Normalization and microbial differential abundance strategies depend upon data characteristics

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Proportionality: A Valid Alternative to Correlation for Relative Data

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Evaluating Bias of Illumina-Based Bacterial 16S rRNA Gene Profiles

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Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

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

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

Estimating coverage in metagenomic data sets and why it matters

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Reply to: "A fair comparison"

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A fair comparison

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Saliva from Obese Individuals Suppresses the Release of Aroma Compounds from Wine

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Bayesian-multiplicative treatment of count zeros in compositional data sets

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

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Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition

(2014) Mihai Pop et al.   GENOME BIOLOGY

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

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

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Variable selection for sparse Dirichlet-multinomial regression with an application to microbiome data analysis

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A comparison of methods for differential expression analysis of RNA-seq data

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Alterations in the Gut Microbiota Associated with HIV-1 Infection

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PERMANOVA, ANOSIM, and the Mantel test in the face of heterogeneous dispersions: What null hypothesis are you testing?

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Diet rapidly and reproducibly alters the human gut microbiome

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Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

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phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

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Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice

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Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

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EMPeror: a tool for visualizing high-throughput microbial community data

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

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Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics

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Hypothesis Testing and Power Calculations for Taxonomic-Based Human Microbiome Data

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Inferring Correlation Networks from Genomic Survey Data

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Classification and clustering of sequencing data using a Poisson model

(2011) Daniela M. Witten   Annals of Applied Statistics

Evaluation of Subsampling-Based Normalization Strategies for Tagged High-Throughput Sequencing Data Sets from Gut Microbiomes

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Measuring Subcompositional Incoherence

(2011) Michael Greenacre   Mathematical Geosciences

Application of Two-Part Statistics for Comparison of Sequence Variant Counts

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Moving pictures of the human microbiome

(2011) J Gregory Caporaso et al.   GENOME BIOLOGY

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

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Statistical Design and Analysis of RNA Sequencing Data

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UniFrac: an effective distance metric for microbial community comparison

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A human gut microbial gene catalogue established by metagenomic sequencing

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QIIME allows analysis of high-throughput community sequencing data

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Forensic identification using skin bacterial communities

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Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

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

Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale

(2009) C. L. Lauber et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

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Testing species abundance models: a new bootstrap approach applied to Indo-Pacific coral reefs

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Bacterial Community Variation in Human Body Habitats Across Space and Time

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Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

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A core gut microbiome in obese and lean twins

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