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.
About the Author
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 – Rhône-Alpes, France.
Table of Contents
Part I: Emergence of Standard Algorithms
What's Behind Blast
Forty Years of Model-Based Phylogeography
David Bryant and Jamie Kydd
How to Infer Ancestral Genome Features by Parsimony
Duplication, Rearrangement and Reconciliation
Cedric Chauve, Nadia El-Mabrouk, Laurent Guéguen, 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
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
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
Marília D.V. Braga, Cedric Chauve, Daniel Doerr, Katharina Jahn, Jens Stoye, Annelyse Thévenin and Roland Wittler
Genetic History of PopulationsDaniel E. Platt, Filippo Utro, Marc Pybus and Laxmi Parida