Comparative Genomics (vol. # 4205) : RECOMB 2006 International Workshop, RECOMB-CG 2006, Montreal, Canada, September 24-26, 2006, Proceedings

From the reviews: "Comparative genomics is an exciting new field of bioinformatics dealing with problems of vital importance for many areas in biology. ... This volume contains the 17 fully refereed papers presented at the fourth meeting, held in Montreal in September 2006. ... I consider this book essential for libraries aiming to support research in any field of bioinformatics." (N. Sapidis, ACM Computing Reviews, Vol. 49 (4), April, 2008) Front Matter....Pages - Reconstructing Domain Compositions of Ancestral Multi-domain Proteins....Pages 1-10 Domain Architecture in Homolog Identification....Pages 11-23 Inferring Positional Homologs with Common Intervals of Sequences....Pages 24-38 On Genome Evolution with Accumulated Change and Innovation....Pages 39-50 Paths and Cycles in Breakpoint Graphs of Random Multichromosomal Genomes....Pages 51-62 Common Intervals and Symmetric Difference in a Model-Free Phylogenomics, with an Application to Streptophyte Evolution....Pages 63-74 How Pseudo-boolean Programming Can Help Genome Rearrangement Distance Computation....Pages 75-86 Sorting by Translocations Via Reversals Theory....Pages 87-98 Inferring Gene Orders from Gene Maps Using the Breakpoint Distance....Pages 99-112 Ordering Partially Assembled Genomes Using Gene Arrangements....Pages 113-128 Evolution of Tandemly Repeated Sequences Through Duplication and Inversion....Pages 129-140 A PQ Framework for Reconstructions of Common Ancestors and Phylogeny....Pages 141-155 Intron Loss Dynamics in Mammals....Pages 156-170 Finding Maximum Likelihood Indel Scenarios....Pages 171-185 Conservation Patterns in cis -Elements Reveal Compensatory Mutations....Pages 186-199 Transcription Factor Centric Discovery of Regulatory Elements in Mammalian Genomes Using Alignment-Independent Conservation Maps....Pages 200-214 Identifiability Issues in Phylogeny-Based Detection of Horizontal Gene Transfer....Pages 215-229 Back Matter....Pages - This book provides an evolutionary conceptual framework for comparative genomics, with the ultimate objective of understanding the loss and gain of genes during evolution, the interactions among gene products, and the relationship between genotype, phenotype and the environment. The many examples in the book have been carefully chosen from primary research literature based on two criteria: their biological insight and their pedagogical merit. The phylogeny-based comparative methods, involving both continuous and discrete variables, often represent a stumbling block for many students entering the field of comparative genomics. They are numerically illustrated and explained in great detail. The book is intended for researchers new to the field, i.e., advanced undergraduate students, postgraduates and postdoctoral fellows, although professional researchers who are not in the area of comparative genomics will also find the book informative This book constitutes the refereed proceedings of the 4th RECOMB Comparative Genomics Satellite Workshop, RECOMB-CG 2006, held in Montreal, Canada in September 2006. The 17 revised full papers presented were carefully reviewed and selected from 34 initial submissions. The papers address a broad variety of aspects and components of the field of comparative genomics, ranging from new quantitative discoveries about genome structure and process to theorems on the complexity of computational problems inspired by genome comparison