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Advancing microbial sciences by individual-based modelling
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Applying “‐omics” Data in Marine Microbial Oceanography
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Analyzing characteristic length scales in biofilm structures
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Biofilm image reconstruction for assessing structural parameters
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Modeling of Biofilm Systems: A Review
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Creating Individual Based Models of the Plankton Ecosystem
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Apparent Surface Associated Lag Time in Growth of Primary Biofilm Cells
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Microscale patchiness leads to large and important intraspecific internal nutrient heterogeneity in phytoplankton
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Molecular Mechanisms Underlying Bacterial Persisters
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Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics
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A bunch of tiny individuals—Individual-based modeling for microbes
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The ODD protocol: A review and first update
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Individual-based modelling of adaptation in marine microbial populations using genetically defined physiological parameters
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Exploring the lag phase and growth initiation of a yeast culture by means of an individual-based model
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Diversity in times of adversity: probabilistic strategies in microbial survival games
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How the chemotactic characteristics of bacteria can determine their population patterns
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Why is metabolic labour divided in nitrification?
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Do simple models lead to generality in ecology?
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Multidimensional modelling to investigate interspecies hydrogen transfer in anaerobic biofilms
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Transcriptome analysis of Pseudomonas aeruginosa biofilm development: anaerobic respiration and iron limitation
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Computational Modeling of Synthetic Microbial Biofilms
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Dynamic Modeling of Cellular Populations within iBioSim
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Cell Polarity-Driven Instability Generates Self-Organized, Fractal Patterning of Cell Layers
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Microzones surrounding phytoplankton form the basis for a stratified marine microbial ecosystem
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Gene expression in Pseudomonas aeruginosa biofilms
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Response of Prochlorococcus ecotypes to co-culture with diverse marine bacteria
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Microbial individuality in the natural environment
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Resource competition and social conflict in experimental populations of yeast
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Local migration promotes competitive restraint in a host–pathogen 'tragedy of the commons'
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Stochasticity of metabolism and growth at the single-cell level
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Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria
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Complete nitrification by a single microorganism
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Complete nitrification by Nitrospira bacteria
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Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
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Non-genetic heterogeneity from stochastic partitioning at cell division
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A microfluidic chemostat for experiments with bacterial and yeast cells
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Microbial cell individuality and the underlying sources of heterogeneity
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Reconstruction of biochemical networks in microorganisms
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Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods
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Going local: technologies for exploring bacterial microenvironments
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Trophic interactions induce spatial self-organization of microbial consortia on rough surfaces
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Evolution of the CRISPR-Cas adaptive immunity systems in prokaryotes: models and observations on virus–host coevolution
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Biofilm formation by Pseudomonas aeruginosa wild type, flagella and type IV pili mutants
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Involvement of bacterial migration in the development of complex multicellular structures in Pseudomonas aeruginosa biofilms
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Tutorial on agent-based modelling and simulation
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Bacterial metapopulations in nanofabricated landscapes
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Relationship between cellular response and behavioral variability in bacterial chemotaxis
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A single-cell view on the ecophysiology of anaerobic phototrophic bacteria
