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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
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
Normalization of Chromosome Contact Maps: Matrix Balancing and Visualization.- Methods to Assess the Reproducibility and Similarity of Hi-C Data.- Methods for the Analysis of Topological Associating Domains (TADs).- Methods for the Differential Analysis of Hi-C D.- Visualising and Annotating Hi-C Data.- Hi-C Data Formats.- Analysis of Hi-C Data for Discovery of Structural Variations In Cancer.- Metagenomes Binning using Proximity-Ligation Data.- Generating High-resolution Hi-C Contact Maps Of Bacteria.- Computational Tools for the Multiscale Analysis of HiC Data in Bacterial Chromosomes.- Analysis of HiChIP Data.- The Physical Behavior of Interphase Chromosomes: Polymer Theory and Coarse-Grain Computer Simulations.- Polymer Folding Simulations from Hi-C Data.- Predictive Polymer Models for 3D Chromosome Organization.- Polymer Modeling of 3D Epigenome Folding: Application to Drosophila.- A Polymer Physics Model To Dissect Genome Organization In Healthy And Pathological Phenotypes.- The 3D Organization of Chromatin Colors in Mammalian Nuclei.- Modeling the 3D Genome using Hi-C and Nuclear Lamin-Genome Contacts.
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