研究者詳細 - 倉田　博之

論文 - 倉田　博之

分割表示252 件中 161 - 180 件目／全件表示 >>

Module-based analysis of robustness tradeoffs in the heat shock response system 査読有り

Kurata H., El-Samad H., Iwasaki R., Ohtake H., Doyle J., Grigorova I., Gross C., Khammash M.

PLoS Computational Biology 2 ( 7 ) 0663 - 0675 2006年08月

担当区分：責任著者掲載種別：研究論文（学術雑誌）

Biological systems have evolved complex regulatory mechanisms, even in situations where much simpler designs seem to be sufficient for generating nominal functionality. Using module-based analysis coupled with rigorous mathematical comparisons, we propose that in analogy to control engineering architectures, the complexity of cellular systems and the presence of hierarchical modular structures can be attributed to the necessity of achieving robustness. We employ the Escherichia coli heat shock response system, a strongly conserved cellular mechanism, as an example to explore the design principles of such modular architectures. In the heat shock response system, the sigma-factor σ32 is a central regulator that integrates multiple feedforward and feedback modules. Each of these modules provides a different type of robustness with its inherent tradeoffs in terms of transient response and efficiency. We demonstrate how the overall architecture of the system balances such tradeoffs. An extensive mathematical exploration nevertheless points to the existence of an array of alternative strategies for the existing heat shock response that could exhibit similar behavior. We therefore deduce that the evolutionary constraints facing the system might have steered its architecture toward one of many robustly functional solutions. © 2006 Kurata et al.

DOI： 10.1371/journal.pcbi.0020059

Scopus

その他リンク： https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=33746639260&origin=inward

大腸菌窒素同化システムのポジティブフィードバック制御のシンプルモデル査読有り

真崎浩一, 倉田博之

情報処理学会研究報告. MPS, 数理モデル化と問題解決研究報告 ( 一般社団法人情報処理学会 ) 59 61 - 64 2006年05月

担当区分：責任著者記述言語：英語掲載種別：研究論文（学術雑誌）

大腸菌の窒素同化システムにおいて、シミュレーションにより環境中のアンモニア濃度の変化に対してシステムがヒステリシスを示すことが予測されている。このヒステリシス挙動がポジティブフィードバック制御に起因することを、シンプルモデルを用いた理論解析により明らかにした。シンプルモデルにおいて立式した3次方程式を解くことによって、システムが複数の定常解を示すアンモニア濃度範囲があることがわかった。また、ポジティブフィードバック制御を強くすると、複数の定常解を示すアンモニアの濃度範囲が拡大し、逆に弱くすると、定常解が1つになることを示した。

CiNii Article

その他リンク： https://ci.nii.ac.jp/naid/110004849753

Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System 査読有り

H. Kurata,H. El Samad,R. Iwasaki,H. Othake,J.C. Doyle,I. Grigorova,C. Gross,and M. Khammash

PLoS Computational Biology 2 e59 - e73 2006年05月

システムバイオロジーの現状と未来査読有り

倉田　博之

生物物理 46 244 - 250 2006年04月

Effective and fast optimization for a dynamic model of the Drosophila circadian oscillator 査読有り

Shin Tanaka,Hiroyuki Kurata,Takeshi Ohashi

IEEE International Conference on Systems, Man, and Cybernetics 3596 - 3601 2006年04月

CADLIVE: Integration for large-scale network data

Yuki Shimokawa,Zazuhiro Maeda,Kentaro Inoue,Hiroyuki Kurata

The 16th International Conference on Genome Informatics S02-1-2 2006年04月

A steady-state approximation-based solver for stiff biochemical models

Emi Shiraishi,Hiroyuki Kurata

The 16th International Conference on Genome Informatics P016-1-2 2006年04月

Comparison of the prediction abilities of FBA, MOMA, and ROOM for a pykF mutant of E. coli

Quanyu Zhao,Hiroyuki Kurata

The 16th International Conference on Genome Informatics P107-1-2 2006年04月

Sensitivity analysis for the E. coli nitrogen assimilation system

Koichi Masaki,Hiroyuki Kurata

未入力 P010-1-2 2006年04月

A simple model of positive feedback of the nitrogen assimilation system in E. coli

Masaki Kouichi,Kurata Hiroyuki

ISPJ SIG Technical Reports 61 - 64 2006年04月

Survival ratio GA for two-evaluation problem in parameter tuning of heat shock response in E. coli 査読有り

Tanaka S., Kurata H., Ohashi T.

