*Corresponding author.
These authors equally contributed.


Shinkai, S., Onami, S., Miyaguchi, T.* (2024) Generalized Langevin dynamics for single beads in linear elastic network. arXiv. Full Text


Ohishi, H., Shinkai, S., Owada, H., Fujii, T., Hosoda, K., Onami, S., Yamamoto, T., Ohkawa, Y., Ochiai, H.* (2023) Transcription-coupled changes in higher-order genomic structure and transcription hub viscosity prolong enhancer-promoter connectivity. bioRxiv. Full Text

Nozaki, T., Shinkai, S., Ide S., Higashi, K., Tamura, S., Shimazoe, M.A., Nakagawa, M., Suzuki, Y., Okada, Y., Sasai, M., Onami, S., Kurokawa, K., Iida, S., Maeshima, K.* (2023) Condensed but liquid-like domain organization of active chromatin regions in living human cells. Science Advances 9, eadf1488. Full Text

Hara, M.*, Ariyoshi, M., Sano, T., Nozawa, R., Shinkai, S., Onami, S., Jansen, I., Hirota, T., Fukagawa, T.* (2023) Centromere/kinetochore is assembled through CENP-C oligomerization. Molecular Cell 83, 2188–2205. Full Text

Okamoto, K., Fujita, H., Okada, Y., Shinkai, S., Onami, S., Abe, K., Fujimoto, K., Sasaki, K., Shioi, G., Watanabe, T.M.* (2023) Single-molecule tracking of Nanog and Oct4 in living mouse embryonic stem cells uncovers a feedback mechanism of pluripotency maintenance. EMBO Journal, e112305. Full Text


Shinkai, S.*, Itoga, H., Kyoda, K., Onami, S.* (2022) PHi-C2: interpreting Hi-C data as the dynamic 3D genome state. Bioinformatics, 38(21), 4984–4986. Full Text

Iida, S., Shinkai, S., Itoh, Y., Tamura, S., Kanemaki, M.T., Onami, S., Maeshima, K.* (2022) Single-nucleosome imaging reveals steady-state motion of interphase chromatin in living human cells. Science Advances 8, eabn5626. Full Text


Shinkai, S.* (2021) The Rheology of the Dynamic 3D Genome Organization. (in Japanese) Seibutsu Butsuri 61(5), 293–297. Full Text


Shinkai, S.*, Onami, S., Nakato, R.* (2020) Toward understanding the dynamic state of 3D genome. Computational and Structural Biotechnology Journal 18, 2259–2269. Full Text

Shinkai, S.*, Sugawara, T., Miura, H., Hiratani, I., Onami, S.* (2020) Microrheology for Hi-C Data Reveals the Spectrum of the Dynamic 3D Genome Organization. Biophysical Journal 118, 2220–2228. Full Text

Shinkai, S.*, Nakagawa, M., Sugawara, T., Togashi, Y., Ochiai, H., Nakato, R., Taniguchi, Y., Onami, S.* (2020) PHi-C: deciphering Hi-C data into polymer dynamics. NAR Genomics and Bioinformatics 2(2), lqaa020. Full Text
Press Release (in Japanese)


Ito, H., Sugawara, T., Shinkai, S., Mizukawa, S., Kondo, A., Senda, H., Sawai, K., Ito, K., Suzuki, S., Takaine, M., Yoshida, S., Imamura, H., Kitamura, K., Namba, T., Tate, S., Ueno, M.* (2019) Spindle pole body movement is affected by glucose and ammonium chloride in fission yeast. Biochemical and Biophysical Research Communications 511(4), 820–825. Link


Shinkai, S.* (2018) Polymer modeling of hierarchical chromatin. (in Japanese) Experimental Medicine 36(17), 65–71.


Shinkai, S.*, Nozaki, T., Maeshima, K., Togashi, Y. (2017) Bridging the dynamics and organization of chromatin domains by mathematical modeling. Nucleus 8(4), 353–359. Full Text

Togashi, Y.*, Shinkai, S., Komatsuzaki, T. (2017) Small Numbers and Individuality of Molecules. (in Japanese) Experimental Medicine 35(19), 3190–3196.


Shinkai, S.*, Nozaki, T., Maeshima, K., Togashi, Y. (2016) Dynamic Nucleosome Movement Provides Structural Information of Topological Chromatin Domains in Living Human Cells. PLOS Computational Biology 12(10), e1005136. Full Text
Cover Article
In the news: EurekAlert!
Press Release (in English)
Press Release (in Japanese)


Shinkai, S.* (2015) Dissipative Heat Decomposition in Stochastic Energetics: Implication of the Instantaneous Diffusion Coefficient in Nonequilibrium Steady States. Journal of the Physical Society of Japan 84, 015001. Full Text

Akimoto, T.*, Nakagawa, M., Shinkai, S., Aizawa, Y. (2015) Generalized Lyapunov exponent as a unified characterization of dynamical instabilities. Physical Review E 91(1), 012926. Link

Akimoto, T.*, Shinkai, S., Aizawa, Y. (2015) Distributional Behavior of Time Averages of Non-L1 Observables in One-dimensional Intermittent Maps with Infinite Invariant Measures. Journal of Statistical Physics 158(2), 476–493. Link

Shinkai, S.* (2015) Analytical theory of individual diffusion trajectories in living cells. Advances in Science, Technology and Environmentology B11, 167–169.

Tamiya, Y.*, Shinkai, S., Aizawa, Y. (2015) Log-Weibull law in Fermi-Pasta-Ulam oscillator chain: Induction time as Nekhoroshev stable time. Advances in Science, Technology and Environmentology B11, 181–183.


Shinkai, S.*, Togashi, Y. (2014) Energetics of single active diffusion trajectories. Europhysics Letters 105(3), 30002. Full Text
Selected in Highlights of 2014


Shinkai, S.*, Aizawa, Y. (2012) 1/f Spectrum and 1-Stable Law in One-Dimensional Intermittent Map with Uniform Invariant Measure and Nekhoroshev Stability. Journal of the Physical Society of Japan 81(2), 024009. Full Text


Shinkai, S.*, Aizawa, Y.(2008) Ergodic properties of the Log-Weibull map with an infinite measure. AIP Conference Proceedings 1076, 219–222. Link


Shinkai, S.*, Aizawa, Y. (2007) The Lempel-Ziv Complexity in Infinite Ergodic Systems. Journal of the Korean Physical Society 50, 261–266. Full Text


Shinkai, S.*, Aizawa, Y. (2006) The Lempel-Ziv complexity of non-stationary chaos in infinite ergodic cases. Progress of Theoretical Physics 116(3), 503–515. Full Text

Shinkai, S.*, Aizawa, Y. (2006) The Lempel-Ziv complexity of 1/f spectral chaos and the infinite ergodic theory. Journal of Physics: Conference Series 31, 213–214. Full Text