A communal catalogue reveals Earth’s multiscale microbial diversity

Invasive Plants Rapidly Reshape Soil Properties in a Grassland Ecosystem

(2017) Sean M. Gibbons et al.   mSystems

pH is the primary determinant of the bacterial community structure in agricultural soils impacted by polycyclic aromatic hydrocarbon pollution

(2017) Yucheng Wu et al.   Scientific Reports

Spatial Gaps in Global Biodiversity Information and the Role of 
Citizen Science

(2016) Tatsuya Amano et al.   BIOSCIENCE

A multiple testing procedure for multi-dimensional pairwise comparisons with application to gene expression studies

(2016) Anjana Grandhi et al.   BMC BIOINFORMATICS

The Mass Production of Redundant, Misleading, and Conflicted Systematic Reviews and Meta-analyses

(2016) JOHN P.A. IOANNIDIS   MILBANK QUARTERLY

Diet-induced extinctions in the gut microbiota compound over generations

(2016) Erica D. Sonnenburg et al.   NATURE

Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies

(2016) Daryl M Gohl et al.   NATURE BIOTECHNOLOGY

Simple and efficient fully-functional succinct trees

(2016) Joshimar Cordova et al.   THEORETICAL COMPUTER SCIENCE

Temperature mediates continental-scale diversity of microbes in forest soils

(2016) Jizhong Zhou et al.   Nature Communications

The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation

(2016) Pier Luigi Buttigieg et al.   Journal of Biomedical Semantics

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals

(2016) Kate L. Ormerod et al.   Microbiome

Quantifying human impact on Earth's microbiome

(2016) Stephen B. Pointing et al.   Nature Microbiology

Metagenomics uncovers gaps in amplicon-based detection of microbial diversity

(2016) Emiley A. Eloe-Fadrosh et al.   Nature Microbiology

A new view of the tree of life

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

Low diversity of planktonic bacteria in the tropical ocean

(2016) Mathias Milici et al.   Scientific Reports

Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton

(2015) A Apprill et al.   AQUATIC MICROBIAL ECOLOGY

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples

(2015) Alma E. Parada et al.   ENVIRONMENTAL MICROBIOLOGY

Decreases in average bacterial community rRNA operon copy number during succession

(2015) Diana R Nemergut et al.   ISME Journal

Determinants of community structure in the global plankton interactome

(2015) G. Lima-Mendez et al.   SCIENCE

A unified initiative to harness Earth's microbiomes

(2015) A. P. Alivisatos et al.   SCIENCE

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys

(2015) William Walters et al.   mSystems

Building Predictive Models inRUsing thecaretPackage

(2015) Max Kuhn   Journal of Statistical Software

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

The Earth Microbiome project: successes and aspirations

(2014) Jack A Gilbert et al.   BMC BIOLOGY

An ontology for microbial phenotypes

(2014) Marcus C Chibucos et al.   BMC MICROBIOLOGY

Assemblage Time Series Reveal Biodiversity Change but Not Systematic Loss

(2014) M. Dornelas et al.   SCIENCE

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences

(2014) Jai Ram Rideout et al.   PeerJ

The founding charter of the Genomic Observatories Network

(2014) Neil Davies et al.   GigaScience

A meta-analysis of changes in bacterial and archaeal communities with time

(2013) Ashley Shade et al.   ISME Journal

Global marine bacterial diversity peaks at high latitudes in winter

(2013) Joshua Ladau et al.   ISME Journal

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

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

Going back to the roots: the microbial ecology of the rhizosphere

(2013) Laurent Philippot et al.   NATURE REVIEWS MICROBIOLOGY

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

The environment ontology: contextualising biological and biomedical entities

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

EMPeror: a tool for visualizing high-throughput microbial community data

(2013) Yoshiki Vázquez-Baeza et al.   GigaScience

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

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

(2012) J Gregory Caporaso et al.   ISME Journal

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Measuring fractions of beta diversity and their relationships to nestedness: a theoretical and empirical comparison of novel approaches

(2012) José C. Carvalho et al.   OIKOS

The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses

(2012) Laurel Cooper et al.   PLANT AND CELL PHYSIOLOGY

Uberon, an integrative multi-species anatomy ontology

(2012) Christopher J Mungall et al.   GENOME BIOLOGY

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

(2012) Daniel McDonald et al.   GigaScience

Marine bacterial, archaeal and protistan association networks reveal ecological linkages

(2011) Joshua A Steele 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

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

(2011) Pelin Yilmaz et al.   NATURE BIOTECHNOLOGY

Bayesian community-wide culture-independent microbial source tracking

(2011) Dan Knights et al.   NATURE METHODS

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

(2011) Patrick D. Schloss et al.   PLoS One

Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project

(2011) Jack A. Gilbert et al.   Standards in Genomic Sciences

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

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

Cython: The Best of Both Worlds

(2010) Stefan Behnel et al.   COMPUTING IN SCIENCE & ENGINEERING

Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes

(2010) Haiyan Chu et al.   ENVIRONMENTAL MICROBIOLOGY

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

(2010) Susan M. Huse et al.   ENVIRONMENTAL MICROBIOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

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

Controlling False Discoveries in Multidimensional Directional Decisions, with Applications to Gene Expression Data on Ordered Categories

(2009) Wenge Guo et al.   BIOMETRICS

Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data

(2009) Micah Hamady et al.   ISME Journal

Worlds within worlds: evolution of the vertebrate gut microbiota

(2008) Ruth E. Ley et al.   NATURE REVIEWS MICROBIOLOGY

A consistent metric for nestedness analysis in ecological systems: reconciling concept and measurement

(2008) Mário Almeida-Neto et al.   OIKOS

A consumer's guide to nestedness analysis

(2008) Werner Ulrich et al.   OIKOS

A latitudinal diversity gradient in planktonic marine bacteria

(2008) J. A. Fuhrman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA