Part I: Phylogenomics

1. Tangled Trees: The Challenge of Inferring Species Trees from Coalescent and Non-Coalescent Genes

Christian Anderson, Liang Liu, Dennis Pearl, and Scott V. Edwards

2. Modeling Gene Family Evolution and Reconciling Phylogenetic Discord

Gergely J Szöllősi and Vincent Daubin

3. Genome-Wide Comparative Analysis of Phylogenetic Trees: The Prokaryotic Forest of Life

Pere Puigbò, Yuri I. Wolf, and Eugene V. Koonin

4. Philosophy and Evolution: Minding the Gap Between Evolutionary Patterns and Tree-Like Patterns

Eric Bapteste, Frederic Bouchard, and Richard M. Burian

Part II: Natural Selection, Recombination, and Innovation in Genomic Sequences

5. Selection on the Protein Coding Genome

Carolin Kosiol and Maria Anisimova

6. Methods to Detect Selection on Non-Coding DNA

Ying Zhen and Peter Andolfatto

7. The Origin and Evolution of New Genes

Margarida Cardoso-Moreira and Manyuan Long

8. Evolution of Protein Domain Architectures

Kristoffer Forslund and Erik L.L. Sonnhammer

9. Estimating Recombination Rates from Genetic Variation in Humans

Adam Auton and Gil McVean

10. Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces

Sergei L. Kosakovsky Pond, Ben Murrell, and Art F.Y. Poon

Part III: Population Genomics

11. Association Mapping and Disease: Evolutionary Perspectives

Søren Besenbacher, Thomas Mailund, and Mikkel H. Schierup

12. Ancestral Population Genomics

Julien Y. Dutheil and Asger Hobolth

13. Non-Redundant Representation of Ancestral Recombinations Graphs

Laxmi Parida

Part IV: The "-omics"

14. Using Genomic Tools to Study Regulatory Evolution

Yoav Gilad

15. Characterization and Evolutionary Analysis of Protein-Protein Interaction Networks

Gabriel Musso, Andrew Emili, and Zhaolei Zhang

16. Statistical Methods in Metabolomics

Alexander Korman, Amy Oh, Alexander Raskind, and David Banks

17. Introduction to the Analysis of Environmental Sequences: Metagenomics with MEGAN

Daniel H. Huson and Suparna Mitra

18. Analyzing Epigenome Data in Context of Genome Evolution and Human Diseases

Lars Feuerbach, Konstantin Halachev, Yassen Assenov, Fabian Müller, Christoph Bock, and Thomas Lengauer

19. Genetical Genomics for Evolutionary Studies

Pjotr Prins, Geert Smant, and Ritsert C. Jansen

Part V: Handling Genomic Data: Resources and Computation

20. Genomics Data Resources: Frameworks and Standards

Mark D. Wilkinson

21. Sharing Programming Resources Between Bio* Projects through Remote Procedure Call and Native Call Stack Strategies

Pjotr Prins, Naohisa Goto, Andrew Yates, Laurent Gautier, Scooter Willis, Christopher Fields, and Toshiaki Katayama

22. Scalable Computing for Evolutionary Genomics

Pjotr Prins, Dominique Belhachemi, Steffen Möller, and Geert Smant