysregulation of Signaling”, eds. Inoue, J-I. & Takekawa, M., Springer, Tokyo, 2015, ISBN 978-4-431-55560-5, ISBN 978-4-431-55561-2 (eBook).
  • Ohshima, D., et al., “Stochastic Simulation of Stress Granules”, pp.77, ”Protein Modifications in Pathogenic Dysregulation of Signaling”, eds. Inoue, J-I. & Takekawa, M., Springer, Tokyo, 2015, ISBN 978-4-431-55560-5, ISBN 978-4-431-55561-2 (eBook).
  • Ichikawa, K., ”Synergistic effect of blocking cancer cell invasion revealed by computer simulations”, Journal of Mathematical Biosciences and Engineering, (2015), 1189, doi: 10.3934/mbe.2015.12.1189.
  • Ohshima, D. and Ichikawa, K., “Regulation of nuclear NF-κB oscillation by nuclear transport: mechanisms determining persistency and frequency”, PLoS ONE, 10 (2015), e0127633, doi:10.1371/journal.pone.0127633.
  • Ohshima, D., Arimoto-Matsuzaki, K., Tomida, T., Takekawa,, and Ichikawa, K., “Spatio-temporal dynamics and mechanisms of stress granule assembly”, PLoS Comp.Biol., 11 (2015), e1004326, doi:10.1371/journal.pcbi.1004326.
  • Sakurai-Yageta, M., Maruyama,T., Suzuki, T., Ichikawa, K., and Murakami, Y., “Dynamic Regulation of a Cell Adhesion Protein Complex Including CADM1 by Combinatorial Analysis of FRAP with Exponential Curve-fitting”, PLoS ONE, 10 (2015), e0116637, doi:10.1371/journal.pone.0116637.


  • Ohshima, D. and Ichikawa, K., “Regulation of nuclear NF-κB oscillation by a diffusion coefficient and its biological implications”, PLoS ONE, 9 (2014), e109895, doi:10.1371/journal.pone.0109895.
  • Ichikawa, K., Ohshima, D., and Sagara, H., “Regulation of signal transduction by spatial parameters: a case in NF–κB oscillation”, IET Systems Biology, 9 (2014), 41-51, doi:10.1049/iet-syb.2013.0020.
  • Isabel Schwende, Tuan D. Pham, and Kazuhisa Ichikawa, “Nuclear Boundary and Pore Detection in SEM Images”, in “Biomedical Informatics and Technology”, Eds. Tuan D. Pham, Kazuhisa Ichikawa, Mayumi Oyama-Higa, and Xiaoyi Jiang, Springer-Verlag Berlin Heidelberg, 2014, pp.235-247, ISBN 978-3-642-54120-9, e-ISBN 978-3-642-54121-6, DOI 10.1007/978-3-642-54121-6.


  • Watanabe, A., Hoshino D., Koshikawa, N., Seiki, M., Suzuki, T., and Ichikawa, K., “Critical role of transient activity of MT1-MMP for ECM degradation in invadopodia”, PLoS Comp.Biol., 9, (2013), e1003086, doi:10.1371/annotation/b41ed85a-11d1-483a-a7ac-9d06f0c8669a.
  • Pham, T.D., and Ichikawa, K., “Spatial chaos and complexity in the intracellular space of cancer and normal cells”, Theoretical Modeling and Medical Biology, 10:62, (2013), doi: 10.1186/1742-4682-10-62.
  • Pham, T.D. and Ichikawa, K., “Characterization of cancer and normal intracellular images by the power law of a fuzzy partition functional”, Conf. Image Analysis and Recognition (ICIAR 2013, June 26-28, (2013), Póvoa de Varzim, Portugal) LNCS 7950, 597–604, 2013.
  • Ohshima, D., Sagara, H., and Ichikawa, K., “Regulation of NF-kB Oscillation by Spatial Parameters in True Intracellular Space (TiCS)”, 2013 International Symposium on Computational Models for Life Sciences, AIP Conf.Proc. 1559, 5-11, (2013); doi: 10.1063/1.4824990.
  • Nguyen-Thanh, N., Pham, T.D., and Ichikawa, K., “Segmentation of mitochondria in intracellular space”,2013 IEEE Symposium Series on Computational Intelligence (IEEE-CIS 2013, 15-19 April 2013, Singapore), 218-221, 2013.
  • Ohshima, D., and Ichikawa, K., “The change in 3-dimensional intracellular parameters alters oscillation pattern of nuclear NF-κB”, Seikagaku, 85, 430-437, June, 2013 (Japanese).


  • Hoshino, D., Koshikawa, N., Suzuki, T., Quaranta, V., Weaver, A.M., Seiki, M., Ichikawa, K., “Establishment and validation of computational model for MT1-MMP dependent ECM degradation and intervention strategies”, PLoS Comp.Biol., 8 (2012), e1002479.
  • Ohshima, D., Inoue, J., Ichikawa, K., “Roles of Spatial Parameters on the Oscillation of Nuclear NF-kB: Computer Simulations of a 3D Spherical Cell”, PLoS ONE, 7 (2012), e46911.
  • Pham, T.D., Vo, D., Nguyen-Thanh, N., Thang, T.C., Ichikawa, K., “Chaotic behavior in intracellular space: an implication for simulation and modeling of cancer”, Computer Modeling and Simulation (EMS), Sixth UKSim/AMSS European Symposium, (2012), 143-147; doi: 1109/EMS.2012.28.
  • Pham, T.D., Vo, D., Nguyen-Thanh, N., Thang, T.C., Ichikawa, K., “How complex is the cancer intracellular signaling space in FIB-SEM images?”, Computer Modeling and Simulation (EMS), Sixth UKSim/AMSS European Symposium, (2012), 139-142; doi: 1109/EMS.2012.25.
  • Saitou,T., Itano, K., Hoshino, D., Koshikawa, N., Seiki, M., Ichikawa, K., Suzuki, T., “Control and Inhibition Analysis of Complex Formation Processes”, Theoretical Biology and Medical Modeling, 9 (2012), 33.
  • Saitou, T., Rouzimaimaiti M., Koshikawa, N., Seiki, M., Ichikawa, K., Suzuki, T., “Mathematical modeling of invadopodia formation”, J.Theor.Biol., 298 (2012), 138-146.
  • Ichikawa, K., Rouzimaimaiti, M., Suzuki, T., “Reaction diffusion equation with non-local term arises as a mean field limit of the master equation”, Discrete and Continuous Dynamical Systems Series S, Vol.5(2012), 105-126.


  • Ichikawa, K., “Localized activation of proteins in a free intracellular space: dependence of cellular morphologies and reaction schemes”, BioSys., Vol.105(2011), 173-180.


  • Ichikawa, K., Suzuki, T., and Murata, T., “Stochastic simulation of biological reactions, and its applications for studying actin polymerization”, Physical Biol., Vol.7(2010), 046010.


  • Suzuki, R., Niki, K., Fujimaki, N., Masaki, S., Ichikawa, K., and Usui, S., “Neuro-Imaging Platform for Neuroinformatics” ICONIP 2007, Part II, LNCS 4985, Ishikawa, M et al.(Eds.), 895-904, 2008.
  • Nozawa, K., and Ichikawa, K., “Can calcium ion contribute to morphological plasticity of a spine?”, BMC Neuroscience, Vol.9, Suppl 1 (2008), 101.


  • Ichikawa, K., Hoshino, A. and Kato, K., “Induction of Synaptic Depression by High Frequency Stimulation in Area CA1 of the Rat Hippocampus: Modeling and Experimental Studies”, Neurocomputing, Vol.70(2007), pp.2055-2059.
  • Imai, H., Kefalov, V., Sakurai, K., Chisaka, O., Ueda, Y., Onishi, A., Morizumi, T., Fu, Y., Ichikawa, K., Nakatani, K., Honda, Y., Chen, J., Yau, K.-W., and Shichida, Y., “Molecular Properties of Rhodopsin and Rod Function”, J.Biol.Chem., Vol.282(2007), pp.6677-6684.


  • Ichikawa, K., “A Modeling Environment with Three-Dimensional Morphology, A-Cell-3D, and Ca2+ Dynamics in a Spine”, Neuroinformatics, Vol.3(2005), pp.49-64.


  • Ichikawa, K., “Localization of Activated Ca2+/calmodulin- Dependent Protein kinase II within a spine: Modeling and computer simulation”, Neurocomputing Vol.58-60(2004), pp.709-714.


  • Kameyama, M., Yamaguchi, I., Ichikawa, K., Sugiyama, T., Hori, H., Ikeda, M., Kuwahata, Y., Eguchi, N., Urade, Y. and Yoshioka, T., “Effect of phospholipase Cβ4 lacking in thalamic neurons on electroencephalogram”, Biochem.Biophys.Res.Comm., Vol.304(2003), pp.153-159.


  • Yamaguchi, I. and Ichikawa, K., “Theta frequency locking by slow GABA(A) synaptic inhibition in a hippocamal SLM interneuronal network model”, Neurocomputing Vol.44-46C(2002), pp.709-714.


  • Yamaguchi, I. and Ichikawa, K., “A model for neuronal gamma and theta oscillations by two networks of hippocampal interneurons”, Neurocomputing Vol.38-40(2001), pp.1043-1049.
  • Ichikawa, K., “A-Cell: graphical user interface for the construction of biochemical reaction models”, Bioinformatics Vol.17(2001), pp.483-484.


