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Modeling the 3D Conformation of Genomes最新文献

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Predictive Models for 3D Chromosome Organization: The Transcription Factor and Diffusive Loop Extrusion Models 三维染色体组织的预测模型:转录因子和扩散环挤压模型
Modeling the 3D Conformation of Genomes Pub Date : 2019-01-15 DOI: 10.1201/9781315144009-5
C. Brackley, M. Pereira, J. Johnson, D. Michieletto, D. Marenduzzo
{"title":"Predictive Models for 3D Chromosome Organization: The Transcription Factor and Diffusive Loop Extrusion Models","authors":"C. Brackley, M. Pereira, J. Johnson, D. Michieletto, D. Marenduzzo","doi":"10.1201/9781315144009-5","DOIUrl":"https://doi.org/10.1201/9781315144009-5","url":null,"abstract":"","PeriodicalId":276713,"journal":{"name":"Modeling the 3D Conformation of Genomes","volume":"13 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116879054","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
The Strings and Binders Switch Model of Chromatin 染色质的“弦”和“键”切换模型
Modeling the 3D Conformation of Genomes Pub Date : 2019-01-15 DOI: 10.1201/9781315144009-3
Simona Bianco, A. Chiariello, Carlo Annunziatella, Andrea Esposito, L. Fiorillo, M. Nicodemi
{"title":"The Strings and Binders Switch Model of Chromatin","authors":"Simona Bianco, A. Chiariello, Carlo Annunziatella, Andrea Esposito, L. Fiorillo, M. Nicodemi","doi":"10.1201/9781315144009-3","DOIUrl":"https://doi.org/10.1201/9781315144009-3","url":null,"abstract":"","PeriodicalId":276713,"journal":{"name":"Modeling the 3D Conformation of Genomes","volume":"17 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114463360","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Modeling the Conformational Ensemble of Mammalian Chromosomes from 5C/Hi-C Data 基于5C/Hi-C数据的哺乳动物染色体构象集合建模
Modeling the 3D Conformation of Genomes Pub Date : 2019-01-15 DOI: 10.1201/9781315144009-12
G. Tiana, L. Giorgetti
{"title":"Modeling the Conformational Ensemble of Mammalian Chromosomes from 5C/Hi-C Data","authors":"G. Tiana, L. Giorgetti","doi":"10.1201/9781315144009-12","DOIUrl":"https://doi.org/10.1201/9781315144009-12","url":null,"abstract":"","PeriodicalId":276713,"journal":{"name":"Modeling the 3D Conformation of Genomes","volume":"14 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128873366","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Chromosome Structure and Dynamics in Bacteria: Theory and Experiments 细菌的染色体结构与动力学:理论与实验
Modeling the 3D Conformation of Genomes Pub Date : 2019-01-15 DOI: 10.1201/9781315144009-9
M. Gherardi, V. Scolari, R. Dame, M. Lagomarsino
{"title":"Chromosome Structure and Dynamics in Bacteria: Theory and Experiments","authors":"M. Gherardi, V. Scolari, R. Dame, M. Lagomarsino","doi":"10.1201/9781315144009-9","DOIUrl":"https://doi.org/10.1201/9781315144009-9","url":null,"abstract":"","PeriodicalId":276713,"journal":{"name":"Modeling the 3D Conformation of Genomes","volume":"14 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134283838","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Modeling the Functional Coupling between 3D Chromatin Organization and Epigenome 三维染色质组织与表观基因组之间的功能耦合建模
Modeling the 3D Conformation of Genomes Pub Date : 2019-01-15 DOI: 10.1201/9781315144009-2
C. Vaillant, D. Jost
{"title":"Modeling the Functional Coupling between 3D Chromatin Organization and Epigenome","authors":"C. Vaillant, D. Jost","doi":"10.1201/9781315144009-2","DOIUrl":"https://doi.org/10.1201/9781315144009-2","url":null,"abstract":"In this chapter, the authors review their efforts to understand the functional coupling between the three-dimensional (3D) dynamical organization of chromatin and the 1D segmentation of genome into active and inactive domains using polymer and statistical physics modeling. They discuss how polymer modeling allows them to better understand the coupling between epigenome and 3D chromosome organization. The observed correlations between epigenome and contactome suggest the existence of epigenomic-specific mechanisms playing major roles in chromatin folding. The authors develop several methods to investigate the