Evolutionary Genomics Statistical And Computational Methods 1910 Methods In Molecular Biology

Part I: Introduction: Bioinformatician's Primers

1. Introduction to Genome Biology and Diversity

            Noor Youssef, Aidan Budd, and Joseph P. Bielawski

2. Probability, Statistics, and Computational Science

            Niko Beerenwinkel and Juliane Siebourg

3. A Not-So-Long Introduction to Computational Molecular Evolution

            Stéphane Aris-Brosou and Nicolas Rodrigue

Part II: Genomic Alignment and Homology Inference

4. Whole-Genome Alignment

            Colin Dewey

5. Inferring Orthology and Paralogy

            Adrian M. Altenhoff, Natasha M. Glover, and Christophe Dessimoz

6. Transposable Elements and Their Identification

            Wojciech Makalowski, Valer Gotea, Amit Pande, and Izabela Makalowska

Part III: Phylogenomics and Genome Evolution

7. Modern Phylogenomics: Building Phylogenetic Trees Using the Multispecies Coalescent Model

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

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

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

9. The Methodology Behind Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution

10. Bayesian Molecular Clock Dating Using Genome-Scale Datasets

            Mario dos Reis and Ziheng Yang

11. Genome Evolution in Outcrossing vs. Selfing vs. Asexual Species

            Sylvain Glémin, Clémentine M. François, and Nicolas Galtier

Part IV: Natural Selection and Innovation in Genomic Sequences

12. Selection Acting on Genomes

            Carolin Kosiol and Maria Anisimova

13. Looking for Darwin in Genomic Sequences: Validity and Success Depends on the Relationship between Model and Data

            Christopher T. Jones, Edward Susko, and Joseph P. Bielawski

14. Evolution of Viral Genomes: Interplay between Selection, Recombination, and Other Forces

            Stephanie J. Spielman, Steven Weaver, Stephen D. Shank, Brittany Rife Magalis, Michael Li, and Sergei L. Kosakovsky Pond

15. Evolution of Protein Domain Architectures

            Sofia K. Forslund, Mateusz Kaduk, and Erik L.L. Sonnhammer

16. New Insights on the Evolution of Genome Content: Population Dynamics of Transposable Elements in Flies and Humans

            Lain Guio and Josefa González

Part V: Population Genomics and Omics in Light of Disease and Evolution

17. Association Mapping and Disease: Evolutionary Perspectives

            Søren Besenbacher, Thomas Mailund, Bjarni J. Vilhjálmsson, and Mikkel H. Schierup

18. Ancestral Population Genomics

            Julien Y. Dutheil and Asger Hobolth

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

            Caner Bagci, Sina Beier, Anna Górska, and Daniel H. Huson

20. Multiple Data Analyses and Statistical Approaches for Analyzing Data from Metagenomic Studies and Clinical Trials

            Suparna Mitra

21. Systems Genetics for Evolutionary Studies

            Pjotr Prins, Geert Smant, Danny Arends, Megan K. Mulligan, Rob W. Williams, and Ritsert