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Heterogeneity in protein expression induces metabolic variability in a modeled Escherichia coli population
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A chemostat array enables the spatio-temporal analysis of the yeast proteome
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Mighty small: Observing and modeling individual microbes becomes big science
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Surface attachment induces Pseudomonas aeruginosa virulence
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Modelling emergence of oscillations in communicating bacteria: a structured approach from one to many cells
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BacSim, a simulator for individual-based modelling of bacterial colony growth
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Microbial community structure in autotrophic nitrifying granules characterized by experimental and simulation analyses
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iDynoMiCS: next‐generation individual‐based modelling of biofilms
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Growth dependence of conjugation explains limited plasmid invasion in biofilms: an individual‐based modelling study
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A unifying hypothesis for the structure of microbial biofilms based on cellular automaton models
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Detecting metabolic activities in single cells, with emphasis on nanoSIMS
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Surface sensing and lateral subcellular localization of WspA , the receptor in a chemosensory‐like system leading to c‐di‐ GMP production
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Bacterial Persistence as a Phenotypic Switch
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Long-Term Monitoring of Bacteria Undergoing Programmed Population Control in a Microchemostat
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Phenotypic Diversity, Population Growth, and Information in Fluctuating Environments
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Pattern-Oriented Modeling of Agent-Based Complex Systems: Lessons from Ecology
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Probing Individual Environmental Bacteria for Viruses by Using Microfluidic Digital PCR
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Acceleration of Emergence of Bacterial Antibiotic Resistance in Connected Microenvironments
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Zooming in to see the bigger picture: Microfluidic and nanofabrication tools to study bacteria
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Microscale Nutrient Patches in Planktonic Habitats Shown by Chemotactic Bacteria
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Mathematical Modeling of Microbial Ecology: Spatial Dynamics of Interactions in Biofilms and Guts
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Isolated Microbial Single Cells and Resulting Micropopulations Grow Faster in Controlled Environments
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Evolutionary Dynamics of the Prokaryotic Adaptive Immunity System CRISPR-Cas in an Explicit Ecological Context
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Pseudomonas aeruginosa Displays Multiple Phenotypes during Development as a Biofilm
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Interactions between Diatoms and Bacteria
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Central Role of the Cell in Microbial Ecology
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Single-Cell Microbiology: Tools, Technologies, and Applications
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Flow cytometry and cell sorting of heterogeneous microbial populations: the importance of single-cell analyses
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Mathematical Description of Microbial Biofilms
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Evolution of Two-Component Signal Transduction Systems
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Individual-Based Modeling of Ecological and Evolutionary Processes
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Single-Cell Ecophysiology of Microbes as Revealed by Raman Microspectroscopy or Secondary Ion Mass Spectrometry Imaging
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Models in biology: ‘accurate descriptions of our pathetic thinking’
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Repair rather than segregation of damage is the optimal unicellular aging strategy
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Revised Estimates for the Number of Human and Bacteria Cells in the Body
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Environments that Induce Synthetic Microbial Ecosystems
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Metabolic and Demographic Feedbacks Shape the Emergent Spatial Structure and Function of Microbial Communities
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The Pseudomonas aeruginosa Transcriptome in Planktonic Cultures and Static Biofilms Using RNA Sequencing
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BSim: An Agent-Based Tool for Modeling Bacterial Populations in Systems and Synthetic Biology
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Assessment of three-dimensional biofilm models through direct comparison with confocal microscopy imaging
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Experimental and simulation analysis of community structure of nitrifying bacteria in a membrane-aerated biofilm
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Microbial motility involvement in biofilm structure formation – a 3D modelling study
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Simulation of single-species bacterial-biofilm growth using the Glazier-Graner-Hogeweg model and the CompuCell3D modeling environment
