Journal article
Signal Processing for Metagenomics: Extracting Information from the Soup
Current genomics, v 10(7), pp 493-510
Nov 2009
PMID: 20436876
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Traditionally, studies in microbial genomics have focused on single-genomes from cultured species, thereby limiting their focus to the small percentage of species that can be cultured outside their natural environment. Fortunately, recent advances in high-throughput sequencing and computational analyses have ushered in the new field of metagenomics, which aims to decode the genomes of microbes from natural communities without the need for cultivation. Although metagenomic studies have shed a great deal of insight into bacterial diversity and coding capacity, several computational challenges remain due to the massive size and complexity of metagenomic sequence data. Current tools and techniques are reviewed in this paper which address challenges in 1) genomic fragment annotation, 2) phylogenetic reconstruction, 3) functional classification of samples, and 4) interpreting complementary metaproteomics and metametabolomics data. Also surveyed are important applications of metagenomic studies, including microbial forensics and the roles of microbial communities in shaping human health and soil ecology.
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Details
- Title
- Signal Processing for Metagenomics: Extracting Information from the Soup
- Creators
- Gail L Rosen - Electrical and Computer Engineering Department, Drexel University, Philadelphia, PA, USABahrad A Sokhansanj - School of Biomedical Engineering, Science, and Health Systems, Drexel University, Philadelphia, PA, USARobi Polikar - Electrical and Computer Engineering Department, Rowan University, Glassboro, NJ, USAMary Ann Bruns - Soil Science/Microbial Ecology, Pennsylvania State University, University Park, PA, USAJacob Russell - Biology Department, Drexel University, Philadelphia, PA, USAElaine Garbarine - Electrical and Computer Engineering Department, Drexel University, Philadelphia, PA, USASteve Essinger - Electrical and Computer Engineering Department, Drexel University, Philadelphia, PA, USANon Yok - Electrical and Computer Engineering Department, Drexel University, Philadelphia, PA, USA
- Publication Details
- Current genomics, v 10(7), pp 493-510
- Publisher
- Bentham Science Publishers Ltd
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Biology; Electrical and Computer Engineering
- Web of Science ID
- WOS:000271381200004
- Scopus ID
- 2-s2.0-70450164082
- Other Identifier
- 991014878385704721
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InCites Highlights
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- Collaboration types
- Domestic collaboration
- Web of Science research areas
- Biochemistry & Molecular Biology
- Genetics & Heredity