Balances: a New Perspective for Microbiome Analysis

A phylogenetic transform enhances analysis of compositional microbiota data

(2017) Justin D Silverman et al.   eLife

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets

(2017) Alex D. Washburne et al.   PeerJ

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

Balance Trees Reveal Microbial Niche Differentiation

(2017) James T. Morton et al.   mSystems

It's all relative: analyzing microbiome data as compositions

(2016) Gregory B. Gloor et al.   ANNALS OF EPIDEMIOLOGY

Gut Microbiota Linked to Sexual Preference and HIV Infection

(2016) Marc Noguera-Julian et al.   EBioMedicine

Testing in Microbiome-Profiling Studies with MiRKAT, the Microbiome Regression-Based Kernel Association Test

(2015) Ni Zhao et al.   AMERICAN JOURNAL OF HUMAN GENETICS

zCompositions — R package for multivariate imputation of left-censored data under a compositional approach

(2015) Javier Palarea-Albaladejo et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

Dysbiotic gut microbiome: A key element of Crohn's disease

(2015) Styrk Furnes Øyri et al.   COMPARATIVE IMMUNOLOGY MICROBIOLOGY AND INFECTIOUS DISEASES

Probiotics Reduce Inflammation in Antiretroviral Treated, HIV-Infected Individuals: Results of the “Probio-HIV” Clinical Trial

(2015) Gabriella d’Ettorre et al.   PLoS One

Processing faecal samples: a step forward for standards in microbial community analysis

(2014) Alba Santiago et al.   BMC MICROBIOLOGY

The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

(2014) Dirk Gevers et al.   Cell Host & Microbe

Bayesian-multiplicative treatment of count zeros in compositional data sets

(2014) Josep-Antoni Martín-Fernández et al.   STATISTICAL MODELLING

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis

(2014) Andrew D Fernandes et al.   Microbiome

Probiotic/prebiotic supplementation of antiretrovirals improves gastrointestinal immunity in SIV-infected macaques

(2013) Nichole R. Klatt et al.   JOURNAL OF CLINICAL INVESTIGATION

ANOVA-Like Differential Expression (ALDEx) Analysis for Mixed Population RNA-Seq

(2013) Andrew D. Fernandes et al.   PLoS One

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

(2012) M.-A. Dillies et al.   BRIEFINGS IN BIOINFORMATICS

Human-Associated Microbial Signatures: Examining Their Predictive Value

(2011) Dan Knights et al.   Cell Host & Microbe

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Coefficients of Determination in Logistic Regression Models—A New Proposal: The Coefficient of Discrimination

(2009) Tue Tjur   AMERICAN STATISTICIAN

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY