Chloroplast sequence variation and the efficacy of peptide nucleic acids for blocking host amplification in plant microbiome studies

Assembly and ecological function of the root microbiome across angiosperm plant species

(2018) Connor R. Fitzpatrick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

lmerTest Package: Tests in Linear Mixed Effects Models

(2017) Alexandra Kuznetsova et al.   Journal of Statistical Software

Identifying the plant-associated microbiome across aquatic and terrestrial environments: the effects of amplification method on taxa discovery

(2017) Sara L. Jackrel et al.   Molecular Ecology Resources

Root microbiota drive direct integration of phosphate stress and immunity

(2017) Gabriel Castrillo et al.   NATURE

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Plant domestication and the assembly of bacterial and fungal communities associated with strains of the common sunflower, Helianthus annuus

(2016) Jonathan W. Leff et al.   NEW PHYTOLOGIST

Composition of the gut microbiota modulates the severity of malaria

(2016) Nicolas F. Villarino et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies

(2016) Jonathan Thorsen et al.   Microbiome

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences

(2015) Siavash Mirarab et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Conducting a Microbiome Study

(2014) Julia K. Goodrich et al.   CELL

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

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

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

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Parasitic plants have increased rates of molecular evolution across all three genomes

(2013) Lindell Bromham et al.   BMC EVOLUTIONARY BIOLOGY

Practical innovations for high-throughput amplicon sequencing

(2013) Derek S Lundberg et al.   NATURE METHODS

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

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

ANOVA-Like Differential Expression (ALDEx) Analysis for Mixed Population RNA-Seq

(2013) Andrew D. Fernandes et al.   PLoS One

The microbiome of medicinal plants: diversity and importance for plant growth, quality and health

(2013) Martina Köberl et al.   Frontiers in Microbiology

Gut Immune Maturation Depends on Colonization with a Host-Specific Microbiota

(2012) Hachung Chung et al.   CELL

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

The evolution of the plastid chromosome in land plants: gene content, gene order, gene function

(2011) Susann Wicke et al.   PLANT MOLECULAR BIOLOGY

Socially transmitted gut microbiota protect bumble bees against an intestinal parasite

(2011) H. Koch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The arcsine is asinine: the analysis of proportions in ecology

(2010) David I. Warton et al.   ECOLOGY

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

Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutions

(2008) M. M. Guisinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA