Rchr
J-GLOBAL ID：201801012877083043
Update date: May. 01, 2024
Shinkai Soya
シンカイ ソウヤ | Shinkai Soya
Affiliation and department：
Job title：
Senior Scientist
Homepage URL (1)：
http://soyashinkai.com/
Research field (4)：
Systems genomics
, Biophysics
, Bio-, chemical, and soft-matter physics
, Mathematical physics and basic theory
Research keywords (9)：
3D genome
, Chromatin Dynamics
, Chromatin Structure
, Chromosome Dynamics
, Chromosome Structure
, Physical Biology
, Statistical Physics
, Microrheology
, Nonlinear Science
Research theme for competitive and other funds (11)：
- 2023 - 2029 マルチモーダル時空間統合オミクス解析による哺乳類細胞運命制御基盤の理解
- 2023 - 2025 Modality of chromatin viscoelasticity and loop formation based on Hi-C data
- 2022 - 2025 クロマチンの運動性から捉える転写制御のゆらぎとがん細胞の悪性化
- 2022 - 2025 Elucidation of the linkage between higher-order genomic structural dynamics and gene expression
- 2021 - 2023 Modality of the dynamic 3D genome organization in hydrodynamic interactions
- 2020 - 2022 Genome information physics based on microrheology of the 3D genome organization
- 2018 - 2020 Polymer modeling for 3D chromosome structure with a deep learning and 4D simulation
- 2016 - 2018 Interactions within chromatin domains by a mathematical model of chromosomes with epigenetic information
- 2016 - 2018 Simultaneous imaging of chromatin fractal dimensions and temperature in living cell nucleus
- 2011 - 2016 Constructing a theoretical framework to study reaction networks involving a small number of molecules: modeling with consideration of minority and hierarchy
- 2009 - 2011 Multi ergodicity in nearly integrable Hamiltonian systems and large deviation properties of infinite ergodic systems
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Papers (28)：
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Hiroaki Ohishi, Soya Shinkai, Hitoshi Owada, Takeru Fujii, Kazufumi Hosoda, Shuichi Onami, Takashi Yamamoto, Yasuyuki Ohkawa, Hiroshi Ochiai. Transcription-coupled changes in higher-order genomic structure and transcription hub viscosity prolong enhancer-promoter connectivity. bioRxiv. 2023
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Kazuko Okamoto, Hideaki Fujita, Yasushi Okada, Soya Shinkai, Shuichi Onami, Kuniya Abe, Kenta Fujimoto, Kensuke Sasaki, Go Shioi, Tomonobu M Watanabe. Single-molecule tracking of Nanog and Oct4 in living mouse embryonic stem cells uncovers a feedback mechanism of pluripotency maintenance. The EMBO Journal. 2023. e112305
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Masatoshi Hara, Mariko Ariyoshi, Tomoki Sano, Ryu-Suke Nozawa, Soya Shinkai, Shuichi Onami, Isabelle Jansen, Toru Hirota, Tatsuo Fukagawa. Centromere/kinetochore is assembled through CENP-C oligomerization. Molecular Cell. 2023. 83. 13. 2188-2205.e13
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Tadasu Nozaki, Soya Shinkai, Satoru Ide, Koichi Higashi, Sachiko Tamura, Masa A Shimazoe, Masaki Nakagawa, Yutaka Suzuki, Yasushi Okada, Masaki Sasai, et al. Condensed but liquid-like domain organization of active chromatin regions in living human cells. Science Advances. 2023. 9. 14. eadf1488
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Soya Shinkai, Hiroya Itoga, Koji Kyoda, Shuichi Onami. PHi-C2: interpreting Hi-C data as the dynamic 3D genome state. BIOINFORMATICS. 2022. 38. 21. 4984-4986
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MISC (14)：
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Soya Shinkai, Yuichi Togashi. Quantitative Theory of Active Diffusion Trajectories by Instantaneous Diffusion Coefficient. BIOPHYSICAL JOURNAL. 2015. 108. 2. 471A-472A
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Tamiya Yuji, Shinkai Soya, Aizawa Yoji. 28aAK-1 Log-Weibull Law and Nekhoroshev Theorem in Hamiltonian Chaos. Meeting abstracts of the Physical Society of Japan. 2014. 69. 1. 317-317
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Shinkai Soya, Togashi Yuichi. A mechanism of anomalous diffusion and the dynamic analysis. Meeting abstracts of the Physical Society of Japan. 2013. 68. 2. 334-334
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Shinkai Soya, Togashi Yuichi. 26aXR-10 Energetics of an Enhanced Diffusion Trajectory. Meeting abstracts of the Physical Society of Japan. 2013. 68. 1. 322-322
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Sugiyama Katsutoshi, Shinkai Soya, Aizawa Yoji. 27aBD-2 Anomalous diffusion driven by infinite ergodicity in nonstationary dynamical systems. Meeting abstracts of the Physical Society of Japan. 2012. 67. 1. 366-366
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Lectures and oral presentations (85)：
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3次元ゲノム構造とクロマチン動態をつなぐ高分子物理学
(第97回 日本薬理学会年会 2023)
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Polymer physics of Hi-C data reveals linear viscoelasticity of the 3D physics
(2023)
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Polymer physics of Hi-C data reveals linear viscoelasticity of the 3D genome
(The Structural Genome: Merging Physics, Biology & Computation 2023)
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Polymer physics of Hi-C data reveals linear viscoelasticity of the 3D physics
(The 4th Genome Modality Annual meeting 2023)
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Polymer physics for Hi-C data reveals rheological features of chromatin
(2022)
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Professional career (1)：
- Ph.D. (Waseda University)
Work history (7)：
- 2023/04 - 現在 RIKEN Center for Biosystems Dynamics Research Senior Scientist
- 2018/04 - 2023/03 RIKEN Center for Biosystems Dynamics Research Research Scientist
- 2017/05 - 2018/03 RIKEN Quantitative Biology Center Research Scientist
- 2017/04 - 2017/04 Hiroshima University Graduate School of Science Research Scientist
- 2013/05 - 2017/03 Hiroshima University Research Center for the Mathematics on Chromatin Live Dynamics Assistant Professor (Special Appointment)
- 2012/04 - 2013/04 Kobe University Graduate School of System Informatics Research Scientist
- 2009/04 - 2012/03 Waseda University Research Associate
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Awards (1)：
- 2016/06 - CREST「生命動態の理解と制御のための基盤技術の創出」研究領域 第6回数理デザイン道場 最優秀ポスター発表賞
Association Membership(s) (4)：
THE PHYSICAL SOCIETY OF JAPAN
, BIOPHYSICAL SOCIETY
, THE MOLECULAR BIOLOGY SOCIETY OF JAPAN
, 日本生物物理学会
