Models and Algorithms for Genome Evolution

Part I. Emergence of Standard Algorithms

1. What’s Behind Blast
Gene Myers

2. Forty Years of Model-Based Phylogeography
David Bryant, Jamie Kydd

3. How to Infer Ancestral Genome Features by Parsimony: Dynamic Programming over an Evolutionary Tree
Miklós Csűrös

4. Duplication, Rearrangement and Reconciliation: A Follow-Up 13 Years Later
Cedric Chauve, Nadia El-Mabrouk, Laurent Guéguen, Magali Semeria, Eric Tannier

5. The Genesis of the DCJ Formula
Anne Bergeron, Jens Stoye

Part II. New Lights on Current Paradigms

6. Large-Scale Multiple Sequence Alignment and Phylogeny Estimation
Tandy Warnow

7. Rearrangements in Phylogenetic Inference: Compare, Model, or Encode?
Bernard M. E. Moret, Yu Lin, Jijun Tang

8. Status of Research on Insertion and Deletion Variations in the Human Population
Liqing Zhang, Mingming Liu, Layne T. Watson

9. A Retrospective on Genomic Preprocessing for Comparative Genomics
Binhai Zhu

10. The Emperor Has No Caps! A Comparison of DCJ and Algebraic Distances
Joao Meidanis, Sophia Yancopoulos

Part III. Promising Directions

11. Fractionation, Rearrangement, Consolidation, Reconstruction
David Sankoff, Chunfang Zheng

12. Error Detection and Correction of Gene Trees
Manuel Lafond, Krister M. Swenson, Nadia El-Mabrouk

13. The Potential of Family-Free Genome Comparison
Marília D. V. Braga, Cedric Chauve, Daniel Doerr, Katharina Jahn, Jens Stoye, Annelyse Thévenin, Roland Wittler

14. Genetic History of Populations: Limits to Inference
Daniel E. Platt, Filippo Utro, Marc Pybus, Laxmi Parida

Avainsanat: Computer Science, Computational Biology/Bioinformatics, Mathematical and Computational Biology, Bioinformatics, Mathematics of Computing