behavior of the block copolymer model of chromatin. In the context of epigenomics, the nano-reactor hypothesis naturally introduces a functional coupling between 3D organization and 1D epigenomic state. In order to progress toward a quantitative description of this 1D–3D coupling, a correct parameter inference would require experiments that can record the large-scale dynamics of both the 1D and 3D organization, during the establishment and the maintenance stages, in both wild-type and mutant backgrounds.","PeriodicalId":276713,"journal":{"name":"Modeling the 3D Conformation of Genomes","volume":"12 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127322265","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
Physical 3D Modeling of Whole Genomes: Exploring Chromosomal Organization Properties and Principles 全基因组的物理三维建模:探索染色体组织特性和原理
Modeling the 3D Conformation of Genomes Pub Date : 2019-01-15 DOI: 10.1201/9781315144009-14
M. D. Stefano, Jonas Paulsen, E. Hovig, C. Micheletti
{"title":"Physical 3D Modeling of Whole Genomes: Exploring Chromosomal Organization Properties and Principles","authors":"M. D. Stefano, Jonas Paulsen, E. Hovig, C. Micheletti","doi":"10.1201/9781315144009-14","DOIUrl":"https://doi.org/10.1201/9781315144009-14","url":null,"abstract":"","PeriodicalId":276713,"journal":{"name":"Modeling the 3D Conformation of Genomes","volume":"297 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114442124","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Restraint-Based Modeling of Genomes and Genomic Domains 基于约束的基因组和基因组域建模
Modeling the 3D Conformation of Genomes Pub Date : 2019-01-15 DOI: 10.1201/9781315144009-10
M. D. Stefano, M. Martí-Renom
{"title":"Restraint-Based Modeling of Genomes and Genomic Domains","authors":"M. D. Stefano, M. Martí-Renom","doi":"10.1201/9781315144009-10","DOIUrl":"https://doi.org/10.1201/9781315144009-10","url":null,"abstract":"","PeriodicalId":276713,"journal":{"name":"Modeling the 3D Conformation of Genomes","volume":"7 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124161565","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Analysis of Chromatin Dynamics and Search Processes in the Nucleus 核中染色质动力学和搜索过程的分析
Modeling the 3D Conformation of Genomes Pub Date : 2019-01-15 DOI: 10.1201/9781315144009-8
A. Amitai, D. Holcman
{"title":"Analysis of Chromatin Dynamics and Search Processes in the Nucleus","authors":"A. Amitai, D. Holcman","doi":"10.1201/9781315144009-8","DOIUrl":"https://doi.org/10.1201/9781315144009-8","url":null,"abstract":"","PeriodicalId":276713,"journal":{"name":"Modeling the 3D Conformation of Genomes","volume":"72 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129946347","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Chromosome Folding: Contributions of Chromosome Conformation Capture and Polymer Physics 染色体折叠:染色体构象捕获和高分子物理的贡献
Modeling the 3D Conformation of Genomes Pub Date : 2019-01-15 DOI: 10.1201/9781315144009-1
J. Dekker
{"title":"Chromosome Folding: Contributions of Chromosome Conformation Capture and Polymer Physics","authors":"J. Dekker","doi":"10.1201/9781315144009-1","DOIUrl":"https://doi.org/10.1201/9781315144009-1","url":null,"abstract":"","PeriodicalId":276713,"journal":{"name":"Modeling the 3D Conformation of Genomes","volume":"26 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126345667","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Genome Structure Calculation through Comprehensive Data Integration 基于综合数据集成的基因组结构计算
Modeling the 3D Conformation of Genomes Pub Date : 2019-01-15 DOI: 10.1201/9781315144009-11
G. Polles, N. Hua, A. Yıldırım, F. Alber
{"title":"Genome Structure Calculation through Comprehensive Data Integration","authors":"G. Polles, N. Hua, A. Yıldırım, F. Alber","doi":"10.1201/9781315144009-11","DOIUrl":"https://doi.org/10.1201/9781315144009-11","url":null,"abstract":"","PeriodicalId":276713,"journal":{"name":"Modeling the 3D Conformation of Genomes","volume":"34 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129841467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
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