Titlebook: Comparative Genomics; International Worksh Craig E. Nelson,Stéphane Vialette Conference proceedings 2008 Springer-Verlag Berlin Heidelberg

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Limitations of Pseudogenes in Identifying Gene Losses,e opportunity to identify cases of gene loss, the best method to do this with is unclear. A number of methods to identify gene losses rely on the presence of a pseudogene for each loss. If genes are completely or largely removed from the genome, however, such methods will fail to identify these case

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Duplication Mechanism and Disruptions in Flanking Regions Influence the Fate of Mammalian Gene Duplransposition accounts for at least half of all predicted duplicate genes in these genomes, with tandem and interspersed duplicates comprising the other half. Estimation of the evolutionary rates in each class revealed greater rate asymmetry between retrotransposed and interspersed segmental duplicat

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Discovering Local Patterns of Co-evolution,n about the functional interdependencies between sets of genes and cellular functions, about their complementary and backup relations, and more generally, for answering fundamental questions about the evolution of biological systems..Orthologs that exhibit strong signal of co-evolution in part of th

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Ancestral Reconstruction by Asymmetric Wagner Parsimony over Continuous Characters and Squared Parsconsider parsimony analysis over numerical characters, where knowing the feature values at terminal taxa allows one to infer ancestral features, namely, by minimizing the total number of changes on the edges using continuous-valued distance measures. In particular, we show that ancestral reconstruct

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Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer,d using their differences to locate HGT events. Another approach is based on augmenting a species tree into a phylogenetic network to improve the fitness of the evolution of the gene sequence data under an optimization criterion, such as maximum parsimony (MP). One major problem with the first appro

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An Evolutionary Study of the Human Papillomavirus Genomes, we found that the existing HPV groups are monophyletic and that the high-risk carcinogenicity taxa are usually clustered together. Then, we present a new algorithm for analyzing the information content of multiple sequence alignments in relation to epidemiologic carcinogenicity data to identify reg

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An Algorithm for Inferring Mitogenome Rearrangements in a Phylogenetic Tree, parsimonious assignment of genomic rearrangement events to the edges of the given phylogenetic tree. An algorithm called algorithm . (tree rearrangement explorer) is proposed for solving this problem heuristically. . is based on an extended version of algorithm . (common interval rearrangement expl