We show the list of publication of our activities.

Publications 2000-

  • Kobayashi K., Maeda K., Tokuoka M. Mochizuki A. and Satou Y. (2018) Controlling Cell Fate Specification System by Key Genes Determined from Network Structure. iScience 4, 281-293.
  • Sakai Y., Mochizuki A., Kinoshita K., Hirano T., Tachikawa M. (2018) Modeling the functions of condensin in chromosome shaping and segregation. PLoS Comput. Biol. 14(6), e1006152.
  • Ogawa N., Hatsuda T., Mochizuki A. and Tachikawa M. (2017) Dynamical pattern selection of growing cellular mosaic in fish retina. Phys. Rev. E 96, 032416.
  • Okada T. and Mochizuki A. (2017) Sensitivity and network topology in chemical reaction systems. Phys. Rev. E 96, 022322.
  • Tachikawa M., Morone N., Senju Y., Sugiura T., Hanawa-Suetsugu K., Mochizuki A. and Suetsugu S. (2017) Measurement of caveolin-1 densities in the cell membrane for quantification of caveolar deformation after exposure to hypotonic membrane tension. Sci. Rep. 7, 7794.
  • Mori F. and Mochizuki A. (2017) Expected Number of Fixed Points in Boolean Networks with Arbitrary Topology. Phys. Rev. Lett. 119, 028301.
  • Kurosawa G., Fujioka A., Koinuma S., Mochizuki A. and Shigeyoshi Y. (2017) Temperature-amplitude coupling for stable biological rhythms at different temperatures. PLoS Comput. Biol. 13(6), e1005501.
  • Tachikawa M. and Mochizuki A. (2017) Golgi apparatus self-organizes into the characteristic shape via postmitotic reassembly dynamics. Proc. Natl. Acad. Sci. USA 114, 5177-5182.
  • Mochizuki A. (2016) Theoretical approaches for the dynamics of complex biological systems from information of networks. Proc. Jpn. Acad. Ser. B 92, 255-264.
  • Sakai Y., Tachikawa M. and Mochizuki A. (2016) Controlling segregation speed of entangled polymers by the shapes: A simple model for eukaryotic chromosome segregation. Phys. Rev. E 94, 042403.
  • Okada T. and Mochizuki A. (2016) Law of Localization in Chemical Reaction Networks. Phys. Rev. Lett. 117, 048101.
  • Hayakawa Y.,Tachikawa M. and Mochizuki A. (2016) Flat leaf formation realized by cell-division control and mutual recessive gene regulation. J. Theor. Biol. 404, 206-214.
  • Ohta N., Waki K., Mochizuki A. and Satou Y. (2015) A Boolean function for neural induction reveals a critical role of direct intercellular interactions in patterning the ectoderm of the ascidian embryo. PLoS Comput. Biol. 11(12), e1004687.
  • Mochizuki A. and Fiedler B. (2015) Sensitivity of chemical reaction networks: a structural approach. 1. Examples and the carbon metabolic network. J. Theor. Biol. 367, 189-202.
  • Ishihara J.,Tachikawa M., Iwasaki H. and Mochizuki A. (2015) Mathematical study of pattern formation accompanied by heterocyst differentiation in multicellular cyanobacterium. J. Theor. Biol. 371, 9-23.
  • Hayakawa Y.,Tachikawa M. and Mochizuki A. (2015) Mathematical study for the mechanism of vascular and spot patterns by auxin and pin dynamics in plant development. J. Theor. Biol. 365, 12-22.
  • Tachikawa M. and Mochizuki A. (2015) Nonlinearity in cytoplasm viscosity can generate an essential symmetry breaking in cellular behaviors. J. Theor. Biol. 364, 260-265.
  • Ishimatsu K., Hata T., Mochizuki A., Sekine R., Yamamura M. and Kiga D. (2014) General applicability of synthetic gene-overexpression for cell-type ratio control via reprogramming. ACS Synth. Biol. 3(9), 638-644.
  • Nonomura K., Yamaguchi Y., Hamachi M., Koike M., Uchiyama Y., Nakazato K., Mochizuki A., Sakaue-Sawano A., Miyawaki A., Yoshida H., Kuida K., and Miura M. (2013) Local Apotosis Modulates Early Mammalian Brain Development through the Elimination of Morphogen-Producing Cells. Developmental Cell, 27(6), 621-634.
  • Ichikawa T., Nakazato K., Keller P.J., Kajiura-Kobayashi H., Stelzer E.H.K, Mochizuki A. and Nonaka S. (2013) Live imaging and quantitative analysis of whole mouse embryos during gastrulation using light-sheet microscopy and three-dimensional tracking tools. Nature Protocols, 9, 575-585.