Conference Proceedings - IEEE International Conference on Systems, Man and Cybernetics 3 2078 - 2083 2005年12月

担当区分：責任著者掲載種別：研究論文（国際会議プロシーディングス）

In the field of bioinformatics, several studies have attempted to reconstruct biological reactions on a computer in order to understand their essence. In this study, we optimized the parameter tuning problem of the heat shock response in E. coli, one of the gene regulatory network simulations, which exhibits a transient peak by genetic algorithms (GAs). However, if the search area is too large, the optimization performance deteriorated significantly. To optimize this problem more efficiently, we defined two evaluation functions that represent two features of the simulation and used the survival ratio GA. This GA has a gene's lifetime as a new concept, that is, the population holds previous search histories. By alternating between two evaluation functions every generation, the population holds both previously evaluated genes and children inherit both properties. In the two-evaluation problem of the heat shock response, the survival ratio GA exhibited a considerably better optimization performance than traditional GA methods. © 2005 IEEE.

Scopus

その他リンク： https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=27944494749&origin=inward

Reverse engineering for a dynamic model of the Drosophila circadian oscillator 査読有り

Tanaka S., Kurata H., Ohashi T.

Proceedings - International Conference on Computational Intelligence for Modelling, Control and Automation, CIMCA 2005 and International Conference on Intelligent Agents, Web Technologies and Internet 1 625 - 632 2005年12月

担当区分：責任著者掲載種別：研究論文（国際会議プロシーディングス）

In the field of bioinformatics, biochemical networks have been reconstructed in computer to understand their dynamic features. A problem is how to estimate the values of many kinetic parameters that are hard to measure experimentally. In this study, we have proposed a novel parameter estimation method based on genetic algorithms (GAs) and applied it to the Drosophila circadian oscillator. We defined two evaluation functions that represent two features of the dynamic model. To optimize the two functions simultaneously, we proposed the survival ratio GA, which has a gene's lifetime as a new concept, that is, the population holds previous search histories. By alternating between two evaluation functions every generation, the population holds both previously evaluated genes and children inherit both properties. In the two-evaluation problem of the Drosophila circadian oscillation system, the survival ratio GA exhibited a considerably better optimizing performance than traditional GA methods. © 2005 IEEE.

Scopus

その他リンク： https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=33847187422&origin=inward

Reverse Engineering for a Dynamic Model of the Drosophila Circadian Oscillator 査読有り

Shin Tanaka,Hiroyuki Kurata,Takeshi Ohashi

International Conference on Computational Intelligence for Modelling, Control and Automation 625 - 631 2005年11月

Survival ratio GA for two-evaluation problem in parameter tuning of heat shock response in E. coli 査読有り

Shin Tanaka,Hiroyuki Kurata,Takeshi Ohashi

Proceedings of the IEEE International Conference on Systems, Man, and Cybernetics 2078 - 2083 2005年10月

A grid layout algorithm for automatic drawing of biochemical networks 査読有り

Li W., Kurata H.

Bioinformatics 21 ( 9 ) 2036 - 2042 2005年05月

担当区分：責任著者掲載種別：研究論文（学術雑誌）

Motivation: Visualization is indispensable in the research of complex biochemical networks. Available graph layout algorithms are not adequate for satisfactorily drawing such networks. New methods are required to visualize automatically the topological architectures and facilitate the understanding of the functions of the networks. Results: We propose a novel layout algorithm to draw complex biochemical networks. A network is modeled as a system of interacting nodes on squared grids. A discrete cost function between each node pair is designed based on the topological relation and the geometric positions of the two nodes. The layouts are produced by minimizing the total cost. We design a fast algorithm to minimize the discrete cost function, by which candidate layouts can be produced efficiently. A simulated annealing procedure is used to choose better candidates. Our algorithm demonstrates its ability to exhibit cluster structures clearly in relatively compact layout areas without any prior knowledge. We developed Windows software to implement the algorithm for CADLIVE. © The Author 2005. Published by Oxford University Press. All rights reserved.

DOI： 10.1093/bioinformatics/bti290

Scopus

その他リンク： https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=18744387729&origin=inward

A Grid Layout Algorithm for Automatic Drawing of Biochemical Networks 査読有り

Weijiang Li,Hiroyuki Kurata

Bioinformatics 21 2036 - 2042 2005年04月

有用物質生産のための細胞設計工学査読有り

倉田博之

ケミカルエンジニヤリング 50 907 - 912 2005年04月

Surviving heat shock: Control strategy for robustness and performance 査読有り

H. El-Samad,H. Kurata,J.C. Doyle,C. A. Gross,M. Khammash

Proc Natl Acad Sci U S A. 102 2736 - 2741 2005年04月