Main description:

This detailed book aims to provide an overview of novel bioinformatics resources for exploring diverse aspects of RNA biology. This edition focuses on methods dealing with non-coding RNA (miRNAs, circRNAs or lncRNAs), RNA modifications (m6A or RNA editing), single cell RNA-seq and statistical models to handle count data from RNA-seq experiments. The book also includes chapters based on the classical RNA bioinformatics methods, such as those for deciphering secondary and tertiary RNA structures; however, they are revised to take into account deep sequencing data. Finally, chapters describing methods to analyze RNA sequencing data from emerging third generation sequencing technologies that could provide interesting insights into the transcriptional process and its regulation are also included.
Written for the highly successful Methods in Molecular Biology series, chapters include the kind of expert implementation advice that encourages quality results. Comprehensive and up-to-date, RNA Bioinformatics, Second Edition serves as an ideal guide for researchers digging ever-deeper into the depths of the study of RNAs.
The chapter 'RNA-Seq Data Analysis in Galaxy' is open access under a CC BY 4.0 license.

Contents:

1. Advanced Design of Structural RNAs Using RNARedPrint

Yann Ponty, Stefan Hammer, Hua-Ting Yao, and Sebastian Will

2. Modeling and Predicting RNA Three-Dimensional Structures

Vladimir Reinharz, Roman Sarrazin-Gendron, and Jerome Waldispuhl

3. Motif Discovery from CLIP Experiments

Marco Pietrosanto, Gabriele Ausiello, and Manuela Helmer-Citterich

4. Profiling of RNA Structure at Single-Nucleotide Resolution Using nextPARS

Uciel Chorostecki, Jesse R. Willis, Ester Saus, and Toni Gabaldon

5. RNA Framework for Assaying the Structure of RNAs by High-Throughput Sequencing

Tycho Marinus and Danny Incarnato

6. Using RNentropy to Detect Significant Variation in Gene Expression across Multiple RNA-Seq or Single Cell RNA-Seq Samples

Federico Zambelli and Giulio Pavesi

7. Statistical Modeling of High Dimensional Counts

Michael I. Love

8. QuickIsoSeq for Isoform Quantification in Large-Scale RNA Sequencing

Ramya Gamini, Reiko Nakashima, Wen He, Ying Huang, Ying Zhang, and Shanrong Zhao

9. Summarizing RNA-Seq Data or Differentially Expressed Genes Using Gene Set, Network or Pathway Analysis

Enrica Calura and Paolo Martini

10. Computational Analysis of circRNA Expression Data

Giulio Ferrero, Nicola Licheri, Michele De Bortoli, Raffaele A Calogero, Marco Beccuti, and Francesca Cordero

11. Differential Expression Analysis of Long Non-Coding RNAs

Qian Li and Xuefeng Wang

12. Micro-RNA Quantification, Target Gene Identification, and Pathway Analysis

Gabriele Sales and Enrica Calura

13. In Silico Analysis of MicroRNA Sequencing Data

Ernesto Aparicio-Puerta, Bastian Fromm, Michael Hackenberg, and Marc K. Halushka

14. RNA Editing Detection in HPC Infrastructures

Claudio Lo Giudice, Luigi Mansi, Tiziano Flati, Silvia Gioiosa, Giovanni Chillemi, Pietro Libro, Tiziana Castrignano, Graziano Pesole, and Ernesto Picardi

15. Identification of Genes Post-Transcriptionally Regulated from RNA-Seq: The Case Study of Liver Hepatocellular Carcinoma

Stefano de Pretis, Mattia Furlan, and Mattia Pelizzola

16. Computational Analysis of Single Cell RNA-Seq Data

Luca Alessandri, Francesca Cordero, Marco Beccuti, Maddalena Arigoni, and Raffaele A. Calogero

17. Normalization of Single-Cell RNA-Seq Data

Davide Risso

18. Dimensionality Reduction of Single-Cell RNA-Seq Data

George C. Linderman

19. Single-Cell RNA Sequencing Analysis: A Step-by-Step Overview

Shaked Slovin, Annamaria Carissimo, Francesco Panariello, Antonio Grimaldi, Valentina Bouche, Gennaro Gambardella, and Davide Cacchiarelli

20. RNA-Seq Data Analysis in Galaxy

Berenice Batut, Marius van den Beek, Maria A. Doyle, and Nicola Soranzo

21. RAP: A Web Tool for RNA-Seq Data Analysis

Mattia D'Antonio, Pietro Libro, Ernesto Picardi, Graziano Pesole, and Tiziana Castrignano

22. iDEP Web Application for RNA-Seq Data Analysis

Xijin Ge

23. Exploring Non-Invasive Biomarkers with the miRandola Database: A Tool for Translational Medicine

Francesco Russo

24. Database Resources for Functional Circular RNAs

Dahui Hu, Peijing Zhang, and Ming Chen

25. Databases for RNA Editing Collections

Claudio Lo Giudice, Luigi Mansi, Graziano Pesole, and Ernesto Picardi

26. MODOMICS: An Operational Guide to the Use of the RNA Modification Pathways Database

Pietro Boccaletto and Blazej Baginski

27. MeT-DB V2.0: Elucidating Context-Specific Functions of N6-Methyl-Adenosine Methyltranscriptome

Hui Liu, Jiani Ma, Jia Meng, and Lin Zhang

28. WHISTLE: A Functionally Annotated High-Accuracy Map of Human m6A Epitranscriptome

Qingru Xu, Kunqi Chen, and Jia Meng

29. Transcript Identification through Long-Read Sequencing

Masahide Seki, Miho Oka, Liu Xu, Ayako Suzuki, and Yutaka Suzuki

30. Transcript Isoform-Specific Estimation of Poly(A) Tail Length by Nanopore Sequencing of Native RNA

Adnan M. Niazi, Maximillian Krause, and Eivind Valen

31. Nanopore RNA Sequencing Analysis

Tommaso Leonardi and Adrien Leger