MixMC: A Multivariate Statistical Framework to Gain Insight into Microbial Communities

Investigating microbial co-occurrence patterns based on metagenomic compositional data

(2015) Yuguang Ban et al.   BIOINFORMATICS

A Linear Mixed Model Spline Framework for Analysing Time Course ‘Omics’ Data

(2015) Jasmin Straube et al.   PLoS One

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

Brief Report: Intestinal Dysbiosis in Ankylosing Spondylitis

(2015) Mary-Ellen Costello et al.   Arthritis & Rheumatology

The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease

(2014)   Cell Host & Microbe

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

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

PLS-DA for compositional data with application to metabolomics

(2014) Alžběta Kalivodová et al.   JOURNAL OF CHEMOMETRICS

Relating the metatranscriptome and metagenome of the human gut

(2014) E. A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle

(2014) Xuesong He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

A novel approach for biomarker selection and the integration of repeated measures experiments from two assays

(2012) Benoit Liquet et al.   BMC BIOINFORMATICS

A framework for human microbiome research

(2012)   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

(2012) Nicholas A Bokulich et al.   NATURE METHODS

Analyses of the Microbial Diversity across the Human Microbiome

(2012) Kelvin Li et al.   PLoS One

Evaluation of 16S rDNA-Based Community Profiling for Human Microbiome Research

(2012)   PLoS One

Visualising associations between paired ‘omics’ data sets

(2012) Ignacio González et al.   BioData Mining

Sparse PLS discriminant analysis: biologically relevant feature selection and graphical displays for multiclass problems

(2011) Kim-Anh Lê Cao et al.   BMC 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

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

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

(2010) Susan M. Huse et al.   ENVIRONMENTAL MICROBIOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Human oral, gut, and plaque microbiota in patients with atherosclerosis

(2010) O. Koren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

Principal component analysis for compositional data with outliers

(2009) Peter Filzmoser et al.   ENVIRONMETRICS

Multivariate paired data analysis: multilevel PLSDA versus OPLSDA

(2009) Johan A. Westerhuis et al.   Metabolomics

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

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

Diet-Induced Obesity Is Linked to Marked but Reversible Alterations in the Mouse Distal Gut Microbiome

(2008) Peter J. Turnbaugh et al.   Cell Host & Microbe

Human colonic microbiota associated with diet, obesity and weight loss

(2008) S H Duncan et al.   INTERNATIONAL JOURNAL OF OBESITY

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE