ReviewACS synthetic biology2022
Agent-Based Modeling of Microbial Communities.
Review in ACS synthetic biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
31 citing papers in PubMed.
- The influence of cell morphology on the dynamics and stability of model bacterial communities.PLoS computational biology · 2026Article
- Systems engineering of engineered live biotherapeutics: A discovery-to-translation framework for streamlining microbiome therapeutic development.Journal of controlled release : official journal of the Controlled Release Society · 2026Review
- Applications of synthetic biology in biomedicine.Molecular biomedicine · 2026Review
- Bacterial degradation of a plant toxin and nutrient competition with commensals trade off to constrain pathogen growth.mSystems · 2026Article
- Identifiability, Sensitivity, and Genetic Algorithms in Bacterial Biofilm Selection Models.Bulletin of mathematical biology · 2026Article
- Review
- Mathematical Modelling and Intuition in Microbiology: A Perspective.Environmental microbiology · 2026Review
- Mathematical modeling of planar cell polarity: principles, approaches, and open questions.NPJ systems biology and applications · 2026Review
- Computational and multi-omics systems biology for precision microbiome therapeutics.Frontiers in microbiomes · 2026Review
- Agent-based model for simulating microbial movement with a preferred target for agricultural biologicals.PeerJ · 2026Article
- Biofilm-associated antibiotic tolerance in the era of multidrug resistance: quorum-sensing mechanisms and emerging therapeutic strategies.Frontiers in cellular and infection microbiology · 2026Review
- Investigating the effects of soil microstructures on bacterial growth via microfluidic channels and an agent-based model.Scientific reports · 2025Article
- Toward the Next Generation of In Silico Modeling of Dynamic Host-Microbiota Interactions in the Skin.JID innovations : skin science from molecules to population health · 2025Review
- Thermodynamically consistent, reduced models of gene regulatory networks.Royal Society open science · 2025Article
- Dissecting the physics of bacterial biofilms with agent-based simulations.Current opinion in solid state & materials science · 2025Article
- Engineering microorganisms for enhanced tolerance to toxic end-products and intermediates.FEMS microbiology reviews · 2025Review
- Individual-based modeling unravels spatial and social interactions in bacterial communities.The ISME journal · 2025Review
- From single cells to communities: Mathematical perspectives on bacterial quorum sensing.Computational and structural biotechnology journal · 2025Review
- Deciphering microbial spatial organization: insights from synthetic and engineered communities.ISME communications · 2025Review
- Optogenetic patterning generates multi-strain biofilms with spatially distributed antibiotic resistance.Nature communications · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Microbial communities are complex living systems that populate the planet with diverse functions and are increasingly harnessed for practical human needs. To deepen the fundamental understanding of their organization and functioning as well as to facilitate their engineering for applications, mathematical modeling has played an increasingly important role. Agent-based models represent a class of powerful quantitative frameworks for investigating microbial communities because of their individualistic nature in describing cells, mechanistic characterization of molecular and cellular processes, and intrinsic ability to produce emergent system properties. This review presents a comprehensive overview of recent advances in agent-based modeling of microbial communities. It surveys the state-of-the-art algorithms employed to simulate intracellular biomolecular events, single-cell behaviors, intercellular interactions, and interactions between cells and their environments that collectively serve as the driving forces of community behaviors. It also highlights three lines of applications of agent-based modeling, namely, the elucidation of microbial range expansion and colony ecology, the design of synthetic gene circuits and microbial populations for desired behaviors, and the characterization of biofilm formation and dispersal. The review concludes with a discussion of existing challenges, including the computational cost of the modeling, and potential mitigation strategies.
Indexed as
Identifiers
What OpenQuestion holds
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.