  • Fiedler B., Mochizuki A., Kurosawa G. and Saito D. (2013) Dynamics and control at feedback vertex sets. I: Informative and determining nodes in regulatory networks. J. Dyn. Differ. Eqns. 25, 563-604.
  • Mochizuki A., Fiedler B., Kurosawa G. and Saito D. (2013) Dynamics and control at feedback vertex sets. II: A faithful monitor to determine the diversity of molecular activities in regulatory networks. J. Theor. Biol. 335, 130-146.
  • Ichikawa T., Nakazato K., Keller P.J., Kajiura-Kobayashi H., Stelzer E.H.K, Mochizuki A. and Nonaka S. (2013) Live imaging of whole mouse embryos during gastrulation: migration analyses of epiblast and mesodermal cells. PLoS ONE, 8(7), e64506
  • Nakamura, T., Saito, D., Kawasumi, A., Shinohara, K., Asai, Y., Takaoka, K., Dong, F., Takamatsu, A., Belo, J. A., Mochizuki, A. and Hamada H., (2012) Fluid Flow and Interlinked Feedback Loops Establish Left-Right Asymmetric Decay of Cerl2 mRNA in the Mouse Embryo. Nat. Commun. 3, 1322.
  • Takasu, N. N., Kurosawa, G., Tokuda, T. I., Mochizuki, A., Todo, T., and Nakamura, W., (2012) Circadian regulation of food-anticipatory activity in molecular clock-deficient mice. PLoS ONE 7, e48892.
  • Fujishima, K., Horie, R., Mochizuki, A., and Kengaku, M., (2012) Principles of branch dynamics governing shape characteristics of cerebellar Purkinje cell dendrites, Development139, 3442-3455.
  • Kubota, Y., Karube, F., Nomura, M., Gulledge, A. T., Mochizuki, A., Schertel, A. and Kawaguchi Y., (2011) Conserved properties of dendritic trees in four cortical interneuron subtypes, Sci. Rep.1, 89.
  • Mochizuki, A. and Saito, D., (2010) Analyzing steady states of dynamics of bio-molecules from the structure of regulatory networks, J. theor. Biol.266, 323-335.
  • Takahashi, J., Ohbayashi, A., Oginuma, M., Saito, D., Mochizuki, A., Saga, Y. and Takada, S. (2010) Analysis of Ripply1/2-deficient mouse embryos reveals a mechanism underlying the rostrocaudal patterning within a somite, Dev. Biol.342, 134-145.
  • Shimono, K., Sugimura, K., Kengaku, M., Uemura, T. and Mochizuki, A. (2010) Computational modeling of dendritic tiling by diffusible extracellular suppressor, Genes Cells15, 137-149.
  • Nakazato K. and Mochizuki A. (2009) Steepness of thermal gradient is essential to obtain a unified view of thermotaxis in C. elegans, J. theor. Biol.260, 56-65.
  • Mochizuki A. (2008) Structure of regulatory networks and diversity of gene expression patterns. J. theor. Biol. 250, 307-321.
  • Sugimura K., Shimono K., Uemura T. and Mochizuki A (2007) Self-organizing mechanism for development of space-filling neuronal dendrites. PLoS Comput Biol. 3(11), 2143-2154.
  • Otsuji, M., Ishihara, S., Co, C., Kaibuchi, K., Mochizuki, A., and Kuroda, K. (2007) A Mass Conserved Reaction-Diffusion System Captures Properties of Cell Polarity. PLoS Comput Biol. 3(6), 1040-1054
  • Ishihara, S., Otsuji, M. and Mochizuki, A. (2007) Transient and steady state of mass-conserved reaction-diffusion systems. Phys. Rev. E 75 (1), 015203-1 - 015203-4.
  • Nakamura, T., Mine, N., Nakaguchi, E., Mochizuki, A., Yamamoto, M., Yashiro, K., Meno, C., & Hamada, H. (2006) Generation of robust left-right asymmetry in the mouse embryo requires a self-enhancement and lateral-inhibition system. Dev. Cell 11, 495-504.
  • Fujita, H. & Mochizuki, A. (2006) The Origin of the Diversity of Leaf Venation Pattern. Dev. Dyn. 235, 2710-2721
  • Takigawa-Imamura, H., Mochizuki, A. (2006) Predicting regulation of the phosphorylation cycle of KaiC clock protein using mathematical analysis. J Biol. Rhythms 21, 405-416.
  • Fujita, H. & Mochizuki, A. (2006) Pattern formation by the positive feedback regulation between flow of diffusible signal molecule and localization of its carrier. J. theor. Biol.241, 541-551.
