Ahmet Arıhan Erözden , Nalan Tavsanli , Mahmut Çalışkan
{"title":"用生物信息学方法研究沙蜥系统发育的进展。","authors":"Ahmet Arıhan Erözden , Nalan Tavsanli , Mahmut Çalışkan","doi":"10.1016/j.compbiolchem.2024.108226","DOIUrl":null,"url":null,"abstract":"<div><div>The quest to discover the evolutionary relationships of organisms is an evolving, long-time topic of research. Such research gave rise to many different taxonomic databases and various definitions of systematic groups. One such group is the phylum Tardigrada. Tardigrades are an important field of study because of their biotechnological potential as well as their complex biological processes, which have the potential to answer questions about animal evolution. The evolutionary relationships within the phyla are subject to rigorous research, and new data is added to the literature constantly. For these studies, a widespread technique is the use of bioinformatic approaches in order to put forward concrete phylogenetic evidence. Bioinformatics is a field of computational biology that interprets large amounts of data in order to compute and demonstrate results. It is widely used not only for phylogeny but also for various different types of analyses and has been growing as a field since its foundation. This review discusses the different aspects, advantages, and methods of the use of bioinformatics in tardigrade phylogeny. It aims to put forward a defining picture of how the bioinformatic methods prove useful for providing phylogenetic results and elaborate on future perspectives.</div></div>","PeriodicalId":10616,"journal":{"name":"Computational Biology and Chemistry","volume":"113 ","pages":"Article 108226"},"PeriodicalIF":2.6000,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Advances in bioinformatic approaches to tardigrade phylogeny\",\"authors\":\"Ahmet Arıhan Erözden , Nalan Tavsanli , Mahmut Çalışkan\",\"doi\":\"10.1016/j.compbiolchem.2024.108226\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><div>The quest to discover the evolutionary relationships of organisms is an evolving, long-time topic of research. Such research gave rise to many different taxonomic databases and various definitions of systematic groups. One such group is the phylum Tardigrada. Tardigrades are an important field of study because of their biotechnological potential as well as their complex biological processes, which have the potential to answer questions about animal evolution. The evolutionary relationships within the phyla are subject to rigorous research, and new data is added to the literature constantly. For these studies, a widespread technique is the use of bioinformatic approaches in order to put forward concrete phylogenetic evidence. Bioinformatics is a field of computational biology that interprets large amounts of data in order to compute and demonstrate results. It is widely used not only for phylogeny but also for various different types of analyses and has been growing as a field since its foundation. This review discusses the different aspects, advantages, and methods of the use of bioinformatics in tardigrade phylogeny. It aims to put forward a defining picture of how the bioinformatic methods prove useful for providing phylogenetic results and elaborate on future perspectives.</div></div>\",\"PeriodicalId\":10616,\"journal\":{\"name\":\"Computational Biology and Chemistry\",\"volume\":\"113 \",\"pages\":\"Article 108226\"},\"PeriodicalIF\":2.6000,\"publicationDate\":\"2024-09-26\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Computational Biology and Chemistry\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S1476927124002147\",\"RegionNum\":4,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Computational Biology and Chemistry","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1476927124002147","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOLOGY","Score":null,"Total":0}
Advances in bioinformatic approaches to tardigrade phylogeny
The quest to discover the evolutionary relationships of organisms is an evolving, long-time topic of research. Such research gave rise to many different taxonomic databases and various definitions of systematic groups. One such group is the phylum Tardigrada. Tardigrades are an important field of study because of their biotechnological potential as well as their complex biological processes, which have the potential to answer questions about animal evolution. The evolutionary relationships within the phyla are subject to rigorous research, and new data is added to the literature constantly. For these studies, a widespread technique is the use of bioinformatic approaches in order to put forward concrete phylogenetic evidence. Bioinformatics is a field of computational biology that interprets large amounts of data in order to compute and demonstrate results. It is widely used not only for phylogeny but also for various different types of analyses and has been growing as a field since its foundation. This review discusses the different aspects, advantages, and methods of the use of bioinformatics in tardigrade phylogeny. It aims to put forward a defining picture of how the bioinformatic methods prove useful for providing phylogenetic results and elaborate on future perspectives.
期刊介绍:
Computational Biology and Chemistry publishes original research papers and review articles in all areas of computational life sciences. High quality research contributions with a major computational component in the areas of nucleic acid and protein sequence research, molecular evolution, molecular genetics (functional genomics and proteomics), theory and practice of either biology-specific or chemical-biology-specific modeling, and structural biology of nucleic acids and proteins are particularly welcome. Exceptionally high quality research work in bioinformatics, systems biology, ecology, computational pharmacology, metabolism, biomedical engineering, epidemiology, and statistical genetics will also be considered.
Given their inherent uncertainty, protein modeling and molecular docking studies should be thoroughly validated. In the absence of experimental results for validation, the use of molecular dynamics simulations along with detailed free energy calculations, for example, should be used as complementary techniques to support the major conclusions. Submissions of premature modeling exercises without additional biological insights will not be considered.
Review articles will generally be commissioned by the editors and should not be submitted to the journal without explicit invitation. However prospective authors are welcome to send a brief (one to three pages) synopsis, which will be evaluated by the editors.