Faculty Profiles - KURATA Hiroyuki

Papers - KURATA Hiroyuki

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Interlocked Feedback is not the Best Choice for PER Oscillators

Fumitaka Ohnishi,Hiroyuki Kurata

The 16th International Conference on Genome Informatics 16 P116-1-2 2005.04

CADLIVE: Computer-Aided Design of Living Systems

Hiroyuki Kurata,Marie Kajiwara,Yuki Shimokawa

The 16th International Conference on Genome Informatics 16 P114-1-1 2005.04

Optimization of a Large-Scale Dynamic Model of the Cell Cycle Network Using Multi Objective GA

Shunsuke Yamamichi,Hiroyuki Kurata

The 16th International Conference on Genome Informatics 16 P122-1-2 2005.04

CADLIVE dynamic simulator: Direct link of biochemical networks to dynamic models Reviewed

Kurata H., Masaki K., Sumida Y., Iwasaki R.

Genome Research 15 ( 4 ) 590 - 600 2005.04

Authorship：Corresponding author Publishing type：Research paper (scientific journal)

We have developed the CADLIVE (Computer-Aided Design of LIVing systEms) Simulator that provided a rule-based automatic way to convert biochemical network maps into dynamic models, which enables simulating their dynamics without going through all of the reactions down to the details of exact kinetic parameters. The simulator supports the biochemical reaction maps that are generated by the previously developed GUI editor. Notice that the part of the GUI editor had been previously published, but, as yet, not the simulator. To directly link biochemical network maps to dynamic simulation, we have created the strategy of three layers and two stages with the efficient conversion rules in an XML representation. This strategy divides a molecular network into three layers, i.e., gene, protein, and metabolic layers, and partitions the conversion process into two stages. Once a biochemical map is provided, CADLIVE automatically builds a mathematical model, thereby facilitating one to simulate and analyze it. In order to demonstrate the feasibility of CADLIVE, we analyzed the Escherichia coli nitrogen-assimilation system (64 equations with 64 variables) that consists of multiple and complicated negative and positive feedback loops. CADLIVE predicted that the glnK gene is responsible for hysteresis or reversibility of nitrogen-related (Ntr) gene expression with respect to the ammonia concentration, supporting the experimental observation of the runaway expression of the Ntr genes. ©2005 by Cold Spring Harbor Laboratory Press.

DOI： 10.1101/gr.3463705

Scopus

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Surviving heat shock: Control strategies for robustness and performance Reviewed

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

Proceedings of the National Academy of Sciences of the United States of America 102 ( 8 ) 2736 - 2741 2005.02

Authorship：Corresponding author Publishing type：Research paper (scientific journal)

Molecular biology studies the cause-and-effect relationships among microscopic processes initiated by individual molecules within a cell and observes their macroscopic phenotypic effects on cells and organisms. These studies provide a wealth of information about the underlying networks and pathways responsible for the basic functionality and robustness of biological systems. At the same time, these studies create exciting opportunities for the development of quantitative and predictive models that connect the mechanism to its phenotype then examine various modular structures and the range of their dynamical behavior. The use of such models enables a deeper understanding of the design principles underlying biological organization and makes their reverse engineering and manipulation both possible and tractable The heat shock response presents an interesting mechanism where such an endeavor is possible. Using a model of heat shock, we extract the design motifs in the system and justify their existence in terms of various performance objectives. We also offer a modular decomposition that parallels that of traditional engineering control architectures. © 2005 by The National Academy of Sciences of the USA.

DOI： 10.1073/pnas.0403510102

Scopus

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Optimization of E.Coli heat shock response parameter tuning using distributed and integrated genetic algorithms Reviewed

Tanaka S., Kurata H., Ohashi T.

Conference Proceedings - IEEE International Conference on Systems, Man and Cybernetics 2 1243 - 1248 2004.12

Authorship：Corresponding author Publishing type：Research paper (international conference proceedings)

The progress of computer made the analysis that was difficult in traditional technology possible. In Gene Regulatory Network Simulation to recreate and understand actual biological reaction, we build a reaction model and find the several unknown parameters in order to show the same behavior as actual. However it is difficult to optimize them because the scopes of them are logarithm scale wide and the fitness space is multidimensional and multimodal. We optimized it using Distributed Genetic Algorithms (DGA) which has multiple populations. DGA showed better performance, if and only if the parameter of the emigrating operation is appropriate. Therefore we propose Distributed and Integrated Genetic Algorithms (DIGA) to reduce the cost to find the appropriate parameters of operation. We carried out some optimizing experiments on parameter tuning of Heat Shock Response simulation of E.Coli and several mathematical functions and inspected the characteristic of DIGA. © 2004 IEEE.

