Models and Algorithms for Genome Evolution

ISBN-13: 9781447152972 / Angielski / Twarda / 2013 / 328 str.

Cedric Chauve; Nadia El-Mabrouk; Eric Tannier

Opis

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 50^th anniversary of his first scientific article.Topics and features: discusses the development of the BLAST algorithm, model-based phylogeography techniques, and the double cut and join (DCJ) distance formula; reviews the reconstruction of evolutionary features of ancestral genomes in a known phylogeny, and presents integrative models of evolution; introduces algorithms to estimate alignment and phylogeny on ultra-large datasets, and an approach for using likelihood methods with rearrangement models; examines the impact of insertion and deletion variants in human biology, evolution and health; surveys novel and recent research on genomic distance and family-free genome comparison; describes consolidation methods for reconstruction of ancestral gene orders, and error detection in gene tree construction; investigates the genetic events recoverable from simulations of human population histories.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.

Spis treści

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
Miklós Csűrös

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
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
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

O autorze

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.