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E-raamat: Gene Regulation and Metabolism: Post-Genomic Computational Approaches

Edited by (UNAM Campus Morelos), Edited by (University Bielefeld)
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As exciting as the new field of genomics is, it has not yet produced a basicconceptual change in biology. The fundamental problems remain: the origin of life, cellorganization, the pathways of differentiation, aging, and the molecular and cellular capabilities ofthe 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. Therapidly expanding role of computers in biology may usher in a profound conceptual change in how westudy living systems in the laboratory.This book focuses on current computational approaches tounderstanding the complex networks of metabolic and gene regulatory capabilities of the cell. Thecontributors look well beyond the state of the art in computational biology to anticipate whatbiological research will be like in a post-genomic world.



An overview of current computational approaches to metabolism and gene regulation.
Preface vii
Are the Eyes Homologous?
1(16)
Jeremy C. Ahouse
I Information and Knowledge Representation 17(68)
Automation of Protein Sequence Characterization and Its Application in Whole Proteome Analysis
19(30)
Rolf Apweiler
Margaret Biswas
Wolfgang Fleischmann
Evgenia V. Kriventseva
Nicola Mulder
Information Fusion and Metabolic Network Control
49(36)
Andreas Freier
Ralf Hofestadt
Matthias Lange
Uwe Scholz
II Gene Regulation: From Sequence to Networks 85(136)
Specificity of Protein-DNA Interactions
87(16)
Gary D. Stormo
Genomics of Gene Regulation: The View
103(26)
Escherichia coli
Julio Collado-Vides
Gabriel Moreno-Hagelsieb
Ernesto Perez-Rueda
Heladia Salgado
Araceli M. Huerta
Rosa Maria Gutierrez
David A. Rosenblueth
Andres Christen
Esperanza Benitez-Bellon
Arturo Medrano-Soto
Socorro Gama-Castro
Alberto Santos-Zavaleta
Cesar Bonavides-Martinez
Edgar Diaz-Peredo
Fabiola Sanchez-Solano
Dulce Maria Millan
Discovery of DNA Regulatory Motifs
129(20)
Abigail Manson McGuire
George M. Church
Gene Networks Description and Modeling in the GeneNet System
149(32)
Nikolay A. Kolchanov
Elena A. Ananko
Vitali A. Likhoshvai
Olga A. Podkolodnaya
Elena V. Ignatieva
Alexander V. Ratushny
Yuri G. Matushkin
Regulation of Cellular States in Mammalian Cells from a Genomewide View
181(40)
Sui Huang
III Postgenomic Approaches 221(68)
Predicting Protein Function and Networks on a Genomewide Scale
223(28)
Edward M. Marcotte
Metabolic Pathways
251(22)
Steffen Schmidt
Thomas Dandekar
Toward Computer Simulation of the Whole Cell
273(16)
Masaru Tomita
Glossary 289(8)
Corresponding Authors 297(2)
Index 299