1. A Predictive Approach to Infer the Activity and Natural Variation of Retrotransposon Families in Plants
Matthias Benoit and Hajk-Georg Drost
2. In silico Identification of Stress Associated Transposable Elements in Arabidopsis thaliana using Public Transcriptome Data
Doğa Eskier and Gökhan Karakülah
3. A Practical Guide on Computational Tools and Databases for Transposable Elements in Plants
Liliane Santana Oliveira, Tharcísio Soares de Amorim, Daniel Longhi Fernandes Pedro, Fábio Fernandes da Rocha Vicente, and Alexandre Rossi Paschoal
4. A Tutorial of EDTA: Extensive de-novo TE Annotator
Weijia Su, Shujun Ou, Matthew B. Hufford, and Thomas Peterson
5. Mining of Miniature Transposable Elements in Brassica species at BrassicaTED
Murukarthick Jayakodi and Tae-Jin Yang
6. Genome-wide Identification of Miniature Inverted-Repeat Transposable Elements by Targeted High-Throughput Sequencing
Yanyan Tang, Fengxia Liu, and Lubin Tan
7. Identification of Extrachromosomal Circular Forms of Active Transposable Elements Using Mobilome-Seq
Sophie Lanciano, Panpan Zhang, Christel Llauro, and Marie Mirouze
8. Identification of Active Transposable Elements in Plants: The mobilome-seq Approach
Michael Thieme and Anne C. Roulin
9. High-throughput Profiling of Extrachromosomal Linear DNAs of Long Terminal Repeat Retrotransposons by ALE-seq
Ling Wang, Eun Yu Kim, and Jungnam Cho
10. Bioinformatics Analysis Guides to LTR Retrotransposon-Derived Extrachromosomal Linear DNAs Identified by ALE-seq
Ling Wang, Jungnam Cho, and Viswanathan Satheesh
11. Determination of TE insertion Positions using Transposon Display
Eun Yu Kim, Wenwen Fan, and Jungnam Cho
12. Detection of Transposition Events from Next-Generation Sequencing Data
Akio Miyao
13. Rapid Detection of Transposon-Induced Genome Rearrangements
Sharu Paul Sharma and Thomas Peterson
14. Detection of Transposable Element Insertions in Arabidopsis Using Sequence Capture
Leandro Quadrana, Amanda Bortolini Silveira, Erwann Caillieux, and Vincent Colot
15. Efficient Detection of Transposable Element Insertion Polymorphisms Between Genomes Using Short-Read Sequencing Data
Baduel P., Quadrana L., and Colot. V.
16. Quantitative Measurement of Transposon Copy Number using the Droplet Digital PCR
Wenwen Fan and Jungnam Cho
17. Detecting Signatures of TE Polymorphisms in Short-read Sequencing Data
Christoph Stritt and Anne C. Roulin
18. How to Activate Heat-responsible Retrotransposon ONSEN in Brassicaceae Species
Hidetaka Ito
19. Measurement of Genetic Mobility Using a Transposon-Based Marker System In Sorghum
Jae Il Lyu, Yeong Deuk Jo, Joon-Woo Ahn, Jin-Baek Kim, and Soon-Jae Kwon
20. Sequence-specific Amplified Polymorphism (SSAP) and Sequence Characterized Amplified Region (SCAR) Markers in Zea mays
Neha Samir Roy, Rahul Vasudeo Ramekar, and Nam-Soo Kim
21. Analysis of Plant DNA Methylation Profiles using R
Marco Catoni and Nicolae Radu Zabet
22. Arabidopsis thaliana Mature Endosperm Dissection and Isolation of Seed Tissue Genomic DNA
Mayumi Iwasaki and Luis Lopez-Molina
23. Transposon-Based Tagging in Silico using FastPCR Software
Ruslan Kalendar, Dana Kospanova, and Alan H. Schulman
24. Bamboo Transposon Research: Current
