Article: Supervised method for periodontitis phenotypes prediction based on microbial composition using 16S rRNA sequences Journal: International Journal of Computational Biology and Drug Design (IJCBDD) 2014 Vol.7 No.2/3 pp.214 - 224 Abstract: Microbes play an important role on human health, however, little is known on microbes in the past decades for the limitation of culture-based techniques. Recently, with the development of next-generation sequencing (NGS) technologies, it is now possible to sequence millions of sequences directly from environments samples, and thus it supplies us a sight to probe the hidden world of microbial communities and detect the associations between microbes and diseases. In the present work, we proposed a supervised learning-based method to mine the relationship between microbes and periodontitis with 16S rRNA sequences. The jackknife accuracy is 94.83% and it indicated the method can effectively predict disease status. These findings not only expand our understanding of the association between microbes and diseases but also provide a potential approach for disease diagnosis and forensics. Inderscience Publishers - linking academia, business and industry through research

Title: Supervised method for periodontitis phenotypes prediction based on microbial composition using 16S rRNA sequences

Authors: Wei Chen; Yong-Mei Cheng; Shao-Wu Zhang; Quan Pan

Addresses: College of Automation, Northwestern Polytechnical University, Xi'an, 710072, China; Department of Biostatistics, Yale University, New Haven, CT 06510, USA ' College of Automation, Northwestern Polytechnical University, Xi'an, 710072, China ' College of Automation, Northwestern Polytechnical University, Xi'an, 710072, China ' College of Automation, Northwestern Polytechnical University, Xi'an, 710072, China

Abstract: Microbes play an important role on human health, however, little is known on microbes in the past decades for the limitation of culture-based techniques. Recently, with the development of next-generation sequencing (NGS) technologies, it is now possible to sequence millions of sequences directly from environments samples, and thus it supplies us a sight to probe the hidden world of microbial communities and detect the associations between microbes and diseases. In the present work, we proposed a supervised learning-based method to mine the relationship between microbes and periodontitis with 16S rRNA sequences. The jackknife accuracy is 94.83% and it indicated the method can effectively predict disease status. These findings not only expand our understanding of the association between microbes and diseases but also provide a potential approach for disease diagnosis and forensics.

Keywords: microbial communities; 16S rRNA genes; OTU; operational taxonomic unit; periodontitis phenotype; supervised learning; human-association diseases; elastic net; microbial composition; 16S rRNA sequences; microbes; next-generation sequencing; NGS; disease diagnosis; forensics; gene sequences.

DOI: 10.1504/IJCBDD.2014.061647

International Journal of Computational Biology and Drug Design, 2014 Vol.7 No.2/3, pp.214 - 224

Published online: 21 Oct 2014 *

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Title: Supervised method for periodontitis phenotypes prediction based on microbial composition using 16S rRNA sequences

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