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Computational Epigenomics and Epitranscriptomics

  • Book
  • © 2023

Overview

Editors:
  1. Pedro H. Oliveira

    1. Genoscope, Évry, France

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2624)

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Table of contents (16 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. DNA Methylation Data Analysis Using Msuite

    • Xiaojian Liu, Pengxiang Yuan, Kun Sun
    Pages 1-6

  3. Interactive DNA Methylation Array Analysis with ShinyÉPICo

    • Octavio Morante-Palacios
    Pages 7-18

  4. Predicting Chromatin Interactions from DNA Sequence Using DeepC

    • Ron Schwessinger
    Pages 19-42

  5. Integrating Single-Cell Methylome and Transcriptome Data with MAPLE

    • Yasin Uzun, Hao Wu, Kai Tan
    Pages 43-54

  6. Quantitative Comparison of Multiple Chromatin Immunoprecipitation-Sequencing (ChIP-seq) Experiments with spikChIP

    • Enrique Blanco, Cecilia Ballaré, Luciano Di Croce, Sergi Aranda
    Pages 55-72

  7. A Guide to MethylationToActivity: A Deep Learning Framework That Reveals Promoter Activity Landscapes from DNA Methylomes in Individual Tumors

    • Karissa Dieseldorff Jones, Daniel Putnam, Justin Williams, Xiang Chen
    Pages 73-85

  8. DNA Modification Patterns Filtering and Analysis Using DNAModAnnot

    • Alexis Hardy, Sandra Duharcourt, Matthieu Defrance
    Pages 87-114

  9. Methylome Imputation by Methylation Patterns

    • Ya-Ting Sabrina Chang, Ming-Ren Yen, Pao-Yang Chen
    Pages 115-126

  10. Sequoia: A Framework for Visual Analysis of RNA Modifications from Direct RNA Sequencing Data

    • Ratanond Koonchanok, Swapna Vidhur Daulatabad, Khairi Reda, Sarath Chandra Janga
    Pages 127-138

  11. Predicting Pseudouridine Sites with Porpoise

    • Xudong Guo, Fuyi Li, Jiangning Song
    Pages 139-151

  12. Pseudouridine Identification and Functional Annotation with PIANO

    • Jiahui Yao, Cuiyueyue Hao, Kunqi Chen, Jia Meng, Bowen Song
    Pages 153-162

  13. Analyzing mRNA Epigenetic Sequencing Data with TRESS

    • Zhenxing Guo, Andrew M. Shafik, Peng Jin, Zhijin Wu, Hao Wu
    Pages 163-183

  14. Nanopore Direct RNA Sequencing Data Processing and Analysis Using MasterOfPores

    • Luca Cozzuto, Anna Delgado-Tejedor, Toni Hermoso Pulido, Eva Maria Novoa, Julia Ponomarenko
    Pages 185-205

  15. Data Analysis Pipeline for Detection and Quantification of Pseudouridine (ψ) in RNA by HydraPsiSeq

    • Florian Pichot, Virginie Marchand, Mark Helm, Yuri Motorin
    Pages 207-223

  16. Analysis of RNA Sequences and Modifications Using NASE

    • Samuel Wein
    Pages 225-239

  17. Mapping of RNA Modifications by Direct Nanopore Sequencing and JACUSA2

    • Amina Lemsara, Christoph Dieterich, Isabel S. Naarmann-de Vries
    Pages 241-260

  18. Back Matter

    Pages 261-262
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Keywords

About this book

This volume details state-of-the-art computational methods designed to manage, analyze, and generally leverage epigenomic and epitranscriptomic data. Chapters guide readers through fine-mapping and quantification of modifications, visual analytics, imputation methods, supervised analysis, and integrative approaches for single-cell data. 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.

 

Cutting-edge and thorough, Computational Epigenomics and Epitranscriptomics aims to provide an overview of epiomic protocols, making it easier for researchers to extract impactful biological insight from their data.

Editors and Affiliations

  • Genoscope, Évry, France

    Pedro H. Oliveira

Bibliographic Information

  • Book Title: Computational Epigenomics and Epitranscriptomics

  • Editors: Pedro H. Oliveira

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-2962-8

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2023

  • Hardcover ISBN: 978-1-0716-2961-1Published: 02 February 2023

  • Softcover ISBN: 978-1-0716-2964-2Published: 02 February 2024

  • eBook ISBN: 978-1-0716-2962-8Published: 01 February 2023

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 262

  • Number of Illustrations: 4 b/w illustrations, 61 illustrations in colour

  • Topics: Genetics and Genomics, Mathematical and Computational Biology

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