Computational Biology of Non-Coding RNA Methods and Protocols

This second edition 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, Second Edition aims to ensure successful results in the further study of this vital field.

Overview of the different classes of small RNAs during B cell development.- A Current Perspective of Medical Informatics Developments for a Clinical Translation of (non-coding)RNAs and Single-Cell Technologies.- Non-coding RNA networks in infection.- The role of non-coding RNAs in tumorigenesis, diagnosis/prognosis, and therapeutic strategies for cutaneous melanoma.- A review on circular RNA translation and its implications in disease.- Modeling ncRNA-Mediated Circuits in Cell Fate Decision: From Systems Biology to Synthetic Biology.- Mathematical modeling for oscillations driven by noncoding RNAs.- Out-of-equilibrium ceRNA crosstalk.- Mechanistic Modelling the Role of MicroRNAs and Transcription Factors in Disease Progression.- Architects and Partners: The Dual Roles of Non-Coding RNAs in Gene Fusion Events.- Unveiling Long Non-Coding RNA Networks from Single-Cell Omics Data through Artificial Intelligence.- LncRNA recognition associated CpG island detection and methylation analysis.- Computational resources for lncRNA functions and targetome.- Temporal expression analysis to unravel gene regulatory dynamics by microRNAs.- Computational prediction of gene regulation by lncRNAs.- Structure-based prediction of lncRNA-protein interactions by deep learning.- Modelling ncRNA Synergistic Regulation in Cancer.- A Practical Guideline for MicroRNA Sequencing Data Analysis in Chronic Lymphocytic Leukemia.- A Network Biology-Guided Investigation of the Long Non-Coding RNAs’ role in Glaucoma.- ncRNA editing: Functional Characterization and Computational Resources.