Research and Interests

Applications & Data, etc.

• Excel spreadsheets implementing nucleosome positioning predictors (Awazu A., Bioinfomatics, 2017)
  
• RNA-seq data of Arabidopsis thaliana with more than 20 replicates for each of 8 conditions (Awazu A. et al., Scientific Reports, 2018)
  
• F.catlas (Database for quantified NGS data of F. catus)
  
• Draft genome sequence and gene annotations of sea urchin Hemicentrotus pulcherrimus (HpBase)
  
  

Publication list

• Biomolecular dynamics and functions.
  
  
  • Komoto, T., Ikeo, K., Yaguchi, S., Yamamoto, T., Sakamoto, N., & Awazu, A.:
    Assembly of continuous high-resolution draft genome sequence of Hemicentrotus pulcherrimus using long-read sequencing.
    Development, Growth & Differentiation. https://doi.org/10.1111/dgd.12924
    
    
  • Watanabe, K., Fujita, M., Okamoto, K., Yoshioka, H., Moriwaki, M., Tagashira, H., Awazu, A., Yamamoto, T., & Sakamoto, N.:
    The crucial role of CTCF in mitotic progression during early development of sea urchin. Development, Growth & Differentiation. https://doi.org/10.1111/dgd.12875
    
    
  • S. Wakao, N. Saitoh, and A. Awazu:
    Mathematical model of structural changes in nuclear speckle
    Biophysics and Physicobiology (2023) 20, e200020
    
    
  • T. Kameda, A. Awazu, Y. Togashi:
    Molecular dynamics analysis of biomolecular systems including nucleic acids.
    Biophysics and Physicobiology 19, e190027 (2022)
    
    
  • M. Shirai, T. Nara, H. Takahashi, K. Takayama, Y. Chen, Y. Hirose, M. Fujii, A. Awazu, N. Shimoda, Y. Kikuchi:
    Identification of aberrant transcription termination at specific gene loci with DNA hypomethylated transcription termination sites caused by DNA methyltransferase deficiency.
    Genes Genet. Syst. 21, 00092 (2022)
    
    
  • T. Komoto, M. Fujii, A. Awazu:
    Epigenetic-structural changes in X chromosomes promote Xic pairing during early differentiation of mouse embryonic stem cells.
    Biophysics and Physicobiology 19, e190018 (2022)
    
    
  • S. Nakahata, T. Komoto, M. Fujii, A. Awazu:
    Mathematical model of chromosomal dynamics during DNA double strand break repair in budding yeast.
    Biophysics and Physicobiology 19, e190012 (2022)
    
    
  • H. Matsumori, K. Watanabe, H. Tachiwana, T. Fujita, Y. Ito, M. Tokunaga, K. Sakata-Sogawa, H. Osakada, T. Haraguchi, A. Awazu, H. Ochiai, Y. Sakata, K. Ochiai, T. Toki, E. Ito, P.G. Goldberg, K.Tokunaga, M. Nakao, N. Saitoh:
    Ribosomal protein L5 facilitates rDNA-bundled condensate and nucleolar assembly
    Life Sci. Alli. 5, e202101045 (2022)
    （粟津は数理モデル構築とシミュレーションを行いました。）
    
    
  • D. Aoki#, A. Awazu#, M. Fujii#, J. Uewaki#, M, Hashimoto, N. Tochio, T. Umehara, S. Tate (#:Equal contribution): Ultrasensitive Change in Nucleosome Binding by Multiple Phosphorylations to the Intrinsically Disordered Region of the Histone Chaperone FACT
    J. Mol. Biol. 432 (2020) 4637-4657, https://doi.org/ 10.1016/j.jmb.2020.06.011.
    
    
  • Y. Kaneshige, F. Hayashi, K. Morigaki, Y. Tanimoto, H. Yamashita, M. Fujii, A. Awazu: Affinity of rhodopsin to raft enables the aligned oligomer formation from dimers: Coarse-grained molecular dynamics simulation of disk membranes
    PLoS ONE 15 (2020) e0226123.
    Press release
    
    
  • T. Kameda, A. Awazu, Y. Togashi: Histone Tail Dynamics in Partially Disassembled Nucleosomes During Chromatin Remodeling
    Front. Mol. Biosci. (2019) 6, 133.
    
