Computational Biology of Non-Coding RNA: Methods and Protocols

✍ Scribed by Xin Lai, Shailendra K. Gupta, Julio Vera

• Publisher: Springer New York;Humana Press
• Year: 2019
• Tongue: English
• Leaves: 454
• Series: Methods in Molecular Biology 1912
• Edition: 1st ed.
• Category: Library

✦ Synopsis

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

Front Matter ....Pages i-xii
Front Matter ....Pages 1-1
ncRNAs in Inflammatory and Infectious Diseases (Leon N. Schulte, Wilhelm Bertrams, Christina Stielow, Bernd Schmeck)....Pages 3-32
p73-Governed miRNA Networks: Translating Bioinformatics Approaches to Therapeutic Solutions for Cancer Metastasis (Stella Logotheti, Stephan Marquardt, Brigitte M. Pützer)....Pages 33-52
Front Matter ....Pages 53-53
Methods for Annotation and Validation of Circular RNAs from RNAseq Data (Disha Sharma, Paras Sehgal, Judith Hariprakash, Sridhar Sivasubbu, Vinod Scaria)....Pages 55-76
Methods to Study Long Noncoding RNA Expression and Dynamics in Zebrafish Using RNA Sequencing (Samatha Mathew, Ambily Sivadas, Paras Sehgal, Kriti Kaushik, Shamsudheen K. Vellarikkal, Vinod Scaria et al.)....Pages 77-110
Workflow Development for the Functional Characterization of ncRNAs (Markus Wolfien, David Leon Brauer, Andrea Bagnacani, Olaf Wolkenhauer)....Pages 111-132
ncRNA Editing: Functional Characterization and Computational Resources (Giovanni Nigita, Gioacchino P. Marceca, Luisa Tomasello, Rosario Distefano, Federica Calore, Dario Veneziano et al.)....Pages 133-174
Computational Prediction of Functional MicroRNA–mRNA Interactions (Müşerref Duygu Saçar Demirci, Malik Yousef, Jens Allmer)....Pages 175-196
Front Matter ....Pages 197-197
Tools for Understanding miRNA–mRNA Interactions for Reproducible RNA Analysis (Andrea Bagnacani, Markus Wolfien, Olaf Wolkenhauer)....Pages 199-214
Computational Resources for Prediction and Analysis of Functional miRNA and Their Targetome (Isha Monga, Manoj Kumar)....Pages 215-250
Noncoding RNAs Databases: Current Status and Trends (Vinicius Maracaja-Coutinho, Alexandre Rossi Paschoal, José Carlos Caris-Maldonado, Pedro Vinícius Borges, Almir José Ferreira, Alan Mitchell Durham)....Pages 251-285
Front Matter ....Pages 287-287
Controllability Methods for Identifying Associations Between Critical Control ncRNAs and Human Diseases (Jose C. Nacher, Tatsuya Akutsu)....Pages 289-300
Network-Based Methods and Other Approaches for Predicting lncRNA Functions and Disease Associations (Rosario Michael Piro, Annalisa Marsico)....Pages 301-321
Integration of miRNA and mRNA Expression Data for Understanding Etiology of Gynecologic Cancers (Sushmita Paul)....Pages 323-338
Front Matter ....Pages 339-339
Quantitative Characteristic of ncRNA Regulation in Gene Regulatory Networks (Federico Bocci, Mohit Kumar Jolly, Herbert Levine, José Nelson Onuchic)....Pages 341-366
Kinetic Modelling of Competition and Depletion of Shared miRNAs by Competing Endogenous RNAs (Araks Martirosyan, Marco Del Giudice, Chiara Enrico Bena, Andrea Pagnani, Carla Bosia, Andrea De Martino)....Pages 367-409
Modeling ncRNA-Mediated Circuits in Cell Fate Decision (Xiao-Jun Tian, Manuela Vanegas Ferro, Hanah Goetz)....Pages 411-426
Modeling Long ncRNA-Mediated Regulation in the Mammalian Cell Cycle (Jomar F. Rabajante, Ricardo C. H. del Rosario)....Pages 427-445
Back Matter ....Pages 447-451

✦ Subjects

Life Sciences; Bioinformatics; Human Genetics; Computational Biology/Bioinformatics