Edge Principal Components and Squash Clustering: Using the Special Structure of Phylogenetic Placement Data for Sample Comparison

The phylogenetic Kantorovich-Rubinstein metric for environmental sequence samples

(2012) Steven N. Evans et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

A Format for Phylogenetic Placements

(2012) Frederick A. Matsen et al.   PLoS One

Bacterial Communities in Women with Bacterial Vaginosis: High Resolution Phylogenetic Analyses Reveal Relationships of Microbiota to Clinical Criteria

(2012) Sujatha Srinivasan et al.   PLoS One

Principal components analysis in the space of phylogenetic trees

(2011) Tom M. W. Nye   ANNALS OF STATISTICS

Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood

(2011) Simon A. Berger et al.   SYSTEMATIC BIOLOGY

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

Alignment and clustering of phylogenetic markers - implications for microbial diversity studies

(2010) James R White et al.   BMC BIOINFORMATICS

Global patterns in the biogeography of bacterial taxa

(2010) Diana R. Nemergut et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2010) Justin Kuczynski et al.   NATURE METHODS

Metagenomic Sequencing of an In Vitro-Simulated Microbial Community

(2010) Jenna L. Morgan et al.   PLoS One

Vaginal microbiome of reproductive-age women

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

Visual and statistical comparison of metagenomes

(2009) Suparna Mitra et al.   BIOINFORMATICS

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

(2009) Arthur Brady et al.   NATURE METHODS

Bacterial Community Variation in Human Body Habitats Across Space and Time

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

Prevalence and Abundance of Uncultivated Megasphaera-Like Bacteria in the Human Vaginal Environment

(2008) M. Zozaya-Hinchliffe et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH