Comparative Genomics

Algorithms for Exploring the Space of Gene Tree/Species Tree Reconciliations.- Limitations of Pseudogenes in Identifying Gene Losses.- Duplication Mechanism and Disruptions in Flanking Regions Influence the Fate of Mammalian Gene Duplicates.- Estimating the Relative Contributions of New Genes from Retrotransposition and Segmental Duplication Events during Mammalian Evolution.- Discovering Local Patterns of Co-evolution.- Ancestral Reconstruction by Asymmetric Wagner Parsimony over Continuous Characters and Squared Parsimony over Distributions.- An Alignment-Free Distance Measure for Closely Related Genomes.- Gene Team Tree: A Compact Representation of All Gene Teams.- Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer.- An Evolutionary Study of the Human Papillomavirus Genomes.- An Algorithm for Inferring Mitogenome Rearrangements in a Phylogenetic Tree.- Perfect DCJ Rearrangement.- Sorting Genomes with Insertions, Deletions and Duplications by DCJ.- A Fast and Exact Algorithm for the Median of Three Problem-A Graph Decomposition Approach.- A Phylogenetic Approach to Genetic Map Refinement.- Sorting Cancer Karyotypes by Elementary Operations.- On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios.- Hurdles Hardly Have to Be Heeded.- Internal Validation of Ancestral Gene Order Reconstruction in Angiosperm Phylogeny.