A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses

Scientific method: Statistical errors

(2014) Regina Nuzzo   NATURE

Resistance and resilience of the forest soil microbiome to logging-associated compaction

(2013) Martin Hartmann et al.   ISME Journal

Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill

(2013) Adam R Rivers et al.   ISME Journal

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

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

Random Sampling Process Leads to Overestimation of  -Diversity of Microbial Communities

(2013) J. Zhou et al.   mBio

Multivariate analyses in soil microbial ecology: a new paradigm

(2012) Jean Thioulouse et al.   ENVIRONMENTAL AND ECOLOGICAL STATISTICS

The energy–diversity relationship of complex bacterial communities in Arctic deep-sea sediments

(2011) Christina Bienhold et al.   ISME Journal

Disconnect of microbial structure and function: enzyme activities and bacterial communities in nascent stream corridors

(2011) Aline Frossard et al.   ISME Journal

Two decades of describing the unseen majority of aquatic microbial diversity

(2011) LUCIE ZINGER et al.   MOLECULAR ECOLOGY

Experimental and analytical tools for studying the human microbiome

(2011) Justin Kuczynski et al.   NATURE REVIEWS GENETICS

Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems

(2011) Lucie Zinger et al.   PLoS One

Distance-based multivariate analyses confound location and dispersion effects

(2011) David I. Warton et al.   Methods in Ecology and Evolution

A Holistic Approach to Marine Eco-Systems Biology

(2011) Eric Karsenti et al.   PLOS BIOLOGY

Regularized Sandwich Estimators for Analysis of High-Dimensional Data Using Generalized Estimating Equations

(2010) David I. Warton   BIOMETRICS

Replicate or lie

(2010) James I. Prosser   ENVIRONMENTAL MICROBIOLOGY

Spatial and Temporal Variation in a Caribbean Herbivorous Fish Assemblage

(2010) Dorothée Kopp et al.   JOURNAL OF COASTAL RESEARCH

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Multivariate Cutoff Level Analysis (MultiCoLA) of large community data sets

(2010) Angélique Gobet et al.   NUCLEIC ACIDS RESEARCH

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

Genetic markers in the playground of multivariate analysis

(2009) T Jombart et al.   HEREDITY

Biodiversity of benthic microbial communities in bioturbated coastal sediments is controlled by geochemical microniches

(2009) Victoria J Bertics et al.   ISME Journal

Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands

(2009) Simone I Böer et al.   ISME Journal

Pseudoreplication conventions are testable hypotheses.

(2009) Richard G. Coss   JOURNAL OF COMPARATIVE PSYCHOLOGY

An ancient black art.

(2009) Thomas J. Koehnle et al.   JOURNAL OF COMPARATIVE PSYCHOLOGY

The ancient black art and transdisciplinary extent of pseudoreplication.

(2009) Stuart H. Hurlbert   JOURNAL OF COMPARATIVE PSYCHOLOGY

Pseudoreplication is a pseudoproblem.

(2009) Jeffrey C. Schank et al.   JOURNAL OF COMPARATIVE PSYCHOLOGY

Megx.net: integrated database resource for marine ecological genomics

(2009) R. Kottmann et al.   NUCLEIC ACIDS RESEARCH

A protocol for data exploration to avoid common statistical problems

(2009) Alain F. Zuur et al.   Methods in Ecology and Evolution

ANALYZING OR EXPLAINING BETA DIVERSITY? COMMENT

(2008) Pierre Legendre et al.   ECOLOGY

ANALYZING OR EXPLAINING BETA DIVERSITY? COMMENT

(2008) Etienne Laliberté   ECOLOGY

ANALYZING OR EXPLAINING BETA DIVERSITY? COMMENT

(2008) Raphaël Pélissier et al.   ECOLOGY

ANALYZING OR EXPLAINING BETA DIVERSITY? REPLY

(2008) Hanna Tuomisto et al.   ECOLOGY