Theoretical Biology Laboratory MOCHIZUKI Lab.

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.

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.

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.

Yamauchi Y., Hishida A., Okada T. and Mochizuki A. (2024) Finding regulatory modules of chemical reaction systems. Phys. Rev. Research 6, 023150.

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.

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.

Mochizuki A.* (2022) A structural approach to understanding enzymatic regulation of chemical reaction networks. Biochem. J. 479(11), 1265–1283.

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.

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.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Okada T. and Mochizuki A. (2016) Law of Localization in Chemical Reaction Networks. Phys. Rev. Lett. 117, 048101. doi:10.1103/PhysRevLett.117.048101

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

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

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

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

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

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.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Fujita, H. & Mochizuki, A. (2006) The Origin of the Diversity of Leaf Venation Pattern. Dev. Dyn. 235, 2710-2721 doi:10.1002/dvdy.20908

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

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

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

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

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

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

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

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

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

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

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

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