KOICHI FUJIMOTO

Last Updated :2024/07/12

Affiliations, Positions
Hiroshima University, Full Professor
Web Site
https://home.hiroshima-u.ac.jp/kfjmt/
https://scholar.google.co.jp/citations?user=DiHpVKwAAAAJ
https://jglobal.jst.go.jp/en/detail?JGLOBAL_ID=201101083147200705
E-mail
kfjmthiroshima-u.ac.jp
Self-introduction
Theoretical study (mathematical modeling and data analysis) of evolving multi-level dynamics (gene expression, shape, and behaviors) in plants, animals, and microbes.

Basic Information

Academic Degrees

  • The University of Tokyo
  • The University of Tokyo
  • The University of Tokyo

Research Keywords

  • symmetry
  • fluctuation
  • morphogenesis
  • mechanobiology
  • flower

Educational Activity

Course in Charge

  1. 2024, Liberal Arts Education Program1, 3Term, Linear AlgebraII
  2. 2024, Undergraduate Education, 1Term, Mathematics for Computation A
  3. 2024, Undergraduate Education, 4Term, Mathematics for Modeling and Simulation
  4. 2024, Undergraduate Education, First Semester, Special Study of Mathematics and Informatics for Graduation
  5. 2024, Undergraduate Education, Second Semester, Special Study of Mathematics and Informatics for Graduation
  6. 2024, Undergraduate Education, Second Semester, Mathematical modeling of rapid evolution and eco-evolutionary feedbacks
  7. 2024, Graduate Education (Master's Program) , Academic Year, Research for Academic Degree Dissertation in Mathematical and Life Sciences
  8. 2024, Graduate Education (Master's Program) , Second Semester, Special Lecture on Mathematical and Life Sciences C
  9. 2024, Graduate Education (Master's Program) , First Semester, Exercises in Applied Mathematics and Computational Science A
  10. 2024, Graduate Education (Master's Program) , Second Semester, Exercises in Applied Mathematics and Computational Science B
  11. 2024, Graduate Education (Doctoral Program) , Academic Year, Research for Academic Degree Dissertation in Integrated Life Sciences
  12. 2024, Graduate Education (Doctoral Program) , Second Semester, Special Lecture on Mathematical and Life Sciences G