  • Takigawa-Imamura, H., Mochizuki, A. (2006) Transcriptional Autoregulation by Phosphorylated and Non-Phosphorylated KaiC in Cyanobacterial Circadian Rhythms. J. theor. Biol. 241, 178-192.
  • Mochizuki, A., Yahara, K., Kobayashi, I. and Iwasa, Y. (2006) Genetic addiction: selfish gene's strategy for symbiosis in the genome. Genetics 172, 1309-1323.
  • Mochizuki, A. (2005) An Analytical Study of The Number of Steady States in Gene Regulatory Networks. J. theor. Biol. 236, 291-310.
  • Feugier, F. G., Mochizuki, A. and Iwasa, Y. (2005) Self-organization of the vascular system in plant leaves: Inter-dependent dynamics of auxin flux and carrier proteins. J. theor. Biol. 236, 366-375.
  • Tohya, S., Mochizuki, A. and Iwasa, Y. (2003) Difference in the Retinal Cone Mosaic Pattern Between Zebrafish and Medaka: Cell-Rearrangement Model. J. Theor. Biol. 221, 289-300.
  • Shoji, H., Mochizuki, A., Iwasa, Y., Hirata, M., Watanabe, T., Hioki, S. and Kondo, S. (2003) Origine of directionality in the fish stripe pattern. Dev. Dyn. 226, 627-633.
    doi: 10.1002/dvdy.10277
  • Ryohji, T., Mochizuki, A. & Iwasa, Y. (2003) Possibility of Tissue Separation Caused by Cell Adhesion. J. theor. Biol. 221, 459-474.
  • Shoji, H., Mochizuki, A., Iwasa, Y. and Kondo, S. (2002) Directionality of Stripes Formed by Anisotropic Reaction-Diffusion Models. J. Theor. Biol. 214, 549-561.
  • Honda, H. and Mochizuki, A. (2002) Formation and maintenance of distinctive cell patterns by co-expression of membrane-bound ligands and their receptors. Dev. Dyn. 223, 180-192.
    doi: 10.1002/dvdy.10042
  • Mochizuki, A. (2002) Pattern formation of cone mosaic in zebrafish retina: A Cell rearrangement model. J. Theor. Biol. 215, 345-361.
  • Kurosawa, G., Mochizuki, A. and Iwasa, Y. (2002) Processes promoting oscillations -- comparative study of circadian clock models. J. Theor. Biol. 216, 193-208.


Publications 1996-1999

  • Mochizuki, A. (1999) Estimating cell lineage from distributions of randomly introduced markers. J. Theor. Biol. 197, (2) 227-245.
  • Tohya, S, Mochizuki, A., and Iwasa, Y. (1999). Formation of cone mosaic of zebrafish retina. J. Theor. Biol. 200, (2) 231-244.
  • Iwasa, Y., Mochizuki, A. and Takeda, Y. (1999). The Evolution of Genomic Imprinting: Abortion and Overshoot Explain Aberrations. Evolutionary Ecology Research 1, (2) 129-150.
  • Mochizuki, A., Wada, N., Ide, H., and Iwasa, Y. (1998). Cell-cell adhesion in limb-formation, estimated from photographs of cell sorting experiments based on a spatial stochastic model. Dev. Dyn. 211, 204-214
  • Takesue, A., Mochizuki, A. and Iwasa, Y. (1998) Cell-Differentiation Rules that Generate Regular Mosaic Patterns: Modelling Motivated by Cone Mosaic Formation in Fish Retina. J. Theor. Biol. 194, 575-586
  • Tohya, S., Mochizuki, A., Imayama, S. and Iwasa, Y. (1998) On Rugged shape of skin tumor (Basal cell epithelioma). J. Theor. Biol. 194, 65-78
  • Mochizuki, A., Takeda, Y., Ide, H. and Iwasa, Y. (1997). A stochastic model for cell sorting and its application. Forma 12, 107-122.
  • Kawasaki, K., Mochizuki, A., Matsushita, M., Umeda, T. and Shigesada, N. (1997). Modeling spatio-temporal patterns generated by Bacillus subtilis. J. Theor. Biol. 188, 177-185.
  • Iwasa. Y., Mochizuki, A. and Takeda, Y. (1997) Evolution of genomic imprinting: Why are so few genes imprinted ? Journal of Reproduction and Development 43 Suppl., 15-16.
  • Mochizuki, A., Takeda, Y. and Iwasa, Y. (1996). The evolution of Genomic Imprinting. Genetics 144, 1283-1295.
  • Mochizuki, A., Iwasa, Y. and Takeda, Y. (1996). A stochastic model for cell sorting and measuring cell-cell adhesion. J. Theor. Biol. 179, 129-146.