Using null models to infer microbial co-occurrence networks

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

(2016) Sophie Weiss et al.   ISME Journal

Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation

(2016) Matthew T. Agler et al.   PLOS BIOLOGY

Resistant Microbial Cooccurrence Patterns Inferred by Network Topology

(2015) Sari Peura et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Investigating microbial co-occurrence patterns based on metagenomic compositional data

(2015) Yuguang Ban et al.   BIOINFORMATICS

Indigenous Bacteria from the Gut Microbiota Regulate Host Serotonin Biosynthesis

(2015) Jessica M. Yano et al.   CELL

Correction methods for ties in rank correlations

(2015) Ilaria L. Amerise et al.   JOURNAL OF APPLIED STATISTICS

Soil microbiome responses to the short-term effects of Amazonian deforestation

(2015) Acacio A. Navarrete et al.   MOLECULAR ECOLOGY

Differentiating between niche and neutral assembly in metacommunities using null models of β-diversity

(2015) Caroline M. Tucker et al.   OIKOS

The ecology of the microbiome: Networks, competition, and stability

(2015) K. Z. Coyte et al.   SCIENCE

Functional group diversity increases with modularity in complex food webs

(2015) D. Montoya et al.   Nature Communications

Abiotic stress tolerance and competition-related traits underlie phylogenetic clustering in soil bacterial communities

(2014) Marta Goberna et al.   ECOLOGY LETTERS

Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria

(2014) Albert Barberán et al.   ECOLOGY LETTERS

Demonstrating microbial co-occurrence pattern analyses within and between ecosystems

(2014) Ryan J. Williams et al.   Frontiers in Microbiology

Loss in microbial diversity affects nitrogen cycling in soil

(2013) Laurent Philippot 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

Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules

(2013) R. Levy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial community assembly, theory and rare functions

(2013) Mujalin K. Pholchan et al.   Frontiers in Microbiology

Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts

(2012) C. Lozupone et al.   GENOME RESEARCH

A decade of seasonal dynamics and co-occurrences within freshwater bacterioplankton communities from eutrophic Lake Mendota, WI, USA

(2012) Emily L Kara et al.   ISME Journal

Phylogenetic conservatism of functional traits in microorganisms

(2012) Adam C Martiny et al.   ISME Journal

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities

(2012) James P. O'Dwyer et al.   PLoS Computational Biology

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Marine bacterial, archaeal and protistan association networks reveal ecological linkages

(2011) Joshua A Steele et al.   ISME Journal

Using network analysis to explore co-occurrence patterns in soil microbial communities

(2011) Albert Barberán et al.   ISME Journal

Stochastic blockmodels and community structure in networks

(2011) Brian Karrer et al.   PHYSICAL REVIEW E

Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water

(2010) THORSTEN STOECK et al.   MOLECULAR ECOLOGY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

The ecological coherence of high bacterial taxonomic ranks

(2010) Laurent Philippot et al.   NATURE REVIEWS MICROBIOLOGY

Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale

(2009) C. L. Lauber et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Missing and spurious interactions and the reconstruction of complex networks

(2009) Roger Guimerà et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems

(2008) Marcel G. A. van der Heijden et al.   ECOLOGY LETTERS

Hierarchical structure and the prediction of missing links in networks

(2008) Aaron Clauset et al.   NATURE