ArticleProceedings of the National Academy of Sciences of the United States of America2022
LOCOM: A logistic regression model for testing differential abundance in compositional microbiome data with false discovery rate control.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers, 3 of them syntheses that pooled it.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
34 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Melody: meta-analysis of microbiome association studies for discovering generalizable microbial signatures.Genome biology · 2025Pooled it
- Meta-analysis of gut microbiome reveals patterns of dysbiosis in colorectal cancer patients.Journal of medical microbiology · 2025Pooled it
- A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules.Cell host & microbe · 2025Pooled it
- Article
- TestNet: a method for inferring microbial networks with false discovery rate control for clustered and unclustered samples.Genome biology · 2026Article
- Article
- Fast and reliable association discovery in large-scale microbiome studies and meta-analyses using PALM.bioRxiv : the preprint server for biology · 2026Article
- MaAsLin 3: refining and extending generalized multivariable linear models for meta-omic association discovery.Nature methods · 2026Article
- The Oral Microbiome Is a Population-Scale Readout of the Exposome, Age, and Systemic Health.bioRxiv : the preprint server for biology · 2026Article
- CAFT: A Compositional Log-Linear Model for Microbiome Data with Zero Cells.bioRxiv : the preprint server for biology · 2025Article
- TCVS: tree-guided compositional variable selection analysis of microbiome data.Bioinformatics (Oxford, England) · 2025Article
- BMDD: A probabilistic framework for accurate imputation of zero-inflated microbiome sequencing data.PLoS computational biology · 2025Article
- Integrative analysis of microbial 16S gene and shotgun metagenomic sequencing data improves statistical efficiency in testing differential abundance.Journal of the American Statistical Association · 2025Article
- Compositional transformations can reasonably introduce phenotype-associated values into sparse features.mSystems · 2025Article
- TphPMF: A microbiome data imputation method using hierarchical Bayesian Probabilistic Matrix Factorization.PLoS computational biology · 2025Article
- Compositional transformations can reasonably introduce phenotype-associated values into sparse features.bioRxiv : the preprint server for biology · 2025Article
- Rectal mucosal inflammation, microbiome, and wound healing in men who have sex with men who engage in receptive anal intercourse.Scientific reports · 2024Article
- Article
- Revisiting microgenderome: detecting and cataloguing sexually unique and enriched species in human microbiomes.BMC biology · 2024Article
- Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Compositional analysis is based on the premise that a relatively small proportion of taxa are differentially abundant, while the ratios of the relative abundances of the remaining taxa remain unchanged. Most existing methods use log-transformed data, but log-transformation of data with pervasive zero counts is problematic, and these methods cannot always control the false discovery rate (FDR). Further, high-throughput microbiome data such as 16S amplicon or metagenomic sequencing are subject to experimental biases that are introduced in every step of the experimental workflow. McLaren et al. [
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Registered trials
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