    
  • Y. Matsushima, N. Sakamoto, A. Awazu: Insulator Activities of Nucleosome-Excluding DNA Sequences Without Bound Chromatin Looping Proteins.
    J. Phys. Chem. B (2019) 123, 1035-1043. DOI: 10.1021/acs.jpcb.8b10518
    
    
  • K. Takao, K. Takamiya, D-Q. Ding, T. Haraguchi, Y. Hiraoka, H. Nishimori, A. Awazu: Torsional turning motion of chromosomes as an accelerating force to align homologous chromosomes during meiosis.
    J. Phys. Soc. Jpn. (2019) 88, 023801
    
    
  • A. Awazu:Formation by Small Numbers: Minority Biological Scenarios in Correlations Among the Structure, Dynamics, and Function of Nuclear Chromosomes.
    Minorities and Small Numbers from Molecules to Organisms in Biology (Springer 2018)
    
    
  • M. Matsushita, H. Ochiai, K. T. Suzuki, S. Hayashi, T. Yamamoto, A. Awazu, N. Sakamoto : Dynamic changes in the interchromosomal interaction of early histone gene loci during early development of sea urchin.
    J. Cell Sci J. Cell Sci (2017) 130, 4097-4107.
    Press release
    
    
  • T. Kameda, S. Isami, Y. Togashi, H. Nishimori, N. Sakamoto and A. Awazu: The 1-Particle-per-k-Nucleotides (1PkN) Elastic Network Model of DNA Dynamics with Sequence-Dependent Geometry
    Frontier in Physiology. (2017) DOI: 10.3389/fphys.2017.00103.
    
    
  • A. Awazu: Prediction of nucleosome positioning by the incorporation of frequencies and distributions of three different nucleotide segment lengths into a general pseudo k-tuple nucleotide composition
    Bioinfomatics. (2017) 33: 42-48.
    　　-> See also (predictors)
    
    
  • S. Seirin Lee, S. Tashiro, A. Awazu, R. Kobayashi: A new application of the phase-field method for understanding the mechanisms of nuclear architecture reorganization
    J. Math. Biol. (2017) 74, 333–354.
    
    
  • Kazunori Takamiya, Keisuke Yamamoto, Shuhei Isami, Hiraku Nishimori, and Akinori Awazu: Excluded volume effect enhances the homology pairing of model chromosomes
    Nonlinear Theory and Its Applications, IEICE 7, (2016) 66-75.
    
    
  • Shuhei Isami, Naoaki Sakamoto, Hiraku Nishimori, and Akinori Awazu: Simple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence
    PLoS One 10, (2015) e0143760
    
    
  • A. Awazu: Nuclear dynamical deformation-induced hetero- and euchromatin positioning
    Phys. Rev. E 92, (2015) 032709
    
    
  • A. Awazu: Segregation and phase inversion of strongly and weakly fluctuating Brownian particle mixtures and a chain of such particle mixtures in spherical containers
    Phys. Rev. E 90 (2014) 042308
    
    
  • M. Fujii, H. Nishimor, and A. Awazu: Influences of Excluded Volume of Molecules on Signaling Processes on Biomembrane
    PLoS One 8 (2013) e62218
    
    
  • R. Kawai, S. Torigoe, K. Yoshida, A. Awazu, and H. Nishimori: Effective stochastic resonance under noise of heterogeneous amplitude
    Phys. Rev. E 82 (2010) 051122
    
    
  • A. Awazu: Transmissions of Rotational Motions by Coupled Deformable Gears
    Prog. Theo. Phys. Sup, 161 (2006) 161
    
    
  • A. Awazu: Forward and Backward Drift Motions and Inversion of Drift Directions in Small Lattice Gas System
    J. Phys. Soc. Jpn. 74 (2005) 3127
    
    
  • A. Awazu: History-dependent Phase Slips and Rectification of a few Coupled Oscillators System
    Physica D 178 (2003) 19
    (cond-mat/0202472 History-dependent Maximum Static Friction and Rectification of a System with a Few Particles in a Periodic Field)
    
    
  
  
• Rreaction dynamics and organizations.
  
