Faculty Profiles - KURATA Hiroyuki

Papers - KURATA Hiroyuki

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Modular decomposition based spectrum for protein-protein interaction network Reviewed

INOUE Kentaro, LI Weijiang, KURATA Hiroyuki

情報処理学会研究報告. BIO, バイオ情報学 = IPSJ SIG technical reports 17 H1 - H4 2009.05

Two-phase search (TPS) method: Nonbiased and high-speed parameter search for dynamic models of biochemical networks Reviewed

IPSJ Transaction on Bioinformatics ２ 2 - 14 2009.04

Maximum entropy decomposition of flux distribution at steady state to elementary modes Reviewed

J Biosci Bioeng 107 84 - 89 2009.03

A gradual update method for simulating the steady-state solution of stiff differential equations in metabolic circuits Reviewed

32 283 - 288 2009.02

Maximum entropy decomposition of flux distribution at steady state to elementary modes Reviewed

Zhao Quanyu, Kurata Hiroyuki

Journal of bioscience and bioengineering 107 ( 1 ) 84 - 89 2009.01

Two-phase Search (TPS) Method: Nonbiased and High-speed Parameter Search for Dynamic Models of Biochemical Networks Reviewed

Maeda Kazuhiro, Kurata Hiroyuki

Information and Media Technologies 4 ( 2 ) 377 - 389 2009.01

Maximum entropy decomposition of flux distribution at steady state to elementary modes Reviewed

Zhao Q., Kurata H.

Journal of Bioscience and Bioengineering 107 ( 1 ) 84 - 89 2009.01

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

Enzyme Control Flux (ECF) is a method of correlating enzyme activity and flux distribution. The advantage of ECF is that the measurement integrates proteome data with metabolic flux analysis through Elementary Modes (EMs). But there are a few methods of effectively determining the Elementary Mode Coefficient (EMC) in cases where no objective biological function is available. Therefore, we proposed a new algorithm implementing the maximum entropy principle (MEP) as an objective function for estimating the EMC. To demonstrate the feasibility of using the MEP in this way, we compared it with Linear Programming and Quadratic Programming for modeling the metabolic networks of Chinese Hamster Ovary, Escherichia coli, and Saccharomyces cerevisiae cells. The use of the MEP presents the most plausible distribution of EMCs in the absence of any biological hypotheses describing the physiological state of cells, thereby enhancing the prediction accuracy of the flux distribution in various mutants. © 2008 Elsevier Inc. All rights reserved.

DOI： 10.1016/j.jbiosc.2008.09.011

Scopus

Other Link： https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=58149279036&origin=inward

CADLIVE: Computer aided design of biochemical systems Reviewed

Supplement of Journal of Biotechnology:13 th International Biotechnology Symposium and Exhibition (IBS2008) I4-O-001 2008.10

Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli. Reviewed

Yousuke Nishio, Yoshihiro Usuda, Kazuhiko Matsui, Hiroyuki Kurata

Supplement of Journal of Biotechnology:13 th International Biotechnology Symposium and Exhibition (IBS2008) I1-O-071 2008.10

バイオテクノロジー Reviewed

酒井康行, 中野秀雄, 吉本誠, 倉田博之, 池田宰, 橋本篤

化学工学 = CHEMICAL ENGINEERING OF JAPAN 72 ( 10 ) 551 - 557 2008.10

Prediction of flux distribution of mutants by enzyme control fluxes with maximum entropy principal Reviewed

Quanyu Zhao, Hiroyuki Kurata

Supplement of Journal of Biotechnology: 13 th International Biotechnology Symposium and Exhibition (IBS2008) 2008.10

Two-phase search (TPS) 法 : 動的生化学ネットワークモデルの偏りのない効率的なパラメータ探索 Reviewed

前田和勲, 倉田博之

情報処理学会研究報告. BIO, バイオ情報学 = IPSJ SIG technical reports 14 9 - 12 2008.09

動的生化学ネットワークモデルの偏りのない効率的なパラメータ探索

前田和勲，倉田博之

情報処理学会研究報告 BIO-14 9 - 12 2008.08

Visualizing global properties of large complex networks Reviewed

Li W., Kurata H.

PLoS ONE 3 ( 7 ) 2008.07

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

For complex biological networks, graphical representations are highly desired for understanding some design principles, but few drawing methods are available that capture topological features of a large and highly heterogenous network, such as a protein interaction network. Here we propose the circular perspective drawing (CPD) method to visualize global structures of large complex networks. The presented CPD combines the quasi-continuous search (QCS) analogous to the steepest descent method with a random node swapping strategy for an enhanced calculation speed. The CPD depicts a network in an aesthetic manner by showing connection patterns between different parts of the network instead of detailed links between nodes. Global structural features of networks exhibited by CPD provide clues toward a comprehensive understanding of the network organizations. © 2008 Li, Kurata.

DOI： 10.1371/journal.pone.0002541

Scopus

Other Link： https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=49749109867&origin=inward

Estimation of Intracellular Flux Distribution under Underdetermined and Uncertain Conditions by Maximum Entropy Principle Reviewed

Quanyu Zhao,Hiroyuki Kurata

Chin J Biotech Chin 24: 24 21352136 - 21352136 2008.04

Maximum entropy decomposition of flux distribution at steadystate to elementary modes Reviewed

Quanyu Zhao,Hiroyuki Kurata

J Biosci Bioeng 107 8489 - 8489 2008.04

A gradual update method for simulating the steady-state solution of stiff differential equations in metabolic circuits Reviewed

Emi Shiraishi Kazuhiro Maeda Hiroyuki Kurata

Bioprocess Biosyst. Eng 32 283288 - 283288 2008.04

Visualizing Global Properties of Large Complex Networks Reviewed

Li W.,Kurata H.

PLoS ONE 3 e2541 - e2541 2008.04

Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli Reviewed

Yousuke Nishio,Yoshihiro Usuda,Kazuhiko Matsui,Hiroyuki Kurata

Molecular Systems Biology 4 160 - 160 2008.04

Two-phase search (TPS) method: Nonbiased and efficient parameter search for dynamic models of biochemical networks.

Maeda,K.,Kurata,H.

IPSJ SIG Technical Report BIO-14 9 - 12 2008.04

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