Modeling the 3D Conformation of Genomes
portes grátis
Modeling the 3D Conformation of Genomes
Tiana, Guido; Giorgetti, Luca
Taylor & Francis Ltd
03/2021
370
Mole
Inglês
9780367780456
15 a 20 dias
716
Descrição não disponível.
Contents Preface vii Contributors xi 1 Chromosome Folding: Contributions of Chromosome Conformation Capture and Polymer Physics 1 Job Dekker Part 1 FIRST-PRINCIPLES MODELS 19 2 Modeling the Functional Coupling between 3D Chromatin Organization and Epigenome 21 Cedric Vaillant and Daniel Jost 3 The Strings and Binders Switch Model of Chromatin 57 Simona Bianco, Andrea M. Chiariello, Carlo Annunziatella, Andrea Esposito, Luca Fiorillo, and Mario Nicodemi 4 Loop Extrusion: A Universal Mechanism of Chromosome Organization 69 Leonid A. Mirny and Anton Goloborodko 5 Predictive Models for 3D Chromosome Organization: The Transcription Factor and Diffusive Loop Extrusion Models 97 C. A. Brackley, M. C. Pereira, J. Johnson, D. Michieletto, and D. Marenduzzo 6 Introducing Supercoiling into Models of Chromosome Structure 115 Fabrizio Benedetti, Dusan Racko, Julien Dorier, and Andrzej Stasiak 7 Structure and Microrheology of Genome Organization: From Experiments to Physical Modeling 139 Andrea Papale and Angelo Rosa 8 Analysis of Chromatin Dynamics and Search Processes in the Nucleus 177 Assaf Amitai and David Holcman 9 Chromosome Structure and Dynamics in Bacteria: Theory and Experiments 207 Marco Gherardi, Vittore Scolari, Remus Thei Dame, and Marco Cosentino Lagomarsino Part 2 DATA -DRIVEN MODELS 231 10 Restraint-Based Modeling of Genomes and Genomic Domains 233 Marco Di Stefano and Marc A. Marti-Renom 11 Genome Structure Calculation through Comprehensive Data Integration 253 Guido Polles, Nan Hua, Asli Yildirim, and Frank Alber 12 Modeling the Conformational Ensemble of Mammalian Chromosomes from 5C/Hi-C Data 285 Guido Tiana and Luca Giorgetti 13 Learning Genomic Energy Landscapes from Experiments 305 Michele Di Pierro, Ryan R. Cheng, Bin Zhang, Jose N. Onuchic, and Peter G. Wolynes 14 Physical 3D Modeling of Whole Genomes: Exploring Chromosomal Organization Properties and Principles 331 Marco Di Stefano, Jonas Paulsen, Eivind Hovig, and Cristian Micheletti 15 Index 361
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Hi-C Data;SMC Complex;chromosome modeling;CTCF Site;three-dimensional genome structure;Hi-C Study;bioinformatics;Loop Extrusion;Chromatin Fiber;DNA Fiber;Tad Boundary;Chromatin Folding;TF Model;Chromatin Type;Cohesin Ring;DNA Ligation;Promoter Enhancer Interactions;TADs;DNA Fish;Anomalous Exponent;Epigenomic State;Alt Cell;Chromatin Interaction;MC;Chromatin Contact;3C Interaction;Negative Supercoiling;Energy Landscape Theory
Contents Preface vii Contributors xi 1 Chromosome Folding: Contributions of Chromosome Conformation Capture and Polymer Physics 1 Job Dekker Part 1 FIRST-PRINCIPLES MODELS 19 2 Modeling the Functional Coupling between 3D Chromatin Organization and Epigenome 21 Cedric Vaillant and Daniel Jost 3 The Strings and Binders Switch Model of Chromatin 57 Simona Bianco, Andrea M. Chiariello, Carlo Annunziatella, Andrea Esposito, Luca Fiorillo, and Mario Nicodemi 4 Loop Extrusion: A Universal Mechanism of Chromosome Organization 69 Leonid A. Mirny and Anton Goloborodko 5 Predictive Models for 3D Chromosome Organization: The Transcription Factor and Diffusive Loop Extrusion Models 97 C. A. Brackley, M. C. Pereira, J. Johnson, D. Michieletto, and D. Marenduzzo 6 Introducing Supercoiling into Models of Chromosome Structure 115 Fabrizio Benedetti, Dusan Racko, Julien Dorier, and Andrzej Stasiak 7 Structure and Microrheology of Genome Organization: From Experiments to Physical Modeling 139 Andrea Papale and Angelo Rosa 8 Analysis of Chromatin Dynamics and Search Processes in the Nucleus 177 Assaf Amitai and David Holcman 9 Chromosome Structure and Dynamics in Bacteria: Theory and Experiments 207 Marco Gherardi, Vittore Scolari, Remus Thei Dame, and Marco Cosentino Lagomarsino Part 2 DATA -DRIVEN MODELS 231 10 Restraint-Based Modeling of Genomes and Genomic Domains 233 Marco Di Stefano and Marc A. Marti-Renom 11 Genome Structure Calculation through Comprehensive Data Integration 253 Guido Polles, Nan Hua, Asli Yildirim, and Frank Alber 12 Modeling the Conformational Ensemble of Mammalian Chromosomes from 5C/Hi-C Data 285 Guido Tiana and Luca Giorgetti 13 Learning Genomic Energy Landscapes from Experiments 305 Michele Di Pierro, Ryan R. Cheng, Bin Zhang, Jose N. Onuchic, and Peter G. Wolynes 14 Physical 3D Modeling of Whole Genomes: Exploring Chromosomal Organization Properties and Principles 331 Marco Di Stefano, Jonas Paulsen, Eivind Hovig, and Cristian Micheletti 15 Index 361
Este título pertence ao(s) assunto(s) indicados(s). Para ver outros títulos clique no assunto desejado.
Hi-C Data;SMC Complex;chromosome modeling;CTCF Site;three-dimensional genome structure;Hi-C Study;bioinformatics;Loop Extrusion;Chromatin Fiber;DNA Fiber;Tad Boundary;Chromatin Folding;TF Model;Chromatin Type;Cohesin Ring;DNA Ligation;Promoter Enhancer Interactions;TADs;DNA Fish;Anomalous Exponent;Epigenomic State;Alt Cell;Chromatin Interaction;MC;Chromatin Contact;3C Interaction;Negative Supercoiling;Energy Landscape Theory