  • Okamoto, H. and Ichikawa, K., “A model for molecular mechanism of synaptic competition for a finite resource”, BioSys., Vol.55(2000), pp.65-71.
  • Okamoto, H. and Ichikawa, K., “Switching characteristics of a model for biochemical-reaction network describing autophosphorylation versus dephosphorylation of Ca2+/calmodulin-dependent protein kinase II”, Bio.Cyber., Vol.82(2000), pp.35-47.
  • Kojima, H., Ichikawa, K., Ileva, L.V., Traynelis, S.F., Yoshioka, T., “Properties of AMPA receptor channel during long-term depression in rat cerebellar Purkinje cells”, in “Slow Synaptic Responses and modulation” ed.Kuba, K., Higashida, H., Brown, D.A., and Yoshioka, T., Springer(Tokyo), 2000, pp.307-314.


  • Shigematsu, Y., Okamoto, H., Ichikawa, K. and Matsumoto, G., “Temporal event association and output-dependent learning”, J.Adv.Comp.Intell., Vol.3(1999), pp.234-244.


  • Okamoto, H., Ichikawa, K., “Amplification of switching characteristics of biochemical-reaction networks involving Ca2+/calmodulin-dependent protein kinase II: Implication for LTP induced by a single burst during the theta oscillation”, in Information Processing in Cells and Tissues, Ed.Holcombe and Paton, Plenum Press(New York), 1998, pp.125-136.
  • Yamaguchi, I., Ichikawa, K., “A novel method of estimating real [Ca2+]i dynamics from fluorescence signals”, Neurosci.Res., Vol.30(1998), pp.91-98.


  • Okamoto, H., Ichikawa, K., “Autophosphorylation versus dephosphorylation of Ca2+/calmodulin-dependent protein kinase II”, Comp.Neurosci., Ed. Bower, Plenum Press New York,1997, pp.23-28.


  • Ichikawa, K., “Modeling and analysis of spatio-temporal change in [Ca2+]i in a retinal rod outer segment”, Neurosci.Res., Vol.25(1996), pp.137-144.


  • Ichikawa, K., “Transduction steps which characterize retinal cone photocurrent induced by flash stimuli”, Neurosci.Res., Vol.20(1994), pp.337-343.
  • Okamoto, H., Ichikawa, K., “Model for an enzymatic reaction-diffusion system realizing storage of graded information”, Phys.Rev.E, Vol.50(1994), pp.1704-1707.
  • Ichikawa, K., “Critical processes which characterize the photocurrent of retinal rod outer segments to flash stimuli”, Neurosci.Res., Vol.19(1994), pp.201-212.
  • Okamoto, H,. Ichikawa, K., “Analysis of a multistable dynamical system describing a competitive interaction between synapses on a neuron”, Phys.Rev.E, Vol.49(1994), pp.3412-3420.


  • Yoshioka, T., Inoue, H., Ichikawa, K.,Sakakibara, M., Tsuda, M., Suzuki, H., “Biophysical aspect of information flow from receptor to channel”, Annals of the New York Academy of Sciences, Vol.707(1993), pp.328-337.
  • Okamoto, H., Ichikawa K., “A model for a molecular mechanism of an interaction between synapses on a neuron”, Proceedings of International Joint Conference on Neural Networks, Vol.1(1993), pp.101-104.
  • Ichikawa, K., Okamoto, H., “A model for the induction of LTP in the hippocampus”, Proceedings of International Joint Conference on Neural Networks, Vol.1(1993), pp.41-44.
  • Ichikawa, K., “Physiological modeling of visual cortex”, Rev.Neurosci., Vol.4(1993), pp.95-111.


  • Ichikawa, K., “A model for self-organization of receptive fields and orientation-selective columns in the striate cortex”, Neurosci.Res., Vol.11(1991), pp.155-178.


  • Ichikawa, K., “Horizontal stripe color arrangement for large-size TFT-LCD”, SID International Symposium, 1990, pp.400-403.


  • Ichikawa, K., “A model for open-close control of cation channels in the plasma membrane of retinal rod outer segments”, Neurosci.Res., Vol.6(1989), pp.377-396.
  • Ichikawa, K., Suzuki, S., Matino, H., Aoki, T., Higuchi, T., Oana, Y., “14.3-in.-diagonal 16 color TFT-LCD panel using a-Si:H TFTs”, Society for Information Display, International Symposium, Baltimore, U.S.A., 1989, 226-229.


  • Ichikawa, K., “Models for quick activation of transducin and spontaneous deactivation of activated rhodopsin in rod outer segments”, Neurosci.Res., Vol.4(1986), pp.74-81.


  • Ichikawa, K., “Models for transmitter activation process in retinal rod outer segments to flash stimuli”, Neurosci.Res., Vol.2(1985), p.349-364.