ArticleNPJ systems biology and applications2023
EMBED: Essential MicroBiomE Dynamics, a dimensionality reduction approach for longitudinal microbiome studies.
Article in NPJ systems biology and applications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Microbiome assembly statistics toward ecosystem-scale insights, forecasting, and management.The ISME journal · 2026Review
- Review
- Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions.Briefings in bioinformatics · 2025Review
- Linear scaling reveals low-dimensional structure in observable microbial dynamics.bioRxiv : the preprint server for biology · 2025Article
- Soft Modes as a Predictive Framework for Low-Dimensional Biological Systems Across Scales.Annual review of biophysics · 2025Review
- Dynamic coexistence driven by physiological transitions in microbial communities.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Article
- TEMPTED: time-informed dimensionality reduction for longitudinal microbiome studies.Genome biology · 2024Article
- Soft Modes as a Predictive Framework for Low Dimensional Biological Systems across Scales.ArXiv · 2024Article
- 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
- TENSOR REGRESSION FOR INCOMPLETE OBSERVATIONS WITH APPLICATION TO LONGITUDINAL STUDIES.The annals of applied statistics · 2024Article
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Authors and funding
3 authors.
Funding
Abstract
Dimensionality reduction offers unique insights into high-dimensional microbiome dynamics by leveraging collective abundance fluctuations of multiple bacteria driven by similar ecological perturbations. However, methods providing lower-dimensional representations of microbiome dynamics both at the community and individual taxa levels are not currently available. To that end, we present EMBED: Essential MicroBiomE Dynamics, a probabilistic nonlinear tensor factorization approach. Like normal mode analysis in structural biophysics, EMBED infers ecological normal modes (ECNs), which represent the unique orthogonal modes capturing the collective behavior of microbial communities. Using multiple real and synthetic datasets, we show that a very small number of ECNs can accurately approximate microbiome dynamics. Inferred ECNs reflect specific ecological behaviors, providing natural templates along which the dynamics of individual bacteria may be partitioned. Moreover, the multi-subject treatment in EMBED systematically identifies subject-specific and universal abundance dynamics that are not detected by traditional approaches. Collectively, these results highlight the utility of EMBED as a versatile dimensionality reduction tool for studies of microbiome dynamics.
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