Rchr
J-GLOBAL ID：201801012877083043
Update date: Jun. 01, 2026
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 (11)：
Physical bioinformatics
, 3D genome
, 4D genome
, Chromatin Dynamics
, Chromatin Structure
, Chromosome Dynamics
, Chromosome Structure
, Statistical Physics
, Physical Biology
, Microrheology
, Nonlinear Science
Research theme for competitive and other funds (13)：
- 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
- 2025 - 2028 4Dゲノム状態の理解と可視化を支援するデータベースの構築
- 2025 - 2027 4Dゲノム状態の理解と可視化を支援するデータベースの構築
- 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 (30)：
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Shunsuke Ando, Tomoya Urashita, Soya Shinkai, Tomoshige Miyaguchi. Exact Generalized Langevin Dynamics of Pair Coordinates in Elastic Networks. arXiv. 2026
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Soya Shinkai, Toshinori Namba, Takeshi Sugawara, Soya Hagiwara, Shuichi Onami, Tokuko Haraguchi, Yasushi Hiraoka, Akinori Awazu, Masaru Ueno, Shin-ichi Tate. Integrative modelling of the genome structure and dynamics in fission yeast. Research Square. 2026
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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 genomic region proximities during transcriptional bursting. Science Advances. 2024. 10. 49. adn0020
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Soya Shinkai, Shuichi Onami, Tomoshige Miyaguchi. Generalized Langevin dynamics for single beads in linear elastic networks. Physical Review E. 2024. 110. 4. 044136
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Soya Shinkai, Shuichi Onami. 4D Genome Analysis Using PHi-C2. Methods in Molecular Biology. 2024. 2856. 271-279
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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 (102)：
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「4Dゲノム」のバイオインフォマティクスに向けて:その理解と可視化を支援する データベースの開発
(学術情報メディアセンターセミナー「次世代ゲノム解析を拓く学術情報メディア技術」 2026)
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「4Dゲノム」バイオインフォマティクスに向けて:その理解と可視化を支援するデータベースの開発
(第3回情報物理数理セミナー 2026)
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Development of a database to support the understanding and visualization of 4D genome states
(BPS2026 2026)
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『4Dゲノム』のバイオインフォマティクスに向けて:その理解と可視化を支援するデータベースの開発
(スーパーコンピュータワークショップ2025 2026)
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4Dゲノム状態の理解と可視化を支援するデータベース開発
(第48回日本分子生物学会年会 2025)
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Education (2)：
- 2004 - 2009 Waseda University Graduate School of Science and Engineering Depertment of Pure and Applied Physics
- 2000 - 2004 Waseda University School of Science and Engineering Depertment of Physics
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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Committee career (2)：
- 2026/01 - 2027/12 日本生物物理学会 会誌編集委員
- 2026/01 - 2026/12 日本生物物理学会 分野別専門委員(ゲノム・データベース)
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) (6)：
日本バイオインフォマティクス学会
, 日本エピジェネティクス研究会
, 日本生物物理学会
, THE MOLECULAR BIOLOGY SOCIETY OF JAPAN
, BIOPHYSICAL SOCIETY
, THE PHYSICAL SOCIETY OF JAPAN
