Molecules: Proteins and RNA -- Modeling Conformational Flexibility and Evolution of Structure: RNA as an Example -- Gene3D and Understanding Proteome Evolution -- The Evolution of the Globins: We Thought We Understood It -- The Structurally Constrained Neutral Model of Protein Evolution -- Towards Unifying Protein Evolution Theory -- Molecules: Genomes -- A Twenty-First Century View of Evolution: Genome System Architecture, Repetitive DNA, and Natural Genetic Engineering -- Genomic Changes in Bacteria: From Free-Living to Endosymbiotic Life -- Phylogenetic Analysis -- Molecular Phylogenetics: Mathematical Framework and Unsolved Problems -- Phylogenetics and Computational Biology of Multigene Families -- SeqinR 1.0-2: A Contributed Package to the R Project for Statistical Computing Devoted to Biological Sequences Retrieval and Analysis -- Networks -- Evolutionary Genomics of Gene Expression -- From Biophysics to Evolutionary Genetics: Statistical Aspects of Gene Regulation -- Populations -- Drift and Selection in Evolving Interacting Systems -- Adaptation in Simple and Complex Fitness Landscapes -- Genetic Variability in RNA Viruses: Consequences in Epidemiology and in the Development of New Stratgies for the Extinction of Infectivity.