Metagenomic biomarker discovery and explanation

Authors

Nicola Segata, Harvard School of Public Health
Jacques Izard, 2.3Follow
Levi Waldron, Harvard School of Public Health
Dirk Gevers, 4
Larisa Miropolsky, Harvard School of Public Health
Wendy S. Garrett, 5.6.7.
Curtis Huttenhower, Harvard School of Public HealthFollow

Date of this Version

6-24-2011

Citation

2011 Segata et al.

Comments

Segata et al. Genome Biology 2011, 12:R60 http://genomebiology.com/2011/11/6/R60 Page 1 of 18

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/.