Himeoka Yusuke 姫岡優介

Researcher Number	70903160
Other IDs
Affiliation (Current)	2025: 東京大学, 大学院理学系研究科(理学部), 助教
Affiliation (based on the past Project Information) *help	2021 – 2025: 東京大学, 大学院理学系研究科(理学部), 助教
Review Section/Research Field	Principal Investigator Transformative Research Areas, Section (II) / Basic Section 43040:Biophysics-related / 0701:Biology at molecular to cellular levels, and related fields
Keywords	Principal Investigator ネットワーク / 力学系 / 数理モデル / 化学反応 / 微分方程式 / 休眠状態 / ダイナミクス / 代謝モデル / 代謝 / システム生物学 … More / デザイン / 分子システム / 適応度地形 / 化学反応ネットワーク / 人工反応系 / 無細胞翻訳系 / シミュレーション / 化学反応動力学 / PUREシステム / 反応動力学 / 動力学モデル / 細胞 / 動力学 / 休眠 / 微生物 Less

Research Projects
(7 results)
Research Products
(44 results)

A unified science of "life/non-life transition" encompassing cells and artificial cellsArea Organizer
- Area Organizer
  
  姫岡優介
- Project Period (FY)
  2025 – 2027
- Research Category
  
  Grant-in-Aid for Transformative Research Areas (B)
『生命-非生命転移』学の創出Principal Investigator
- Principal Investigator
  
  姫岡優介
- Project Period (FY)
  2025 – 2027
- Research Category
  
  Grant-in-Aid for Transformative Research Areas (B)
- Review Section
  
  Transformative Research Areas, Section (II)
- Research Institution
  The University of Tokyo
大腸菌における『生命-非生命転移境界』の可逆的横断Principal Investigator
- Principal Investigator
  
  姫岡優介
- Project Period (FY)
  2025 – 2027
- Research Category
  
  Grant-in-Aid for Transformative Research Areas (B)
- Review Section
  
  Transformative Research Areas, Section (II)
- Research Institution
  The University of Tokyo
数理モデルを用いた分子システム適応度地形のデザイン原理の解明Principal Investigator
- Principal Investigator
  
  姫岡優介
- Project Period (FY)
  2024 – 2025
- Research Category
  
  Grant-in-Aid for Transformative Research Areas (A)
- Review Section
  
  Transformative Research Areas, Section (II)
- Research Institution
  The University of Tokyo
人工的代謝ネットワークを用いた静止相における細胞代謝ダイナミクスの研究Principal Investigator
- Principal Investigator
  
  姫岡優介
- Project Period (FY)
  2022 – 2026
- Research Category
  
  Grant-in-Aid for Early-Career Scientists
- Review Section
  
  Basic Section 43040:Biophysics-related
- Research Institution
  The University of Tokyo
化学反応動力学理論を用いた頑健な反応経路設計アルゴリズムの開発Principal Investigator
- Principal Investigator
  
  姫岡優介
- Project Period (FY)
  2022 – 2023
- Research Category
  
  Grant-in-Aid for Transformative Research Areas (A)
- Review Section
  
  Transformative Research Areas, Section (II)
- Research Institution
  The University of Tokyo
Exploring roles of the metabolic network structure in bacterial dormancyPrincipal Investigator
- Principal Investigator
  
  Himeoka Yusuke
- Project Period (FY)
  2021 – 2022
- Research Category
  
  Grant-in-Aid for Research Activity Start-up
- Review Section
  
  0701:Biology at molecular to cellular levels, and related fields
- Research Institution
  The University of Tokyo

All 2024 2023 2022

All Journal Article Presentation Book

[Book] システム生物学入門2023
- Author(s)
  畠山哲央、姫岡優介
- Total Pages
  288
- Publisher
  講談社
- ISBN
  9784065334348
- Data Source
  KAKENHI-PROJECT-22K15069
[Journal Article] Perturbation-response analysis of<i>in silico</i>metabolic dynamics in nonlinear regime: Hard-coded responsiveness in the cofactors and network sparsity2024
- Author(s)
  Himeoka Yusuke、Furusawa Chikara
- Journal Title
  
  eLife (to be appeared)
  
  Volume: -
- DOI
  10.1101/2023.10.18.562862
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-22K15069, KAKENHI-PROJECT-22K21344, KAKENHI-PUBLICLY-22H05403
[Journal Article] Evolution of hierarchy and irreversibility in theoretical cell differentiation model2023
- Author(s)
  Nakamura Yoshiyuki T、Himeoka Yusuke、Saito Nen、Furusawa Chikara
- Journal Title
  