Research Activities

Academic Papers

  1. Image recognition-based petal arrangement estimation, FRONTIERS IN PLANT SCIENCE, 15, 20240404
    Link to Paper Search Results by DOI
  2. Diffusive mediator feedbacks control the health-to-disease transition of skin inflammation, PLOS COMPUTATIONAL BIOLOGY, 20(1), 202401
    Link to Paper Search Results by DOI
  3. Size-correlated polymorphisms in phyllotaxis-like periodic and symmetric tentacle arrangements in hydrozoan Coryne uchidai, FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY, 11, 20231122
    Link to Paper Search Results by DOI
  4. Spatiotemporal remodeling of extracellular matrix orients epithelial sheet folding, SCIENCE ADVANCES, 9(35), 202309
    Link to Paper Search Results by DOI
  5. Geodesic theory of long association fibers arrangement in the human fetal cortex, CEREBRAL CORTEX, 33(17), 9778-9786, 20230823
    Link to Paper Search Results by DOI
  6. Patterned proliferation orients tissue-wide stress to control root vascular symmetry in Arabidopsis, Current Biology, 33(5), 886-898.e8, 202303
  7. GRAS transcription factors regulate cell division planes in moss overriding the default rule., Proceedings of the National Academy of Sciences of the United States of America, 120(4), e2210632120, 20230124
  8. Neural mechanism of experience-dependent sensory gain control in C. elegans, Neuroscience Research, 202301
  9. Collective Cell Movement under Cell-Scale Tension Gradient at Tissue Interface, Journal of the Physical Society of Japan, 91(5), 20220515
  10. Traveling wave of inflammatory response to regulate the expansion or shrinkage of skin erythema., PloS one, 17(2), e0263049, 2022
  11. Polymorphism in the symmetries of gastric pouch arrangements in the sea anemone D. lineata., Zoological letters, 7(1), 12-12, 20210906
  12. Polarity Fluctuation Inhibition by Memory in Collective Cell Motion, JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN, 90(5), 202105
  13. Rotation angle of stem cell division plane controls spiral phyllotaxis in mosses., Journal of plant research, 134(3), 457-473, 202105
  14. Tissue growth constrains root organ outlines into an isometrically scalable shape., Development (Cambridge, England), 148(4), 20210226
  15. A Mechanical Instability in Planar Epithelial Monolayers Leads to Cell Extrusion., Biophysical journal, 118(10), 2549-2560, 20200519
  16. Perianth Phyllotaxis Is Polymorphic in the Basal Eudicot Anemone and Eranthis Species, Frontiers in Ecology and Evolution, 8, 20200327
  17. A design principle for floral organ number and arrangement in flowers with bilateral symmetry., Development (Cambridge, England), 147(3), 20200204
  18. Crowding-Boosting Polarity and Motion Order of Cells, Proceedings of the Symposium on Simulation of Traffic Flow, 25, 21-24, 201912
  19. Optimal Scaling of Critical Size for Metamorphosis in the Genus Drosophila., iScience, 20, 348-358, 20191025
  20. Cell Motion Alignment as a Polarity Memory Effect, Journal of the Physical Society of Japan, 88(10), 103801-103801, 20191015
  21. Curved surface geometry-induced topological change of an excitable planar wavefront., Chaos (Woodbury, N.Y.), 29(9), 093120-093120, 201909
  22. Lateral Inhibition by a Peptide Hormone-Receptor Cascade during Arabidopsis Lateral Root Founder Cell Formation., Developmental cell, 48(1), 64-75, 20190107
  23. Cell Migration driven by Receptor Density Polarity of Cell-Matrix Adhesion, Proseeding of the Symposium on Simulation of Traffic Flow, 24, 5-8, 201812
  24. Competition for Space Is Controlled by Apoptosis-Induced Change of Local Epithelial Topology., Current biology : CB, 28(13), 2115-2128, 20180709
  25. A quantitative study of the diversity of stripe-forming processes in an arthropod cell-based field undergoing axis formation and growth., Developmental biology, 437(2), 84-104, 20180515
  26. Spiral phyllotaxis underlies constrained variation in Anemone (Ranunculaceae) tepal arrangement., Journal of plant research, 131(3), 459-468, 201805
  27. Plant-inspired pipettes., Journal of the Royal Society, Interface, 15(140), 201803
  28. Mouse spermatozoa with higher fertilization rates have thinner nuclei., PeerJ, 5, e3913, 2017
  29. Inference of Cell Mechanics in Heterogeneous Epithelial Tissue Based on Multivariate Clone Shape Quantification., Frontiers in cell and developmental biology, 5, 68-68, 2017
  30. Stochastic occurrence of trimery from pentamery in floral phyllotaxis of Anemone (Ranunculaceae), Acta Societatis Botanicorum Poloniae, 85(4), 201612
  31. Relationship between the species-representative phenotype and intraspecific variation in Ranunculaceae floral organ and Asteraceae flower numbers., Annals of botany, 117(5), 925-35, 201604
  32. Neural field dynamics for growing brains, Nonlinear Theory and Its Applications, IEICE, 7(2), 226-233, 2016
  33. A dynamical phyllotaxis model to determine floral organ number., PLoS computational biology, 11(5), e1004145, 201505
  34. A developmental basis for stochasticity in floral organ numbers., Frontiers in plant science, 5, 545-545, 2014
  35. Robustness of self-organizing chemoattractant field arising from precise pulse induction of its breakdown enzyme: a single-cell level analysis of PDE expression in Dictyostelium., Biophysical journal, 104(5), 1191-202, 20130305
  36. A design principle of group-level decision making in cell populations., PLoS computational biology, 9(6), e1003110, 2013
  37. COLLECTIVE DECISION-MAKING AND OSCILLATORY BEHAVIORS IN CELL POPULATIONS, ENGINEERING OF CHEMICAL COMPLEXITY, 11, 279-297, 2013
  38. Collective oscillations in developing cells: insights from simple systems., Development, growth & differentiation, 53(4), 503-17, 201105
  39. Inter-origin cooperativity of geminin action establishes an all-or-none switch for replication origin licensing., Genes to cells : devoted to molecular & cellular mechanisms, 16(4), 380-96, 201104
  40. The onset of collective behavior in social amoebae., Science (New York, N.Y.), 328(5981), 1021-5, 20100521
  41. Network evolution of body plans., PloS one, 3(7), e2772, 20080723
  42. Emergence of multi-time scales in coupled oscillators with plastic frequencies, Europhysics Letters (EPL), 78(2), 20004, 200704
  43. Relation between Adaptation and Irreversible Circulation in Bacteria Chemotaxis, Progress of Theoretical Physics Supplement, 161(161), 251-254, 2006
  44. Cross talking of network motifs in gene regulation that generates temporal pulses and spatial stripes., Genes to cells : devoted to molecular & cellular mechanisms, 10(11), 1025-1038, 200511
  45. Noisy signal amplification in ultrasensitive signal transduction., Proceedings of the National Academy of Sciences of the United States of America, 102(2), 331-336, 20050101
  46. Convective instability with time scale translation of the transmitted fluctuation, Physica D: Nonlinear Phenomena, 196(1-2), 67-89, 200409
  47. Bifurcation cascade as chaotic itinerancy with multiple time scales., Chaos (Woodbury, N.Y.), 13(3), 1041-1056, 200309
  48. How fast elements can affect slow dynamics, Physica D: Nonlinear Phenomena, 180(1-2), 1-16, 200306
  49. Sensitive boundary condition dependence of noise-sustained structure., Physical Review E, 63(3 Pt 2), 036218, 200103
  50. Noise-induced input dependence in a convectively unstable dynamical system, Physica D: Nonlinear Phenomena, 129(3-4), 203-222, 199905

