Incorporating Phylogenetic Information in Microbiome Differential Abundance Studies Has No Effect on Detection Power and FDR Control

In situ relationships between microbiota and potential pathobiota in Arabidopsis thaliana

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Predictive Modeling of Microbiome Data Using a Phylogeny-Regularized Generalized Linear Mixed Model

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GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data

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MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data

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Where less may be more: how the rare biosphere pulls ecosystems strings

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Proteomic insight into the mitigation of wheat root drought stress by arbuscular mycorrhizae

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Linking Statistical and Ecological Theory: Hubbell's Unified Neutral Theory of Biodiversity as a Hierarchical Dirichlet Process

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Gut microbiome influences efficacy of PD-1–based immunotherapy against epithelial tumors

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Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets

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Discrete False-Discovery Rate Improves Identification of Differentially Abundant Microbes

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Tiny Microbes, Big Yields: enhancing food crop production with biological solutions

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Gut Microbial Diversity Is Reduced in Smokers with Crohnʼs Disease

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The Human Intestinal Microbiome in Health and Disease

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A reference gene catalogue of the pig gut microbiome

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Swarm v2: highly-scalable and high-resolution amplicon clustering

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structSSI: Simultaneous and Selective Inference for Grouped or Hierarchically Structured Data

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Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences

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Alterations of the human gut microbiome in liver cirrhosis

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An integrated catalog of reference genes in the human gut microbiome

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Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

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Identification of important regressor groups, subgroups and individuals via regularization methods: application to gut microbiome data

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A comparison of methods for differential expression analysis of RNA-seq data

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Edge Principal Components and Squash Clustering: Using the Special Structure of Phylogenetic Placement Data for Sample Comparison

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A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

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The Inheritance Procedure: Multiple Testing of Tree-structured Hypotheses

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Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

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Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria

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Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

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QIIME allows analysis of high-throughput community sequencing data

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The ecological coherence of high bacterial taxonomic ranks

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FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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Hierarchical False Discovery Rate–Controlling Methodology

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