NDLI: Identifying enterotype in human microbiome by decomposing probabilistic topics into components

Content Provider	IEEE Xplore Digital Library
Author	Xingpeng Jiang Dushoff, J. Xin Chen Xiaohua Hu
Copyright Year	2012
Description	Author affiliation: College of Information Science and Technology, Drexel University, Philadelphia, PA, United States (Xingpeng Jiang; Xin Chen; Xiaohua Hu) \|\| Department of Biology, McMaster University, Hamilton, Ontario, CA (Dushoff, J.)
Abstract	Discovering the global structures of microbial community using large-scale metagenomes is a significant challenge in the era of post-genomics. Data-driven methods such as dimension reduction have shown to be useful when they applied on a metagenomics profile matrix which summarize the abundance of functional or taxonomic categorizations in metagenomic samples. Analogously, model-driven method such as probability topic model (PTM) has been used to build a generative model to simulate the generating of a microbial community based on metagenomic profiles. Data-driven methods are direct and simple, they provide intuitive visualization and understanding of metagenomic profiles. Model-driven methods are often complicated but give a generative mechanism of microbial community which is helpful in understanding the generating process of complex microbial ecology. However, results from model-driven methods are usually hard to visualize and there is less an intuitive understanding of them. We developed a new computational framework to incorporate the strength of data-driven methods into model-based methods and applied the framework to discover and interpret enterotype in human microbiome.
Starting Page	1
Ending Page	4
File Size	2773669
Page Count	4
File Format	PDF
ISBN	9781467325592
e-ISBN	9781467325608
e-ISBN	9781467325585
DOI	10.1109/BIBM.2012.6392720
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2012-10-04
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Dimension reduction metagenomic profile Correlation Biological system modeling Computational modeling Communities Humans probability topic model non-negative matrix factorization Diseases
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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