A Novel Sparse Compositional Technique Reveals Microbial Perturbations

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information

(2018) Stefan Janssen et al.   mSystems

Balances: a New Perspective for Microbiome Analysis

(2018) J. Rivera-Pinto et al.   mSystems

Intermittent Hypoxia and Hypercapnia, a Hallmark of Obstructive Sleep Apnea, Alters the Gut Microbiome and Metabolome

(2018) Anupriya Tripathi et al.   mSystems

Qiita: rapid, web-enabled microbiome meta-analysis

(2018) Antonio Gonzalez et al.   NATURE METHODS

Integrated metabolism in sponge–microbe symbiosis revealed by genome-centered metatranscriptomics

(2017) Lucas Moitinho-Silva et al.   ISME Journal

The gut microbiome in atherosclerotic cardiovascular disease

(2017) Zhuye Jie et al.   Nature Communications

A phylogenetic transform enhances analysis of compositional microbiota data

(2017) Justin D Silverman et al.   eLife

The sponge microbiome project

(2017) Lucas Moitinho-Silva et al.   GigaScience

Uncovering the Horseshoe Effect in Microbial Analyses

(2017) James T. Morton et al.   mSystems

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

(2017) Amnon Amir et al.   mSystems

Structured Matrix Completion with Applications to Genomic Data Integration

(2016) Tianxi Cai et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Inhabitancy of active Nitrosopumilus-like ammonia-oxidizing archaea and Nitrospira nitrite-oxidizing bacteria in the sponge Theonella swinhoei

(2016) Guofang Feng et al.   Scientific Reports

Erratum: Corrigendum: SparRec: An effective matrix completion framework of missing data imputation for GWAS

(2016) Bo Jiang et al.   Scientific Reports

Functional Intestinal Bile Acid 7α-Dehydroxylation by Clostridium scindens Associated with Protection from Clostridium difficile Infection in a Gnotobiotic Mouse Model

(2016) Nicolas Studer et al.   Frontiers in Cellular and Infection Microbiology

zCompositions — R package for multivariate imputation of left-censored data under a compositional approach

(2015) Javier Palarea-Albaladejo et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

Intestinal Colonization by a Lachnospiraceae Bacterium Contributes to the Development of Diabetes in Obese Mice

(2014) Keishi Kameyama et al.   MICROBES AND ENVIRONMENTS

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

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

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

Associating microbiome composition with environmental covariates using generalized UniFrac distances

(2012) Jun Chen et al.   BIOINFORMATICS

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

(2012) Daniel McDonald et al.   GigaScience

Robust principal component analysis?

(2011) Emmanuel J. Candès et al.   JOURNAL OF THE ACM

Microbial community resemblance methods differ in their ability to detect biologically relevant patterns

(2010) Justin Kuczynski et al.   NATURE METHODS

Forensic identification using skin bacterial communities

(2010) N. Fierer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Succession of microbial consortia in the developing infant gut microbiome

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

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

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges

(2009) M. Hamady et al.   GENOME RESEARCH

Distributional Equivalence and Subcompositional Coherence in the Analysis of Compositional Data, Contingency Tables and Ratio-Scale Measurements

(2009) Michael Greenacre et al.   JOURNAL OF CLASSIFICATION

The ecology and phylogeny of cyanobacterial symbionts in sponges

(2008) Kayley M. Usher   Marine Ecology-An Evolutionary Perspective

Cryptic diversity of the symbiotic cyanobacterium Synechococcus spongiarum among sponge hosts

(2008) PATRICK M. ERWIN et al.   MOLECULAR ECOLOGY