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Foundations of Systems Biology - Hiroaki Kitano

Contents


1 Systems Biology: Toward System-level
Understanding of Biological Systems 1
Hiroaki Kitano
I ADVANCED MEASUREMENT SYSTEMS
2 Automatic Acquisition of Cell Lineage through
4D Microscopy and Analysis of Early C. elegans
Embryogenesis 39
Shuichi Onami, Shugo Hamahashi, Masao Nagasaki,
Satoru Miyano, and Hiroaki Kitano
II REVERSE ENGINEERING AND DATA MINING FROM GENE
EXPRESSION DATA
3 The DBRF Method for Inferring a Gene Network
from Large-Scale Steady-State Gene Expression Data 59
Shuichi Onami, Koji M. Kyoda, Mineo Morohashi, and
Hiroaki Kitano
4 The Analysis of Cancer Associated Gene Expression
Matrices 77
MattiasWahde and Zoltan Szallasi
5 Automated Reverse Engineering of Metabolic
Pathways from Observed Data by Means of Genetic
Programming 95
John R. Koza,William Mydlowec, Guido Lanza, Jessen
Yu, and Martin A. Keane

III SOFTWARE FOR MODELING AND SIMULATION

The ERATO Systems Biology Workbench: An
Integrated Environment for Multiscale and
Multitheoretic Simulations in Systems Biology 125
Michael Hucka, Andrew Finney, Herbert Sauro,
Hamid Bolouri, John Doyle, and Hiroaki Kitano
7 Automatic Model Generation for Signal
Transduction with Applications to MAP-Kinase
Pathways 145
Bruce E. Shapiro, Andre Levchenko, and Eric
Mjolsness
8 Modeling Large Biological Systems From Functional
Genomic Data: Parameter Estimation 163
Pedro Mendes
IV CELLULAR SIMULATION
9 Towards a Virtual Biological Laboratory 189
J ¨org Stelling, Andreas Kremling, Martin Ginkel, Katja
Bettenbrock and Ernst Dieter Gilles
10 Computational Cell Biology — The Stochastic
Approach 213
Thomas Simon Shimizu and Dennis Bray
11 Computer Simulation of the Cell: Human
Erythrocyte Model and its Application 233
Yoichi Nakayama and Masaru Tomita
V SYSTEM-LEVEL ANALYSIS
12 Constructing Mathematical Models of Biological
Signal Transduction Pathways: An Analysis of
Robustness 251
Tau-Mu Yi
13 Combination of Biphasic Response Regulation
and Positive Feedback as a General Regulatory
Mechanism in Homeostasis and Signal Transduction 263
Andre Levchenko, Jehoshua Bruck, and Paul W.
Sternberg
14 Distinct Roles of Rho-kinase Pathway and Myosin
Light Chain Kinase Pathway in Phosphorylation of
Myosin Light Chain: Kinetic Simulation Study 279
Shinya Kuroda, Nicolas Schweighofer, Mutsuki
Amano, Kozo Kaibuchi, and Mitsuo Kawato


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