Main description:

This detailed book provides a comprehensive state-of-the-art presentation of all aspects of miRNA target identification, from the prediction of miRNA binding sites on their target molecules to their experimental validation and downstream functional analysis. It also explores methodologies and tools for target prediction and related analysis, as well as tutorials on specific tasks, tools, and analysis pipelines. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and practical, MicroRNA Target Identification: Methods and Protocols updates on basic and advanced concepts involving miRNA target identification and delivers an extremely useful guide to specific computational tasks and analysis in miRNA research.

Contents:

1. A Practical Guide to miRNA Target Prediction

Most Mauluda Akhtar, Luigina Micolucci, Md Soriful Islam, Fabiola Olivieri, and Antonio Domenico Procopio

2. miRandb: A Meta-Database of Online Resources of miRNA and miRNA Targets

Seyed Hamid Aghaee-Bakhtiari

3. Sfold Tools for MicroRNA Target Prediction

William Rennie, Shaveta Kanoria, Chaochun Liu, C. Steven Carmack, Jun Lu, and Ye Ding

4. The Role of Tertiary Structure in MicroRNA Target Recognition

Hin Hark Gan and Kristin C. Gunsalus

5. Protocols for miRNA Target Prediction in Plants

Gaurav Sablok, Kun Yang, and Xiaopen Wen

6. Improving miRNA-Target Prediction Using CLASH Data

Xiaoman Li and Haiyan Hu

7. Integration of Omics Data to Identify Cancer-Related MicroRNA

Luciano Cascione

8. Functional Analysis of Genetic Variants and Somatic Mutations Impacting MicroRNA-Target Recognition: Bioinformatics Resources

Jesse D. Ziebarth, Anindya Bhattacharya, and Yan Cui

9. Construction and Analysis of miRNA Regulatory Networks

Antonella Mensi, Vincenzo Bonnici, Simone Caligola, and Rosalba Giugno

10. Identification of Disease-miRNA Networks across Different Cancer Types Using SWitchMiner (SWIM)

Giulia Fiscon, Federica Conte, Lorenzo Farina, Marco Pellegrini, Francesco Russo, and Paola Paci

11. Computational Methods to Investigate the Impact of miRNAs on Pathways

Salvatore Alaimo, Giovanni Micale, Alessandro La Ferlita, Alfredo Ferro, and Alfredo Pulvirenti

12. Consensus Target Prediction with Enrichment Analysis for MicroRNAs Harboring Editing Sites and Other Variations

Giovanni Nigita, Rosario Distefano, Dario Veneziano, Giulia Romano, Mario Acunzo, and Carlo M. Croce

13. A Roadmap for the Computational Prediction and Experimental Validation of Competitive Endogenous RNAs

Florian A. Karreth

14. Investigating miRNA-lncRNA Interactions: Computational Tools and Resources

Dario Veneziano, Gioacchino P. Marceca, Sebastiano Di Bella, Giovanni Nigita, Rosario Distefano, and Carlo M. Croce

15. Combing the Hairball: Improving Visualization of miRNA-Target Interaction Networks

Francesco Russo, Jessica Xin Hu, Jose Alejandro Romero Herrera, and Soren Brunak

16. Inconsistencies and Limitations of Current MicroRNA Target Identification Methods

Sophie Mockly and Herve Seitz

17. Experimental Validation of MicroRNA Targets: Luciferase Reporter Assay

Luisa Tomasello, Landon Cluts, and Carlo M. Croce

18. Experimental Validation of MicroRNA Targets: Mutagenesis of the Binding Regions

Luisa Tomasello, Landon Cluts, and Carlo M. Croce

19. Experimental Validation of MicroRNA Targets: Analysis of MicroRNA Targets through Western Blotting

Luisa Tomasello, Landon Cluts, and Carlo M. Croce