ArticleGenome biology2022
mbDenoise: microbiome data denoising using zero-inflated probabilistic principal components analysis.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Robust and Interpretable Metagenomic Modeling Through Structure-Aware Multi-View Learning and Attribution-Guided Biological Insight.Research square · 2026Article
- Environmental stress strengthens plant-mycorrhizal associations: A novel extension of the stress gradient hypothesis.Ecology · 2026Article
- Truncated Gaussian copula principal component analysis with application to pediatric acute lymphoblastic leukemia patients' gut microbiome.Statistical methods in medical research · 2026Article
- mbSparse: an autoencoder-based imputation method to address sparsity in microbiome data.Gut microbes · 2025Article
- Denoising single-cell RNA-seq data with a deep learning-embedded statistical framework.BMC bioinformatics · 2025Article
- BMDD: A probabilistic framework for accurate imputation of zero-inflated microbiome sequencing data.PLoS computational biology · 2025Article
- Linear Dimensionality Reduction Methods for Analyzing Structured Biomedical Data: Existing Research and Future Opportunities.Wiley interdisciplinary reviews. Computational statistics · 2025Review
- Article
- Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives.Briefings in bioinformatics · 2025Review
- TphPMF: A microbiome data imputation method using hierarchical Bayesian Probabilistic Matrix Factorization.PLoS computational biology · 2025Article
- Exposome Burden Scores to Summarize Environmental Chemical Mixtures: Creating a Fair and Common Scale for Cross-study Harmonization, Report-back and Precision Environmental Health.Current environmental health reports · 2025Review
- SpeSpeNet: an interactive and user-friendly tool to create and explore microbial correlation networks.ISME communications · 2025Article
- Wise Roles and Future Visionary Endeavors of Current Emperor: Advancing Dynamic Methods for Longitudinal Microbiome Meta-Omics Data in Personalized and Precision Medicine.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Review
- Semisynthetic simulation for microbiome data analysis.Briefings in bioinformatics · 2024Review
- mbDriver: identifying driver microbes in microbial communities based on time-series microbiome data.Briefings in bioinformatics · 2024Article
- A strategy for differential abundance analysis of sparse microbiome data with group-wise structured zeros.Scientific reports · 2024Article
- Article
- Structure-adaptive canonical correlation analysis for microbiome multi-omics data.Frontiers in genetics · 2024Article
- Unique Gut Microbiome Signatures among Adult Patients with Moderate to Severe Atopic Dermatitis in Southern Chinese.International journal of molecular sciences · 2023Article
- Author Correction: mbDenoise: microbiome data denoising using zero-inflated probabilistic principal components analysis.Genome biology · 2023Article
Corrections and comments
- Erratum issued
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The analysis of microbiome data has several technical challenges. In particular, count matrices contain a large proportion of zeros, some of which are biological, whereas others are technical. Furthermore, the measurements suffer from unequal sequencing depth, overdispersion, and data redundancy. These nuisance factors introduce substantial noise. We propose an accurate and robust method, mbDenoise, for denoising microbiome data. Assuming a zero-inflated probabilistic PCA (ZIPPCA) model, mbDenoise uses variational approximation to learn the latent structure and recovers the true abundance levels using the posterior, borrowing information across samples and taxa. mbDenoise outperforms state-of-the-art methods to extract the signal for downstream analyses.
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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.