Structural Approaches to Sequence Evolution

Part I. Molecules: Proteins and RNA

1. Modeling Conformational Flexibility and Evolution of Structure: RNA as an Example
Peter Schuster, Peter F. Stadler

2. Gene3D and Understanding Proteome Evolution
Juan Garcia Ranea, Corin Yeats, Russell Marsden, Christine Orengo

3. The Evolution of the Globins: We Thought We Understood It
Arthur M. Lesk

4. The Structurally Constrained Neutral Model of Protein Evolution
Ugo Bastolla, Markus Porto, H. Eduardo Roman, Michele Vendruscolo

5. Towards Unifying Protein Evolution Theory
Nikolay V. Dokholyan, Eugene I. Shakhnovich

Part II. Molecules: Genomes

6. A Twenty-First Century View of Evolution: Genome System Architecture, Repetitive DNA, and Natural Genetic Engineering
James A. Shapiro

7. Genomic Changes in Bacteria: From Free-Living to Endosymbiotic Life
Francisco J. Silva, Amparo Latorre, Laura Gómez-Valero, Andres Moya

Part III. Phylogenetic Analysis

8. Molecular Phylogenetics: Mathematical Framework and Unsolved Problems
Xuhua Xia

9. Phylogenetics and Computational Biology of Multigene Families
Pietro Liò, Matteo Brilli, Renato Fani

10. SeqinR 1.0-2: A Contributed Package to the R Project for Statistical Computing Devoted to Biological Sequences Retrieval and Analysis
Delphine Charif, Jean R. Lobry

Part IV. Networks

11. Evolutionary Genomics of Gene Expression
I. King Jordan, Leonardo Mariñno-Ramírez

12. From Biophysics to Evolutionary Genetics: Statistical Aspects of Gene Regulation
Michael Lässig

Part V. Populations

13. Drift and Selection in Evolving Interacting Systems
Tomoko Ohta

14. Adaptation in Simple and Complex Fitness Landscapes
Kavita Jain, Joachim Krug

15. Genetic Variability in RNA Viruses: Consequences in Epidemiology and in the Development of New Stratgies for the Extinction of Infectivity
Ester Lázaro

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Nyckelord: SCIENCE / Physics SCI055000