Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets

phylosignal: an R package to measure, test, and explore the phylogenetic signal

(2016) François Keck et al.   Ecology and Evolution

Microbiomes in light of traits: A phylogenetic perspective

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

VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data

(2015) Cedric C Laczny et al.   Microbiome

Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution

(2014) Mikhail Tikhonov et al.   ISME Journal

Dynamics and associations of microbial community types across the human body

(2014) Tao Ding et al.   NATURE

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

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

Biogeographic patterns in below-ground diversity in New York City's Central Park are similar to those observed globally

(2014) K. S. Ramirez et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

The rhizosphere microbiome and plant health

(2012) Roeland L. Berendsen et al.   TRENDS IN PLANT SCIENCE

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

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

Moving pictures of the human microbiome

(2011) J Gregory Caporaso et al.   GENOME BIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Human oral, gut, and plaque microbiota in patients with atherosclerosis

(2010) O. Koren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems

(2008) Marcel G. A. van der Heijden et al.   ECOLOGY LETTERS

Microbial contributions to climate change through carbon cycle feedbacks

(2008) Richard D Bardgett et al.   ISME Journal

The Microbial Engines That Drive Earth's Biogeochemical Cycles

(2008) P. G. Falkowski et al.   SCIENCE