Papers

Ph.D. thesis

“Two design frameworks for optimizing microbial community functions” Link

Abstracts for scientists and non-scientist are available in English. Les résumés pour scientifiques et non-scientifiques sont disponibles en français. Link

 

Journal paper

  1. S. Shibasaki** and A. Terui** (under review) Food web complexity modulates
    environmental impacts on food chain length preprint
  2.  S. Shibasaki*, R. Nakadai, and Y. Nakawake. (under review) “Biogeographical
    distributions of trickster animals”. preprint
  3. S. Shibasaki, and S. Mitri. (2023) A spatially-structured mathematical model
    of the gut microbiome reveals factors that increase community stability. iScience.
    DOI:doi.org/10.1016/j.isci.2023.107499 preprint
  4. A. Picot‡, S. Shibasaki‡, O. Peacock J., and S. Mitri (2023) Microbial interactions
    in theory and practice: when are measurements compatible with models? Curr. Opin.
    in Microbiol. 75:102354 DOI: 10.1016/j.mib.2023.102354
  5. R. Nakadai**, Y. Nakawake**, and S. Shibasaki** (2023) AI language tools risk sci-
    entific diversity and innovation. Nat. Hum. Behav. DOI: 10.1038/s41562-023-01652-3.
    All authors equally contributed
  6.  A. Yamauchi, K. Ito, and S. Shibasaki (2023). Competition model explains trends
    of long-term fertilization in plant communities. Ecol. Evol. DOI: 10.1002/ece3.9832
  7.  A. Yamauchi, K. Ito, S. Shibasaki, and T. Namba (2023). Continuous irregular
    dynamics with multiple neutral trajectories permit species coexistence in competitive
    communities. Theor. Pop. Biol. DOI: 10.1016/j.tpb.2022.12.003
  8. S. Shibasaki**, M, Mobilia, and S. Mitri (2021). Exclusion of the fittest
    predicts microbial community diversity in fluctuating environments.  J. R. Soc.
    Interface 18:2021061320210613. https://doi.org/10.1098/rsif.2021.0613 preprint
  9. A. Yamauchi, K. Ito, and S. Shibasaki (2021). Colonization process determines species diversity via competitive quasi-exclusion. Ecol. Evol. Pages 11: 4470-4480. https://doi.org/10.1002/ece3.7342
  10. S. Shibasaki and S. Mitri (2020) Controlling evolutionary dynamics to optimize microbial bioremediation. Evol. Appl. 2020;00:1–12. preprint, https://doi.org/10.1111/eva.13050
  11. S. Shibasaki* (2019). The evolutionary game of interspecific mutualism in the multi-species model. J. Theo. Biol. (471), 51-58.https://doi.org/10.1016/j.jtbi.2019.03.026  preprint
  12. S. Shibasaki* and M. Shimada. (2018). Cyclic dominance emerges from the evolution of two inter-linked cooperative behaviours in the social amoeba. Proc. R. Soc. B. 285. 20180905. http://dx.doi.org/10.1098/rspb.2018.0905.
    preprint at bioRxiv
  13. S. Shibasaki*, Y. Shirokawa, and M. Shimada. (2017).  Cooperation Induces Other Cooperation: Fruiting Bodies Promote the Evolution of Macrocysts in Dictyostelium discoideum. J.Theo. Biol.  (421), 136-145. http://doi.org/10.1016/j.jtbi.2017.04.002

*corresponding author, **co-corresponding author, ‡ Equal contribution

Conference paper

  1. S. Shibasaki* and M. Shimada. (2017). Stochastic sexual interaction facilitates the evolution of asexual cooperation in the social amoeba.  Proceedings of European Conference of Artificial Life 2017. 372-379. link.