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Elemental composition of single cells of various strains of marine Prochlorococcus and Synechococcus using X‐ray microanalysis
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Agent‐based modeling of the complex life cycle of a cyanobacterium (Anabaena) in a shallow reservoir
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Environmental selection and resource allocation determine spatial patterns in picophytoplankton cell size
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Food-borne microbes: shaping the host ecosystem
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Strong inter-population cooperation leads to partner intermixing in microbial communities
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Spatial self-organization favors heterotypic cooperation over cheating
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Model-aided targeted volatile fatty acid production from food waste using a defined co-culture microbial community
inferred← citeshttps://doi.org/10.1016/j.scitotenv.2024.171091openalex-snapshot
Cooperation between autotrophic and heterotrophic denitrifiers under low C/N ratios revealed by individual-based modelling
inferred← citeshttps://doi.org/10.1016/j.soilbio.2024.109698openalex-snapshot
Trait-based modeling of microbial interactions and carbon turnover in the rhizosphere
inferred← citeshttps://doi.org/10.1016/j.tim.2021.05.003openalex-snapshot
Biofilms vs. cities and humans vs. aliens – a tale of reproducibility in biofilms
inferred← citeshttps://doi.org/10.1016/j.watres.2022.118814openalex-snapshot
Impacts of atmospheric stilling and climate warming on cyanobacterial blooms: An individual-based modelling approach
inferred← citeshttps://doi.org/10.1016/j.watres.2024.122647openalex-snapshot
Role of biogeochemical and hydrodynamic characteristics in simulating nitrogen dynamics in river confluence
inferred← citeshttps://doi.org/10.1016/j.yexcr.2022.113218openalex-snapshot
Leveraging the model-experiment loop: Examples from cellular slime mold chemotaxis
inferred← citeshttps://doi.org/10.1021/acs.biochem.8b01006openalex-snapshot
Understanding and Engineering Distributed Biochemical Pathways in Microbial Communities
inferred← citeshttps://doi.org/10.1021/acs.est.1c05258openalex-snapshot
Roadmap from Microbial Communities to Individuality Modeling for Anaerobic Digestion of Sewage Sludge
inferred← citeshttps://doi.org/10.1021/acs.est.3c05476openalex-snapshot
In Situ and Individual-Based Analysis of the Influence of Polystyrene Microplastics on Escherichia coli Conjugative Gene Transfer at the Single-Cell Level
inferred← citeshttps://doi.org/10.1021/acsbiomaterials.2c01079openalex-snapshot
Computational Design of Antimicrobial Active Surfaces via Automated Bayesian Optimization
inferred← citeshttps://doi.org/10.1021/acssynbio.2c00411openalex-snapshot
Agent-Based Modeling of Microbial Communities
inferred← citeshttps://doi.org/10.1021/acssynbio.7b00003openalex-snapshot
A New Improved and Extended Version of the Multicell Bacterial Simulator gro
inferred← citeshttps://doi.org/10.1021/acssynbio.7b00406openalex-snapshot
Quantitative Investigation of the Role of Intra-/Intercellular Dynamics in Bacterial Quorum Sensing
inferred← citeshttps://doi.org/10.1029/2018ms001452openalex-snapshot
Considering the Role of Adaptive Evolution in Models of the Ocean and Climate System
inferred← citeshttps://doi.org/10.1038/ismej.2017.190openalex-snapshot
Phage mobility is a core determinant of phage–bacteria coexistence in biofilms
inferred← citeshttps://doi.org/10.1038/s41396-017-0023-7openalex-snapshot
Carbon limitation drives GC content evolution of a marine bacterium in an individual-based genome-scale model
inferred← citeshttps://doi.org/10.1038/s41396-018-0112-2openalex-snapshot
Micro-scale intermixing: a requisite for stable and synergistic co-establishment in a four-species biofilm
inferred← citeshttps://doi.org/10.1038/s41467-018-03187-yopenalex-snapshot
Spatial organization of bacterial populations in response to oxygen and carbon counter-gradients in pore networks
inferred← citeshttps://doi.org/10.1038/s41467-019-09306-7openalex-snapshot
Dispersal homogenizes communities via immigration even at low rates in a simplified synthetic bacterial metacommunity
inferred← citeshttps://doi.org/10.1038/s41522-024-00572-yopenalex-snapshot
Metabolic interactions shape emergent biofilm structures in a conceptual model of gut mucosal bacterial communities
inferred← citeshttps://doi.org/10.1038/s41559-019-0952-9openalex-snapshot
Uncovering the rules of microbial community invasions
inferred← citeshttps://doi.org/10.1038/s41559-022-01746-7openalex-snapshot
Ecological modelling approaches for predicting emergent properties in microbial communities
inferred← citeshttps://doi.org/10.1038/s41559-023-02230-6openalex-snapshot
Community composition and the environment modulate the population dynamics of type VI secretion in human gut bacteria
inferred← citeshttps://doi.org/10.1038/s41564-023-01518-4openalex-snapshot
Simultaneous spatiotemporal transcriptomics and microscopy of Bacillus subtilis swarm development reveal cooperation across generations
inferred← citeshttps://doi.org/10.1038/s41567-018-0356-9openalex-snapshot
Emergence of three-dimensional order and structure in growing biofilms
inferred← citeshttps://doi.org/10.1038/s41579-019-0255-9openalex-snapshot
Common principles and best practices for engineering microbiomes
inferred← citeshttps://doi.org/10.1038/s41598-019-39773-3openalex-snapshot
Environmental structure drives resistance to phages and antibiotics during phage therapy and to invading lysogens during colonisation
inferred← citeshttps://doi.org/10.1038/s41598-025-23995-9openalex-snapshot
Investigating the effects of soil microstructures on bacterial growth via microfluidic channels and an agent-based model
inferred← citeshttps://doi.org/10.1038/s42003-024-06218-1openalex-snapshot
Integrative analysis of yeast colony growth
