Signal processing for metagenomics: Extracting information from the soup

Gail L. Rosen, Bahrad A. Sokhansanj, Robi Polikar, Mary Ann Bruns, Jacob Russell, Elaine Garbarine, Steve Essinger, Non Yok

Research output: Contribution to journalReview article

19 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)493-510
Number of pages18
JournalCurrent Genomics
Volume10
Issue number7
DOIs
StatePublished - Nov 27 2009

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Metagenomics
Genome
Genomics
Ecology
Soil
Health

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)

Cite this

Rosen, G. L., Sokhansanj, B. A., Polikar, R., Bruns, M. A., Russell, J., Garbarine, E., ... Yok, N. (2009). Signal processing for metagenomics: Extracting information from the soup. Current Genomics, 10(7), 493-510. https://doi.org/10.2174/138920209789208255
Rosen, Gail L. ; Sokhansanj, Bahrad A. ; Polikar, Robi ; Bruns, Mary Ann ; Russell, Jacob ; Garbarine, Elaine ; Essinger, Steve ; Yok, Non. / Signal processing for metagenomics : Extracting information from the soup. In: Current Genomics. 2009 ; Vol. 10, No. 7. pp. 493-510.
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Rosen, GL, Sokhansanj, BA, Polikar, R, Bruns, MA, Russell, J, Garbarine, E, Essinger, S & Yok, N 2009, 'Signal processing for metagenomics: Extracting information from the soup', Current Genomics, vol. 10, no. 7, pp. 493-510. https://doi.org/10.2174/138920209789208255

Signal processing for metagenomics : Extracting information from the soup. / Rosen, Gail L.; Sokhansanj, Bahrad A.; Polikar, Robi; Bruns, Mary Ann; Russell, Jacob; Garbarine, Elaine; Essinger, Steve; Yok, Non.

In: Current Genomics, Vol. 10, No. 7, 27.11.2009, p. 493-510.

Research output: Contribution to journalReview article

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Rosen GL, Sokhansanj BA, Polikar R, Bruns MA, Russell J, Garbarine E et al. Signal processing for metagenomics: Extracting information from the soup. Current Genomics. 2009 Nov 27;10(7):493-510. https://doi.org/10.2174/138920209789208255