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- 原著論文 2000-
Hosoda, S., Iwata, H., Miura, T., Tanabe, M., Okada, T., Mochizuki, A. and Sato, M. (2024) BayesianSSA: a Bayesian statistical model based on structural sensitivity analysis for predicting responses to enzyme perturbations in metabolic networks. BMC Bioinformatics 25, 297.
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Yu, Q., Ascensao, J.A., Okada, T., COVID-19 Genomics UK (COG-UK) Consortium, Boyd, O., Volz, E. and Hallatschek, O. (2024) Lineage frequency time series reveal elevated levels of genetic drift in SARS-CoV-2 transmission in England. Plos Pathogens, 20(4), p.e1012090.
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Honjo, M., Suzuki, K., Katai, J., Tashiro, Y., Aoyagi, T., Hori, T., Okada, T., Saito, Y. and Futamata, H. (2024) Stable States of a Microbial Community Are Formed by Dynamic Metabolic Networks with Members Functioning to Achieve Both Robustness and Plasticity. Microbes and environments, 39(1), p.ME23091.
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Yamauchi Y., Hishida A., Okada T. and Mochizuki A. (2024) Finding regulatory modules of chemical reaction systems. Phys. Rev. Research 6, 023150.
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Hishida A., Okada T. and Mochizuki A. (2024) Patterns of change in regulatory modules of chemical reaction systems induced by network modification. PNAS nexus, 3(1), pgad441.
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Ishikawa M., Sugino S., Masuda Y., Tarumoto Y., Seto Y., Taniyama N., Wagai F., Yamauchi Y., Kojima Y., Kiryu H., Yusa K., Eiraku M., Mochizuki A. (2023) RENGE infers gene regulatory networks using time-series single-cell RNA-seq data with CRISPR perturbations. Communications Biology, 6(1), 1290.
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Kinoshita A, Naito M., Wang Z., Inoue Y., Mochizuki A. and Tsukaya H. (2022) Position of meristems and the angles of the cell division plane regulate the uniqueness of lateral organ shape. Development 149(23), dev199733.
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Mochizuki A.* (2022) A structural approach to understanding enzymatic regulation of chemical reaction networks. Biochem. J. 479(11), 1265–1283.
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Okada T., Miyagi H., Sako Y., Hiroshima M.*, and Mochizuki A.* (2022) Origin of diverse phosphorylation patterns in the ERBB system Biophysical Journal 121, 470–480.
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Akaki K., Ogata K., Yamauchi Y., Iwai No., Tse K. M., Hia F., Mochizuki A., Ishihama Y., Mino T., Takeuchi O. (2021) IRAK1-dependentRegnase-1-14-3-3 complex formation controls Regnase-1-mediated mRNA decay. eLife 10, e71966. doi: 10.7554/eLife.71966
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Okada T., Mochizuki A., Furuta M., Tsai J-C.. (2021) Flux-augmented bifurcation analysis in chemical reaction network systems. Phys. Rev. E 103, 062212. doi: 10.1103/PhysRevE.103.062212
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Mii Y., Nakazato K., Pack C. G., Ikeda T., Sako Y., Mochizuki A., Taira M. and Takada S. (2021) Quantitative analyses reveal extracellular dynamics of Wnt ligands in Xenopus embryos. eLife 10, e55108. doi: 10.7554/eLife.55108
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Tokuoka M., Maeda K., Kobayashi K., Mochizuki A. and Satou Y. (2021) The gene regulatory system for specifying germ layers in an early chordate embryo. Sci. Adv. 7, eabf8210. doi: 10.1126/sciadv.abf8210
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Kobayashi K., Maeda K., Tokuoka M., Mochizuki A. and Satou Y. (2021) Using linkage logic theory to control dynamics of a gene regulatory network of a chordate embryo. Sci. Rep. 11, 4001. doi:10.1038/s41598-021-83045-y
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Sakai Y., Koyama-Honda I.,Tachikawa M., Knorr R.L. and Mizushima N. (2020) Modeling Membrane Morphological Change during Autophagosome Formation. iScience 23, 101466. doi:10.1016/j.isci.2020.101466
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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.doi:10.1371/journal.pcbi.1006152
- 原著論文 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. doi:10.1016/j.isci.2018.05.004
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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. doi:10.1103/PhysRevE.96.032416
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Okada T. and Mochizuki A. (2017) Sensitivity and network topology in chemical reaction systems. Phys. Rev. E 96, 022322. doi:10.1103/PhysRevE.96.022322
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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. doi:10.1038/s41598-017-08259-5
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Mori F. and Mochizuki A. (2017) Expected Number of Fixed Points in Boolean Networks with Arbitrary Topology. Phys. Rev. Lett. 119, 028301. doi:10.1103/PhysRevLett.119.028301
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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. doi:10.1371/journal.pcbi.1005501
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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. doi:10.1073/pnas.1619264114
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Mochizuki A. (2016) Theoretical approaches for the dynamics of complex biological systems from information of networks. Proc. Jpn. Acad. Ser. B 92, 255-264. doi:10.2183/pjab.92.255
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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. doi:10.1103/PhysRevE.94.042403
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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. doi:10.1016/j.jtbi.2016.06.005
