Faculty Profiles - KURATA Hiroyuki

Papers - KURATA Hiroyuki

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CADLIVE Automatic Visualizing System for Large-Scale Biochemical Maps

Weijiang Li,Hiroyuki Kurata

Genome Informatics Series ( 14 ) 388 - 389 2003.12

CADLIVE-Based Analysis for the Budding Yeast Cell Cycle

Natsumi Shimizu,Shunsuke Yamamichi,Hiroyuki Kurata

Genome Informatics Series ( 14 ) 609 - 610 2003.12

Deterministic and Stochastic Models Analyze the Robustness of Circadian Rhythms

Yoshiyuki Sumida,Fumitaka Ohnishi,Hiroyuki Kurata

Genome Informatics Series ( 14 ) 611 - 612 2003.12

Verification of the optimization performance of Real-Corded Genetic Algorithm with Dominant Direction Priority Searching Method Reviewed

TANAKA Shin, KURATA Hiroyuki, OHASHI Takeshi

IPSJ SIG Notes ( Information Processing Society of Japan (IPSJ) ) 47 49 - 52 2003.12

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

Real-Corded GA is used in optimization problems in a lot of fields. But, there is a problem that GA demands a large quantity of computational complexity. Therefore Hybrid Genetic Algorithm (gradient GA) to use a gradient shows high optimization performance. But we cannot apply gradient GA for the optimization problem that it is impossible to calculate a gradient value of fitness function. So Dominant Direction Priority search method (DDP Searching Method) is suggested in order to reduce these problems. In DDP Searching method, we suppose a vector facing a superior gene from an inferior gene in population to be an indirect gradient direction (a dominant direction) And we carry out prior local search of dominant direction and GA crossover simultaneously. In this paper, we inspected the optimization performance in some mathematical benchmark functions and gene regulatory network simulation using DDP Searching Method.

CiNii Article

Other Link： https://ci.nii.ac.jp/naid/110002914187

Dominant direction priority searching method for real-corded genetic algorithm Reviewed

Shin T., Hiroyuki K., Takeshi O.

Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications 3 1113 - 1119 2003.12

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

GA is used in optimization problems in a lot of fields. But, there is a problem that GA demands a large quantity of computational complexity. Therefore we propose DDP algorithm in order to reduce this problem. DDP calculates DDP vector from the inferior gene to superior of population and create multiple new genes on the DDP vector. We carried out computer simulation to optimize some functions. As a result, DDP adds a search of a global area at early stage of optimization and a search of local area at a late stage to GA. GA+DDP showed the effectiveness in optimization problems of mathematical function and gene regulatory network simulation.

Scopus

Other Link： https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=1642264306&origin=inward

CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle Reviewed

Kurata H., Matoba N., Shimizu N.

Nucleic Acids Research 31 ( 14 ) 4071 - 4084 2003.07

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

The further understanding of the mechanisms of gene regulatory networks requires comprehensive tools for both the representation of complicated signal transduction pathways and the in silico, identification of genomic signals that govern the regulation of gene expression. Consequently, sophisticated notation must be developed to represent the signal transduction pathways in a form that can be readily processed by both computers and humans. We propose the regulator-reaction equations combined with detailed attributes including the associated cellular component, molecular function, and biological process and present the simulation-directed graphical notation that is derived from modification of Kohn's method. We have developed the software suite, CADLIVE (Computer-Aided Design of LIVing systEms), which features a graphical user interface (GUI) to edit large-scale maps of complicated signal transduction pathways using a conventional XML-based representation. The regulator-reaction equations represent not only mechanistic reactions, but also semantic models containing ambiguous and incomplete processes. In order to demonstrate the feasibility of CADLIVE, we constructed a detailed map of the budding yeast cell cycle, which consists of 184 molecules and 152 reactions, in a really compact space. CADLIVE enables one to look at the whole view of a large-scale map, to integrate postgenomic data into the map, and to computationally simulate the signal transduction pathways, which greatly facilitates exploring novel or unexpected interactions.