Scopus

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モジュール分割統合法による大規模生命分子ネットワークの最適化

吉田圭介,倉田博之

数理モデル化と問題解決シンポジウム論文集 97 - 102 2004.10

生命における振動システムのモデリングとシステム解析

山道俊介，大西史高，倉田博之

数理モデル化と問題解決シンポジウム論文集 379 - 382 2004.10

Computer-Aided Design of Metabolic and Gene Regulatory Networks Reviewed

Proceedings of The 10th APCChE Congress 2L - 06 2004.10

Optimization of E.Coli Heat Shock Response Parameter Tuning Using Distributed and Integrated Genetic Algorithms Reviewed

Shin Tanaka,Hiroyuki Kurata,Takeshi Ohashi

Proceedings of the IEEE International Conference on Systems, Man and Cybernetics 1243 - 1248 2004.10

Statistical And Integrative Approach For Constructing Biological Network Maps Reviewed

Hiroyuki Kurata,Natsumi Shimizu,Kanako Misumi

Genome Informatics 15 161 - 170 2004.04

Optimization and System Analysis of the Heat Shock Response by CADLIVE

Kouji Mitsukiyo,Marie Kajiwara,Hiroyuki Kurata

Genome Informatics Series 15 P006 2004.04

Simulation of Circadian Rhythms Using Grid Computing

Takayuki Tanaka,Hiroyuki Kurata

Genome Informatics Series 15 P011 2004.04

A Large-Scale Dynamic Model of the Yeast Cell Cycle

Shunsuke Yamamichi,Hiroyuki Kurata

Genome Informatics Series 15 P007 2004.04

CADLIVE: New Modules for Domain Expansions and Topological Analysis

Hiroyuki Kurata,Yuki Shimokawa,Tomoko Noguchi,Natsumi Shimizu

Genome Informatics Series 15 S05 2004.04

Statistical and Integrative Approach for Constructing Biological Network Maps Reviewed

Kurata Hiroyuki, Shimizu Natsumi, Misumi Kanako

Genome Informatics 15 ( 2 ) 161 - 170 2004.01

Statistical and integrative approach for constructing biological network maps. Reviewed

Kurata H., Shimizu N., Misumi K.

Genome informatics. International Conference on Genome Informatics 15 ( 2 ) 161 - 170 2004.01

Authorship：Corresponding author Language：English Publishing type：Research paper (scientific journal)

A goal of systems biology is to build a concrete biochemical network map, which provides an important instruction to trace the pathways of interest or to understand the mechanism of a biological system. In the postgenomic era, not only the concrete biochemical maps, but also postgenomic maps (mRNA coexpression and protein-protein interaction networks) have been extensively produced. In the biochemical map, the individual reactions are reliable, but the number of the reactions is limited, because molecular biology requires extensive experiments to verify them. By contrast, postgenomic data provide much information regarding interactions, but are coarse-grained. To expand the biochemical network, an intuitional approach, which superposes postgenomic data on the map one by one, has been carried out, but it is not effective when a large amount of the coarse-grained data is handled. In order to effectively integrate such postgenomic interactions into a biochemical map, a statistical approach would be suitable rather than intuition. In this article, we proposed a novel statistical approach that integrates postgenomic interaction networks into the biochemical network, predicting novel pathways. A statistical correlation for such different types of networks identifies functional modules; subsequently the superposition of the different networks on the functional modules predicts inter-modular relations, which are the key pathways to construct a large-scale biochemical network.

Scopus

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Computer-Aided Design of Metabolic and Gene Regulatory Networks Reviewed

Kurata Hiroyuki

アジア・太平洋化学工学会議発表論文要旨集 2004 ( 0 ) 419 - 419 2004.01

Integration of Postgenomic Data for GMA to Simulate a Metabolic Circuit

Takayuki Tanaka,Hiroyuki Kurata

Genome Informatics Series ( 14 ) 613 - 614 2003.12

CADLIVE SYSTEM: Map-based dynamic simulation of biochemical networks. Genome Informatics Series

Hiroyuki Kurata,Rei Iwasaki,Kouichi Masaki,Takayuki Tanaka,Kouji Mitsukiyo,Yoshiyuki Sumida

Genome Informatics Series ( 14 ) 270 - 271 2003.12

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Papers - KURATA Hiroyuki