Investigating microbial associations from sequencing survey data with co‐correspondence analysis

Characterizing both bacteria and fungi improves understanding of the Arabidopsis root microbiome

(2019) Joy Bergelson et al.   Scientific Reports

Algorithms and biplots for double constrained correspondence analysis

(2018) Cajo J. F. ter Braak et al.   ENVIRONMENTAL AND ECOLOGICAL STATISTICS

Distinct patterns and processes of abundant and rare eukaryotic plankton communities following a reservoir cyanobacterial bloom

(2018) Yuanyuan Xue et al.   ISME Journal

Fungi stabilize connectivity in the lung and skin microbial ecosystems

(2018) Laura Tipton et al.   Microbiome

Dynamic microbial populations along the Cuyahoga River

(2017) Matthew V. Cannon et al.   PLoS One

Microorganisms and ocean global change

(2017) David A. Hutchins et al.   Nature Microbiology

Microbial interactions and community assembly at microscales

(2016) Otto X Cordero et al.   CURRENT OPINION IN MICROBIOLOGY

Network-based metabolic analysis and microbial community modeling

(2016) Cesar Cardona et al.   CURRENT OPINION IN MICROBIOLOGY

Merging evolutionary history into species interaction networks

(2016) Guadalupe Peralta   FUNCTIONAL ECOLOGY

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

(2016) Bin Ma et al.   ISME Journal

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

(2016) Sophie Weiss et al.   ISME Journal

Small-scale variability of protistan planktonic communities relative to environmental pressures and biotic interactions at two adjacent coastal stations

(2016) S Genitsaris et al.   MARINE ECOLOGY PROGRESS SERIES

Application of multivariate statistical techniques in microbial ecology

(2016) O. Paliy et al.   MOLECULAR ECOLOGY

Network analysis reveals functional redundancy and keystone taxa amongst bacterial and fungal communities during organic matter decomposition in an arable soil

(2016) Samiran Banerjee et al.   SOIL BIOLOGY & BIOCHEMISTRY

A comprehensive insight into functional profiles of free-living microbial community responses to a toxic Akashiwo sanguinea bloom

(2016) Caiyun Yang et al.   Scientific Reports

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

(2016) Emily B. Graham et al.   Frontiers in Microbiology

Small-scale variability of protistan planktonic communities relative to environmental pressures and biotic interactions at two adjacent coastal stations

(2016) S Genitsaris et al.   MARINE ECOLOGY PROGRESS SERIES

CCLasso: correlation inference for compositional data through Lasso

(2015) Huaying Fang et al.   BIOINFORMATICS

Investigating microbial co-occurrence patterns based on metagenomic compositional data

(2015) Yuguang Ban et al.   BIOINFORMATICS

Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers

(2015) Sarah J Spencer et al.   ISME Journal

Marked seasonality and high spatial variability of protist communities in shallow freshwater systems

(2015) Marianne Simon et al.   ISME Journal

Inhibitory bacteria reduce fungi on early life stages of endangered Colorado boreal toads (Anaxyrus boreas)

(2015) Jordan G Kueneman et al.   ISME Journal

Data visualization: Mapping the topical space

(2015) Rikke Schmidt Kjærgaard   NATURE

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

(2015) Zachary D. Kurtz et al.   PLoS Computational Biology

Microbiome, Metagenomics, and High-Dimensional Compositional Data Analysis

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

Unveiling of the Diversity of Prasinoviruses (Phycodnaviridae) in Marine Samples by Using High-Throughput Sequencing Analyses of PCR-Amplified DNA Polymerase and Major Capsid Protein Genes

(2014) Camille Clerissi et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Cross-taxon congruence in lake plankton largely independent of environmental gradients

(2014) Korhan Özkan et al.   ECOLOGY

Complex communities of small protists and unexpected occurrence of typical marine lineages in shallow freshwater systems

(2014) Marianne Simon et al.   ENVIRONMENTAL MICROBIOLOGY

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

The unseen world: environmental microbial sequencing and identification methods for ecologists

(2014) Naupaka Zimmerman et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

Global meta-analysis reveals low consistency of biodiversity congruence relationships

(2014) Martin J. Westgate et al.   Nature Communications

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Photosynthetic picoeukaryote assemblages in the South China Sea from the Pearl River estuary to the SEATS station

(2013) W Wu et al.   AQUATIC MICROBIAL ECOLOGY

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

Morphology, Genome Plasticity, and Phylogeny in the Genus Ostreococcus Reveal a Cryptic Species, O. mediterraneus sp. nov. (Mamiellales, Mamiellophyceae)

(2013) Lucie Subirana et al.   PROTIST

A method for detecting modules in quantitative bipartite networks

(2013) Carsten F. Dormann et al.   Methods in Ecology and Evolution

How much metagenomic sequencing is enough to achieve a given goal?