Invited Lecture, Oral Presentation, Poster Presentation

  1. 単純な力学模型による脳の皺形成のシミュレーション, 松下勝義; 堀部和也; 鎌本直也; 廣中謙一; 藤本仰一, 日本物理学会講演概要集(CD-ROM), 2018/09/21
  2. 2種類の細胞間の真っ直ぐで滑らかな境界は,境界から離れた局所的な細胞成長により促進される, 藤原基洋; 宮島俊介; 中島敬二; 藤本仰一, 日本植物学会大会研究発表記録, 2018/09/01
  3. 形の空間にみる制約された揺らぎと多様性:花器官配置の数理解析, 北沢美帆; 北沢美帆; 藤本仰一, 日本植物学会大会研究発表記録, 2018/09/01
  4. 細胞分裂面制御からみるボディプランの進化, 鎌本直也; 松下勝義; 長谷部光泰; 藤本仰一, 日本進化学会大会プログラム・講演要旨集(Web), 2018/08/22
  5. Evo‐Devoの数理;発展と未来, 藤本仰一, 日本進化学会大会プログラム・講演要旨集(Web), 2018/08/22
  6. 形の空間にみる制約された揺らぎと多様性:花器官配置の数理解析, 北沢美帆; 北沢美帆; 藤本仰一, 日本進化学会大会プログラム・講演要旨集(Web), 2018/08/22
  7. 花器官配置の多様性を数理モデルから読み解く, 北沢美帆; 北沢美帆; 藤本仰一, 日本植物学会大会研究発表記録, 2017/09/01
  8. 植物組織では異方的な細胞成長が細胞間の滑らかな境界形成を促進する, 藤原基洋; 藤本仰一; 宮島俊介, 日本植物学会大会研究発表記録, 2017/09/01
  9. 花器官配置の制約された揺らぎ:花器官数の多様化との相関, 藤本仰一; 北沢美帆, 日本進化学会大会プログラム・講演要旨集(Web), 2017/08/24
  10. 完全変態昆虫における変態のための臨界重量の適応的意義, 廣中謙一; 廣中謙一; 西村隆史; 藤本仰一, 日本物理学会講演概要集(CD-ROM), 2017/03/21,

    完全変態昆虫では、幼虫がある臨界重量に到達したときに蛹化が確約される。今回、我々は臨界重量の適応的意義を明らかにするため、完全変態昆虫の最適生活史モデルを構築し、理論的予測を実測データと比較した。

  11. 曲面による進行パルス波の分裂, 堀部和也; 廣中謙一; 松下勝義; 藤本仰一, 日本物理学会講演概要集(CD-ROM), 2017/03/21
  12. 細胞壁をもつ植物における器官形成の解析―側根形成をモデルとして―, 郷達明; 郷達明; 藤原基洋; 藤本仰一; 深城英弘, 日本細胞生物学会大会(Web), 2017
  13. 細胞死により空いた隙間をめぐる力学的な細胞競合, 坪井有寿; 大澤志津江; 井垣達吏; 藤本仰一, 日本細胞生物学会大会(Web), 2017
  14. Curvature-driven splitting of a planar traveling wave, Horibe Kazuya; Hironaka Ken-ichi; Matsushita Katsuyoshi; Fujimoto Koichi, Meeting Abstracts of the Physical Society of Japan, 2017,

    反応拡散系による進行パルス波は，平面上で反射，対消滅，分裂といった様々な時空間パターンが知られているが，それらに対する曲面の影響はまだよく調べられていない．今回我々は進行パルス波が二次元ガウス関数型曲面によって曲がり，その一部が対消滅し，分裂することを数値計算で示す．分裂が生じるまでの波の経時変化は測地線方程式から導いた曲面の最短経路から予測できた．この進行波の分裂は，ガウス関数型曲面の幅と高さの比が閾値を越えると生じた．さらに曲面の高さが波の幅以下のときには幅と高さの比によらず分裂が起きず、進行波は波の幅より小さな曲面から影響を受けないという一種のロバストネスを示した。これらの性質は、ヒトなどの大脳皮質の折れ畳んだ曲面上における神経活動の伝搬波でも働いているかもしれない。

  15. Mechanical occupation of the lost territory by winners during cell competition, Tsuboi Alice; Ohsawa Shizue; Igaki Tatsushi; Fujimoto Koichi, Meeting Abstracts of the Physical Society of Japan, 2017,

    胞競合は、遺伝的に異なる2種類の細胞が、その境界において互いに適応度を競い合う現象である。適応度の低い細胞(敗者)がアポトーシスにより排除され、そのアポトーシスで空いた隙間を適応度の高い細胞(勝者)が埋めていく。細胞の適応度に応じて埋める仕組みは、よくわかっていない。我々は、多細胞組織における細胞の増殖、細胞死、および、力学的な変形を考慮した数理モデルの数値実験を通じて、その仕組みを提示する。その一部をショウジョウバエの遺伝学実験により検証した。

