Hi-C Data Analysis: Methods and Protocols

ISBN-13: 9781071613894 / Angielski / Twarda / 2021 / 356 str.

Silvio Bicciato; Francesco Ferrari

Spis treści

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

Agnès Thierry and Charlotte Cockram

10.         Computational Tools for the Multiscale Analysis of HiC Data in Bacterial Chromosomes

Nelle Varoquaux, Virginia S. Lioy, Frédéric 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

Blurb

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.