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2024
Dead in the water – Role of relic DNA and primer choice for targeted sequencing surveys of anaerobic sewage sludge intended for biological monitoring
Water Research
2024
A flexible Bayesian tool for CoDa mixed models: logistic-normal distribution with Dirichlet covariance
Statistics and Computing
2023
Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses
Genome Biology
2023
Pitfalls in the statistical analysis of microbiome amplicon sequencing data
Molecular Ecology Resources
2023
Dynamics of the Apostichopus californicus-associated flavivirus under suboxic conditions and organic matter amendment
Frontiers in Marine Science
2023
Best practice for wildlife gut microbiome research: A comprehensive review of methodology for 16S rRNA gene investigations
Frontiers in Microbiology
2023
Impact of HIV on the Oral Microbiome of Children Living in Sub-Saharan Africa, Determined by Using an rpoC Gene Fragment Metataxonomic Approach
Microbiology Spectrum
2023
Homogeneous Environmental Selection Structures the Bacterial Communities of Benthic Biofilms in Proglacial Floodplain Streams
Applied and Environmental Microbiology
2023
Plant microbiota dysbiosis and the Anna Karenina Principle
Trends in Plant Science
2023
Bioinformatic and Statistical Analysis of Microbiome Data
2023
The Integrated Nested Laplace Approximation for Fitting Dirichlet Regression Models
Journal of Computational and Graphical Statistics
2023
A Synthetic Formula Amino Acid Diet Leads to Microbiome Dysbiosis, Reduced Colon Length, Inflammation, and Altered Locomotor Activity in C57BL/6J Mice
Microorganisms
2022
Phenol and Polyaromatic Hydrocarbons Are Stronger Drivers Than Host Plant Species in Shaping the Arbuscular Mycorrhizal Fungal Component of the Mycorrhizosphere
International Journal of Molecular Sciences
2022
Principal microbial groups: compositional alternative to phylogenetic grouping of microbiome data
Briefings in Bioinformatics
2022
Hierarchical phylogenetic community assembly of soil protists in a temperate agricultural field
Environmental Microbiology
2022
Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade
Frontiers in Bioinformatics
2022
Biochar reduced extractable dieldrin concentrations and promoted oligotrophic growth including microbial degraders of chlorinated pollutants
Journal of Hazardous Materials
2022
Glacier shrinkage will accelerate downstream decomposition of organic matter and alters microbiome structure and function
Global Change Biology
2022
Microdiversity characterizes prevalent phylogenetic clades in the glacier-fed stream microbiome
The ISME Journal
2022
Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy
mSystems
2021
Assessment of phylo-functional coherence along the bacterial phylogeny and taxonomy
Scientific Reports
2021
Geographic differences in gut microbiota composition impact susceptibility to enteric infection
Cell Reports
2021
The Adult Phenylketonuria (PKU) Gut Microbiome
Microorganisms
2021
EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets
mSystems
2021
Plant‐bacteria associations are phylogenetically structured in the phyllosphere
Molecular Ecology
2021
Advances in Compositional Data Analysis
2021
Evidence That Microorganisms at the Animal-Water Interface Drive Sea Star Wasting Disease
Frontiers in Microbiology
2021
Quantification of the covariation of lake microbiomes and environmental variables using a machine learning‐based framework
Molecular Ecology
2021
Chemically informed analyses of metabolomics mass spectrometry data with Qemistree
Nature Chemical Biology
2021
Tree-aggregated predictive modeling of microbiome data
Scientific Reports
2021
Learning sparse log-ratios for high-throughput sequencing data
Bioinformatics
2021
Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions
Frontiers in Microbiology
2021
Highly decomposed organic carbon mediates the assembly of soil communities with traits for the biodegradation of chlorinated pollutants
Journal of Hazardous Materials
2020
A phylogenetic model for the recruitment of species into microbial communities and application to studies of the human microbiome
The ISME Journal
2020
Incorporating Phylogenetic Information in Microbiome Differential Abundance Studies Has No Effect on Detection Power and FDR Control
Frontiers in Microbiology
2020
A Bayesian analysis for pseudo-compositional data with spatial structure
Statistical Methods in Medical Research
2020
Applications of weighted association networks applied to compositional data in biology
Environmental Microbiology
2020
Amalgams: data-driven amalgamation for the dimensionality reduction of compositional data
NAR Genomics and Bioinformatics
2020
The Lizard Gut Microbiome Changes with Temperature and Is Associated with Heat Tolerance
Applied and Environmental Microbiology
2020
Variable selection in microbiome compositional data analysis
NAR Genomics and Bioinformatics
2020
Comparison of the Bacterial Gut Microbiome of North American Triatoma spp. With and Without Trypanosoma cruzi
Frontiers in Microbiology
2020
Rare microbial taxa emerge when communities collide: freshwater and marine microbiome responses to experimental mixing
Ecology
2020
Environmental Atlas of Prokaryotes Enables Powerful and Intuitive Habitat-Based Analysis of Community Structures
iScience
2020
Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data
Bioinformatics
2020
Analysis of microbial compositions: a review of normalization and differential abundance analysis
npj Biofilms and Microbiomes
2020
Subspecies Niche Specialization in the Oral Microbiome Is Associated with Nasopharyngeal Carcinoma Risk
mSystems
2020
A Bayesian model of microbiome data for simultaneous identification of covariate associations and prediction of phenotypic outcomes
The Annals of Applied Statistics
2020
Interpretable Log Contrasts for the Classification of Health Biomarkers: a New Approach to Balance Selection
mSystems
2020
Identifying Suspect Bat Reservoirs of Emerging Infections
Vaccines
2020
Phylogenetic conservation of soil bacterial responses to simulated global changes
Philosophical Transactions of the Royal Society B: Biological Sciences
2019
The intestinal environment as an evolutionary adaptation to mouthbrooding in the Astatotilapia burtoni cichlid
FEMS Microbiology Ecology
2019
The Microbiome Stress Project: Toward a Global Meta-Analysis of Environmental Stressors and Their Effects on Microbial Communities
Frontiers in Microbiology
2019
Establishing microbial composition measurement standards with reference frames
Nature Communications
2019
Phylogenetic conservation of bacterial responses to soil nitrogen addition across continents
Nature Communications
2019
Microbiome data science
Journal of Biosciences
2019
A field guide for the compositional analysis of any-omics data
GigaScience
2019
Phylofactorization: a graph partitioning algorithm to identify phylogenetic scales of ecological data
Ecological Monographs
2019
Scalable methods for analyzing and visualizing phylogenetic placement of metagenomic samples
PLOS ONE
2019
Gut microbial diversity increases with social rank in the African cichlid fish, Astatotilapia burtoni
Animal Behaviour
2018
Dynamic linear models guide design and analysis of microbiota studies within artificial human guts
Microbiome
2018
Toward Personalized Control of Human Gut Bacterial Communities
mSystems
2018
Ecophylogenetics Clarifies the Evolutionary Association between Mammals and Their Gut Microbiota
mBio
2018
Best practices for analysing microbiomes
Nature Reviews Microbiology
2018
Methods for phylogenetic analysis of microbiome data
Nature Microbiology
2018
Balances: a New Perspective for Microbiome Analysis
mSystems
2018
Guiding longitudinal sampling in IBD cohorts
Gut
2018
Understanding sequencing data as compositions: an outlook and review
Bioinformatics
2018
Taxonomic patterns in the zoonotic potential of mammalian viruses
PeerJ
2017
Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment
PLOS Computational Biology
2017
SigTree : A Microbial Community Analysis Tool to Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree
Computational and Structural Biotechnology Journal
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