  
  • Awazu, A., Takemoto, D., Watanabe, K., & Sakamoto, N.:
    Possibilities of skin coat color-dependent risks and risk factors of squamous cell carcinoma and deafness of domestic cats inferred via RNA-seq data.
    Genes to Cells 28. 893-905 (2023). https://doi.org/10.1111/gtc.13076
    
    
  • T. Nakanishi and A. Awazu:
    Formation of Small-World Network Containing Module Networks in Globally and Locally Coupled Map System with Changes in Global Connection with Time Delay Effects
    J. Phys. Soc. Jpn. 92, 034801.1-9 (2023)
    
    
  • K. Watanabe, Y. Yasui, Y. Kurose, M. Fujii, T. Yamamoto, N. Sakamoto, A. Awazu:
    Partial exogastrulation due to apical-basal polarity of F-actin distribution disruption in sea urchin embryo by omeprazole.
    Genes to Cells 1-17 (2022) doi/epdf/10.1111/gtc.12934
    プレスリリース
    
    
  • T. Nakanishi, M. Fujii, and A. Awazu:
    Self-Organization of Diverse Directional Hierarchical Networks in Simple Coupled Maps with Connection Changes
    J. Phys. Soc. Jpn. 91, 023801.1-4 (2022)
    
    
  • Ohara, A., Fujii, M., & Awazu, A.: Spontaneous Organizations of Diverse Network Structures in Coupled Logistic Maps with a Delayed Connection Change.
    J. Phys. Soc. Jpn, 89, 114801 (2020).
    
    
  • D. Liu, A. Awazu, T. Sakuma, T. Yamamoto, N. Sakamoto: Establishment of knockout adult sea urchins by using a CRISPR-Cas9 system
    Development Growrh and Differentiation 10.1111/dgd.12624
    Press release
    
    
  • A. Awazu, T. Tanabe, M. Kamitani, A. Tezuka, A. J. Nagano : Broad distribution spectrum from Gaussian to power law appears in stochastic variations in RNA-seq data.
    Scientific Reports 8, (2018) 8339.
    Commentary in Japanese (BSJ-Review 10:3 (2019))
    
    
  • L. Shi, K. Fujioka, N. Sakurai-Ozato, W. Fukumoto, K. Satoh, J. Sun, A. Awazu, et al.: Chromosomal Abnormalities in Human Lymphocytes after Computed Tomography Scan Procedure
    Radiation Research (2018), https://doi.org/10.1667/RR14976.1.
    
    
  • H. Kawazoe, Y. Nakano, ..., A. Awazu, ... : Risk stratification of ventricular fibrillation in Brugada syndrome using noninvasive scoring methods
    Heart Rhythm (2016) 13, 1947-1954.
    
    
  • A. Takemoto, T. Miyamoto, F. Simono, N. Kurogi, M. Shirae-Kurabayashi, A. Awazu, K. T. Suzuki1, T. Yamamoto, N. Sakamoto: Cilia play a role in breaking left–right symmetry of the sea urchin embryo
    Genes to Cells (2016) 12362
    
    
  • Koudai Hirao, Atsushi J. Nagano, and Akinori Awazu: Noise-plasticity correlations of gene expression in the multicellular organism Arabidopsis thaliana
    J. Theo. Bio. 387, (2015) 13-22
    
    
  • T. Tokuyama, Y. Nakano, A. Awazu, et al.: Deterioration of the circadian variation of heart rate variability in Brugada syndrome may contribute to the pathogenesis of ventricular fibrillation
    Journal of Cardiology 64 (2014) 133-138
    
    
  • R. Kawai, A. Awazu, and H. Nishimori: Effective stochastic resonance of coupled excitable elements under noise of unequal amplitude
    Phys. Rev. E 84 (2011) 021135-1-5
    
