Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Developing climate-smart restoration: Can plant microbiomes be hardened against heat waves?

(2018) Rachel L. Rubin et al.   ECOLOGICAL APPLICATIONS

Creating a 3D microbial and chemical snapshot of a human habitat

(2018) Clifford A. Kapono et al.   Scientific Reports

Heterogeneity of Microbiota Dysbiosis in Chronic Rhinosinusitis: Potential Clinical Implications and Microbial Community Mechanisms Contributing to Sinonasal Inflammation

(2018) Keehoon Lee et al.   Frontiers in Cellular and Infection Microbiology

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

(2018) Nicholas A. Bokulich et al.   Microbiome

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information

(2018) Stefan Janssen et al.   mSystems

Qiita: rapid, web-enabled microbiome meta-analysis

(2018) Antonio Gonzalez et al.   NATURE METHODS

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

Evaluating the Information Content of Shallow Shotgun Metagenomics

(2018) Benjamin Hillmann et al.   mSystems

q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data

(2018) Nicholas A. Bokulich et al.   mSystems

Tree genetics defines fungal partner communities that may confer drought tolerance

(2017) Catherine A. Gehring et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients

(2017) V. Gopalakrishnan et al.   SCIENCE

Steering Soil Microbiomes to Suppress Aboveground Insect Pests

(2017) Ana Pineda et al.   TRENDS IN PLANT SCIENCE

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

(2016) Mingxun Wang et al.   NATURE BIOTECHNOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Microbial community assembly and metabolic function during mammalian corpse decomposition

(2015) J. L. Metcalf et al.   SCIENCE

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

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

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

Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor

(2013) M. I. Smith et al.   SCIENCE

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

(2012) Daniel McDonald et al.   GigaScience

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Shotgun metaproteomics of the human distal gut microbiota

(2008) Nathan C Verberkmoes et al.   ISME Journal