  PNAS Nexus
  
  Volume: 3 Issue: 1 Pages: 454-454
- DOI
  10.1093/pnasnexus/pgad454
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-22K15069, KAKENHI-PROJECT-22K21344, KAKENHI-PUBLICLY-22H05403
[Journal Article] Emergence of growth and dormancy from a kinetic model of the <i>Escherichia coli</i> central carbon metabolism2022
- Author(s)
  Himeoka Yusuke、Mitarai Namiko
- Journal Title
  
  Physical Review Research
  
  Volume: 4 Issue: 4 Pages: 043223-043223
- DOI
  10.1103/physrevresearch.4.043223
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K20626
[Journal Article] Structural determinants of relaxation dynamics in chemical reaction networks2022
- Author(s)
  Himeoka Yusuke、Kirkegaard Julius B.、Mitarai Namiko、Krishna Sandeep
- Journal Title
  
  bioRxiv
  
  Volume: -
- DOI
  10.1101/2022.05.25.493374
- Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K15069, KAKENHI-PUBLICLY-22H05403
[Presentation] 大腸菌代謝動力学モデルの恒常性と死2024
- Author(s)
  姫岡優介
- Organizer
  第11回定量生物学の会年会
- Invited
- Data Source
  KAKENHI-PUBLICLY-22H05403
[Presentation] Terraced NK modelにおける遺伝子型の自由度と進化速度の関係2024
- Author(s)
  池田雄太郎, 姫岡優介, 古澤力
- Organizer
  第11回定量生物学の会年会
- Data Source
  KAKENHI-PUBLICLY-22H05403
[Presentation] 細菌の休眠状態と代謝ダイナミクスの安定性2024
- Author(s)
  姫岡優介
- Organizer
  多細胞休止を研究する会
- Invited
- Data Source
  KAKENHI-PUBLICLY-22H05403
[Presentation] Solving differential equations for chemical kinetics using quantics tensor train2024
- Author(s)
  Rihito Sakurai, Wataru Mizukami, Yuta Mizuno, Yusuke Himeoka, Hiroshi Shinaoka
- Organizer
  APS March Meeting 2024
- Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-22H05403
[Presentation] Updating parameters of in silico PURE system model ePURE ) based on experimental observations2024
- Author(s)
  Shunnosuke Ban, Yusuke Himeoka, Tomoaki Matsuura, Yoshihiro Shimizu, Chikara Furusawa
- Organizer
  Korea-Japan Joint Workshop of Bottom-up Synthetic Biology
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K15069
[Presentation] Solving differential equations for chemical kinetics using quantics tensor train2024
- Author(s)
  Rihito Sakurai, Wataru Mizukami, Yuta Mizuno, Yusuke Himeoka, Hiroshi Shinaoka
- Organizer
  APS March Meeting 2024
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K15069
[Presentation] in silico細胞死2024
- Author(s)
  姫岡優介
- Organizer
  非平衡系の物理
- Data Source
  KAKENHI-PUBLICLY-22H05403
[Presentation] Updating parameters of in silico PURE system model ePURE ) based on experimental observations2024
- Author(s)
  Shunnosuke Ban, Yusuke Himeoka, Tomoaki Matsuura, Yoshihiro Shimizu, Chikara Furusawa
- Organizer
  Korea-Japan Joint Workshop of Bottom-up Synthetic Biology
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-22H05403
[Presentation] Emergence of Complex Host-Parasite networks of replicating RNA molecules: A Computational Analysis2023
- Author(s)
  Kei Nishida, Yusuke Himeoka, Chikara Furusawa
- Organizer
  Statphys28 Satellite meeting Statistical Physics and Information-Processing in Living Systems
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K15069
[Presentation] Disruption of homeostasis and death in kinetic models of Escherichia coli metabolism2023
- Author(s)
  Yusuke HImeoka, Chikara Furusawa
- Organizer
  Statphys28
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K15069
[Presentation] Solving differential equations for chemical kinetics using quantics tensor train2023
- Author(s)
  Rihito Sakurai, Wataru Mizukami, Yuta Mizuno, Yusuke Himeoka, Hiroshi Shinaoka
- Organizer
  Computational Approaches to Quantum Many-Body Systems
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K15069
[Presentation] 代謝ネットワークの構造と摂動への応答性の関係2023
- Author(s)
  姫岡優介, 古澤力
- Organizer
  「細胞を創る」研究会16.0
- Data Source
  KAKENHI-PUBLICLY-22H05403
[Presentation] Simulating fast and slow chemical kinetics with dynamic mode decomposition2023
- Author(s)
  Yuta Mizuno, Yosuke Sumiya, Yusuke Himeoka
- Organizer
  38th Symposium on Chemical Kinetics and Dynamics
- Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-22H05403
[Presentation] Solving differential equations for chemical kinetics using quantics tensor train2023
- Author(s)
  Rihito Sakurai, Wataru Mizukami, Yuta Mizuno, Yusuke Himeoka, Hiroshi Shinaoka
- Organizer
  Computational Approaches to Quantum Many-Body Systems
- Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-22H05403
[Presentation] Disruption of metabolic homeostasis: Responsiveness due to the cofactor dynamics and network sparsity2023
- Author(s)
  姫岡優介, 古澤力
- Organizer
  日本生物物理学会第61回年会
- Data Source
  KAKENHI-PUBLICLY-22H05403
[Presentation] Disruption of metabolic homeostasis: Sensitivity due to the network structure2023
- Author(s)
  Yusuke HImeoka, Chikara Furusawa
- Organizer
  Statphys28 Satellite meeting Statistical Physics and Information-Processing in Living Systems
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K15069
[Presentation] Exploring Host-Parasite Networks of Replicating RNA through Computational Simulations2023
- Author(s)
  西田慧,姫岡優介,古澤力
- Organizer
  日本進化学会第25回大会
- Data Source
  KAKENHI-PUBLICLY-22H05403
[Presentation] Disruption of metabolic homeostasis: Sensitivity due to the network structure2023
