pldist: ecological dissimilarities for paired and longitudinal microbiome association analysis

A highly adaptive microbiome-based association test for survival traits

(2018) Hyunwook Koh et al.   BMC GENOMICS

Variance Component Selection With Applications to Microbiome Taxonomic Data

(2018) Jing Zhai et al.   Frontiers in Microbiology

A small-sample kernel association test for correlated data with application to microbiome association studies

(2018) Xiang Zhan et al.   GENETIC EPIDEMIOLOGY

Gut microbiome influences efficacy of PD-1–based immunotherapy against epithelial tumors

(2017) Bertrand Routy et al.   SCIENCE

A phylogenetic transform enhances analysis of compositional microbiota data

(2017) Justin D Silverman et al.   eLife

Microbiome Datasets Are Compositional: And This Is Not Optional

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

MiRKAT-S: a community-level test of association between the microbiota and survival times

(2017) Anna Plantinga et al.   Microbiome

A powerful microbiome-based association test and a microbial taxa discovery framework for comprehensive association mapping

(2017) Hyunwook Koh et al.   Microbiome

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

Dynamics of the human gut microbiome in inflammatory bowel disease

(2017) Jonas Halfvarson et al.   Nature Microbiology

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

(2016) Zheng-Zheng Tang et al.   BIOINFORMATICS

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

(2016) Gregory B. Gloor et al.   CANADIAN JOURNAL OF MICROBIOLOGY

A small-sample multivariate kernel machine test for microbiome association studies

(2016) Xiang Zhan et al.   GENETIC EPIDEMIOLOGY

An adaptive association test for microbiome data

(2016) Chong Wu et al.   Genome Medicine

Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics

(2016) Juan Jovel et al.   Frontiers in Microbiology

Randomised clinical trial: gut microbiome biomarkers are associated with clinical response to a low FODMAP diet in children with the irritable bowel syndrome

(2015) B. P. Chumpitazi et al.   ALIMENTARY PHARMACOLOGY & THERAPEUTICS

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

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

Intestinal Blautia Is Associated with Reduced Death from Graft-versus-Host Disease

(2015) Robert R. Jenq et al.   BIOLOGY OF BLOOD AND MARROW TRANSPLANTATION

National Institutes of Health Consensus Development Project on Criteria for Clinical Trials in Chronic Graft-versus-Host Disease: I. The 2014 Diagnosis and Staging Working Group Report

(2015) Madan H. Jagasia et al.   BIOLOGY OF BLOOD AND MARROW TRANSPLANTATION

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease

(2015) James D. Lewis et al.   Cell Host & Microbe

Metagenomics meets time series analysis: unraveling microbial community dynamics

(2015) Karoline Faust et al.   CURRENT OPINION IN MICROBIOLOGY

Metagenomic Analysis of the Stool Microbiome in Patients Receiving Allogeneic Stem Cell Transplantation: Loss of Diversity Is Associated with Use of Systemic Antibiotics and More Pronounced in Gastrointestinal Graft-versus-Host Disease

(2014) Ernst Holler et al.   BIOLOGY OF BLOOD AND MARROW TRANSPLANTATION

Rethinking “Enterotypes”

(2014) Dan Knights et al.   Cell Host & Microbe

Complete Suppression of the Gut Microbiome Prevents Acute Graft-Versus-Host Disease following Allogeneic Bone Marrow Transplantation

(2014) Jaak M. Vossen 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

Associating microbiome composition with environmental covariates using generalized UniFrac distances

(2012) Jun Chen et al.   BIOINFORMATICS

Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis

(2012) H. H. Kong et al.   GENOME RESEARCH

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

(2012) Junjie Qin et al.   NATURE

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

Categorization of the gut microbiota: enterotypes or gradients?

(2012) Ian B. Jeffery et al.   NATURE REVIEWS MICROBIOLOGY

Variance adjusted weighted UniFrac: a powerful beta diversity measure for comparing communities based on phylogeny

(2011) Qin Chang et al.   BMC BIOINFORMATICS

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Analysis of the Lung Microbiome in the “Healthy” Smoker and in COPD

(2011) John R. Erb-Downward et al.   PLoS One

Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans

(2011) B. D. Muegge et al.   SCIENCE

Disordered Microbial Communities in the Upper Respiratory Tract of Cigarette Smokers

(2010) Emily S. Charlson et al.   PLoS One

Principal component analysis for compositional data with outliers

(2009) Peter Filzmoser et al.   ENVIRONMETRICS

Graft-versus-host disease

(2009) James LM Ferrara et al.   LANCET

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE