A phylogenetic transform enhances analysis of compositional microbiota data

Balance Trees Reveal Microbial Niche Differentiation

(2017) James T. Morton et al.   mSystems

Compositional data analysis of the microbiome: fundamentals, tools, and challenges

(2016) Matthew C.B. Tsilimigras et al.   ANNALS OF EPIDEMIOLOGY

It's all relative: analyzing microbiome data as compositions

(2016) Gregory B. Gloor et al.   ANNALS OF EPIDEMIOLOGY

The evolution of cooperation within the gut microbiota

(2016) Seth Rakoff-Nahoum et al.   NATURE

Cospeciation of gut microbiota with hominids

(2016) A. H. Moeller et al.   SCIENCE

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

MixMC: A Multivariate Statistical Framework to Gain Insight into Microbial Communities

(2016) Kim-Anh Lê Cao et al.   PLoS One

CCLasso: correlation inference for compositional data through Lasso

(2015) Huaying Fang et al.   BIOINFORMATICS

Microbiomes in light of traits: A phylogenetic perspective

(2015) J. B. H. Martiny et al.   SCIENCE

Where Next for Microbiome Research?

(2015) Matthew K. Waldor et al.   PLOS BIOLOGY

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

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

Proportionality: A Valid Alternative to Correlation for Relative Data

(2015) David Lovell et al.   PLoS Computational Biology

BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies

(2015) Ke Yuan et al.   GENOME BIOLOGY

Microbiome, Metagenomics, and High-Dimensional Compositional Data Analysis

(2015) Hongzhe Li   Annual Review of Statistics and Its Application

Variable selection in regression with compositional covariates

(2014) W. Lin et al.   BIOMETRIKA

Age-Related Decrease in TCR Repertoire Diversity Measured with Deep and Normalized Sequence Profiling

(2014) O. V. Britanova et al.   JOURNAL OF IMMUNOLOGY

PyClone: statistical inference of clonal population structure in cancer

(2014) Andrew Roth et al.   NATURE METHODS

A Taxonomic Signature of Obesity in the Microbiome? Getting to the Guts of the Matter

(2014) Mariel M. Finucane et al.   PLoS One

Bayesian-multiplicative treatment of count zeros in compositional data sets

(2014) Josep-Antoni Martín-Fernández et al.   STATISTICAL MODELLING

Phylogenetics and the Human Microbiome

(2014) Frederick A. Matsen   SYSTEMATIC BIOLOGY

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

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

Helminth Colonization Is Associated with Increased Diversity of the Gut Microbiota

(2014) Soo Ching Lee et al.   PLoS Neglected Tropical Diseases

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

(2014) Andrew D Fernandes et al.   Microbiome

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

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

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses

(2013) Tomáš Větrovský et al.   PLoS One

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

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

Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules

(2013) R. Levy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Associating microbiome composition with environmental covariates using generalized UniFrac distances

(2012) Jun Chen et al.   BIOINFORMATICS

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

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

(2012) Patricio S. La Rosa et al.   PLoS One

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Analysis of a data matrix and a graph: Metagenomic data and the phylogenetic tree

(2011) Elizabeth Purdom   Annals of Applied Statistics

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Ecology drives a global network of gene exchange connecting the human microbiome

(2011) Chris S. Smillie et al.   NATURE

The skin microbiome

(2011) Elizabeth A. Grice et al.   NATURE REVIEWS MICROBIOLOGY

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives

(2010) Jesse R. Zaneveld et al.   NUCLEIC ACIDS RESEARCH

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

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

Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

(2010) C. De Filippo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

What are the consequences of the disappearing human microbiota?

(2009) Martin J. Blaser et al.   NATURE REVIEWS MICROBIOLOGY

Bacterial Community Variation in Human Body Habitats Across Space and Time

(2009) E. K. Costello et al.   SCIENCE

Evolution of Mammals and Their Gut Microbes

(2008) R. E. Ley et al.   SCIENCE

Resource Partitioning and Sympatric Differentiation Among Closely Related Bacterioplankton

(2008) D. E. Hunt et al.   SCIENCE