RNA Bioinformatics

ISBN-13: 9781071613092 / Angielski / Miękka / 2022 / 600 str.

Ernesto Picardi

Spis treści

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 Jérôme Waldispühl

 

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 Castrignanò, 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 Alessandrì, 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 Bouché, Gennaro Gambardella, and Davide Cacchiarelli

 

20. RNA-Seq Data Analysis in Galaxy

            Bérénice 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 Castrignanò

 

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 Błażej Bagiński

 

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

Blurb

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.