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Okada T. and Mochizuki A. (2016) Law of Localization in Chemical Reaction Networks. Phys. Rev. Lett. 117, 048101. doi:10.1103/PhysRevLett.117.048101
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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. doi:10.1371/journal.pcbi.1004687
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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. doi:10.1016/j.jtbi.2015.01.034
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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. doi:10.1016/j.jtbi.2014.10.025
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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. doi:10.1016/j.jtbi.2014.09.039
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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. doi:10.1016/j.jtbi.2014.09.023
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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. doi:10.1038/nprot.2014.035.
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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. doi:10.1016/j.devcel.2013.11.015
- 原著論文 2000-
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. doi:10.1021/sb400102w
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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. doi:10.1016/j.jtbi.2013.06.009
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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 doi:10.1371/journal.pone.0064506
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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. doi:10.1007/s10884-013-9312-7
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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. doi:10.1038/ncomms2319
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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. doi:10.1371/journal.pone.0048892
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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. doi:10.1242/dev.081315
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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. doi:10.1038/srep00089
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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. doi:10.1016/j.jtbi.2010.06.007
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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. doi:10.1016/j.ydbio.2010.03.015
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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. doi:10.1111/j.1365-2443.2009.01367.x
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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. doi:10.1016/j.jtbi.2009.05.027
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Mochizuki A. (2008) Structure of regulatory networks and diversity of gene expression patterns. J. theor. Biol. 250, 307-321. doi:10.1016/j.jtbi.2007.09.019
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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. doi:10.1371/journal.pcbi.0030212
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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 doi:10.1371/journal.pcbi.0030108.eor
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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. doi:10.1103/PhysRevE.75.015203
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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.
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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. doi:10.1016/j.devcel.2006.08.002
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Fujita, H. & Mochizuki, A. (2006) The Origin of the Diversity of Leaf Venation Pattern. Dev. Dyn. 235, 2710-2721 doi:10.1002/dvdy.20908
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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. doi:10.1016/j.jtbi.2005.12.016
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Takigawa-Imamura, H., Mochizuki, A. (2006) Transcriptional Autoregulation by Phosphorylated and Non-Phosphorylated KaiC in Cyanobacterial Circadian Rhythms. J. theor. Biol. 241, 178-192. doi:10.1016/j.jtbi.2005.11.013
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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. doi:10.1534/genetics.105.042895
- 原著論文 2000-
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. doi:10.1016/j.jtbi.2005.03.017
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Mochizuki, A. (2005) An Analytical Study of The Number of Steady States in Gene Regulatory Networks. J. theor. Biol. 236, 291-310. doi:10.1016/j.jtbi.2005.03.015
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Ryohji, T., Mochizuki, A. & Iwasa, Y. (2003) Possibility of Tissue Separation Caused by Cell Adhesion. J. theor. Biol. 221, 459-474. doi:10.1006/jtbi.2003.3193
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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. doi:10.1006/jtbi.2003.3192
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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
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Kurosawa, G., Mochizuki, A. and Iwasa, Y. (2002) Processes promoting oscillations — comparative study of circadian clock models. J. Theor. Biol. 216, 193-208. doi:10.1006/jtbi.2002.2546
- 原著論文 2000-
Mochizuki, A. (2002) Pattern formation of cone mosaic in zebrafish retina: A Cell rearrangement model. J. Theor. Biol. 215, 345-361. doi:10.1006/jtbi.2001.2508
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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. doi:10.1006/jtbi.2001.2480
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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