Computational biology of non-coding RNA : methods and protocols
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Bibliographic Information
Computational biology of non-coding RNA : methods and protocols
（Methods in molecular biology / John M. Walker, series editor, 1912）（Springer protocols）
Humana Press, c2019
- : [hardback]
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Includes bibliographical references and index
Description and Table of Contents
Description
This volume details a collection of state-of-art methods including identification of novel ncRNAs and their targets, functional annotation and disease association in different biological contexts. Chapters guide readers through an overview of disease-specific ncRNAs, computational methods and workflows for ncRNA discovery, annotation based on high-throughput sequencing data, bioinformatics tools and databases for ncRNA analyses, network-based methods, and kinetic modelling of ncRNA-mediated gene regulation. Written in the highly successful Methods in Molecular Biology series format, 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 cutting-edge, Computational Biology of Non-Coding RNA: Methods and Protocols aims to provide a state-of-the-art collection of computational methods and approaches that will be of value to researchers interested in ncRNA field.
Table of Contents
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. Putzer
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
Disha Sharma, Paras Sehgal, Judith Hariprakash, Sridhar Sivasubbu, and Vinod Scaria
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
Muserref Duygu Sacar 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, Jose Carlos Caris-Maldonado, Pedro Vinicius Borges, Almir Jose 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
Jose C. Nacher and Tatsuya Akutsu
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 Jose 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
Xiao-Jun Tian, Manuela Vanegas Ferro, and Hanah Goetz
17. Modeling Long ncRNA-mediated Regulation in the Mammalian Cell Cycle
Jomar F. Rabajante and Ricardo C.H. del Rosario
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