Computational Biology of Non-Coding RNA: Methods and Protocols

Part I: Overview of Disease-Specific ncRNAs

1. ncRNAs in Inflammatory and Infectious Diseases

Leon Schulte, Wilhelm Bertrams, Christina Stielow, and Bernd Schmeck

2. p73-Governed miRNA Networks: Translating Bioinformatics Approaches to Therapeutic Solutions for Cancer Metastasis

Stella Logotheti, Stephan Marquardt, and Brigitte M. Pützer

Part II: Computational Methods and Workflows for ncRNA discovery and annotation based on High-Throughput Sequencing Data

3. Methods for Annotation and Validation of Circular RNAs from RNAseq Data

4. Methods to Study Long Non-coding RNA Expression and Dynamics in Zebrafish using RNA Sequencing

Samatha Mathew, Ambily Sivadas, Paras Sehgal,  Kriti Kaushik, Shamsudheen K. Vellarikkal, Vinod Scaria, and Sridhar Sivasubbu

5. Workflow Development for the Functional Characterization of ncRNAs

Markus Wolfien, David Leon Brauer, Andrea Bagnacani, and Olaf Wolkenhauer

6. ncRNA Editing: Functional Characterization and Computational Resources

Giovanni Nigita, Gioacchino P. Marceca, Luisa Tomasello, Rosario Distefano, Federica Calore, Dario Veneziano, Giulia Romano, Serge Patrick Nana-Sinkam, Mario Acunzo, and Carlo M. Croce

7. Computational Prediction of Functional microRNA - mRNA Interactions

Müserref Duygu Saçar Demirci, Malik Yousef, and Jens Allmer

Part III: Bioinformatics Tools and Databases for ncRNA Analyses

8. Tools for Understanding miRNA-mRNA Interactions for Reproducible RNA Analysis

Andrea Bagnacani, Markus Wolfien, and Olaf Wolkenhauer

9. Computational Resources for Prediction and Analysis of Functional miRNA and their Targetome

Isha Monga and Manoj Kumar

10. Non-coding RNAs Databases: Current Status and Trends

Vinicius Maracaja-Coutinho, Alexandre Rossi Paschoal, José Carlos Caris-Maldonado, Pedro Vinícius Borges, Almir José Ferreira, and Alan Mitchell Durham

Part IV: Network-based Methods for Characterizing ncRNA Fuction

11. Controllability Methods for Identifying Associations between Critical Control ncRNAs

and Human Diseases

12. Network-based Methods and Other Approaches for Predicting lncRNA Functions and Disease Associations

Rosario Michael Piro and Annalisa Marsico

13. Integration of miRNA and mRNA Expression Data for Understanding Etiology of Gynecologic Cancers

Sushmita Paul

Part V: Kinetic Modeling of ncRNA-mediated Gene Regulation

14. Quantitative Characteristic of ncRNA Regulation in Gene Regulatory Networks

Federico Bocci, Mohit Kumar Jolly, Herbert Levine, and José N. Onuchic

15. Kinetic Modeling of Competition and Depletion of Shared miRNAs by Competing Endogenous RNAs

Araks Martirosyan, Marco Del Giudice, Chiara Enrico Bena, Andrea Pagnani,

Carla Bosia, and Andrea De Martino

16. Modeling ncRNA-mediated Circuits in Cell Fate Decision

17. Modeling Long ncRNA-mediated Regulation in the Mammalian Cell Cycle