ArticleGenome biology2022
LinDA: linear models for differential abundance analysis of microbiome compositional data.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 267 papers, 1 of them a synthesis that pooled it.
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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
267 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Melody: meta-analysis of microbiome association studies for discovering generalizable microbial signatures.Genome biology · 2025Pooled it
- Effect of pasteurizedGut microbes · 2026Trial
- Increasing gut short-chain fatty acids protects intestinal barrier function but does not spare muscle glycogen or impact aerobic performance.The Journal of physiology · 2026Trial
- Baseline gut microbiome and metabolome profiles predict weight loss after a structured lifestyle intervention.Microbiome · 2026Trial
- The Effects of a Powdered Meal Replacement on Inflammation, Gut Microbiota, and Metabolism in People With Excess Body Weight-A Randomized Controlled Trial.The Journal of nutrition · 2026Trial
- Pasteurized Akkermansia muciniphila MucNature medicine · 2026Trial
- Trial
- Early Microbiological and Immunological Parameters in Sandblasted, Large-Grit Acid-Etched Implant Surfaces: A Split Mouth Randomized Clinical Trial.Clinical oral implants research · 2026Trial
- Cholesterol-lowering effects of oats induced by microbially produced phenolic metabolites in metabolic syndrome: a randomized controlled trial.Nature communications · 2026Trial
- A young child formula with Limosilactobacillus reuteri and GOS modulates gut microbiome and enhances bone and muscle development: a randomized trial.Nature communications · 2025Trial
- Consecutive fecal microbiota transplantation for metabolic dysfunction-associated steatotic liver disease: a randomized controlled trial.Gut microbes · 2025Trial
- Effect of sweeteners and sweetness enhancers on weight management and gut microbiota composition in individuals with overweight or obesity: the SWEET study.Nature metabolism · 2025Trial
- Neoadjuvant cobimetinib and atezolizumab with or without vemurafenib for stage III melanoma: outcomes and the impact of the microbiome from the NeoACTIVATE trial.Journal for immunotherapy of cancer · 2025Trial
- Trial
- Trial
- Article
- Sex modulates the long-term effects of delivery mode on microbiota-gut barrier crosstalk and colitis susceptibility in mice.Gut microbes · 2026Article
- Dynamic flexibility of the murine gut microbiota during morphine disturbance enables escape from the stable dysbiosis that is associated with addiction-like behavior.Gut microbes · 2026Article
- The role of gut microbiota in chronic intestinal pseudo-obstruction: exploring fecal microbiota transplantation as a treatment option.Gut microbes · 2026Article
- From gut to brain: data-driven evidence suggests causal contribution of gut-microbiota to major depressive disorder in humans.Gut microbes · 2026Article
207 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Differential abundance analysis is at the core of statistical analysis of microbiome data. The compositional nature of microbiome sequencing data makes false positive control challenging. Here, we show that the compositional effects can be addressed by a simple, yet highly flexible and scalable, approach. The proposed method, LinDA, only requires fitting linear regression models on the centered log-ratio transformed data, and correcting the bias due to compositional effects. We show that LinDA enjoys asymptotic FDR control and can be extended to mixed-effect models for correlated microbiome data. Using simulations and real examples, we demonstrate the effectiveness of LinDA.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.