Dejun Lin, Giancarlo Bonora, Galip Gürkan Yardımcı, William S Noble
{"title":"用于分析和建模基因组结构和组织的计算方法。","authors":"Dejun Lin, Giancarlo Bonora, Galip Gürkan Yardımcı, William S Noble","doi":"10.1002/wsbm.1435","DOIUrl":null,"url":null,"abstract":"<p><p>Recent advances in chromosome conformation capture technologies have led to the discovery of previously unappreciated structural features of chromatin. Computational analysis has been critical in detecting these features and thereby helping to uncover the building blocks of genome architecture. Algorithms are being developed to integrate these architectural features to construct better three-dimensional (3D) models of the genome. These computational methods have revealed the importance of 3D genome organization to essential biological processes. In this article, we review the state of the art in analytic and modeling techniques with a focus on their application to answering various biological questions related to chromatin structure. We summarize the limitations of these computational techniques and suggest future directions, including the importance of incorporating multiple sources of experimental data in building a more comprehensive model of the genome. This article is categorized under: Analytical and Computational Methods > Computational Methods Laboratory Methods and Technologies > Genetic/Genomic Methods Models of Systems Properties and Processes > Mechanistic Models.</p>","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":null,"pages":null},"PeriodicalIF":7.9000,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/wsbm.1435","citationCount":"30","resultStr":"{\"title\":\"Computational methods for analyzing and modeling genome structure and organization.\",\"authors\":\"Dejun Lin, Giancarlo Bonora, Galip Gürkan Yardımcı, William S Noble\",\"doi\":\"10.1002/wsbm.1435\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Recent advances in chromosome conformation capture technologies have led to the discovery of previously unappreciated structural features of chromatin. Computational analysis has been critical in detecting these features and thereby helping to uncover the building blocks of genome architecture. Algorithms are being developed to integrate these architectural features to construct better three-dimensional (3D) models of the genome. These computational methods have revealed the importance of 3D genome organization to essential biological processes. In this article, we review the state of the art in analytic and modeling techniques with a focus on their application to answering various biological questions related to chromatin structure. We summarize the limitations of these computational techniques and suggest future directions, including the importance of incorporating multiple sources of experimental data in building a more comprehensive model of the genome. This article is categorized under: Analytical and Computational Methods > Computational Methods Laboratory Methods and Technologies > Genetic/Genomic Methods Models of Systems Properties and Processes > Mechanistic Models.</p>\",\"PeriodicalId\":49254,\"journal\":{\"name\":\"Wiley Interdisciplinary Reviews-Systems Biology and Medicine\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":7.9000,\"publicationDate\":\"2019-01-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://sci-hub-pdf.com/10.1002/wsbm.1435\",\"citationCount\":\"30\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Wiley Interdisciplinary Reviews-Systems Biology and Medicine\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1002/wsbm.1435\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2018/7/18 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q1\",\"JCRName\":\"Medicine\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1002/wsbm.1435","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2018/7/18 0:00:00","PubModel":"Epub","JCR":"Q1","JCRName":"Medicine","Score":null,"Total":0}
Computational methods for analyzing and modeling genome structure and organization.
Recent advances in chromosome conformation capture technologies have led to the discovery of previously unappreciated structural features of chromatin. Computational analysis has been critical in detecting these features and thereby helping to uncover the building blocks of genome architecture. Algorithms are being developed to integrate these architectural features to construct better three-dimensional (3D) models of the genome. These computational methods have revealed the importance of 3D genome organization to essential biological processes. In this article, we review the state of the art in analytic and modeling techniques with a focus on their application to answering various biological questions related to chromatin structure. We summarize the limitations of these computational techniques and suggest future directions, including the importance of incorporating multiple sources of experimental data in building a more comprehensive model of the genome. This article is categorized under: Analytical and Computational Methods > Computational Methods Laboratory Methods and Technologies > Genetic/Genomic Methods Models of Systems Properties and Processes > Mechanistic Models.
期刊介绍:
Journal Name:Wiley Interdisciplinary Reviews-Systems Biology and Medicine
Focus:
Strong interdisciplinary focus
Serves as an encyclopedic reference for systems biology research
Conceptual Framework:
Systems biology asserts the study of organisms as hierarchical systems or networks
Individual biological components interact in complex ways within these systems
Article Coverage:
Discusses biology, methods, and models
Spans systems from a few molecules to whole species
Topical Coverage:
Developmental Biology
Physiology
Biological Mechanisms
Models of Systems, Properties, and Processes
Laboratory Methods and Technologies
Translational, Genomic, and Systems Medicine