- Author(s)
  Yusuke HImeoka, Chikara Furusawa
- Organizer
  Statphys28 Satellite meeting Statistical Physics and Information-Processing in Living Systems
- Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-22H05403
[Presentation] Emergence of Complex Host-Parasite networks of replicating RNA molecules: A Computational Analysis2023
- Author(s)
  Kei Nishida, Yusuke Himeoka, Chikara Furusawa
- Organizer
  Statphys28 Satellite meeting Statistical Physics and Information-Processing in Living Systems
- Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-22H05403
[Presentation] 代謝反応ダイナミクスの摂動応答関係とネットワーク構造2023
- Author(s)
  姫岡優介, 古澤力
- Organizer
  研究会「理論と実験」
- Data Source
  KAKENHI-PUBLICLY-22H05403
[Presentation] Disruption of homeostasis and death in kinetic models of Escherichia coli metabolism2023
- Author(s)
  Yusuke HImeoka, Chikara Furusawa
- Organizer
  Statphys28
- Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-22H05403
[Presentation] Solving differential equations for chemical kinetics using quantics tensor train2023
- Author(s)
  Rihito Sakurai, Wataru Mizukami, Yuta Mizuno, Yusuke Himeoka, Hiroshi Shinaoka
- Organizer
  Trends in the Theory of Quantum Materials 2023
- Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-22H05403
[Presentation] Solving differential equations for chemical kinetics using quantics tensor train2023
- Author(s)
  Rihito Sakurai, Wataru Mizukami, Yuta Mizuno, Yusuke Himeoka, Hiroshi Shinaoka
- Organizer
  Trends in the Theory of Quantum Materials 2023
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K15069
[Presentation] Perturbation-response analysis of in silico metabolic dynamics: Hard-coded responsiveness in the cofactor and network sparsity2023
- Author(s)
  Yusuke Himeoka
- Organizer
  Asia Synthetic Biology Association meeting 2023
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-22H05403
[Presentation] ネットワークの構造と代謝状態の恒常性2023
- Author(s)
  姫岡優介
- Organizer
  日本生物物理学会サブグループ人工細胞モデル＆分子ロボティクス第4回研究会
- Invited
- Data Source
  KAKENHI-PUBLICLY-22H05403
[Presentation] Perturbation-response analysis of in silico metabolic dynamics: Hard-coded responsiveness in the cofactor and network sparsity2023
- Author(s)
  Yusuke Himeoka
- Organizer
  Asia Synthetic Biology Association meeting 2023
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K15069
[Presentation] 代謝ホメオスタシスの擾乱とネットワークの構造の関係2023
- Author(s)
  姫岡優介, 古澤力
- Organizer
  第46回日本分子生物学会年会
- Data Source
  KAKENHI-PUBLICLY-22H05403
[Presentation] Structure of catalytic reaction network for specialized compartments evolution2023
- Author(s)
  Shunsuke Ichii, Yusuke Himeoka, Chikara Furusawa
- Organizer
  STATPHYS28 Satellite Meeting 窶彜tatistical Physics and Information-Processing in Living Systems窶?
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K15069
[Presentation] Simulating fast and slow chemical kinetics with dynamic mode decomposition2023
- Author(s)
  Yuta Mizuno, Yosuke Sumiya, Yusuke Himeoka
- Organizer
  38th Symposium on Chemical Kinetics and Dynamics
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K15069
[Presentation] Structure of catalytic reaction network for specialized compartments evolution2023
- Author(s)
  Shunsuke Ichii, Yusuke Himeoka, Chikara Furusawa
- Organizer
  STATPHYS28 Satellite Meeting Statistical Physics and Information-Processing in Living Systems窶?
- Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-22H05403
[Presentation] Emergence of growth and dormancy from a kinetic model of the Escherichia coli central carbon metabolism2022
- Author(s)
  Yusuke Himeoka
- Organizer
  Roles of Heterogeneity in Nonequilibrium Collective Dynamics 2022
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K20626
[Presentation] 大腸菌中心代謝ネットワークから生じる休眠状態様のダイナミクス2022
- Author(s)
  姫岡優介
- Organizer
  理論合成インシリコ生物学セミナー
- Invited
- Data Source
  KAKENHI-PROJECT-21K20626
[Presentation] 大腸菌代謝モデルを用いた休眠状態への遷移ダイナミクスの研究2022
- Author(s)
  姫岡優介
- Organizer
  第2回深津ERATOプロジェクト全体会議
- Data Source
  KAKENHI-PROJECT-21K20626
[Presentation] Emergence of growth and dormancy from a kinetic model of the Escherichia coli central carbon metabolism2022
- Author(s)
  Yusuke Himeoka
- Organizer
  RIKEN iTHEMS Seminar
- Invited
- Data Source
  KAKENHI-PROJECT-21K20626
[Presentation] 人工的な代謝ネットワークの緩和特性とネットワーク構造2022
- Author(s)
  姫岡優介
- Organizer
  日本物理学会
- Data Source
  KAKENHI-PROJECT-21K20626
[Presentation] Disruption of metabolic homeostasis : Sensitivity due to the network structure2022
- Author(s)
  Yusuke Himeoka
- Organizer
  Quantitative Biology of Non-growing Microbes,
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K20626
[Presentation] 人工的な代謝ネットワークの緩和特性とネットワーク構造2022
- Author(s)
  姫岡優介
- Organizer
  日本物理学会第 77 回年次大会
- Data Source
  KAKENHI-PROJECT-22K15069
[Presentation] Emergence of growth and dormancy from a kinetic model of the Escherichia coli central carbon metabolism2022
- Author(s)
  Yusuke HImeoka
- Organizer
  , Major ideas in quantitative microbial physiology: Past, Present and Future,
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K20626
[Presentation] 細胞の休眠ダイナミクスと代謝ネットワーク構造2022
- Author(s)
  姫岡優介
- Organizer
  ネットワーク科学研究会2022
- Invited
- Data Source
  KAKENHI-PROJECT-21K20626

