ArticleNature methods2026
MaAsLin 3: refining and extending generalized multivariable linear models for meta-omic association discovery.
Article in Nature methods, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers.
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Who cites it
92 citing papers in PubMed.
- Combined high-quality metagenomics reveals off-target effects of albendazole, ivermectin-albendazole and moxidectin-albendazole on the human gut bacteria.NPJ biofilms and microbiomes · 2026Trial
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- Polyphenol-rich sugarcane extract reduces circulatingFrontiers in nutrition · 2026Trial
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- GutMIND: A multi-cohort machine learning framework for integrative characteristics of the microbiota-gut-brain axis in neuropsychiatric disorders.Gut microbes · 2026Article
- Maternal diet shapes neonatal microbiome ontogenesis and neurometabolic resilience.Gut microbes · 2026Article
- CRISPR-Cas immune repertoires as an ecological record of bacterial interactions with mobile genetic elements in the human gut.Gut microbes · 2026Article
- High dietary BGut microbes · 2026Article
- Lung microbiome features associated with ICU delirium in mechanically ventilated patients: a secondary cohort analysis.Brain, behavior, & immunity - health · 2026Article
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- The effect of pectin supplementation on geriatric individuals with frailty: a randomised placebo-controlled dietary intervention study.GeroScience · 2026Article
- Environmental microbial community signatures associated withApplied and environmental microbiology · 2026Article
- Cervicovaginal Virome Restructuring Associated with HPV Status, Bacterial Dysbiosis, and Cervical Cytological Abnormalities.Viruses · 2026Article
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- The planktonic microbiome of the Great Barrier Reef.Nature · 2026Article
- IRS: iterative reference selection improves normalization of microbiome sequencing data.Briefings in bioinformatics · 2026Article
- Identification of Microbiome Associations with Tacrolimus Pharmacokinetics in Adult Hematopoietic Cell Transplantation Using Population Pharmacokinetic and Machine Learning.Pharmaceutical research · 2026Observational
- Gardnerella enrichment in the vaginal microbiome of women with gestational diabetes mellitus is associated with lower fetal birthweight percentiles.Diabetologia · 2026Observational
- Intestinal fructose catabolism promotes obesity and insulin resistance via ileal lacteal remodeling.Science advances · 2026Article
32 more citing papers are in PubMed but not listed here.
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9 authors.
Funding
Abstract
Microbial community analysis typically involves determining which microbial features are associated with properties such as environmental or health phenotypes. This task is impeded by data characteristics, including sparsity (technical or biological) and compositionality. Here we introduce MaAsLin 3 (microbiome multivariable associations with linear models) to simultaneously identify both abundance and prevalence relationships in microbiome studies with modern, potentially complex designs. MaAsLin 3 can newly account for compositionality either experimentally (for example, quantitative PCR or spike-ins) or computationally, and it expands the range of testable biological hypotheses and covariate types. On a variety of synthetic and real datasets, MaAsLin 3 outperformed state-of-the-art differential abundance methods, and when applied to the Inflammatory Bowel Disease Multi-omics Database, MaAsLin 3 corroborated previously reported associations, identifying 77% with feature prevalence rather than abundance. In summary, MaAsLin 3 enables researchers to identify microbiome associations more accurately and specifically, especially in complex datasets.
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