    
  • A. Awazu and K. Kaneko: Discreteness-Induced Slow Relaxation in Reversible Catalytic Reaction Networks
    Phys. Rev. E 81 (2010) 051920
    
    
  • A. Awazu and K. Kaneko: Ubiquitous ``glassy'' relaxation in catalytic reaction networks
    Phys. Rev. E 80 (2009) 041931
    
    
  • A. Awazu and K. Kaneko: Self-organized criticality of a catalytic reaction network under flow
    Phys. Rev. E 80 (2009) 010902(R)
    
    
  • A. Awazu: Input-dependent wave propagations in asymmetric cellular automata: Possible behaviors of feed-forward loop in biological reaction network
    Math. Biosci. Eng. 5 (2008) 419
    
    
  • A. Awazu and K. Kaneko: Discreteness-induced Transition in Catalytic Reaction Networks
    Phys. Rev. E 76 (2007) 041915
    
    
  • A. Awazu and K. Kaneko: Pulse Replications and Spatially Differentiated Structure Formation in One dimensional lattice dynamical System
    Math. Biosci 201 (2006) 90
    
    
  • A. Awazu and K. Kaneko: Relaxation to Equilibrium Can Be Hindered by Transient Dissipative Structures
    Phys. Rev. Lett. 92, (2004) 258302
    
    
  
  
• Structure formation and rheology.
  
  
  • T. Niiya, A. Awazu, H. Nishimori: Stability of transverse dunes against perturbations: A theoretical study using dune skeleton model
    AEOLIAN RESEARCH 9, (2013) 63-68
    
    
  • M. Fujii, A. Awazu, and H. Nishimori: Segregation pattern reorientation of granular mixture on horizontally oscillating tray
    Phys. Rev. E 85, (2012) 041304 1-4
    
    
  • T. Niiya, A. Awazu, H. Nishimori: Bifurcation Analysis of the Transition of Dune Shapes Under a Unidirectional Wind
    Phys. Rev. Lett. 108, (2012) 158001 1-4
    
    
  • H. Niiya, A. Awazu, H. Nishimori: Three-Dimensional Dune Skeleton Model as a Coupled Dynamical System of Two-Dimensional Cross Sections
    J. Phys. Soc. Jpn. (2010) 063002
    
    
  • A. Awazu: Complex Transport Phenomena in a Simple Lattice Gas System
    Physica A 373 (2007) 425
    
    
  • A. Awazu: Segregation and Phase Inversion in a Simple Granular System.
    J. Phys. Soc. Jpn. 72 (2003) 1832 (cond-mat/0301087)
    
    
  • A. Awazu: Dynamic and Static Frictions of the System with Twoparticles in a box
    J. Phys. Soc. Jpn 71 (2002) 15 (cond-mat/0102246 Liquid-Solid Phase Transition and Change of Frictional Forces of the System with Two Particles in a Box)
    
    
  • A. Awazu: Liquid-Solid Phase Transition of the System with Two particles in a Rectangular Box
    Phys. Rev. E 63, (2001) 032102
    
    
  • A. Awazu: Size Segregation and Convection of Granular Mixtures Almost Completely Packed in the Rotating Thin Box.
    Phys. Rev. Lett. 84, (2000) 4585
    
    
  • A. Awazu: Effective Dimension Transition of the Dynamics of Granular Materials in the Pipe
    (cond-mat/0010059)
    (System Width Dependency of Dynamics of Grains: Transition Between One Dimensional States and Two Dimensional States.
    Powder and Grains 2001 413 (edited by Y Kishino)).
    
    
  
  
• Active particle populations.
  
  
  • O. Yamanaka, Y. Oki, Y. Imamura, Y. Tamura, M. Shiraishi*, S. Izumi, A. Awazu, H. Nishimori:
    Ants Alter Collective Behavior After Feeding and Generate Shortcut Paths on a Two-Dimensional Foraging Area.
    Front. Phys. 10, 896717 (2022)
    
    
  • O. Yamanaka, M. Shiraishi, A. Awazu, H. Nishimori: Verification of mathematical models of response threshold through statistical characterisation of the foraging activity in ant societies
    Scientific Reports 9, (2019) 8845.
    
