Incorporating phylogenetic metrics to microbial co‐occurrence networks based on amplicon sequences to discern community assembly processes

A New Method to Correct for Habitat Filtering in Microbial Correlation Networks

(2019) Vanessa Brisson et al.   Frontiers in Microbiology

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Fundamental contradictions among observational and experimental estimates of non-trophic species interactions

(2018) Allison K. Barner et al.   ECOLOGY

Species co-occurrence networks: Can they reveal trophic and non-trophic interactions in ecological communities?

(2018) Mara A. Freilich et al.   ECOLOGY

Soil pH mediates the balance between stochastic and deterministic assembly of bacteria

(2018) Binu M. Tripathi et al.   ISME Journal

Phylogenetic-scale disparities in the soil microbial diversity–ecosystem functioning relationship

(2018) Marta Goberna et al.   ISME Journal

Why do microbes exhibit weak biogeographic patterns?

(2018) Kyle M. Meyer et al.   ISME Journal

The social network of microorganisms — how auxotrophies shape complex communities

(2018) Karsten Zengler et al.   NATURE REVIEWS MICROBIOLOGY

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

Niche and fitness differences determine invasion success and impact in laboratory bacterial communities

(2018) Shao-peng Li et al.   ISME Journal

When can competition and dispersal lead to checkerboard distributions?

(2018) Tad Dallas et al.   JOURNAL OF ANIMAL ECOLOGY

Fire modifies the phylogenetic structure of soil bacterial co-occurrence networks

(2017) Eduardo Pérez-Valera et al.   ENVIRONMENTAL MICROBIOLOGY

A meta-analysis of nestedness and turnover components of beta diversity across organisms and ecosystems

(2017) Janne Soininen et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

Using null models to infer microbial co-occurrence networks

(2017) Nora Connor et al.   PLoS One

Antagonism correlates with metabolic similarity in diverse bacteria

(2017) Jakob Russel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China

(2016) Bin Ma et al.   ISME Journal

Predicting microbial traits with phylogenies

(2015) Marta Goberna et al.   ISME Journal

Marine microbial community dynamics and their ecological interpretation

(2015) Jed A. Fuhrman et al.   NATURE REVIEWS MICROBIOLOGY

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

(2014) Marta Goberna et al.   ECOLOGY LETTERS

A role for biotic filtering in driving phylogenetic clustering in soil bacterial communities

(2014) Marta Goberna et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Type VI secretion system effectors: poisons with a purpose

(2014) Alistair B. Russell et al.   NATURE REVIEWS MICROBIOLOGY

Nurses experience reciprocal fitness benefits from their distantly related facilitated plants

(2014) Lugui Sortibrán et al.   PERSPECTIVES IN PLANT ECOLOGY EVOLUTION AND SYSTEMATICS

What nurse shrubs can do for barren soils: rapid productivity shifts associated with a 40 years ontogenetic gradient

(2014) Jose Antonio Navarro-Cano et al.   PLANT AND SOIL

Plant Facilitation and Phylogenetics

(2013) Alfonso Valiente-Banuet et al.   Annual Review of Ecology Evolution and Systematics

Characterizing the distribution and rates of microbial sulfate reduction at Middle Valley hydrothermal vents

(2013) Kiana L Frank et al.   ISME Journal

Bacterial Communities in Pigmented Biofilms Formed on the Sandstone Bas-Relief Walls of the Bayon Temple, Angkor Thom, Cambodia

(2013) Asako Kusumi et al.   MICROBES AND ENVIRONMENTS

Plant phylodiversity enhances soil microbial productivity in facilitation-driven communities

(2013) José Antonio Navarro-Cano et al.   OECOLOGIA

Soil microbial community under a nurse-plant species changes in composition, biomass and activity as the nurse grows

(2013) S. Hortal et al.   SOIL BIOLOGY & BIOCHEMISTRY

Evolutionary history predicts the stability of cooperation in microbial communities

(2013) Alexandre Jousset et al.   Nature Communications

Rethinking Community Assembly through the Lens of Coexistence Theory

(2012) J. HilleRisLambers et al.   Annual Review of Ecology Evolution and Systematics

treePL: divergence time estimation using penalized likelihood for large phylogenies

(2012) Stephen A. Smith et al.   BIOINFORMATICS

Competition, Not Cooperation, Dominates Interactions among Culturable Microbial Species

(2012) Kevin R. Foster et al.   CURRENT BIOLOGY

Stochastic and deterministic assembly processes in subsurface microbial communities

(2012) James C Stegen 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

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

(2012) J. J. Morris et al.   mBio

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

(2012) Steven W. Kembel et al.   PLoS Computational Biology

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

(2011) Albert Barberán et al.   ISME Journal

Differential Growth Responses of Soil Bacterial Taxa to Carbon Substrates of Varying Chemical Recalcitrance

(2011) Katherine C. Goldfarb et al.   Frontiers in Microbiology

Planctomycetes dominate biofilms on surfaces of the kelp Laminaria hyperborea

(2010) Mia M Bengtsson et al.   BMC MICROBIOLOGY

Opposing effects of competitive exclusion on the phylogenetic structure of communities

(2010) Margaret M. Mayfield et al.   ECOLOGY LETTERS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Bacterial Quorum-Sensing Network Architectures

(2009) Wai-Leung Ng et al.   Annual Review of Genetics

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

Partitioning the turnover and nestedness components of beta diversity

(2009) Andrés Baselga   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Bacterial competition: surviving and thriving in the microbial jungle

(2009) Michael E. Hibbing et al.   NATURE REVIEWS MICROBIOLOGY

Dispersal leads to spatial autocorrelation in species distributions: A simulation model

(2008) Volker Bahn et al.   ECOLOGICAL MODELLING