Faculty Profiles - KURATA Hiroyuki

Papers - KURATA Hiroyuki

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

MASAKI Koichi, KURATA Hiroyuki

IPSJ SIG Notes ( Information Processing Society of Japan (IPSJ) ) 59 61 - 64 2006.05

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

Computer simulation predicted that the nitrogen assimilation system shows hysteresis with respect to the change in ammonia concentration in environment. To theoretically elucidate the mechanism of how hysteresis is generated, we reduced the dynamic model to the simple model with the third-order equations. Theoretical analysis of the simple model shows that the positive feedback control is responsible for hysteresis. The system has two steady-state solutions for the ammonia concentration within specific ranges. The range of an ammonia concentration that provides two solutions expands when the positive feedback becomes strong, while the system has only one solution when the positive feedback is weakened.

CiNii Article

Other Link： https://ci.nii.ac.jp/naid/110004849753

Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System Reviewed

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 2006.05

システムバイオロジーの現状と未来 Reviewed

倉田　博之

生物物理 46 244 - 250 2006.04

Effective and fast optimization for a dynamic model of the Drosophila circadian oscillator Reviewed

Shin Tanaka,Hiroyuki Kurata,Takeshi Ohashi

IEEE International Conference on Systems, Man, and Cybernetics 3596 - 3601 2006.04

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 2006.04

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

Emi Shiraishi,Hiroyuki Kurata

The 16th International Conference on Genome Informatics P016-1-2 2006.04

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 2006.04

Sensitivity analysis for the E. coli nitrogen assimilation system

Koichi Masaki,Hiroyuki Kurata

P010-1-2 2006.04

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

Masaki Kouichi,Kurata Hiroyuki

ISPJ SIG Technical Reports 61 - 64 2006.04

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

Tanaka S., Kurata H., Ohashi T.

Conference Proceedings - IEEE International Conference on Systems, Man and Cybernetics 3 2078 - 2083 2005.12

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

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

Other Link： https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=27944494749&origin=inward

Reverse engineering for a dynamic model of the Drosophila circadian oscillator Reviewed

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 2005.12

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

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

Other Link： https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=33847187422&origin=inward

Reverse Engineering for a Dynamic Model of the Drosophila Circadian Oscillator Reviewed

Shin Tanaka,Hiroyuki Kurata,Takeshi Ohashi

International Conference on Computational Intelligence for Modelling, Control and Automation 625 - 631 2005.11

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

Shin Tanaka,Hiroyuki Kurata,Takeshi Ohashi

Proceedings of the IEEE International Conference on Systems, Man, and Cybernetics 2078 - 2083 2005.10

A grid layout algorithm for automatic drawing of biochemical networks Reviewed

Li W., Kurata H.

Bioinformatics 21 ( 9 ) 2036 - 2042 2005.05

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

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

Other Link： https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=18744387729&origin=inward

A Grid Layout Algorithm for Automatic Drawing of Biochemical Networks Reviewed

Weijiang Li,Hiroyuki Kurata

Bioinformatics 21 2036 - 2042 2005.04

有用物質生産のための細胞設計工学 Reviewed

倉田博之

ケミカルエンジニヤリング 50 907 - 912 2005.04

Surviving heat shock: Control strategy for robustness and performance Reviewed

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

Proc Natl Acad Sci U S A. 102 2736 - 2741 2005.04