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Statistical approaches for differential expression analysis in metatranscriptomics

(2021) Yancong Zhang et al.   BIOINFORMATICS

A statistical model for describing and simulating microbial community profiles

(2021) Siyuan Ma et al.   PLoS Computational Biology

Sequence count data are poorly fit by the negative binomial distribution

(2020) Stijn Hawinkel et al.   PLoS One

CAMISIM: simulating metagenomes and microbial communities

(2019) Adrian Fritz et al.   Microbiome

The Integrative Human Microbiome Project

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Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

(2019) Jason Lloyd-Price et al.   NATURE

A Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome

(2019) Courtney R. Armour et al.   mSystems

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome

(2018) Melanie Schirmer et al.   Nature Microbiology

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

Methods for normalizing microbiome data: an ecological perspective

(2018) Donald T. McKnight et al.   Methods in Ecology and Evolution

Variability in Metagenomic Count Data and Its Influence on the Identification of Differentially Abundant Genes

(2017) Viktor Jonsson et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

The MetaCyc database of metabolic pathways and enzymes

(2017) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Analysis of Microbiome Data in the Presence of Excess Zeros

(2017) Abhishek Kaul et al.   Frontiers in Microbiology

Microbiome Datasets Are Compositional: And This Is Not Optional

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

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

Development of Inflammatory Bowel Disease Is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice

(2017) Thomas Sharpton et al.   mSystems

Mediation Analysis: A Practitioner's Guide

(2016) Tyler J. VanderWeele   Annual Review of Public Health

A two-part mixed-effects model for analyzing longitudinal microbiome compositional data

(2016) Eric Z. Chen et al.   BIOINFORMATICS

Statistical evaluation of methods for identification of differentially abundant genes in comparative metagenomics

(2016) Viktor Jonsson et al.   BMC GENOMICS

The Human Intestinal Microbiome in Health and Disease

(2016) Susan V. Lynch et al.   NEW ENGLAND JOURNAL OF MEDICINE

Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies

(2016) Jonathan Thorsen et al.   Microbiome

The gut microbiome in health and in disease

(2015) Andrew B. Shreiner et al.   CURRENT OPINION IN GASTROENTEROLOGY

Zero-Inflated Beta Regression for Differential Abundance Analysis with Metagenomics Data

(2015) Xiaoling Peng et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Sequencing and beyond: integrating molecular 'omics' for microbial community profiling

(2015) Eric A. Franzosa et al.   NATURE REVIEWS MICROBIOLOGY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease

(2015) Xochitl C Morgan et al.   GENOME BIOLOGY

Regression Models for Count Data inR

(2015) Achim Zeileis et al.   Journal of Statistical Software

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

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

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

(2014) Charity W Law et al.   GENOME BIOLOGY

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

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

(2013) Paul J. McMurdie et al.   PLoS One

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

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

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

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

(2009) M. D. Robinson et al.   BIOINFORMATICS