Hi-C Data Analysis: Methods and Protocols (Methods in Molecular Biology)

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 Agns Thierry and Charlotte Cockram 10. Computational Tools for the Multiscale Analysis of HiC Data in Bacterial Chromosomes Nelle Varoquaux, Virginia S. Lioy, Frdric 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