A statistical model for describing and simulating microbial community profiles

A zero inflated log-normal model for inference of sparse microbial association networks

(2021) Vincent Prost et al.   PLoS Computational Biology

Analysis of compositions of microbiomes with bias correction

(2020) Huang Lin et al.   Nature Communications

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

(2019) Jason Lloyd-Price et al.   NATURE

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer

(2019) Jakob Wirbel et al.   NATURE MEDICINE

Chronic obstructive pulmonary disease upper airway microbiome is associated with select clinical characteristics

(2019) Alexa A. Pragman et al.   PLoS One

Cooking shapes the structure and function of the gut microbiome

(2019) Rachel N. Carmody et al.   Nature Microbiology

metaSPARSim: a 16S rRNA gene sequencing count data simulator

(2019) Ilaria Patuzzi et al.   BMC BIOINFORMATICS

The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

(2019) Adrian Tett et al.   Cell Host & Microbe

Large Covariance Estimation for Compositional Data via Composition-Adjusted Thresholding

(2018) Yuanpei Cao et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

gCoda: Conditional Dependence Network Inference for Compositional Data

(2017) Huaying Fang et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Quantitative microbiome profiling links gut community variation to microbial load

(2017) Doris Vandeputte et al.   NATURE

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium

(2017) Rashmi Sinha et al.   NATURE BIOTECHNOLOGY

A Bayesian method for detecting pairwise associations in compositional data

(2017) Emma Schwager et al.   PLoS Computational Biology

Microbiome Datasets Are Compositional: And This Is Not Optional

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

PERMANOVA-S: association test for microbial community composition that accommodates confounders and multiple distances

(2016) Zheng-Zheng Tang et al.   BIOINFORMATICS

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

(2016) Sophie Weiss et al.   ISME Journal

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

Testing the Neutral Theory of Biodiversity with Human Microbiome Datasets

(2016) Lianwei Li et al.   Scientific Reports

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

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

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

(2015) Kristoffer Forslund et al.   NATURE

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

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

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

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

(2013) Jun Chen et al.   Annals of Applied Statistics

Bayesian Gaussian Copula Factor Models for Mixed Data

(2013) Jared S. Murray et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

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

A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets

(2013) Omry Koren et al.   PLoS Computational Biology

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

A powerful and flexible approach to the analysis of RNA sequence count data

(2011) Yi-Hui Zhou et al.   BIOINFORMATICS

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

Vaginal microbiome of reproductive-age women

(2010) J. Ravel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA