The Construction of Observational Heterarchy on One-Dimensional Map System. - Kohei Nakajima; Soya Shinkai (BIOCOMP, 2007)

Formal Model of Embodiment on Abstract Systems: From Hierarchy to Heterarchy. - Kohei Nakajima; Soya Shinkai; Takashi Ikegami (ECAL, 2007)

Dynamic Nucleosome Movement Provides Structural Information of Topological Chromatin Domains in Living Human Cells. - Soya Shinkai; Tadasu Nozaki; Kazuhiro Maeshima; Yuichi Togashi (PLoS Comput. Biol., 2016)

PHi-C2: interpreting Hi-C data as the dynamic 3D genome state. - Soya Shinkai; Hiroya Itoga; Koji Kyoda; Shuichi Onami (Bioinform., 2022)