,Foundations of Systems Biology
edited by
Hiroaki Kitano
The MIT Press
Cambridge, Massachusetts
London, England
,
c 2001 Massachusetts Institute of Technology
All rights reserved. No part of this 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 LATEX document preparation system.
Printed on recycled paper and bound in the United States of America.
Library of Congress Cataloging-in-Publication Data
Foundations of systems 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 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
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 SOFTWARE FOR MODELING AND SIMULATION
edited by
Hiroaki Kitano
The MIT Press
Cambridge, Massachusetts
London, England
,
c 2001 Massachusetts Institute of Technology
All rights reserved. No part of this 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 LATEX document preparation system.
Printed on recycled paper and bound in the United States of America.
Library of Congress Cataloging-in-Publication Data
Foundations of systems 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 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
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 SOFTWARE FOR MODELING AND SIMULATION
