ArticlePloS one2013
Novel multiscale modeling tool applied to Pseudomonas aeruginosa biofilm formation.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
- Beyond Resistance Genes:Life (Basel, Switzerland) · 2026Review
- Precision nutrition through diet-gut microbiome interactions: Emerging insights driven by artificial intelligence, microbiome health metrics, and mechanistic modeling.Gut microbes reports · 2026Review
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- Agent-based model of the human colon to investigate mechanisms of pathogen colonization resistance.Biophysical journal · 2025Article
- Bacterial community dynamics as a result of growth-yield trade-off and multispecies metabolic interactions toward understanding the gut biofilm niche.BMC microbiology · 2024Article
- Computer simulation study of nutrient-driven bacterial biofilm stratification.Journal of the Royal Society, Interface · 2024Article
- Spatial transcriptome-guided multi-scale framework connects P. aeruginosa metabolic states to oxidative stress biofilm microenvironment.PLoS computational biology · 2024Article
- A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia.PLoS computational biology · 2023Article
- Integrating Omics Data in Genome-Scale Metabolic Modeling: A Methodological Perspective for Precision Medicine.Metabolites · 2023Review
- A Holistic Approach from Systems Biology Reveals the Direct Influence of the Quorum-Sensing Phenomenon onMetabolites · 2023Article
- Genome-scale model of Pseudomonas aeruginosa metabolism unveils virulence and drug potentiation.Communications biology · 2023Article
- Emerging computational paradigms to address the complex role of gut microbial metabolism in cardiovascular diseases.Frontiers in cardiovascular medicine · 2022Review
- McComedy: A user-friendly tool for next-generation individual-based modeling of microbial consumer-resource systems.PLoS computational biology · 2022Article
- Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels.Frontiers in microbiology · 2022Review
- A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS).Nature protocols · 2021Article
- Spatio-temporal modeling of the crowding conditions and metabolic variability in microbial communities.PLoS computational biology · 2021Article
- The influence of the crowding assumptions in biofilm simulations.PLoS computational biology · 2021Article
- Mechanistic models of microbial community metabolism.Molecular omics · 2021Review
- Metabolic modeling predicts specific gut bacteria as key determinants for Candida albicans colonization levels.The ISME journal · 2021Article
- Addressing uncertainty in genome-scale metabolic model reconstruction and analysis.Genome biology · 2021Review
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Multiscale modeling is used to represent biological systems with increasing frequency and success. Multiscale models are often hybrids of different modeling frameworks and programming languages. We present the MATLAB-NetLogo extension (MatNet) as a novel tool for multiscale modeling. We demonstrate the utility of the tool with a multiscale model of Pseudomonas aeruginosa biofilm formation that incorporates both an agent-based model (ABM) and constraint-based metabolic modeling. The hybrid model correctly recapitulates oxygen-limited biofilm metabolic activity and predicts increased growth rate via anaerobic respiration with the addition of nitrate to the growth media. In addition, a genome-wide survey of metabolic mutants and biofilm formation exemplifies the powerful analyses that are enabled by this computational modeling tool.
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Registered trials
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