Himeoka Yusuke 姫岡 優介

Research Projects

Research Products

A unified science of "life/non-life transition" encompassing cells and artificial cellsArea Organizer

Area Organizer

Project Period (FY)

Research Category

『生命-非生命転移』学の創出Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

大腸菌における『生命-非生命転移境界』の可逆的横断Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

数理モデルを用いた分子システム適応度地形のデザイン原理の解明Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

人工的代謝ネットワークを用いた静止相における細胞代謝ダイナミクスの研究Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

化学反応動力学理論を用いた頑健な反応経路設計アルゴリズムの開発Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Exploring roles of the metabolic network structure in bacterial dormancyPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

[Book] システム生物学入門2023

Author(s)

Total Pages

Publisher

ISBN

Data Source

[Journal Article] Perturbation-response analysis of<i>in silico</i>metabolic dynamics in nonlinear regime: Hard-coded responsiveness in the cofactors and network sparsity2024

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Evolution of hierarchy and irreversibility in theoretical cell differentiation model2023

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Emergence of growth and dormancy from a kinetic model of the <i>Escherichia coli</i> central carbon metabolism2022

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Structural determinants of relaxation dynamics in chemical reaction networks2022

Author(s)

Journal Title

DOI

Data Source

[Presentation] 大腸菌代謝動力学モデルの恒常性と死2024

Author(s)

Organizer

Data Source

[Presentation] Terraced NK modelにおける遺伝子型の自由度と進化速度の関係2024

Author(s)

Organizer

Data Source

[Presentation] 細菌の休眠状態と代謝ダイナミクスの安定性2024

Author(s)

Organizer

Himeoka Yusuke 姫岡優介