This book provides a timely summary of physical modeling approaches applied to biological datasets that describe conformational properties of chromosomes in the cell nucleus. Chapters explain how to convert raw experimental data into 3D conformations, and how to use models to better understand biophysical mechanisms that control chromosome conformation. The coverage ranges from introductory chapters to modeling aspects related to polymer physics, and data-driven models for genomic domains, the entire human genome, epigenome folding, chromosome structure and dynamics, and predicting 3D genome structure.
| Preface |
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vii | |
| Editor |
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xi | |
| Contributors |
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xiii | |
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1 Chromosome Folding: Contributions of Chromosome Conformation Capture and Polymer Physics |
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1 | (18) |
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PART 1 FIRST-PRINCIPLES MODELS |
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19 | (212) |
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2 Modeling the Functional Coupling between 3D Chromatin Organization and Epigenome |
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21 | (36) |
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3 The Strings and Binders Switch Model of Chromatin |
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57 | (12) |
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4 Loop Extrusion: A Universal Mechanism of Chromosome Organization |
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69 | (28) |
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5 Predictive Models for 3D Chromosome Organization: The Transcription Factor and Diffusive Loop Extrusion Models |
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97 | (18) |
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6 Introducing Supercoiling into Models of Chromosome Structure |
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115 | (24) |
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1 Structure and Microrheology of Genome Organization: From Experiments to Physical Modeling |
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139 | (38) |
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8 Analysis of Chromatin Dynamics and Search Processes in the Nucleus |
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177 | (30) |
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9 Chromosome Structure and Dynamics in Bacteria: Theory and Experiments |
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207 | (24) |
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Marco Cosentino Lagomarsino |
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PART 2 DATA-DRIVEN MODELS |
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231 | (130) |
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10 Restraint-Based Modeling of Genomes and Genomic Domains |
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233 | (20) |
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11 Genome Structure Calculation through Comprehensive Data Integration |
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253 | (32) |
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12 Modeling the Conformational Ensemble of Mammalian Chromosomes from 5C/Hi-C Data |
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285 | (20) |
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13 Learning Genomic Energy Landscapes from Experiments |
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305 | (26) |
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14 Physical 3D Modeling of Whole Genomes: Exploring Chromosomal Organization Properties and Principles |
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331 | (30) |
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| Index |
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361 | |
Guido Tiana, PhD, is Associate Professor of Theoretical Biophysics at the University of Milano. He obtained the PhD at the Niels Bohr Institute (Copenhagen) in 2000 and since then has worked on the physics of complex systems of biological interest, such as proteins, DNA, RNA, chromosomes and genetic networks. The methods come from the realm of statistical mechanics, making heavy use of computational tools and some experimental work.
Luca Giorgetti, PhD, is a group leader at the Friedrich Miescher Institute for Biomedical Research in Basel. He obtained his PhD at the European Institute of Oncology (IEO) and University of Milan followed by a postdoctoral training at the Curie Institute in Paris. He is an expert in combining physical modeling and experimental research in chromosome conformation and transcriptional regulation.
Lisainfo e-raamatute kohta