MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments

Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing

(2017) Michael Tessler et al.   Scientific Reports

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

(2016) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

EuPathDB: the eukaryotic pathogen genomics database resource

(2016) Cristina Aurrecoechea et al.   NUCLEIC ACIDS RESEARCH

Antibiotics, birth mode, and diet shape microbiome maturation during early life

(2016) Nicholas A. Bokulich et al.   Science Translational Medicine

The Ontology for Biomedical Investigations

(2016) Anita Bandrowski et al.   PLoS One

Longitudinal analysis of microbial interaction between humans and the indoor environment

(2014) S. Lax et al.   SCIENCE

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

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

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

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

The environment ontology: contextualising biological and biomedical entities

(2013) Pier Buttigieg et al.   Journal of Biomedical Semantics

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

(2012) Daniel McDonald et al.   GigaScience

The genomic standards consortium: bringing standards to life for microbial ecology

(2011) Pelin Yilmaz et al.   ISME Journal

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

(2011) Daniel McDonald et al.   ISME Journal

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level

(2010) P. Rocca-Serra et al.   BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

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

BioPortal: ontologies and integrated data resources at the click of a mouse

(2009) N. F. Noy et al.   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2008) E. W. Sayers et al.   NUCLEIC ACIDS RESEARCH