Metagenomic biomarker discovery and explanation

Nicola Segata, Jacques Izard, Levi Waldron, Dirk Gevers, Larisa Miropolsky, Wendy S. Garrett, Curtis Huttenhower

Research output: Contribution to journalArticle

2246 Citations (Scopus)

Abstract

This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/ .

Original languageEnglish (US)
Article numberR60
JournalGenome biology
Volume12
Issue number6
DOIs
StatePublished - Jun 24 2011

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Metagenomics
biomarker
biomarkers
Biomarkers
Microbiota
microbial communities
microbial community
methodology
gene
organisms
Genes
method
genes
testing

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

Cite this

Segata, N., Izard, J., Waldron, L., Gevers, D., Miropolsky, L., Garrett, W. S., & Huttenhower, C. (2011). Metagenomic biomarker discovery and explanation. Genome biology, 12(6), [R60]. https://doi.org/10.1186/gb-2011-12-6-r60

Metagenomic biomarker discovery and explanation. / Segata, Nicola; Izard, Jacques; Waldron, Levi; Gevers, Dirk; Miropolsky, Larisa; Garrett, Wendy S.; Huttenhower, Curtis.

In: Genome biology, Vol. 12, No. 6, R60, 24.06.2011.

Research output: Contribution to journalArticle

Segata, N, Izard, J, Waldron, L, Gevers, D, Miropolsky, L, Garrett, WS & Huttenhower, C 2011, 'Metagenomic biomarker discovery and explanation', Genome biology, vol. 12, no. 6, R60. https://doi.org/10.1186/gb-2011-12-6-r60
Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS et al. Metagenomic biomarker discovery and explanation. Genome biology. 2011 Jun 24;12(6). R60. https://doi.org/10.1186/gb-2011-12-6-r60
Segata, Nicola ; Izard, Jacques ; Waldron, Levi ; Gevers, Dirk ; Miropolsky, Larisa ; Garrett, Wendy S. ; Huttenhower, Curtis. / Metagenomic biomarker discovery and explanation. In: Genome biology. 2011 ; Vol. 12, No. 6.
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