Models and Algorithms for Genome Evolution (Computational Biology)

This authoritative text/reference presents a review of the history, current status, and potential future directions of computational biology in molecular evolution. Gathering together the unique insights of an international selection of prestigious researchers, this must-read volume examines the latest developments in the field, the challenges that remain, and the new avenues emerging from the growing influx of sequence data. These viewpoints build upon the pioneering work of David Sankoff, one of the founding fathers of computational biology, and mark the 50th anniversary of his first scientific article. The broad spectrum of rich contributions in this essential collection will appeal to all computer scientists, mathematicians and biologists involved in comparative genomics, phylogenetics and related areas. Dr. Cedric Chauve is an associate professor at the Department of Mathematics of Simon Fraser University, Canada. Dr. Nadia El-Mabrouk is a full professor at the Computer Science Department of the University of Montreal, Canada. Dr. Eric Tannier is a researcher at the Bioinformatics and Evolutionary Genomics Group of Inria Grenoble - Rhne-Alpes, France. Part I: Emergence of Standard Algorithms What's Behind Blast Gene Myers Forty Years of Model-Based Phylogeography David Bryant and Jamie Kydd How to Infer Ancestral Genome Features by Parsimony Mikls Csurs Duplication, Rearrangement and Reconciliation Cedric Chauve, Nadia El-Mabrouk, Laurent Guguen, Magali Semeria and Eric Tannier The Genesis of the DCJ Formula Anne Bergeron and Jens Stoye Part II: New Lights on Current Paradigms Large-Scale Multiple Sequence Alignment and Phylogeny Estimation Tandy Warnow Rearrangements in Phylogenetic Inference Bernard M.E. Moret, Yu Lin and Jijun Tang Status of Research on Insertion and Deletion Variations in the Human Population Liqing Zhang, Mingming Liu and Layne T. Watson A Retrospective on Genomic Preprocessing for Comparative Genomics Binhai Zhu A Comparison of DCJ and Algebraic Distances Joao Meidanis and Sophia Yancopoulos Part III: Promising Directions Fractionation, Rearrangement, Consolidation, Reconstruction David Sankoff and Chunfang Zheng Error Detection and Correction of Gene Trees Manuel Lafond, Krister M. Swenson and Nadia El-Mabrouk The Potential of Family-Free Genome Comparison Marlia D.V. Braga, Cedric Chauve, Daniel Doerr, Katharina Jahn, Jens Stoye, Annelyse Thvenin and Roland Wittler Genetic History of PopulationsDaniel E. Platt, Filippo Utro, Marc Pybus and Laxmi Parida