(2013) Jiajia Ni et al.   Scientific Reports

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

The role of biotic interactions in shaping distributions and realised assemblages of species: implications for species distribution modelling

(2012) Mary Susanne Wisz et al.   BIOLOGICAL REVIEWS

Community congruence of plants, invertebrates and birds in natural and constructed shallow open-water wetlands: Do we need to monitor multiple assemblages?

(2012) Rebecca C. Rooney et al.   ECOLOGICAL INDICATORS

Temporal variability in the diversity and composition of stream bacterioplankton communities

(2012) Maria C. Portillo et al.   ENVIRONMENTAL MICROBIOLOGY

Multi-scale structure and geographic drivers of cross-infection within marine bacteria and phages

(2012) Cesar O Flores et al.   ISME Journal

The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

(2012) Laure Guillou et al.   NUCLEIC ACIDS RESEARCH

Metagenomes of the Picoalga Bathycoccus from the Chile Coastal Upwelling

(2012) Daniel Vaulot et al.   PLoS One

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Evaluating and interpreting cross-taxon congruence: Potential pitfalls and solutions

(2011) Margherita Gioria et al.   ACTA OECOLOGICA-INTERNATIONAL JOURNAL OF ECOLOGY

Genomic Analysis at the Single-Cell Level

(2011) Tomer Kalisky et al.   Annual Review of Genetics

Marine Protistan Diversity

(2011) David A. Caron et al.   Annual Review of Marine Science

Unveiling in situ interactions between marine protists and bacteria through single cell sequencing

(2011) Manuel Martinez-Garcia et al.   ISME Journal

Statistical structure of host-phage interactions

(2011) C. O. Flores et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Visualizing Uncertainty About the Future

(2011) D. Spiegelhalter et al.   SCIENCE

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Spatial congruency of benthic diatom, invertebrate, macrophyte, and fish assemblages in European streams

(2010) Richard K. Johnson et al.   ECOLOGICAL APPLICATIONS

Significant CO2 fixation by small prymnesiophytes in the subtropical and tropical northeast Atlantic Ocean

(2010) Ludwig Jardillier et al.   ISME Journal

Abundance, spatial distribution and genetic diversity ofOstreococcus tauriviruses in two different environments

(2010) Laure Bellec et al.   Environmental Microbiology Reports

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

Community concordance between bryophyte and insect assemblages in boreal springs: a broad-scale study in isolated habitats

(2009) RISTO VIRTANEN et al.   FRESHWATER BIOLOGY

Increasing importance of small phytoplankton in a warmer ocean

(2009) XOSÉ ANXELU G. MORÁN et al.   GLOBAL CHANGE BIOLOGY

Simple to sample: Vascular plants as surrogate group in a nature reserve

(2009) E. Santi et al.   JOURNAL FOR NATURE CONSERVATION

Microbial community structure and its functional implications

(2009) Jed A. Fuhrman   NATURE

A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit Ribosomal RNA Genes

(2009) Linda A. Amaral-Zettler et al.   PLoS One

Rules of Engagement: Interspecies Interactions that Regulate Microbial Communities

(2008) Ainslie E.F. Little et al.   Annual Review of Microbiology

Microbial services: challenges for microbial ecologists in a changing world

(2008) H Ducklow   AQUATIC MICROBIAL ECOLOGY

Power transformations in correspondence analysis

(2008) Michael Greenacre   COMPUTATIONAL STATISTICS & DATA ANALYSIS

Wide genetic diversity of picoplanktonic green algae (Chloroplastida) in the Mediterranean Sea uncovered by a phylum-biased PCR approach

(2008) Manon Viprey et al.   ENVIRONMENTAL MICROBIOLOGY

Review: Ecological networks - beyond food webs

(2008) Thomas C. Ings et al.   JOURNAL OF ANIMAL ECOLOGY

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

(2008) Mário Almeida-Neto et al.   OIKOS

The Microbial Engines That Drive Earth's Biogeochemical Cycles

(2008) P. G. Falkowski et al.   SCIENCE