Gene Regulation and Metabolism: Postgenomic Computational Approaches

Julio Collado-Vides , Ralf Hofestdt

  • 出版商: A Bradford Book
  • 出版日期: 2004-08-20
  • 售價: $1,050
  • 貴賓價: 9.8$1,029
  • 語言: 英文
  • 頁數: 320
  • 裝訂: Paperback
  • ISBN: 0262532689
  • ISBN-13: 9780262532686

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Description:

As exciting as the new field of genomics is, it has not yet produced a basic conceptual change in biology. The fundamental problems remain: the origin of life, cell organization, the pathways of differentiation, aging, and the molecular and cellular capabilities of the brain. What has occurred is an explosion of molecular information obtained by genomic sequences, which will soon be followed by exhaustive catalogs of protein interactions and protein function. This wealth of information can be analyzed and manipulated only with the help of computers. The rapidly expanding role of computers in biology may usher in a profound conceptual change in how we study living systems in the laboratory.

This book focuses on current computational approaches to understanding the complex networks of metabolic and gene regulatory capabilities of the cell. The contributors look well beyond the state of the art in computational biology to anticipate what biological research will be like in a post-genomic world.

Julio Collado-Vides is Professor and Head of the Laboratory of Computational Biology at the Universidad Nacional Autónoma de México, Cuernavaca. He is coeditor of Integrative Approaches to Molecular Biology (MIT Press, 1996).

Ralf Hofestädt is Professor of Bioinformatics and Medical Informatics at the University of Bielefeld.

 

Table of Contents:

Preface vii
1 Are the Eyes Homologous?
Jeremy C. Ahouse
 
1
I Information and Knowledge Representation 17
2 Automation of Protein Sequence Characterization and Its Application in Whole Proteome Analysis
Rolf Apweiler, Margaret Biswas, Wolfgang Fleischmann, Evgenia V. Kriventseva and Nicola Mulder
19
3 Information Fusion and Metabolic Network Control
Andreas Freier, Ralf Hofestädt, Matthias Lange and Uwe Scholz
49
II Gene Regulation: From Sequence to Networks 85
4 Specificity of Protein-DNA Interactions
Gary D. Stormo
87
5 Genomics of Gene Regulation: The View from Escherichia coli
Julio Collado-Vides, Gabriel Moreno-Hagelsieb, Ernesto Pérez-Rueda, Heladia Salgado, Araceli M. Huerta, Rosa Maria Gutiérrez, David A. Rosenblueth, Andrés Christen, Esperanza Benitez-Bellon, Arturo Medrano-Soto, Socorro Gama-Castro, Alberto Santos-Zavaleta, César Bonavides-Martinez, Edgar Diaz-Peredo, Fabiola Sanchez-Solano and Dulce Maria Millan
103
6 Discovery of DNA Regulatory Motifs
Abigail Manson McGuire and George M. Church
129
7 Gene Networks Description and Modeling in the GeneNet System
Nikolay A. Kolchanov, Elena A. Ananko, Vitali A. Likhoshvai, Olga A. Podkolodnaya, Elena V. Ignatieva, Alexander V. Ratushny and Yuri G. Matushkin
149
8 Regulation of Cellular States in Mammalian Cells from a Genomewide View
Sui Huang
181
III Postgenomic Approaches 221
9 Predicting Protein Function and Networks on a Genomewide Scale
Edward M. Marcotte
223
10 Metabolic Pathways
Steffen Schmidt and Thomas Dandekar
251
11 Toward Computer Simulation of the Whole Cell
Masaru Tomita
273
Glossary 289
Corresponding Authors 297
Index
 
299