Hi-C data analysis : methods and protocols
著者
書誌事項
Hi-C data analysis : methods and protocols
（Methods in molecular biology / John M. Walker, series editor, 2301）（Springer protocols）
Humana Press, c2022
- : [hardback]
大学図書館所蔵 全1件
注記
Includes bibliographical references and index
内容説明・目次
内容説明
This volume details a comprehensive set of methods and tools for Hi-C data processing, analysis, and interpretation. Chapters cover applications of Hi-C to address a variety of biological problems, with a specific focus on state-of-the-art computational procedures adopted for the data analysis. 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, Hi-C Data Analysis: Methods and Protocols aims to help computational and molecular biologists working in the field of chromatin 3D architecture and transcription regulation.
目次
1. Normalization of Chromosome Contact Maps: Matrix Balancing and Visualization
Cyril Matthey Doret, Lyam Baudry, Shogofa Mortaza, Pierrick Moreau, Romain Koszul, and Axel Cournac
2. Methods to Assess the Reproducibility and Similarity of Hi-C Data
Tao Yang, Xi He, Lin An, and Qunhua Li
3. Methods for the Analysis of Topological Associating Domains (TADs)
Marie Zufferey, Daniele Tavernari, and Giovanni Ciriello
4. Methods for the Differential Analysis of Hi-C D
Chiara Nicoletti
5. Visualising and Annotating Hi-C Data
Koustav Pal and Francesco Ferrari
6. Hi-C Data Formats
Soohyun Lee
7. Analysis of Hi-C Data for Discovery of Structural Variations In Cancer
Fan Song, Jie Xu, Jesse Dixon, and Feng Yue
8. Metagenomes Binning using Proximity-Ligation Data
Martial Marbouty and Romain Koszul
9. Generating High-resolution Hi-C Contact Maps Of Bacteria
Agnes Thierry and Charlotte Cockram
10. Computational Tools for the Multiscale Analysis of HiC Data in Bacterial Chromosomes
Nelle Varoquaux, Virginia S. Lioy, Frederic Boccard, and Ivan Junier
11. Analysis of HiChIP Data
Martina Dori and Mattia Forcato
12. The Physical Behavior of Interphase Chromosomes: Polymer Theory and Coarse-Grain Computer Simulations
Angelo Rosa
13. Polymer Folding Simulations from Hi-C Data
Yinxiu Zhan, Luca Giorgetti, and Guido Tiana
14. Predictive Polymer Models for 3D Chromosome Organization
Michael Chiang, Giada Forte, Nick Gilbert, Davide Marenduzzo, and Chris A. Brackley
15. Polymer Modeling of 3D Epigenome Folding: Application to Drosophila
Daniel Jost
16. A Polymer Physics Model To Dissect Genome Organization In Healthy And Pathological Phenotypes
Mattia Conte, Luca Fiorillo, Simona Bianco, Andrea M. Chiariello, Andrea Esposito, Francesco Musella, Francesco Flora, Alex Abraham, and Mario Nicodemi
17. The 3D Organization of Chromatin Colors in Mammalian Nuclei
Leopold Carron, Jean-Baptiste Morlot, Annick Lesne and Julien Mozziconacci
18. Modeling the 3D Genome using Hi-C and Nuclear Lamin-Genome Contacts
Jonas Paulsen and Philippe Collas
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