Comparative Genomics

1. Front Matter

   PDF

2. Algorithms for Exploring the Space of Gene Tree/Species Tree Reconciliations

   • Jean-Philippe Doyon, Cedric Chauve, Sylvie Hamel

   Pages 1-13

3. Limitations of Pseudogenes in Identifying Gene Losses

   • James C. Costello, Mira V. Han, Matthew W. Hahn

   Pages 14-25

4. Duplication Mechanism and Disruptions in Flanking Regions Influence the Fate of Mammalian Gene Duplicates

   • Paul Ryvkin, Jin Jun, Edward Hemphill, Craig Nelson

   Pages 26-39

5. Estimating the Relative Contributions of New Genes from Retrotransposition and Segmental Duplication Events during Mammalian Evolution

   • Jin Jun, Paul Ryvkin, Edward Hemphill, Ion Măndoiu, Craig Nelson

   Pages 40-54

6. Discovering Local Patterns of Co-evolution

   • Yifat Felder, Tamir Tuller

   Pages 55-71

7. Ancestral Reconstruction by Asymmetric Wagner Parsimony over Continuous Characters and Squared Parsimony over Distributions

   • Miklós Csűrös

   Pages 72-86

8. An Alignment-Free Distance Measure for Closely Related Genomes

   • Bernhard Haubold, Mirjana Domazet-Los̆o, Thomas Wiehe

   Pages 87-99

9. Gene Team Tree: A Compact Representation of All Gene Teams

   • Melvin Zhang, Hon Wai Leong

   Pages 100-112

10. Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer

    • Cuong Than, Guohua Jin, Luay Nakhleh

    Pages 113-127

11. An Evolutionary Study of the Human Papillomavirus Genomes

    • Dunarel Badescu, Abdoulaye Baniré Diallo, Mathieu Blanchette, Vladimir Makarenkov

    Pages 128-142

12. An Algorithm for Inferring Mitogenome Rearrangements in a Phylogenetic Tree

    • Matthias Bernt, Daniel Merkle, Martin Middendorf

    Pages 143-157

13. Perfect DCJ Rearrangement

    • Sèverine Bérard, Annie Chateau, Cedric Chauve, Christophe Paul, Eric Tannier

    Pages 158-169

14. Sorting Genomes with Insertions, Deletions and Duplications by DCJ

    • Sophia Yancopoulos, Richard Friedberg

    Pages 170-183

15. A Fast and Exact Algorithm for the Median of Three Problem—A Graph Decomposition Approach

    • Andrew Wei Xu

    Pages 184-197

16. A Phylogenetic Approach to Genetic Map Refinement

    • Denis Bertrand, Mathieu Blanchette, Nadia El-Mabrouk

    Pages 198-210

17. Sorting Cancer Karyotypes by Elementary Operations

    • Michal Ozery-Flato, Ron Shamir

    Pages 211-225

18. On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios

    • Anne Bergeron, Julia Mixtacki, Jens Stoye

    Pages 226-240

19. Hurdles Hardly Have to Be Heeded

    • Krister M. Swenson, Yu Lin, Vaibhav Rajan, Bernard M. E. Moret

    Pages 241-251

20. Internal Validation of Ancestral Gene Order Reconstruction in Angiosperm Phylogeny

    • David Sankoff, Chunfang Zheng, P. Kerr Wall, Claude dePamphilis, Jim Leebens-Mack, Victor A. Albert

    Pages 252-264

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.

• ancestral genomes
• computational biology
• data mining
• dna sequence
• evolution
• gene tree
• genome
• genome distance
• genomics
• mitogenome rearrangement
• phylogenetic tree
• pseudogene

• Molecular and Cell Biology, University of Connecticut, Division of Genetics and Genomics, Storrs, USA

  Craig E. Nelson

• Université Paris-Est, IGM-LabInfo, Marne la Vallée, France

  Stéphane Vialette

Policies and ethics