Part I: Introductory Chapters
1. Pseudogene Redux with New Biological Significance
Leonardo Salmena
2. Contribution of Pseudogenes to Sequence Diversity
Mauno Vihinen
Part II: Methods to Identify Pseudogenes
3. Computational Methods for Pseudogene Annotation Based on Sequence Homology
Paul M. Harrison
4. Computational Methods of Identification of Pseudogenes Based on Functionality: Entropy and GC Content
Evgeniy S. Balakirev, Vladimir R. Chechetkin, Vasily V. Lobzin, and Francisco J. Ayala
5. Computational Methods of Identification of Pseudogenes Based on Functionality: Hybridization of 18S rRNA and mRNA During Translation
Chuanhua Xing
6. Whole Genome Identification of Neutrally Evolving Pseudogenes Using the Evolutionary Measure dN/dS
Lisa O. Andrieux and David Torrents Arenales
7. Methods to Study the Occurrence and the Evolution of Pseudogenes Through a Phylogenetic Approach
Jacques Dainat and Pierre Pontarotti
Part III: Methods to Detect Transcribed Pseudogenes of a Parental Gene of Interest
8. Methods for Detecting Transcribed Pseudogenes: PCR on Regions of High Sequence Similarity Followed by Cloning and Sequencing
Wenyong Ding and Jianwu Dai
Part IV: High-Throughput Methods to Detect Transcribed Pseudogenes
9. RNA Amplification for Pseudogene Detection Using RNA-Seq
Stephen C.M. Tsoi and Michael K. Dyck
10. GENCODE Pseudogenes
Adam Frankish and Jennifer Harrow
11. Methods to Detect Transcribed Pseudogenes: RNA-Seq Discovery Allows Learning Through Features
Camilo Valdes and Enrico Capobianco
Part V: High-Throughput Methods to Detect Translated Pseudogenes
12. Proteomics Techniques for the Detection of Translated Pseudogenes
Nadia Ucciferri and Silvia Rocchiccioli
Part VI: Methods to Study Transcribed Pseudogenes
13. Pseudogenes as Competitive Endogenous RNAs: Target Prediction and Validation
Florian A. Karreth, Ugo Ala, Paolo Provero, and Pier Paolo Pandolfi
14. Pseudogenes: A Novel Source of Trans Acting Antisense RNAs
Per Johnsson, Kevin V. Morris, and Dan Grander
15. Pseudogene-Derived Endogenous siRNAs and Their Function
Wen-Ling Chan and Jan-Gowth Chang
Part VII: Methods to Study Translated Pseudogenes
16. Methods to Study Translated Pseudogenes: In Vitro Translation, Fusion with a Tag/Reporter Gene, and Complementation Assay
Anne Parle-McDermott
Part VIII: Methods to Study Translated Pseudogenes
17. Targeted and Robust Amplification of Mitochondrial DNA in the Presence of Nuclear Encoded Mitochondrial Pseudogenes Using 29 DNA Polymerases
Jonci N. Wolff
18. Discrimination of Pseudogene and Parental Gene DNA Methylation Using Allelic Bisulphite Sequencing
Luke B. Hesson and Robyn L. Ward
19. Mutational Analysis of CYP21A2 Gene and CYP21A1P Pseudogene: Long Range PCR on Genomic DNA
Hsien-Hsiung Lee
20. PMS2 Gene Mutational Analysis: RNA-Based Direct cDNA Sequencing to Circumvent Pseudogene Interference
Katharina Wimmer and Annekatrin Wernstedt
21. Dealing with Pseudogenes in Molecular Diagnostics in the Next Generation Sequencing Era
Kathleen Claes and Kim De Leeneer