Ebook: Comparative Genomics: International Workshop, RECOMB-CG 2008, Paris, France, October 13-15, 2008. Proceedings

This book constitutes the refereed proceedings of the 6th RECOMB Comparative Genomics Satellite Workshop, RECOMB-CG 2008, held in Paris, France, in October 2008.

The 19 revised full papers presented were carefully reviewed and selected from 48 initial submissions. The papers illustrate the crucial role of comparative genomics in understanding genome function and address a broad variety of aspects, ranging from the inference of evolution in genetic regulatory networks to the divergent fates of gene and genome duplication events and to the importance of new computational approaches to unraveling the structural evolution of genomes.

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This book constitutes the refereed proceedings of the 6th RECOMB Comparative Genomics Satellite Workshop, RECOMB-CG 2008, held in Paris, France, in October 2008.

The 19 revised full papers presented were carefully reviewed and selected from 48 initial submissions. The papers illustrate the crucial role of comparative genomics in understanding genome function and address a broad variety of aspects, ranging from the inference of evolution in genetic regulatory networks to the divergent fates of gene and genome duplication events and to the importance of new computational approaches to unraveling the structural evolution of genomes.

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This book constitutes the refereed proceedings of the 6th RECOMB Comparative Genomics Satellite Workshop, RECOMB-CG 2008, held in Paris, France, in October 2008.

The 19 revised full papers presented were carefully reviewed and selected from 48 initial submissions. The papers illustrate the crucial role of comparative genomics in understanding genome function and address a broad variety of aspects, ranging from the inference of evolution in genetic regulatory networks to the divergent fates of gene and genome duplication events and to the importance of new computational approaches to unraveling the structural evolution of genomes.

Content:
Front Matter....Pages -
Algorithms for Exploring the Space of Gene Tree/Species Tree Reconciliations....Pages 1-13
Limitations of Pseudogenes in Identifying Gene Losses....Pages 14-25
Duplication Mechanism and Disruptions in Flanking Regions Influence the Fate of Mammalian Gene Duplicates....Pages 26-39
Estimating the Relative Contributions of New Genes from Retrotransposition and Segmental Duplication Events during Mammalian Evolution....Pages 40-54
Discovering Local Patterns of Co-evolution....Pages 55-71
Ancestral Reconstruction by Asymmetric Wagner Parsimony over Continuous Characters and Squared Parsimony over Distributions....Pages 72-86
An Alignment-Free Distance Measure for Closely Related Genomes....Pages 87-99
Gene Team Tree: A Compact Representation of All Gene Teams....Pages 100-112
Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer....Pages 113-127
An Evolutionary Study of the Human Papillomavirus Genomes....Pages 128-142
An Algorithm for Inferring Mitogenome Rearrangements in a Phylogenetic Tree....Pages 143-157
Perfect DCJ Rearrangement....Pages 158-169
Sorting Genomes with Insertions, Deletions and Duplications by DCJ....Pages 170-183
A Fast and Exact Algorithm for the Median of Three Problem—A Graph Decomposition Approach....Pages 184-197
A Phylogenetic Approach to Genetic Map Refinement....Pages 198-210
Sorting Cancer Karyotypes by Elementary Operations....Pages 211-225
On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios....Pages 226-240
Hurdles Hardly Have to Be Heeded....Pages 241-251
Internal Validation of Ancestral Gene Order Reconstruction in Angiosperm Phylogeny....Pages 252-264
Back Matter....Pages -

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This book constitutes the refereed proceedings of the 6th RECOMB Comparative Genomics Satellite Workshop, RECOMB-CG 2008, held in Paris, France, in October 2008.

The 19 revised full papers presented were carefully reviewed and selected from 48 initial submissions. The papers illustrate the crucial role of comparative genomics in understanding genome function and address a broad variety of aspects, ranging from the inference of evolution in genetic regulatory networks to the divergent fates of gene and genome duplication events and to the importance of new computational approaches to unraveling the structural evolution of genomes.

Content:
Front Matter....Pages -
Algorithms for Exploring the Space of Gene Tree/Species Tree Reconciliations....Pages 1-13
Limitations of Pseudogenes in Identifying Gene Losses....Pages 14-25
Duplication Mechanism and Disruptions in Flanking Regions Influence the Fate of Mammalian Gene Duplicates....Pages 26-39
Estimating the Relative Contributions of New Genes from Retrotransposition and Segmental Duplication Events during Mammalian Evolution....Pages 40-54
Discovering Local Patterns of Co-evolution....Pages 55-71
Ancestral Reconstruction by Asymmetric Wagner Parsimony over Continuous Characters and Squared Parsimony over Distributions....Pages 72-86
An Alignment-Free Distance Measure for Closely Related Genomes....Pages 87-99
Gene Team Tree: A Compact Representation of All Gene Teams....Pages 100-112
Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer....Pages 113-127
An Evolutionary Study of the Human Papillomavirus Genomes....Pages 128-142
An Algorithm for Inferring Mitogenome Rearrangements in a Phylogenetic Tree....Pages 143-157
Perfect DCJ Rearrangement....Pages 158-169
Sorting Genomes with Insertions, Deletions and Duplications by DCJ....Pages 170-183
A Fast and Exact Algorithm for the Median of Three Problem—A Graph Decomposition Approach....Pages 184-197
A Phylogenetic Approach to Genetic Map Refinement....Pages 198-210
Sorting Cancer Karyotypes by Elementary Operations....Pages 211-225
On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios....Pages 226-240
Hurdles Hardly Have to Be Heeded....Pages 241-251
Internal Validation of Ancestral Gene Order Reconstruction in Angiosperm Phylogeny....Pages 252-264
Back Matter....Pages -
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