DOI： 10.1093/nar/gkg461

Scopus

Other Link： https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=0242380634&origin=inward

CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle Reviewed

H. Kurata,N. Matoba,N. Shimizu

Nucleic Acids Res. 31 4071 - 4084 2003.07

代謝シュミレーションの新展開 Reviewed

倉田博之

生物工学会誌 : seibutsu-kogaku kaishi 81 ( 6 ) 2003.06

Dominant Direction Priority Searching Method for Real-Corded Genetic Algorithm Reviewed

TANAKA Shin, KURATA Hiroyuki, OHASHI Takeshi

IPSJ SIG Notes ( Information Processing Society of Japan (IPSJ) ) 45 9 - 12 2003.06

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

GA is used in optimization problems in a lot of fields. But, there is a problem that GA demands a large quantity of computational complexity. Therefore we propose DDP algorithm in order to reduce this problem. GA+DDP showed the effectiveness in optimization problems of mathematical function and gene regulatory network simulation.

CiNii Article

Other Link： https://ci.nii.ac.jp/naid/110002914201

Dominant direction priority searching method for real-coded genetic algorithm Reviewed

Shin Tanaka,Hiroyuki Kurata,Ken Ohashi

Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications PDPTA'03 1113 - 1119 2003.06

Feedback Regulation of the Heat Shock Response in E. coli Reviewed

Hana El-Samad,Mustafa Khammash,Hiroyuki Kurata,John C. Doyle

Lecture Notes in Control and Information Sciences 289 115 - 128 2003.04

Deterministic and Stochastic Models Analyze the Robustness of Circadian Rhythms Reviewed

Sumida Yoshiyuki, Ohnishi Fumitaka, Kurata Hiroyuki

Genome Informatics 14 611 - 612 2003.01

CADLIVE-Based Analysis for the Budding Yeast Cell Cycle Reviewed

Shimizu Natsumi, Yamamichi Shunsuke, Kurata Hiroyuki

Genome Informatics 14 609 - 610 2003.01

CADLIVE Automatic Visualizing System for Large-Scale Biochemical Maps Reviewed

Li Weijiang, Kurata Hiroyuki

Genome Informatics 14 388 - 389 2003.01

Building common patterns of transcription factor binding sites of Escherichia coli

W. Li,H. Kurata

Genome Informatics Series 13 301 - 302 2002.12

SANAC: Mathematical simulator for elucidating the architecture of biochemical networks

H. Kurata,H. Kitano

Genome Informatics Series 13 242 - 243 2002.12

BIOCAD project for synthesis and analysis of gene regulatory networks

Hiroyuki Kurata,Yoshiyuki Sumida,Shin Tanaka,Kouichi Masaki,Takayuki Tanaka,Yuki Urago,Ken Ohashi

Genome Informatics Series 13 467 - 477 2002.12

Screening for transgenic plant cells that highly express a target gene from genetically mixed cells Reviewed

H. Akashi,H.Kurata,M. Seki,K. Taira,S. Furusaki

Biochem. Eng. J. 10 175 - 182 2002.07

Robustness Analysis of the heat shock response in E. coli Reviewed

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

Proceedings of the 2002 American Control Conference 1742 - 1747 2002.05

Screening for transgenic plant cells that highly express a target gene from genetically mixed cells Reviewed

Akashi H., Kurata H., Seki M., Taira K., Furusaki S.

Biochemical Engineering Journal 10 ( 3 ) 175 - 182 2002.04

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

To establish a strategy for stably and highly expressing a target gene in transformed plant cell suspensions, we developed the co-selection method that linked the hygromycin phosphotransferase gene (hph) to the β-glucuronidase (uidA, GUS) gene in the opposite direction under the same transcriptional regulation of the cauliflower mosaic virus (CaMV) 35S promoter. The linked genes were transferred into a tobacco BY-2 cell suspension, which was cultivated under various levels of the antibiotic pressure. Under the high pressure of hygromycin, GUS expression was increased and maintained over 1.5 years. We presented a successful example for selecting the plant cell suspension that highly expressed the target gene out of genetically heterogeneous cells. © 2002 Elsevier Science B.V. All rights reserved.

DOI： 10.1016/S1369-703X(01)00182-6

Scopus

Other Link： https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=0036211936&origin=inward

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Papers - KURATA Hiroyuki