Ebook: Structural Approaches to Sequence Evolution: Molecules, Networks, Populations
- Tags: Biophysics and Biological Physics, Bioinformatics
- Series: Biological and Medical Physics Biomedical Engineering
- Year: 2007
- Publisher: Springer-Verlag Berlin Heidelberg
- Edition: 1
- Language: English
- pdf
Structural requirements constrain the evolution of biological entities at all levels, from macromolecules to their networks, right up to populations of biological organisms. Classical models of molecular evolution, however, are focused at the level of the symbols - the biological sequence - rather than that of their resulting structure. Now recent advances in understanding the thermodynamics of macromolecules, the topological properties of gene networks, the organization and mutation capabilities of genomes, and the structure of populations make it possible to incorporate these key elements into a broader and deeply interdisciplinary view of molecular evolution. This book gives an account of such a new approach, through clear tutorial contributions by leading scientists specializing in the different fields involved.
Structural requirements constrain the evolution of biological entities at all levels, from macromolecules to their networks, right up to populations of biological organisms. Classical models of molecular evolution, however, are focused at the level of the symbols - the biological sequence - rather than that of their resulting structure. Now recent advances in understanding the thermodynamics of macromolecules, the topological properties of gene networks, the organization and mutation capabilities of genomes, and the structure of populations make it possible to incorporate these key elements into a broader and deeply interdisciplinary view of molecular evolution. This book gives an account of such a new approach, through clear tutorial contributions by leading scientists specializing in the different fields involved.
Structural requirements constrain the evolution of biological entities at all levels, from macromolecules to their networks, right up to populations of biological organisms. Classical models of molecular evolution, however, are focused at the level of the symbols - the biological sequence - rather than that of their resulting structure. Now recent advances in understanding the thermodynamics of macromolecules, the topological properties of gene networks, the organization and mutation capabilities of genomes, and the structure of populations make it possible to incorporate these key elements into a broader and deeply interdisciplinary view of molecular evolution. This book gives an account of such a new approach, through clear tutorial contributions by leading scientists specializing in the different fields involved.
Content:
Front Matter....Pages I-XIX
Front Matter....Pages 1-1
Modeling Conformational Flexibility and Evolution of Structure: RNA as an Example....Pages 3-36
Gene3D and Understanding Proteome Evolution....Pages 37-55
The Evolution of the Globins: We Thought We Understood It....Pages 57-74
The Structurally Constrained Neutral Model of Protein Evolution....Pages 75-112
Towards Unifying Protein Evolution Theory....Pages 113-126
Front Matter....Pages 128-128
A Twenty-First Century View of Evolution: Genome System Architecture, Repetitive DNA, and Natural Genetic Engineering....Pages 129-147
Genomic Changes in Bacteria: From Free-Living to Endosymbiotic Life....Pages 149-165
Front Matter....Pages 168-168
Molecular Phylogenetics: Mathematical Framework and Unsolved Problems....Pages 169-189
Phylogenetics and Computational Biology of Multigene Families....Pages 191-205
SeqinR 1.0-2: A Contributed Package to the R Project for Statistical Computing Devoted to Biological Sequences Retrieval and Analysis....Pages 207-232
Front Matter....Pages 234-234
Evolutionary Genomics of Gene Expression....Pages 235-252
From Biophysics to Evolutionary Genetics: Statistical Aspects of Gene Regulation....Pages 253-282
Front Matter....Pages 284-284
Drift and Selection in Evolving Interacting Systems....Pages 285-298
Adaptation in Simple and Complex Fitness Landscapes....Pages 299-339
Genetic Variability in RNA Viruses: Consequences in Epidemiology and in the Development of New Stratgies for the Extinction of Infectivity....Pages 341-362
Back Matter....Pages 363-367
Structural requirements constrain the evolution of biological entities at all levels, from macromolecules to their networks, right up to populations of biological organisms. Classical models of molecular evolution, however, are focused at the level of the symbols - the biological sequence - rather than that of their resulting structure. Now recent advances in understanding the thermodynamics of macromolecules, the topological properties of gene networks, the organization and mutation capabilities of genomes, and the structure of populations make it possible to incorporate these key elements into a broader and deeply interdisciplinary view of molecular evolution. This book gives an account of such a new approach, through clear tutorial contributions by leading scientists specializing in the different fields involved.
Content:
Front Matter....Pages I-XIX
Front Matter....Pages 1-1
Modeling Conformational Flexibility and Evolution of Structure: RNA as an Example....Pages 3-36
Gene3D and Understanding Proteome Evolution....Pages 37-55
The Evolution of the Globins: We Thought We Understood It....Pages 57-74
The Structurally Constrained Neutral Model of Protein Evolution....Pages 75-112
Towards Unifying Protein Evolution Theory....Pages 113-126
Front Matter....Pages 128-128
A Twenty-First Century View of Evolution: Genome System Architecture, Repetitive DNA, and Natural Genetic Engineering....Pages 129-147
Genomic Changes in Bacteria: From Free-Living to Endosymbiotic Life....Pages 149-165
Front Matter....Pages 168-168
Molecular Phylogenetics: Mathematical Framework and Unsolved Problems....Pages 169-189
Phylogenetics and Computational Biology of Multigene Families....Pages 191-205
SeqinR 1.0-2: A Contributed Package to the R Project for Statistical Computing Devoted to Biological Sequences Retrieval and Analysis....Pages 207-232
Front Matter....Pages 234-234
Evolutionary Genomics of Gene Expression....Pages 235-252
From Biophysics to Evolutionary Genetics: Statistical Aspects of Gene Regulation....Pages 253-282
Front Matter....Pages 284-284
Drift and Selection in Evolving Interacting Systems....Pages 285-298
Adaptation in Simple and Complex Fitness Landscapes....Pages 299-339
Genetic Variability in RNA Viruses: Consequences in Epidemiology and in the Development of New Stratgies for the Extinction of Infectivity....Pages 341-362
Back Matter....Pages 363-367
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