You must choose, but choose wisely: Model-based approaches for microbial community analysis

Putting science back into microbial ecology: a question of approach

(2020) James I. Prosser   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Novel Sparse Compositional Technique Reveals Microbial Perturbations

(2019) Cameron Martino et al.   mSystems

Rarity of microbial species: In search of reliable associations

(2019) Arnaud Cougoul et al.   PLoS One

A comprehensive evaluation of predictive performance of 33 species distribution models at species and community levels

(2019) Anna Norberg et al.   ECOLOGICAL MONOGRAPHS

Uncovering the drivers of host-associated microbiota with joint species distribution modelling

(2018) Johannes R. Björk et al.   MOLECULAR ECOLOGY

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

A global atlas of the dominant bacteria found in soil

(2018) Manuel Delgado-Baquerizo et al.   SCIENCE

Forecasting biodiversity in breeding birds using best practices

(2018) David J. Harris et al.   PeerJ

Balances: a New Perspective for Microbiome Analysis

(2018) J. Rivera-Pinto et al.   mSystems

The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies

(2018) Jolinda Pollock et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Biotic interactions in species distribution modelling: 10 questions to guide interpretation and avoid false conclusions

(2018) Carsten F. Dormann et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing

(2017) Luisa W. Hugerth et al.   Frontiers in Microbiology

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

Modeling Through Latent Variables

(2017) Geert Verbeke et al.   Annual Review of Statistics and Its Application

Successive DNA extractions improve characterization of soil microbial communities

(2017) Mauricio R. Dimitrov et al.   PeerJ

Accuracy of microbial community diversity estimated by closed- and open-reference OTUs

(2017) Robert C. Edgar   PeerJ

Modelling of species distributions, range dynamics and communities under imperfect detection: advances, challenges and opportunities

(2016) Gurutzeta Guillera-Arroita   ECOGRAPHY

Study of biological communities subject to imperfect detection: bias and precision of community N-mixture abundance models in small-sample situations

(2016) Yuichi Yamaura et al.   ECOLOGICAL RESEARCH

A family of interaction-adjusted indices of community similarity

(2016) Thomas Sebastian Benedikt Schmidt et al.   ISME Journal

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

(2016) Sophie Weiss et al.   ISME Journal

Application of multivariate statistical techniques in microbial ecology

(2016) O. Paliy et al.   MOLECULAR ECOLOGY

A comparison of tools for the simulation of genomic next-generation sequencing data

(2016) Merly Escalona et al.   NATURE REVIEWS GENETICS

Three points to consider when choosing a LM or GLM test for count data

(2016) David I. Warton et al.   Methods in Ecology and Evolution

boral - Bayesian Ordination and Regression Analysis of Multivariate Abundance Data in r

(2016) Francis K.C. Hui   Methods in Ecology and Evolution

Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System

(2016) Adrian Ho et al.   Frontiers in Microbiology

A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity

(2016) Nam-Phuong Nguyen et al.   npj Biofilms and Microbiomes

Determinants of community structure in the global plankton interactome

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

So Many Variables: Joint Modeling in Community Ecology

(2015) David I. Warton et al.   TRENDS IN ECOLOGY & EVOLUTION

For testing the significance of regression coefficients, go ahead and log-transform count data

(2015) Anthony R. Ives   Methods in Ecology and Evolution

Proportionality: A Valid Alternative to Correlation for Relative Data

(2015) David Lovell et al.   PLoS Computational Biology

Microbiome, Metagenomics, and High-Dimensional Compositional Data Analysis

(2015) Hongzhe Li   Annual Review of Statistics and Its Application

Estimating the Effects of Habitat and Biological Interactions in an Avian Community

(2015) Robert M. Dorazio et al.   PLoS One

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

(2014) Pier Luigi Buttigieg et al.   FEMS MICROBIOLOGY ECOLOGY

Bi-level variable selection via adaptive sparse group Lasso

(2014) Kuangnan Fang et al.   JOURNAL OF STATISTICAL COMPUTATION AND SIMULATION

Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data

(2014) Gentile F. Ficetola et al.   Molecular Ecology Resources

A fair comparison

(2014) Paul I Costea et al.   NATURE METHODS

Model-based thinking for community ecology

(2014) David I. Warton et al.   PLANT ECOLOGY

Strengths and Limitations of 16S rRNA Gene Amplicon Sequencing in Revealing Temporal Microbial Community Dynamics

(2014) Rachel Poretsky et al.   PLoS One

Model-based approaches to unconstrained ordination

(2014) Francis K.C. Hui et al.   Methods in Ecology and Evolution

Understanding co-occurrence by modelling species simultaneously with a Joint Species Distribution Model (JSDM)

(2014) Laura J. Pollock et al.   Methods in Ecology and Evolution

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

A Logistic Normal Multinomial Regression Model for Microbiome Compositional Data Analysis

(2013) Fan Xia et al.   BIOMETRICS

More than the sum of the parts: forest climate response from joint species distribution models

(2013) James S. Clark et al.   ECOLOGICAL APPLICATIONS

PERMANOVA, ANOSIM, and the Mantel test in the face of heterogeneous dispersions: What null hypothesis are you testing?

(2013) Marti J. Anderson et al.   ECOLOGICAL MONOGRAPHS

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

Detecting diversity: emerging methods to estimate species diversity

(2013) Kelly J. Iknayan et al.   TRENDS IN ECOLOGY & EVOLUTION

A Poisson–Gamma model for analysis of ecological non-negative continuous data

(2012) Scott D. Foster et al.   ENVIRONMENTAL AND ECOLOGICAL STATISTICS

Unlocking the potential of metagenomics through replicated experimental design

(2012) Rob Knight et al.   NATURE BIOTECHNOLOGY

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Defining seasonal marine microbial community dynamics

(2011) Jack A Gilbert et al.   ISME Journal

Distance-based multivariate analyses confound location and dispersion effects

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

Making more out of sparse data: hierarchical modeling of species communities

(2010) Otso Ovaskainen et al.   ECOLOGY

Do not log-transform count data

(2010) Robert B. O’Hara et al.   Methods in Ecology and Evolution