Computational biology of non-coding RNA : methods and protocols

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書誌事項

Computational biology of non-coding RNA : methods and protocols

edited by Xin Lai, Shailendra K. Gupta, Julio Vera

（Methods in molecular biology / John M. Walker, series editor, 1912）（Springer protocols）

Humana Press, c2019

  • : [hardback]

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注記

Includes bibliographical references and index

内容説明・目次

内容説明

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.

目次

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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