  16. 陸上植物の根端分裂組織に見られるドーム形状の曲線は共通する, 藤原基洋; 藤本仰一, 日本植物学会大会研究発表記録, 2016/09/01
  17. 花器官配置の対称性の発生進化を数理モデルでたどる, 中川愛子; 北沢美帆; 藤本仰一, 日本植物学会大会研究発表記録, 2016/09/01
  18. 細胞競合 その本質と生理的意義に迫る 細胞競合の数理モデル 不均一な増殖に対する上皮組織の恒常的な変形, 坪井 有寿; 大澤 志津江; 井垣 達吏; 藤本 仰一, 日本生化学会大会・日本分子生物学会年会合同大会講演要旨集, 2015/12
  19. 細胞社会を支える適者生存システム 細胞競合の分子基盤とその役割 細胞競合の数理モデル 不均一な増殖により生じる細胞の形の恒常性破綻とその維持, 坪井 有寿; 大澤 志津江; 井垣 達吏; 藤本 仰一, 日本細胞生物学会大会講演要旨集, 2015/06
  20. 花の左右対称と回転対称を切り替える仕組み, 中川愛子; 北沢美帆; 藤本仰一, 形の科学会誌, 2015/06
  21. 上皮細胞がくさび形に変形するのに必要な力の探索―頂底極性に基づく細胞変形モデル, 藤原基洋; 藤本仰一, 形の科学会誌, 2015/06
  22. 力が細胞競合の適応度を調節する, 坪井有寿; 大澤志津江; 井垣達吏; 藤本仰一, 日本細胞生物学会大会要旨集, 2014/05/15
  23. 細胞競合の数理モデル:分裂速度の差により生じる恒常性の破綻とその維持, 坪井有寿; 大澤志津江; 井垣達吏; 藤本仰一, 日本分子生物学会年会プログラム・要旨集(Web), 2014
  24. 力を介して細胞の増殖速度の差を感知する仕組み, 坪井有寿; 赤井菜々美; 井垣達吏; 藤本仰一, 日本物理学会講演概要集, 2013/08/26
  25. 細胞の集団的な応答の設計原理 1―双安定系, 藤本仰一; 澤井哲, 日本物理学会講演概要集, 2013/08/26
  26. 細胞の集団的な応答の設計原理 2―興奮振動系, 藤本仰一; 澤井哲, 日本物理学会講演概要集, 2013/08/26
  27. 細胞競合の数理モデリング―力を介した遺伝的な差異の認識, 藤本仰一; 坪井有寿, 日本分子生物学会年会プログラム・要旨集(Web), 2013
  28. 細胞競合における力を介した境界形成メカニズム, 坪井有寿; 藤本仰一, 日本分子生物学会年会プログラム・要旨集(Web), 2013
  29. A design principle of collective decision-making of cell populations 1 : bistable circuits, Fujimoto Koichi; Sawai Satoshi, Meeting Abstracts of the Physical Society of Japan, 2013
  30. A design principle of collective decision-making of cell populations 2 : excitatory-oscillatory circuits, Fujimoto Koichi; Sawai Satoshi, Meeting Abstracts of the Physical Society of Japan, 2013
  31. Mechanical dynamics at the interface between two clonal cell populations with different growth rate, Tsuboi Arisu; Akai Nanami; Igaki Tatsushi; Fujimoto Koichi, Meeting Abstracts of the Physical Society of Japan, 2013
  32. The onset of collective cellular oscillations that capture remote information (Theory of Biomathematics and Its Applications VIII), Fujimoto Koichi; Sawai Satoshi, RIMS Kokyuroku, 2012/06
  33. 24aBD-12 Synchronized Onset of Cell Density Dependent Transition, Fujimoto Koichi, Meeting Abstracts of the Physical Society of Japan, 2012
  34. 27aPS-41 Formation and splitting of striped pattern on growing domain in animal segmentation, Matsuura H; Fujimoto K, Meeting Abstracts of the Physical Society of Japan, 2012
  35. 形づくりの遺伝子ネットワーク進化理論, 藤本仰一; 石原秀至; 金子邦彦, 生化学, 2009/09/25
  36. フィードバックループと形づくり 形づくりの遺伝子ネットワーク進化理論, 藤本 仰一; 石原 秀至; 金子 邦彦, 日本生化学会大会プログラム・講演要旨集, 2009/09
  37. 21aPS-53 Network modules organizing spatio-temporal gene expression leading to diverse animal body plans., Fujimoto Koichi, Meeting Abstracts of the Physical Society of Japan, 2007
  38. Self-Organization in Frequency Space. 1, Tachikawa Masashi; Fujimoto Kouichi, Meeting Abstracts of the Physical Society of Japan, 2003

Awards

  1. Drosophila image award HONORABLE MENTION – VIDEO, Spatiotemporal remodeling of extracellular matrix orients epithelial sheet folding

External Funds

Acceptance Results of Competitive Funds

  1. 2021, 2026
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  2. 2022/04/01, 2024/03/31
  3. 2021/07/09, 2024/03/31
  4. 2020/04/01, 2023/03/31
  5. 2020/04/01, 2022/03/31
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  6. Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), 2017/06/30, 2022/03/31
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  7. Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (S), Spatiotemporal regulation of cell division axis as a grand plan of plant developmental evolution, 2016/05/31, 2021/03/31
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  8. Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), Mathematical analysis of cell competition: Differential fitness-driven multicellular mechanics, 2017/04/01, 2019/03/31
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  9. Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (S), Developmental dynamics of human brain from pattern formation to generation of behaviors, 2014/05/30, 2019/03/31
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  10. Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), 2016/04/01, 2018/03/31
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  11. Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B), Making a model of Economic circulation and environmental conservation in the hilly and mountainous areas by the self-employed and self-harvesting forestry, 2015/04/01, 2018/03/31
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  12. Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), 2015/04/01, 2017/03/31
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  13. Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), 2014/04/01, 2016/03/31
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  14. Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B), Molecular network design toward group-level decision making of cell populations, 2011/04/28, 2015/03/31
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