ArticleBiometrics2021
Zero-inflated Poisson factor model with application to microbiome read counts.
Article in Biometrics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 45 citations in OpenAlex.
- A joint mixture Tobit method with latent microbial abundance improves detection of microbiome-disease associations in zero-inflated data.PLoS computational biology · 2026Article
- Spatial mixed models for assessing environmental exposure effects on the microbiome.Genome medicine · 2026Article
- Upper Respiratory Tract Resistome Exhibits SARS-CoV-2-associated Antimicrobial Resistance Patterns.Current microbiology · 2026Article
- Truncated Gaussian copula principal component analysis with application to pediatric acute lymphoblastic leukemia patients' gut microbiome.Statistical methods in medical research · 2026Article
- Variational inference for microbiome survey data with application to global ocean data.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
- MicroNet-MIMRF: a microbial network inference approach based on mutual information and Markov random fields.Bioinformatics advances · 2024Article
- A GLM-based zero-inflated generalized Poisson factor model for analyzing microbiome data.Frontiers in microbiology · 2024Article
- Bayesian biclustering for microbial metagenomic sequencing data via multinomial matrix factorization.Biostatistics (Oxford, England) · 2022Article
- Negative binomial factor regression with application to microbiome data analysis.Statistics in medicine · 2022Article
- mbDenoise: microbiome data denoising using zero-inflated probabilistic principal components analysis.Genome biology · 2022Article
- Applications and Comparison of Dimensionality Reduction Methods for Microbiome Data.Frontiers in bioinformatics · 2022Review
- Assessing the Relationship Between Nitrate-Reducing Capacity of the Oral Microbiome and Systemic Outcomes.Methods in molecular biology (Clifton, N.J.) · 2021Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Dimension reduction of high-dimensional microbiome data facilitates subsequent analysis such as regression and clustering. Most existing reduction methods cannot fully accommodate the special features of the data such as count-valued and excessive zero reads. We propose a zero-inflated Poisson factor analysis model in this paper. The model assumes that microbiome read counts follow zero-inflated Poisson distributions with library size as offset and Poisson rates negatively related to the inflated zero occurrences. The latent parameters of the model form a low-rank matrix consisting of interpretable loadings and low-dimensional scores that can be used for further analyses. We develop an efficient and robust expectation-maximization algorithm for parameter estimation. We demonstrate the efficacy of the proposed method using comprehensive simulation studies. The application to the Oral Infections, Glucose Intolerance, and Insulin Resistance Study provides valuable insights into the relation between subgingival microbiome and periodontal disease.
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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.