ArticleGenome biology2021
mbImpute: an accurate and robust imputation method for microbiome data.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Periodontitis during pregnancy: The effect on the gut microbiome and intestinal inflammation.Journal of periodontology · 2026Article
- Chimeric reference panels for genomic imputation.Genetics · 2026Article
- DeepIMB: Imputation of non-biological zero counts in microbiome data.Genes & genomics · 2026Article
- Reducing bias and enhancing equity in AI-enabled precision nutrition: addressing measurement error across wearables, multiomics, and dietary data.Frontiers in digital health · 2026Review
- mbSparse: an autoencoder-based imputation method to address sparsity in microbiome data.Gut microbes · 2025Article
- BMDD: A probabilistic framework for accurate imputation of zero-inflated microbiome sequencing data.PLoS computational biology · 2025Article
- mcRigor: a statistical method to enhance the rigor of metacell partitioning in single-cell data analysis.Nature communications · 2025Article
- Article
- TphPMF: A microbiome data imputation method using hierarchical Bayesian Probabilistic Matrix Factorization.PLoS computational biology · 2025Article
- SpeSpeNet: an interactive and user-friendly tool to create and explore microbial correlation networks.ISME communications · 2025Article
- Semisynthetic simulation for microbiome data analysis.Briefings in bioinformatics · 2024Review
- PhyImpute and UniFracImpute: two imputation approaches incorporating phylogeny information for microbial count data.Briefings in bioinformatics · 2024Article
- Article
- mbtransfer: Microbiome intervention analysis using transfer functions and mirror statistics.PLoS computational biology · 2024Article
- A strategy for differential abundance analysis of sparse microbiome data with group-wise structured zeros.Scientific reports · 2024Article
- Relative dispersion ratios following fecal microbiota transplant elucidate principles governing microbial migration dynamics.Nature communications · 2024Article
- The impact of antibiotics on the gut microbiota of children recovering from watery diarrhoea.npj antimicrobials and resistance · 2024Article
- A comprehensive overview of microbiome data in the light of machine learning applications: categorization, accessibility, and future directions.Frontiers in microbiology · 2024Review
- Structure-adaptive canonical correlation analysis for microbiome multi-omics data.Frontiers in genetics · 2024Article
- mb-PHENIX: diffusion and supervised uniform manifold approximation for denoizing microbiota data.Bioinformatics (Oxford, England) · 2023Article
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Authors and funding
3 authors.
Funding
Abstract
A critical challenge in microbiome data analysis is the existence of many non-biological zeros, which distort taxon abundance distributions, complicate data analysis, and jeopardize the reliability of scientific discoveries. To address this issue, we propose the first imputation method for microbiome data-mbImpute-to identify and recover likely non-biological zeros by borrowing information jointly from similar samples, similar taxa, and optional metadata including sample covariates and taxon phylogeny. We demonstrate that mbImpute improves the power of identifying disease-related taxa from microbiome data of type 2 diabetes and colorectal cancer, and mbImpute preserves non-zero distributions of taxa abundances.
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Registered trials
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