RNA bioinformatics
著者
書誌事項
RNA bioinformatics
（Methods in molecular biology / John M. Walker, series editor, 2284）（Springer protocols）
Humana Press, c2021
2nd ed
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注記
Includes bibliographical references and index
内容説明・目次
内容説明
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.
目次
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
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