Craig Nelson

Stéphane Vialette

Over the last decade great investments have been made in the acquisition of enormous amounts of gene sequence data from a diverse collection of org- isms. Realizing the full potential of these investments will require the continued development of computational tools for comparative genomics and the intel- gent application of these tools to address biologically relevant questions. The RECOMB Workshop on Comparative Genomics (RECOMB-CG) is devoted to bringingtogetherscientistsworkingonallaspectsofcomparativegenomics,from the development of new computational approaches to genome sequence analysis andcomparison,to the genome-wideapplicationofcomputationaltools to study the evolutionary dynamics of prokaryotic and eukaryotic genomes. This volume contains the 19 papers presented at the 6th Annual RECOMB- ´ CG workshop held during October 13–15 at the Ecole Normale Sup´ erieure, in Paris, France. The papers selected for presentation and published in these p- ceedings were selected from 48 submissions from scientists around the world. Each paper was reviewed by at least three members of the Program Committee in a stringent and thoughtful peer-review process.

International Workshop, RECOMB-CG 2008, Paris, France, October 13-15, 2008, Proceedings

Comparative Genomics

Guillaume Fertin

Anthony Labarre

Irena Rusu

Eric Tannier

A comprehensive survey of a rapidly expanding field of combinatorial optimization, mathematically oriented but offering biological explanations when required. From one cell to another, from one individual to another, and from one species to another, the content of DNA molecules is often similar. The organization of these molecules, however, differs dramatically, and the mutations that affect this organization are known as genome rearrangements. Combinatorial methods are used to reconstruct putative rearrangement scenarios in order to explain the evolutionary history of a set of species, often formalizing the evolutionary events that can explain the multiple combinations of observed genomes as combinatorial optimization problems. This book offers the first comprehensive survey of this rapidly expanding application of combinatorial optimization. It can be used as a reference for experienced researchers or as an introductory text for a broader audience. Genome rearrangement problems have proved so interesting from a combinatorial point of view that the field now belongs as much to mathematics as to biology. This book takes a mathematically oriented approach, but provides biological background when necessary. It presents a series of models, beginning with the simplest (which is progressively extended by dropping restrictions), each constructing a genome rearrangement problem. The book also discusses an important generalization of the basic problem known as the median problem, surveys attempts to reconstruct the relationships between genomes with phylogenetic trees, and offers a collection of summaries and appendixes with useful additional information.

Stéphane Vialette

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