title: Metagenomic biomarker discovery and explanation.
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/.
authors.affiliation: Department of Biostatistics, 677 Huntington Avenue, Harvard School of Public Health, Boston, MA 02115, USA.
authors.forename: Nicola
authors.initials: N
authors.lastname: Segata
authors.forename: Jacques
authors.initials: J
authors.lastname: Izard
authors.forename: Levi
authors.initials: L
authors.lastname: Waldron
authors.forename: Dirk
authors.initials: D
authors.lastname: Gevers
authors.forename: Larisa
authors.initials: L
authors.lastname: Miropolsky
authors.forename: Wendy S
authors.initials: WS
authors.lastname: Garrett
authors.forename: Curtis
authors.initials: C
authors.lastname: Huttenhower
mesh_terms: D000328:Adult; D000818:Animals; D001419:Bacteria / Q000145:classification; D015415:Biomarkers; D003093:Colitis, Ulcerative / Q000382:microbiology; D057225:Data Mining; D006801:Humans; D007223:Infant; D054892:Metagenome; D056186:Metagenomics / Q000379:methods*; D051379:Mice; D008807:Mice, Inbred BALB C; D018345:Mice, Knockout; D009092:Mucous Membrane / Q000382:microbiology; D012680:Sensitivity and Specificity; D012984:Software; D014780:Viruses / Q000145:classification
chemical_list: D015415:Biomarkers