Compositional analysis: a valid approach to analyze microbiome high-throughput sequencing data

Displaying Variation in Large Datasets: Plotting a Visual Summary of Effect Sizes

(2016) Gregory B. Gloor et al.   JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS

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

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

(2015) Zachary D. Kurtz et al.   PLoS Computational Biology

Proportionality: A Valid Alternative to Correlation for Relative Data

(2015) David Lovell et al.   PLoS Computational Biology

16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice

(2015) Alan W. Walker et al.   Microbiome

Microbiota of Human Breast Tissue

(2014) Camilla Urbaniak et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Short-term probiotic therapy alleviates small intestinal bacterial overgrowth, but does not improve intestinal permeability in chronic liver disease

(2014) Dong Shin Kwak et al.   EUROPEAN JOURNAL OF GASTROENTEROLOGY & HEPATOLOGY

Alterations in the Intestinal Microbiome (Dysbiosis) as a Predictor of Relapse After Infliximab Withdrawal in Crohnʼs Disease

(2014) Sylvie Rajca et al.   INFLAMMATORY BOWEL DISEASES

Microbial signature profiles of periodontally healthy and diseased patients

(2014) Talita Gomes Baêta Lourenço et al.   JOURNAL OF CLINICAL PERIODONTOLOGY

Recovery of the Gut Microbiome following Fecal Microbiota Transplantation

(2014) A. M. Seekatz et al.   mBio

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

High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients

(2013) Marc Frémont et al.   ANAEROBE

Microbiota Modulate Behavioral and Physiological Abnormalities Associated with Neurodevelopmental Disorders

(2013) Elaine Y. Hsiao et al.   CELL

High throughput sequencing methods and analysis for microbiome research

(2013) Julia M. Di Bella et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

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

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

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Distance-based multivariate analyses confound location and dispersion effects

(2011) David I. Warton et al.   Methods in Ecology and Evolution

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Pyrosequencing of the Chaperonin-60 Universal Target as a Tool for Determining Microbial Community Composition

(2009) J. Schellenberg et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Univariate statistical analysis of environmental (compositional) data: Problems and possibilities

(2009) Peter Filzmoser et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

(2009) James Robert White et al.   PLoS Computational Biology