{"title":"基因组尺度代谢模型在人类疾病研究中的应用:系统综述","authors":"","doi":"10.1016/j.cmpb.2024.108397","DOIUrl":null,"url":null,"abstract":"<div><h3>Background and Objectives:</h3><p>Genome-scale metabolic networks (GEMs) represent a valuable modeling and computational tool in the broad field of systems biology. Their ability to integrate constraints and high-throughput biological data enables the study of intricate metabolic aspects and processes of different cell types and conditions. The past decade has witnessed an increasing number and variety of applications of GEMs for the study of human diseases, along with a huge effort aimed at the reconstruction, integration and analysis of a high number of organisms. This paper presents a systematic review of the scientific literature, to pursue several important questions about the application of constraint-based modeling in the investigation of human diseases. Hopefully, this paper will provide a useful reference for researchers interested in the application of modeling and computational tools for the investigation of metabolic-related human diseases.</p></div><div><h3>Methods:</h3><p>This systematic review was conducted according to the <em>Preferred Reporting Items for Systematic Reviews and Meta-Analyses</em> (PRISMA) guidelines. Elsevier Scopus®, National Library of Medicine PubMed® and Clarivate Web of Science™ databases were enquired, resulting in 566 scientific articles. After applying exclusion and eligibility criteria, a total of 169 papers were selected and individually examined.</p></div><div><h3>Results:</h3><p>The reviewed papers offer a thorough and up-to-date picture of the latest modeling and computational approaches, based on genome-scale metabolic models, that can be leveraged for the investigation of a large variety of human diseases. The numerous studies have been categorized according to the clinical research area involved in the examined disease. Furthermore, the paper discusses the most typical approaches employed to derive clinically-relevant information using the computational models.</p></div><div><h3>Conclusions:</h3><p>The number of scientific papers, utilizing GEM-based approaches for the investigation of human diseases, suggests an increasing interest in these types of approaches; hopefully, the present review will represent a useful reference for scientists interested in applying computational modeling approaches to investigate the aetiopathology of human diseases; we also hope that this work will foster the development of novel applications and methods for the discovery of clinically-relevant insights on metabolic-related diseases.</p></div>","PeriodicalId":10624,"journal":{"name":"Computer methods and programs in biomedicine","volume":null,"pages":null},"PeriodicalIF":4.9000,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0169260724003900/pdfft?md5=84ba91d2da746a463bbd24ee7f1ef111&pid=1-s2.0-S0169260724003900-main.pdf","citationCount":"0","resultStr":"{\"title\":\"Applications of genome-scale metabolic models to the study of human diseases: A systematic review\",\"authors\":\"\",\"doi\":\"10.1016/j.cmpb.2024.108397\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><h3>Background and Objectives:</h3><p>Genome-scale metabolic networks (GEMs) represent a valuable modeling and computational tool in the broad field of systems biology. Their ability to integrate constraints and high-throughput biological data enables the study of intricate metabolic aspects and processes of different cell types and conditions. The past decade has witnessed an increasing number and variety of applications of GEMs for the study of human diseases, along with a huge effort aimed at the reconstruction, integration and analysis of a high number of organisms. This paper presents a systematic review of the scientific literature, to pursue several important questions about the application of constraint-based modeling in the investigation of human diseases. Hopefully, this paper will provide a useful reference for researchers interested in the application of modeling and computational tools for the investigation of metabolic-related human diseases.</p></div><div><h3>Methods:</h3><p>This systematic review was conducted according to the <em>Preferred Reporting Items for Systematic Reviews and Meta-Analyses</em> (PRISMA) guidelines. Elsevier Scopus®, National Library of Medicine PubMed® and Clarivate Web of Science™ databases were enquired, resulting in 566 scientific articles. After applying exclusion and eligibility criteria, a total of 169 papers were selected and individually examined.</p></div><div><h3>Results:</h3><p>The reviewed papers offer a thorough and up-to-date picture of the latest modeling and computational approaches, based on genome-scale metabolic models, that can be leveraged for the investigation of a large variety of human diseases. The numerous studies have been categorized according to the clinical research area involved in the examined disease. Furthermore, the paper discusses the most typical approaches employed to derive clinically-relevant information using the computational models.</p></div><div><h3>Conclusions:</h3><p>The number of scientific papers, utilizing GEM-based approaches for the investigation of human diseases, suggests an increasing interest in these types of approaches; hopefully, the present review will represent a useful reference for scientists interested in applying computational modeling approaches to investigate the aetiopathology of human diseases; we also hope that this work will foster the development of novel applications and methods for the discovery of clinically-relevant insights on metabolic-related diseases.