†These authors equally contributed.
2025
Shinkai, S.*, Onami, S. (2025)
4D Genome Analysis Using PHi-C2.
In: Nakato, R. (eds) Computational Methods for 3D Genome Analysis.
Methods in Molecular Biology 2856, 271–279.
Link
2024
Ohishi, H., Shinkai, S.,
Owada, H., Fujii, T., Hosoda, K., Onami, S., Yamamoto, T., Ohkawa, Y., Ochiai, H.* (2024)
Transcription-coupled changes in genomic region proximities during transcriptional bursting.
Science Advances 10, eadn0020.
Full Text
Press Release (in Japanese)
Shinkai, S., Onami, S., Miyaguchi, T.* (2024)
Generalized Langevin dynamics for single beads in linear elastic network.
Physical Review E 110, 044136.
Full Text
Kusano, Y., Shinkai, S., Nozawa, R., Sun, J., Onami, S., Tashiro, S., Hirota, T.* (2024)
Spatial organization of supercoil dynamics during DNA replication.
bioRxiv.
Full Text
2023
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
Press Release (in Japanese)
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
Press Release (in Japanese)
2022
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
Press Release (in Japanese)
2021
Shinkai, S.* (2021) The Rheology of the Dynamic 3D Genome Organization. (in Japanese) Seibutsu Butsuri 61(5), 293–297. Full Text
2020
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)
2019
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
2018
Shinkai, S.* (2018) Polymer modeling of hierarchical chromatin. (in Japanese) Experimental Medicine 36(17), 65–71.
2017
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.
2016
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
Press Release (in English)
Press Release (in Japanese)
2015
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.
2014
Shinkai, S.*, Togashi, Y. (2014)
Energetics of single active diffusion trajectories.
Europhysics Letters 105(3), 30002.
Full Text
Selected in Highlights of 2014
2012
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
2008
Shinkai, S.*, Aizawa, Y.(2008) Ergodic properties of the Log-Weibull map with an infinite measure. AIP Conference Proceedings 1076, 219–222. Link
2007
Shinkai, S.*, Aizawa, Y. (2007) The Lempel-Ziv Complexity in Infinite Ergodic Systems. Journal of the Korean Physical Society 50, 261–266. Full Text
2006
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