Kitano H. (ed) Foundations of Systems Biology (The MIT Press, biologia

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Foundations of Systems Biology
edited by
Hiroaki Kitano
The MIT Press
Cambridge, Massachusetts
London, England
c
2001 Massachusetts Institute ofTechnology
All rights reserved. No part ofthis book may be reproduced in any form by any electronic or
mechanical means (including photocopying, recording, or information storage and retrieval)
without permission in writing from the publisher.
This book was set in Palatino by the author using the L
A
T
E
X document preparation system.
Printed on recycled paper and bound in the United States ofAmerica.
Library ofCongress Cataloging-in-Publication Data
Foundations ofsystems biology
edited by Hiroaki Kitano. - 1st ed.
p.cm.
Included bibliographical references (p.).
ISBN 0-262-11266-3 (hc.: alk. paper)
1. Biological systems-Research-Methodology
2. Biological systems-Research-Case studies.
I. Kitano, Hiroaki, 1961-
QH313.F662002
573-dc21
2001042807
Contents
Contributors
ix
Preface
xiii
1 Systems Biology: Toward System-level
Understanding of Biological Systems
1
Hiroaki Kitano
I ADVANCEDMEASUREMENT 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
fromLarge-ScaleSteady-StateGene ExpressionData
59
Shuichi Onami, Koji M. Kyoda, Mineo Morohashi, and
Hiroaki Kitano
4 The Analysis of Cancer Associated Gene Expression
Matrices
77
Mattias Wahde 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 SOFTWAREFOR MODELING AND SIMULATION
6 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
Jorg 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
MechanisminHomeostasisandSignalTransduction
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
vi
Contents
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