</p></div>\",\"PeriodicalId\":10624,\"journal\":{\"name\":\"Computer methods and programs in biomedicine\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":4.9000,\"publicationDate\":\"2024-08-29\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.sciencedirect.com/science/article/pii/S0169260724003900/pdfft?md5=84ba91d2da746a463bbd24ee7f1ef111&pid=1-s2.0-S0169260724003900-main.pdf\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Computer methods and programs in biomedicine\",\"FirstCategoryId\":\"5\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S0169260724003900\",\"RegionNum\":2,\"RegionCategory\":\"医学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Computer methods and programs in biomedicine","FirstCategoryId":"5","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0169260724003900","RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS","Score":null,"Total":0}
引用次数: 0
摘要
背景与目的:基因组尺度代谢网络(GEM)是系统生物学广泛领域中一种宝贵的建模和计算工具。它能够整合约束条件和高通量生物数据,有助于研究不同细胞类型和条件下错综复杂的代谢问题和过程。在过去的十年中,GEMs 在人类疾病研究中的应用越来越多,种类也越来越丰富,同时在重建、整合和分析大量生物体方面也做出了巨大努力。本文对科学文献进行了系统回顾,探讨了基于约束的建模在人类疾病研究中的应用的几个重要问题。希望本文能为那些对应用建模和计算工具研究代谢相关人类疾病感兴趣的研究人员提供有用的参考。方法:本系统综述是根据系统综述和元分析首选报告项目(PRISMA)指南进行的。查询了 Elsevier Scopus®、美国国家医学图书馆 PubMed® 和 Clarivate Web of Science™ 数据库,共获得 566 篇科学文章。结果:综述论文全面介绍了基于基因组尺度代谢模型的最新建模和计算方法,可用于研究多种人类疾病。众多研究根据所研究疾病涉及的临床研究领域进行了分类。结论:利用基于 GEM 的方法研究人类疾病的科学论文数量表明,人们对这类方法的兴趣与日俱增;希望本综述能为有意应用计算建模方法研究人类疾病病因病理学的科学家提供有用的参考;我们还希望这项工作能促进新型应用和方法的开发,以发现代谢相关疾病的临床相关见解。
Applications of genome-scale metabolic models to the study of human diseases: A systematic review
Background and Objectives:
Genome-scale metabolic networks (GEMs) represent a valuable modeling and computational tool in the broad field of systems biology. Their ability to integrate constraints and high-throughput biological data enables the study of intricate metabolic aspects and processes of different cell types and conditions. The past decade has witnessed an increasing number and variety of applications of GEMs for the study of human diseases, along with a huge effort aimed at the reconstruction, integration and analysis of a high number of organisms. This paper presents a systematic review of the scientific literature, to pursue several important questions about the application of constraint-based modeling in the investigation of human diseases. Hopefully, this paper will provide a useful reference for researchers interested in the application of modeling and computational tools for the investigation of metabolic-related human diseases.
Methods:
This systematic review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Elsevier Scopus®, National Library of Medicine PubMed® and Clarivate Web of Science™ databases were enquired, resulting in 566 scientific articles. After applying exclusion and eligibility criteria, a total of 169 papers were selected and individually examined.
Results:
The reviewed papers offer a thorough and up-to-date picture of the latest modeling and computational approaches, based on genome-scale metabolic models, that can be leveraged for the investigation of a large variety of human diseases. The numerous studies have been categorized according to the clinical research area involved in the examined disease. Furthermore, the paper discusses the most typical approaches employed to derive clinically-relevant information using the computational models.
Conclusions:
The number of scientific papers, utilizing GEM-based approaches for the investigation of human diseases, suggests an increasing interest in these types of approaches; hopefully, the present review will represent a useful reference for scientists interested in applying computational modeling approaches to investigate the aetiopathology of human diseases; we also hope that this work will foster the development of novel applications and methods for the discovery of clinically-relevant insights on metabolic-related diseases.
期刊介绍:
To encourage the development of formal computing methods, and their application in biomedical research and medical practice, by illustration of fundamental principles in biomedical informatics research; to stimulate basic research into application software design; to report the state of research of biomedical information processing projects; to report new computer methodologies applied in biomedical areas; the eventual distribution of demonstrable software to avoid duplication of effort; to provide a forum for discussion and improvement of existing software; to optimize contact between national organizations and regional user groups by promoting an international exchange of information on formal methods, standards and software in biomedicine.
Computer Methods and Programs in Biomedicine covers computing methodology and software systems derived from computing science for implementation in all aspects of biomedical research and medical practice. It is designed to serve: biochemists; biologists; geneticists; immunologists; neuroscientists; pharmacologists; toxicologists; clinicians; epidemiologists; psychiatrists; psychologists; cardiologists; chemists; (radio)physicists; computer scientists; programmers and systems analysts; biomedical, clinical, electrical and other engineers; teachers of medical informatics and users of educational software.