Comparative Genomics

1. Front Matter

   PDF

2. Genome Aliquoting Revisited

   • Robert Warren, David Sankoff

   Pages 1-12

3. The Problem of Chromosome Reincorporation in DCJ Sorting and Halving

   • Jakub Kováč, Marília D. V. Braga, Jens Stoye

   Pages 13-24

4. Advances on Genome Duplication Distances

   • Yves Gagnon, Olivier Tremblay Savard, Denis Bertrand, Nadia El-Mabrouk

   Pages 25-38

5. Listing All Parsimonious Reversal Sequences: New Algorithms and Perspectives

   • Ghada Badr, Krister M. Swenson, David Sankoff

   Pages 39-49

6. Ultra-Perfect Sorting Scenarios

   • Aïda Ouangraoua, Anne Bergeron, Krister M. Swenson

   Pages 50-61

7. On Sorting Genomes with DCJ and Indels

   • Marília D. V. Braga

   Pages 62-73

8. The Zero Exemplar Distance Problem

   • Minghui Jiang

   Pages 74-82

9. Scaffold Filling under the Breakpoint Distance

   • Haitao Jiang, Chunfang Zheng, David Sankoff, Binhai Zhu

   Pages 83-92

10. An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers

    • Jean-Philippe Doyon, Celine Scornavacca, K. Yu. Gorbunov, Gergely J. Szöllősi, Vincent Ranwez, Vincent Berry

    Pages 93-108

11. Detecting Highways of Horizontal Gene Transfer

    • Mukul S. Bansal, J. Peter Gogarten, Ron Shamir

    Pages 109-120

12. On Exploring Genome Rearrangement Phylogenetic Patterns

    • Andrew Wei Xu

    Pages 121-136

13. Fast and Accurate Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Novel Robustness Estimator

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

    Pages 137-148

14. A Simple Measure of the Dynamics of Segmented Genomes: An Application to Influenza

    • Stéphane Aris-Brosou

    Pages 149-160

15. Novel Definition and Algorithm for Chaining Fragments with Proportional Overlaps

    • Raluca Uricaru, Alban Mancheron, Eric Rivals

    Pages 161-172

16. Assessing the Robustness of Complete Bacterial Genome Segmentations

    • Hugo Devillers, Hélène Chiapello, Sophie Schbath, Meriem El Karoui

    Pages 173-187

17. An Algorithm to Solve the Motif Alignment Problem for Approximate Nested Tandem Repeats

    • Atheer A. Matroud, Michael D. Hendy, Christopher P. Tuffley

    Pages 188-197

18. Limited Lifespan of Fragile Regions in Mammalian Evolution

    • Max A. Alekseyev, Pavel A. Pevzner

    Pages 198-215

19. Mapping Association between Long-Range Cis-Regulatory Regions and Their Target Genes Using Comparative Genomics

    • Emmanuel Mongin, Ken Dewar, Mathieu Blanchette

    Pages 216-227

20. A New Genomic Evolutionary Model for Rearrangements, Duplications, and Losses That Applies across Eukaryotes and Prokaryotes

    • Yu Lin, Bernard M. E. Moret

    Pages 228-239

The complexity of genome evolution has given birth to exciting challenges for computational biologists. A various range of algorithmic, statistical, mathem- ical techniques to elucidate the histories of molecules are developed each year and many are presented at the RECOMB satellite workshop on Comparative Genomics. It is a place where scientists working on all aspects of comparative genomics can share ideas on the development of tools and their application to relevant questions. This volume contains the papers presented at RECOMB-CG 2010, held on October 9–11 in Ottawa. The ?eld is still ?ourishing as seen from the papers presented this year: many developments enrich the combinatorics of genome rearrangements, while gene order phylogenies are becoming more and more - curate, thanks to a mixing of combinatorial and statistical principles, associated with rapid and thoughtful heuristics. Several papers tend to re?ne the models of genome evolution, and more and more genomic events can be modeled, from single nucleotide substitutions in whole genome alignments to large structural mutations or horizontal gene transfers.

• DCJ
• DNA sequences
• ancestral genomes
• cancer genomics
• comparative genomics
• comparative tools
• computational complexity
• data analysis
• double cut and join
• duplication
• evolution
• gene treee
• genome
• halving
• sorting

• INRIA Rhône-Alpes, Université de Lyon 1, Villeurbanne, France

  Eric Tannier

Policies and ethics