Part I: Introduction: Bioinformatician’s Primers

Aidan Budd

Rajeev K. Azad and Jeffrey G. Lawrence

Part III: Genome Evolution: Insights from Statistical Analyses

11.

2. Diversity of Genome Organization

Aidan Budd

3. Probability, Statistics, and Computational Science

Niko Beerenwinkel and Juliane Siebourg

4. The Essentials of Computational Molecular Evolution

Stéphane Aris-Brosou and Nicolas Rodrigue

Part II: Genomic Data Assembly, Alignment, and Homology Inference

5. Next-Generation Sequencing Technologies and Fragment Assembly Algorithms

Heewook Lee and Haixu Tang

6. Gene Prediction

Rajeev K. Azad and Jeffrey G. Lawrence

Part III: Genome Evolution: Insights from Statistical Analyses

11.

Tyler Alioto

Rajeev K. Azad and Jeffrey G. Lawrence

Part III: Genome Evolution: Insights from Statistical Analyses

11.

7. Alignment Methods: Strategies, Challenges, Benchmarking, and Comparative Overview

Ari Löytynoja

8. Whole-Genome Alignment

Colin N. Dewey

9. Inferring Orthology and Paralogy

Adrian M. Altenho and Christophe Dessimoz

10. Detecting Laterally Transferred Genes

Rajeev K. Azad and Jeffrey G. Lawrence

Part III: Genome Evolution: Insights from Statistical Analyses

11.

Sylvain Glémin and Nicolas Galtier

12. Transposable Elements And Their Identification

Wojciech Makałowski, Amit Pande, Valer Gotea, and Izabela Makałowska

13. Evolution of Genome Content: Population Dynamics of Transposable Elements in Flies and Humans

Josefa González and Dmitri A. Petrov

14. Detection and Phylogenetic Assessment of Conserved Synteny Derived from Whole Genome Duplications

Shigehiro Kuraku and Axel Meyer

15. Analysis of Gene Order Evolution Beyond Single-Copy Genes

Nadia El-Mabrouk and David Sankoff

16. Discovering Patterns in Gene Order

Laxmi Parida and Niina Haiminen

1. Introduction to Genome Biology: Features, Processes, and Structures

Rajeev K. Azad and Jeffrey G. Lawrence

Part III: Genome Evolution: Insights from Statistical Analyses

11.

Aidan Budd

Rajeev K. Azad and Jeffrey G. Lawrence

Part III: Genome Evolution: Insights from Statistical Analyses

11.

2. Diversity of Genome Organization

Aidan Budd

3. Probability, Statistics, and Computational Science

Niko Beerenwinkel and Juliane Siebourg

4. The Essentials of Computational Molecular Evolution

Stéphane Aris-Brosou and Nicolas Rodrigue

Part II: Genomic Data Assembly, Alignment, and Homology Inference

5. Next-Generation Sequencing Technologies and Fragment Assembly Algorithms

Heewook Lee and Haixu Tang

6. Gene Prediction

Rajeev K. Azad and Jeffrey G. Lawrence

Part III: Genome Evolution: Insights from Statistical Analyses

11.

Tyler Alioto

Rajeev K. Azad and Jeffrey G. Lawrence

Part III: Genome Evolution: Insights from Statistical Analyses

11.

7. Alignment Methods: Strategies, Challenges, Benchmarking, and Comparative Overview

Ari Löytynoja

8. Whole-Genome Alignment

Colin N. Dewey

9. Inferring Orthology and Paralogy

Adrian M. Altenho and Christophe Dessimoz

10. Detecting Laterally Transferred Genes

Rajeev K. Azad and Jeffrey G. Lawrence

Part III: Genome Evolution: Insights from Statistical Analyses

11.

Sylvain Glémin and Nicolas Galtier

12. Transposable Elements And Their Identification

Wojciech Makałowski, Amit Pande, Valer Gotea, and Izabela Makałowska

13. Evolution of Genome Content: Population Dynamics of Transposable Elements in Flies and Humans

Josefa González and Dmitri A. Petrov

14. Detection and Phylogenetic Assessment of Conserved Synteny Derived from Whole Genome Duplications

Shigehiro Kuraku and Axel Meyer

15. Analysis of Gene Order Evolution Beyond Single-Copy Genes

Nadia El-Mabrouk and David Sankoff

16. Discovering Patterns in Gene Order

Laxmi Parida and Niina Haiminen