A computational framework for integrative analysis of large microbial genomics data

Wei Zhang; Scott Emrich; Dan Liu; Josh Livermore; Erliang Zeng; Stuart Jones

doi:10.1109/BIBM.2015.7359837

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Conference proceeding

A computational framework for integrative analysis of large microbial genomics data

Wei Zhang, Scott Emrich, Dan Liu, Josh Livermore, Erliang Zeng and Stuart Jones

2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp.1109-1116

11/2015

DOI: 10.1109/BIBM.2015.7359837

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Abstract

The availability of huge amount of genome sequence data from natural microbial consortia enables integrated analysis to resolve the genetic and metabolic potential of microbial communities, to establish how functions are partitioned in and among populations, and to reveal how microbial communities evolve and adapt across multiple environments. In this paper, we propose to analyze comparative microbial genomes using a computational framework. The framework is designed to investigate genome context patterns of microbial diversity. With an application to investigate functions of three environments (human gut, soil, and marine), we demonstrated that the developed computational framework was able to identify functional modules and evaluate the functional roles of those modules in microbial communities as response to environmental change. We found different gene networks among microbial communities living in different environments. We showed that modules identified by our framework can be computationally annotated to study their biological functions.

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Title: Subtitle: A computational framework for integrative analysis of large microbial genomics data
Creators: Wei Zhang - Dept. of Comput. Sci. & Eng., Univ. of Notre Dame, Notre Dame, IN, USA
Scott Emrich - Dept. of Comput. Sci. & Eng., Univ. of Notre Dame, Notre Dame, IN, USA
Dan Liu - Dept. of Biol. Sci., Univ. of Notre Dame, Notre Dame, IN, USA
Josh Livermore - Dept. of Biol. Sci., Univ. of Notre Dame, Notre Dame, IN, USA
Erliang Zeng - University of Iowa, Dental Research
Stuart Jones - Dept. of Biol. Sci., Univ. of Notre Dame, Notre Dame, IN, USA
Resource Type: Conference proceeding
Publication Details: 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp.1109-1116
DOI: 10.1109/BIBM.2015.7359837
Publisher: IEEE
Language: English
Date published: 11/2015
Academic Unit: Preventive and Community Dentistry; Roy J. Carver Department of Biomedical Engineering; Iowa Neuroscience Institute; Biostatistics; Dental Research
Record Identifier: 9984071900202771

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