Structural Approaches to Sequence Evolution (eBook)

Ugo Bastolla is researcher in the laboratory of bioinformatics of theCentro de Astrobiologia in Madrid (Spain), on leave to the Centro deBiologia Molecular of the Spanish CSIC. Since his degree in physicswith Luca Peliti he has always been interested in biological topics,above all evolution. He got is PhD in Rome with Giorgio Parisi workingon disordered dynamical systems inspired to biology and was postdoc inJulich (Germany) with Peter Grassberger, studying statistical mechanicalmodels of polymers, in Berlin (Germany) with E.W. Knapp studying simpleprotein models, in Golm (Germany) with Michael Laessig, studyingecological models, and finally in Madrid (Spain) in the bioinformaticsgroup of Alfonso Valencia. His main research interest consists in combiningsimple models of protein thermodynamics and evolution. Markus Porto is professor of Theoretical Solid State Physics at theInstitut fur Festkorperphysik at the Technische Universitat Darmstadt(Germany). He received his PhD at the Universitat Giessen (Germany). Hisresearch interests cover many aspects of solid state and statisticalphysics, including transport and relaxation in disordered systems andbiophysics, as well as applying methods of statistical physics to modelmolecular evolution. H. Eduardo Roman is Research Fellow at the Department of Physics of theUniversity of Milan-Bicocca. He earned his Ph.D at the International Schoolfor Advanced Studies, Trieste (Italy), and has been Privat Dozent at theUniversities of Hamburg and Giessen (Germany). His research interests covermany aspects of Statistical Physics, from fractals to stochastic phenomena,biophysics, proteins and evolution, and ab-initio electronic calculations inmolecules. Michele Vendruscolo is a Royal Society University Research Fellow at theDepartment of Chemistry, University of Cambridge. He received his PhD inCondensed Matter Physics in 1996 at the International School for AdvancedStudies, Trieste (Italy). His research is mainly focussed on understandingthe biophysical principles regulating the behaviour and the evolution ofproteins.

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.