    
  • M. Shiraishi, R. Takeuchi, H. Nakaghawa, S-I. Nishimura, A. Awazu, H. Nishimori: Diverse stochasticity leads a colony of ants to optimal foraging
    J. Theo. Bio. (2019) https://doi.org/10.1016/j.jtbi.2019.01.002
    
    
  • T. Ogawa, E. Shoji, N. J. Suematsu, H. Nishimori, S. Izumi, A. Awazu, M. Iima : The Flux of Euglena gracilis Cells Depends on the Gradient of Light Intensity
    PLOS ONE. (2016) DOI:http://dx.doi.org/10.1371/journal.pone.0168114
    
    
  • E. Shoji, H. Nishimori, A. Awazu, S. Izumi, and M. Iima: Localized Bioconvection Patterns and Their Initial State Dependency in Euglena gracilis Suspensions in an Annular Container
    J. Phys. Soc. Jpn. 83 (2014) 043001 1-4
    
    
  • S. Nakata, M. Hata, Y. S. Ikura, E. Heisler, A. Awazu, H. Kitahata, and H. Nishimori: Motion with Memory of a Self-Propelled Object
    J. Phys. Chem. C 117, (2013) 24490-24495
    
    
  • Y S. Ikura, E. Heisler, A. Awazu, H. Nishimori, and S. Nakata: Collective motion of symmetric camphor papers in an annular water channel
    Phys. Rev. E 88, (2013) 012911 1-5
    
    
  • E. Heisler, N. J. Suematsu, A. Awazu, and H. Nishimor: Swarming of self-propelled camphor boats
    Phys. Rev. E 85, (2012) 055201(R) 1-4
    
    
  • E. Heisler, N. J. Suematsu, A. Awazu, and H. Nishimor: Collective motion and phase transitions of symmetric camphor boats
    J. Phys. Soc. Jpn. 81 (2012) 074605
    
    
  • N. J. Suematsu, A. Awazu, S. Izumi, S. Nakata, H. Nishimori: Localized bioconvection of Euglena caused by phototaxis in the lateral direction
    J. phys. Soc. Jpn. 80 (2011) 064003 1-8
    
    
  • M. Fujii, A. Awazu, and H. Nishimori: Saddle-Node Bifurcation to Jammed State for Quasi-One-Dimensional Counter Chemotactic Flow
    Phys. Rev. E 82 (2010) 015102(R)
    
    
  • N. J. Suematsu, S. Nakata, A. Awazu, and H. Nishimori: Collective behavior of inanimate boats
    Phys. Rev. E 81 (2010) 056210
    
    
  • M. Fujii, A. Awazu, and H. Nishimori: Counter Chemotactic Flow in Quasi-One-Dimensional Path
    J.Phys.Soc.Jpn. 78,(2009) 073801
    
    
  • A. Awazu: Network Structure Formations in Pulsating Particle Populations
    Phys. Rev. E 76 (2007) 055101(R)
    
    
  • A. Awazu: Cellular Automaton Rule184++C. A Simple Model for the Complex Dynamics of Various Particles Flow
    Phys. Lett. A 261, (1999) 309
    
    
  • A. Awazu: Dynamics of Two Equivalent Lanes Traffic Flow Model:Self-Organization of the Slow Lane and Fast Lane
    J.Phys.Soc.Jpn. 67,(1998) 1071
    
    
  
  

Doctoral Thesis (Osaka Prefecture University in 2001.)


過去に参加したプロジェクト

• 少数性生物学－個と多数の狭間が織りなす生命現象の探求－　
  
• 植物環境突破力：大地環境変動に対する植物の生存・成長突破力の分子的統合解析
  
• スパースモデリングの深化と高次元データ駆動科学の創成
  
• 核内クロマチンライブダイナミックスの数理研究拠点（広島大学）
  
  
  

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