ArticleGenome biology2016
MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses.
Article in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 165 papers.
What it found
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Who cites it
165 citing papers in PubMed.
- LGTM: Gaussian process modulated neural topic modeling for longitudinal microbiome.Gut microbes · 2026Article
- Advances in causal discovery methods for ecological time series.Biological reviews of the Cambridge Philosophical Society · 2026Review
- Quantifying antibiotic susceptibility and inoculum effects using transient dynamics of Pseudomonas aeruginosa.PLoS computational biology · 2026Article
- Deciphering microbial community dynamics using cross-sectional data-informed NeuralODE.Microbiome · 2026Article
- CoDaLoMic: An R package for modeling microbiome compositional and longitudinal data.PLoS computational biology · 2026Article
- Dissimilarity measures for generalized Lotka-Volterra systems on networks.Scientific reports · 2026Article
- Dynamical Systems-Constrained Metabolic Modeling Enables Forecasting of Host-Microbiome Dynamics.bioRxiv : the preprint server for biology · 2026Article
- The importance of regulated resource reallocation during dynamic environmental shifts in yeast.The EMBO journal · 2026Article
- Physics-constrained neural ordinary differential equation models to discover and predict microbial community dynamics.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- KeySDL: sparse dictionary learning for keystone microbe identification from steady-state observations using a dynamical-systems model.BioData mining · 2026Article
- Gut-lung microbial dynamics with lumacaftor/ivacaftor in children with cystic fibrosis: a prospective multicenter study.Pediatric research · 2026Article
- Resource landscape shapes the composition and stability of the human vaginal microbiota.PLoS biology · 2026Article
- Bayesian Pairwise Compositional Lotka-Volterra Modeling Infers Potential Rhizosphere Microbial Suppressors of Ralstonia pseudosolanacearum.The plant pathology journal · 2026Article
- DepMicroDiff: Diffusion-Based Dependency-Aware Multimodal Imputation for Microbiome Data.Computational and structural biotechnology journal · 2026Article
- gNODE: gLV model-informed neural ordinary differential equations for modeling microbial community dynamics.Frontiers in cellular and infection microbiology · 2026Article
- A temporal-aware machine learning framework enables microbial community dynamics prediction with personalized precision.Microbiome · 2025Article
- MCSPACE: inferring microbiome spatiotemporal dynamics from high-throughput co-localization data.Microbiome · 2025Article
- Emergence of alternative states in a synthetic human gut microbial community.Nature communications · 2025Article
- Credible inferences in microbiome research: ensuring rigour, reproducibility and relevance in the era of AI.Nature reviews. Gastroenterology & hepatology · 2025Review
- Quantifying microbial interactions based on compositional data using an iterative approach for solving generalized Lotka-Volterra equations.PLoS computational biology · 2025Article
105 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
15 authors.
Funding
Abstract
Predicting dynamics of host-microbial ecosystems is crucial for the rational design of bacteriotherapies. We present MDSINE, a suite of algorithms for inferring dynamical systems models from microbiome time-series data and predicting temporal behaviors. Using simulated data, we demonstrate that MDSINE significantly outperforms the existing inference method. We then show MDSINE's utility on two new gnotobiotic mice datasets, investigating infection with Clostridium difficile and an immune-modulatory probiotic. Using these datasets, we demonstrate new capabilities, including accurate forecasting of microbial dynamics, prediction of stable sub-communities that inhibit pathogen growth, and identification of bacteria most crucial to community integrity in response to perturbations.
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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.