KMS Of Academy of mathematics and systems sciences, CAS
| Infer Metagenomic Abundance and Reveal Homologous Genomes Based on the Structure of Taxonomy Tree | |
Qiu, Yu-Qing1; Tian, Xue2; Zhang, Shihua1
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| 2015-09-01 | |
| Source Publication | IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
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| ISSN | 1545-5963 |
| Volume | 12Issue:5Pages:1112-1122 |
| Abstract | Metagenomic research uses sequencing technologies to investigate the genetic biodiversity of microbiomes presented in various ecosystems or animal tissues. The composition of a microbial community is highly associated with the environment in which the organisms exist. As large amount of sequencing short reads of microorganism genomes obtained, accurately estimating the abundance of microorganisms within a metagenomic sample is becoming an increasing challenge in bioinformatics. In this paper, we describe a hierarchical taxonomy tree-based mixture model (HTTMM) for estimating the abundance of taxon within a microbial community by incorporating the structure of the taxonomy tree. In this model, genome-specific short reads and homologous short reads among genomes can be distinguished and represented by leaf and intermediate nodes in the taxonomy tree, respectively. We adopt an expectation-maximization algorithm to solve this model. Using simulated and real-world data, we demonstrate that the proposed method is superior to both flat mixture model and lowest common ancestry-based methods. Moreover, this model can reveal previously unaddressed homologous genomes. |
| Keyword | Metagenomics abundance estimation taxonomy tree expectation-maximization algorithm |
| DOI | 10.1109/TCBB.2015.2415814 |
| Language | 英语 |
| Funding Project | National Natural Science Foundation of China[61379092] ; National Natural Science Foundation of China[61422309] ; Strategic Priority Research Program of the Chinese Academy of Sciences (CAS)[XDB13040600] ; Foundation for Members of Youth Innovation Promotion Association, CAS ; Outstanding Young Scientist Program of CAS ; Key Laboratory of Random Complex Structures and Data Science, CAS |
| WOS Research Area | Biochemistry & Molecular Biology ; Computer Science ; Mathematics |
| WOS Subject | Biochemical Research Methods ; Computer Science, Interdisciplinary Applications ; Mathematics, Interdisciplinary Applications ; Statistics & Probability |
| WOS ID | WOS:000362909500014 |
| Publisher | IEEE COMPUTER SOC |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.amss.ac.cn/handle/2S8OKBNM/21018 |
| Collection | 应用数学研究所 |
| Corresponding Author | Qiu, Yu-Qing |
| Affiliation | 1.Chinese Acad Sci, Natl Ctr Math & Interdisciplinary Sci, Acad Math & Syst Sci, Beijing 100190, Peoples R China 2.Hangzhou Dianzi Univ, Sch Sci, Hangzhou 310018, Zhejiang, Peoples R China |
| Recommended Citation GB/T 7714 | Qiu, Yu-Qing,Tian, Xue,Zhang, Shihua. Infer Metagenomic Abundance and Reveal Homologous Genomes Based on the Structure of Taxonomy Tree[J]. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS,2015,12(5):1112-1122. |
| APA | Qiu, Yu-Qing,Tian, Xue,&Zhang, Shihua.(2015).Infer Metagenomic Abundance and Reveal Homologous Genomes Based on the Structure of Taxonomy Tree.IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS,12(5),1112-1122. |
| MLA | Qiu, Yu-Qing,et al."Infer Metagenomic Abundance and Reveal Homologous Genomes Based on the Structure of Taxonomy Tree".IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 12.5(2015):1112-1122. |
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