Fundamentals of Systems Analysis and Modeling of Biosystems and Metabolism


by

Kazuyuki Shimizu, Yu Matsuoka

DOI: 10.2174/97816810808641150101
eISBN: 978-1-68108-086-4, 2015
ISBN: 978-1-68108-087-1



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Indexed in: EBSCO.

An understanding of biological systems at cellular and molecular levels helps researchers to model cellular behavior in different expe...[view complete introduction]

Table of Contents

About the Authors

- Pp. i

Kazuyuki Shimizu and Yu Matsuoka

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Foreword

- Pp. iii

Johnjoe Mcfadden

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Preface

- Pp. v

Kazuyuki Shimizu and Yu Matsuoka

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Background

- Pp. 3-19 (17)

Kazuyuki Shimizu and Yu Matsuoka

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Basis for Biosystems Analysis

- Pp. 21-79 (59)

Kazuyuki Shimizu and Yu Matsuoka

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Fundamentals of Modeling of Biosystems

- Pp. 81-132 (52)

Kazuyuki Shimizu and Yu Matsuoka

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Kinetic Modeling for the Main Metabolic Pathways

- Pp. 133-186 (54)

Kazuyuki Shimizu and Yu Matsuoka

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Model Identification, Sensitivity Analysis, and Optimization

- Pp. 187-224 (38)

Kazuyuki Shimizu and Yu Matsuoka

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Steady-State and Dynamic Characteristics

- Pp. 225-257 (33)

Kazuyuki Shimizu and Yu Matsuoka

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Metabolic Regulation of the Main Metabolism

- Pp. 259-290 (32)

Kazuyuki Shimizu and Yu Matsuoka

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Modeling and Computer Simulation for the Main Metabolism

- Pp. 297-327 (31)

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Concluding Summary

- Pp. 329-331 (3)

Kazuyuki Shimizu and Yu Matsuoka

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Subject Index

- Pp. 333-342 (10)

Kazuyuki Shimizu and Yu Matsuoka

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Foreword

I am honored to be able to contribute to this exciting eBook about microbial systems biology, modeling, and metabolic regulation of the main metabolism of a cell. The eBook has excellent credentials for describing important knowledge and approaches for the understanding of metabolic regulation of a cell system in general, since the main metabolism is common and conserved in a variety of living organisms.

Professor Kazuyuki Shimizu and I have been the project leaders of UK-Japan microbial systems biology research for long time. He has been involved in 13C-metabolic flux analysis and systems biology to clarify the metabolic regulation of Esherichia coli. He has published many articles in this area.

In summary, I am delighted to see such expertly produced and well referenced eBook which will contribute for both biochemical science and metabolic engineering as well as bioinformatics.

Johnjoe Mcfadden
Associate Dean (International)
Faculty of Health and Medical Sciences
University of Surrey
Guildford, Surrey
UK


Preface

The ultimate goal of systems biology is to reconstruct the cell system into the computer which can predict observable phenotypes. If this could be attained, the effects of culture environment and/or the specific genes knockout on the metabolism can be predicted without many exhaustive experiments, and thus more efficient metabolic engineering can be made. For this, it is quite important to understand the metabolic regulation mechanism and properly express it in the computer. Construction of a “virtual cell” will be an ambitious but realistic target that will provide significant benefits in the variety of practical applications from both scientific and metabolic engineering points of view.

The present book gives fundamentals of systems analysis and modeling as well as model identification, optimization and dynamics together with computer simulation toward the above ultimate goal. It is also critical to understand the metabolic regulation for the modeling, and thus some of the metabolic regulation of the main metabolism is also explained.

About the Authors

Prof. Kazuyuki Shimizu is based at the Kyushu Institute of Technology (KIT) and the Institute of Advanced Biosciences (IAB), Keio University, Japan. Following a BS and an MS in Chemical Engineering at Nagoya University, and a PhD in Chemical Engineering at Northwestern University, USA, he started his career in 1981 as a research associate at Nagoya University, Japan, and was promoted to associate professor in 1990. He then moved to the KIT as a professor in 1991. In 2000, he became an adjunct professor at IAB, Keio University, Japan. He has long been involved in research into 13C-metabolic flux analysis (13C–MFA), and studies on modeling and systems biology with the aim of gaining insight into the basic principles governing living cell systems. He recognizes the importance of uncovering the metabolic regulation mechanism of a cell system, based on both experimental (wet) and computational (dry) approaches. He has also organized a UK–Japan collaboration project on microbial systems biology toward developing virtual microbes by integration of the different levels of hierarchical omics information, such as transcriptomics, proteomics, metabolomics, and fluxomics data.

Dr.Yu Matsuoka is based at Kyushu Institute of Technology (KIT). Following a BS and PhD in Bioscience and Bioinformatics at KIT, she started her career in 2009 as a postdoctoral fellow at KIT. Her research interest is the systems biology, modeling, and computer simulation of a cell system.

ACKNOWLEDGEMENTS

Declared None.

CONFLICT OF INTEREST

The authors confirm that this ebook contents have no conflict of interest.

Keizo Watanabe
Tokyo Metropolitan University
Japan
E-mail: keizo@tmu.ac.jp

&

Yu Matsuoka
Kyushu Institute of Technology
Iizuka
Fukuoka 820-8502
Japan

List of Contributors

Editor(s):
Kazuyuki Shimizu
Keio University
Japan


Yu Matsuoka
Kyushu Institute of Technology
Japan




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