Universität zu KölnFachgruppe PhysikTheoretische PhysikAG PortoMarkus Porto

(E2): Structural approaches to sequence evolution: Molecules, networks, populations

U. Bastolla, M. Porto, H.E. Roman, and M. Vendruscolo, eds.
Springer Series `Biological and Medical Physics/Biomedical Engineering´, Springer, Berlin, Heidelberg, 2007.

About this book

Structural requirements constrain the evolution of biological entities at all levels, from macromolecules to their networks and up through populations of biological organisms. Classical models of molecular evolution, however, are focused at the level of the symbols - the biological sequence - rather than 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.


  • Bioinformatics
  • Molecular evolution
  • Population genetics
  • Systems biology
  • Thermodynamics of macromolecules

Table of contents

Part I: Molecules: Proteins and RNA
  1. Modeling Conformational Flexibility and Evolution of Structure: RNA as an Example
    Peter Schuster and Peter F. Stadler
  2. Gene3D and Understanding Proteome Evolution
    Juan G. Ranea, Corin Yeats, Russell Marsden, and 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, and Michele Vendruscolo
  5. Towards Unifying Protein Evolution Theory
    Nikolay V. Dokholyan and Eugene I. Shakhnovich

Part II: Molecules: Genomes
  1. A 21st Century View of Evolution: Genome System Architecture, Repetitive DNA, and Natural Genetic Engineering
    James A. Shapiro
  2. Genomic Changes in Bacteria: From Free-Living to Endosymbiotic Life
    Francisco J. Silva, Amparo Latorre, Laura Gómez-Valero, and Andrés Moya

Part III: Phylogenetic Analysis
  1. Molecular Phylogenetics: Mathematical Framework and Unsolved Problems
    Xuhua Xia
  2. Phylogenetics and Computational Biology of Multigene Families
    Pietro Liò, Matteo Brilli, and Renato Fani
  3. SeqinR 1.0-2: A Contributed Package to the R Project for Statistical Computing Devoted to Biological Sequences Retrieval and Analysis
    Delphine Charif and Jean R. Lobry

Part IV: Networks
  1. Evolutionary Genomics of Gene Expression
    I. King Jordan and Leonardo Mariño-Ramírez
  2. From Biophysics to Evolutionary Genetics: Statistical Aspects of Gene Regulation
    Michael Lässig

Part V: Populations
  1. Drift and Selection in Evolving Interaction Systems
    Tomoko Ohta
  2. Adaptation in Simple and Complex Fitness Landscapes
    Kavita Jain and Joachim Krug
  3. Genetic Varability in RNA Viruses: Consequences in Epidemiology and in the Development of New Strategies for the Extinction of Infectivity
    Ester Lázaro

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Universität zu KölnFachgruppe PhysikTheoretische PhysikAG PortoMarkus Porto