inferred← citeshttps://doi.org/10.1039/d3bm01674aopenalex-snapshot
ABCD of IA: A multi-scale agent-based model of T cell activation in inflammatory arthritis
inferred← citeshttps://doi.org/10.1039/d3sm01032eopenalex-snapshot
Residual cells and nutrient availability guide wound healing in bacterial biofilms
inferred← citeshttps://doi.org/10.1042/bst20170242openalex-snapshot
Competitive resource allocation to metabolic pathways contributes to overflow metabolisms and emergent properties in cross-feeding microbial consortia
inferred← citeshttps://doi.org/10.1042/bst20200972openalex-snapshot
Biofilm and swarming emergent behaviours controlled through the aid of biophysical understanding and tools
inferred← citeshttps://doi.org/10.1042/ebc20160037openalex-snapshot
Agent-based modelling in synthetic biology
inferred← citeshttps://doi.org/10.1063/5.0021126openalex-snapshot
Influence of cell interaction forces on growth of bacterial biofilms
inferred← citeshttps://doi.org/10.1088/1367-2630/aa5483openalex-snapshot
Multiscale modeling of bacterial colonies: how pili mediate the dynamics of single cells and cellular aggregates
inferred← citeshttps://doi.org/10.1088/1478-3975/aac473openalex-snapshot
Complex microbial systems across different levels of description
inferred← citeshttps://doi.org/10.1093/ismejo/wraf116openalex-snapshot
Individual-based modeling unravels spatial and social interactions in bacterial communities
inferred← citeshttps://doi.org/10.1098/rsos.211553openalex-snapshot
Agent-based modelling of iron cycling bacteria provides a framework for testing alternative environmental conditions and modes of action
inferred← citeshttps://doi.org/10.1098/rstb.2019.0256openalex-snapshot
Understanding the evolution of interspecies interactions in microbial communities
inferred← citeshttps://doi.org/10.1101/086462openalex-snapshot
Phage mobility is a core determinant of phage-bacteria coexistence in biofilms
inferred← citeshttps://doi.org/10.1101/2020.09.15.297721openalex-snapshot
Self-organisation and persistence of antibiotic resistance in evolving plasmid communities
inferred← citeshttps://doi.org/10.1101/2020.11.18.387787openalex-snapshot
Substrate traits shape the structure of microbial community engaged in metabolic division of labor
inferred← citeshttps://doi.org/10.1101/2021.10.11.463942openalex-snapshot
Investigating the growth of an engineered strain of Cyanobacteria with an Agent-Based Model and a Recurrent Neural Network
inferred← citeshttps://doi.org/10.1101/2023.06.30.547165openalex-snapshot
ISiCell: involving biologists in the design process of agent-based models in cell biology
inferred← citeshttps://doi.org/10.1101/2025.02.27.640280openalex-snapshot
Spatial Dynamics and Emergent Properties of pLS20 Conjugation on Solid Surfaces
inferred← citeshttps://doi.org/10.1101/2025.03.09.642204openalex-snapshot
Individual-Based Modeling of Microbial Communities Integrating Genetic Mechanisms: A Case Study of LuxS-Mediated Quorum Sensing in Salmonella Typhimurium
inferred← citeshttps://doi.org/10.1101/291328openalex-snapshot
Modelling phage-bacteria interactions driving predation and horizontal gene transfer
inferred← citeshttps://doi.org/10.1101/363093openalex-snapshot
Deriving general conditions and mechanisms for division of labor using the cell-based simulator gro
inferred← citeshttps://doi.org/10.1101/621490openalex-snapshot
Predation strategies of the bacterium Bdellovibrio bacteriovorus result in overexploitation and bottlenecks
inferred← citeshttps://doi.org/10.1109/access.2019.2915575openalex-snapshot
An Individual Based Model of Wound Closure in Plant Stems
inferred← citeshttps://doi.org/10.1111/1462-2920.14397openalex-snapshot
Heterotrophic substrate specificity in the aquatic environment: The role of microscale patchiness investigated using modelling
inferred← citeshttps://doi.org/10.1111/1751-7915.12803openalex-snapshot
Bioprocess scale‐up/down as integrative enabling technology: from fluid mechanics to systems biology and beyond
inferred← citeshttps://doi.org/10.1111/1751-7915.13026openalex-snapshot
Editorial: The microbiome as a source of new enterprises and job creation
inferred← citeshttps://doi.org/10.1111/1751-7915.14396openalex-snapshot
Community‐scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing
inferred← citeshttps://doi.org/10.1111/2041-210x.14129openalex-snapshot
miaSim: an R/Bioconductor package to easily simulate microbial community dynamics
inferred← citeshttps://doi.org/10.1111/lam.13657openalex-snapshot
Kinetics and mathematical model of killer/sensitive interaction under different physicochemical conditions of must/wine: a study from a biological point of view
inferred← citeshttps://doi.org/10.1126/science.abm6791openalex-snapshot
Models predict planned phosphorus load reduction will make Lake Erie more toxic
inferred← citeshttps://doi.org/10.1128/jb.00865-16openalex-snapshot
A Diverse Community To Study Communities: Integration of Experiments and Mathematical Models To Study Microbial Consortia
inferred← citeshttps://doi.org/10.1128/mbio.00672-17openalex-snapshot
Division of Labor, Bet Hedging, and the Evolution of Mixed Biofilm Investment Strategies
inferred← citeshttps://doi.org/10.1128/msphere.00656-22openalex-snapshot
Corrected and Republished from: “Understanding Lactobacillus paracasei and Streptococcus oralis Biofilm Interactions through Agent-Based Modeling”
inferred← citeshttps://doi.org/10.1128/msphere.00875-21openalex-snapshot
Understanding Lactobacillus paracasei and Streptococcus oralis Biofilm Interactions through Agent-Based Modeling
inferred← citeshttps://doi.org/10.1128/msystems.00186-18openalex-snapshot
Mobile Compensatory Mutations Promote Plasmid Survival
inferred← citeshttps://doi.org/10.1128/spectrum.00842-25openalex-snapshot
Exploring novel kinetics of automated H 2 O 2 nebulization: a breakthrough in SARS-CoV-2 elimination
inferred← citeshttps://doi.org/10.1146/annurev-marine-010419-010829openalex-snapshot
Combining Molecular Observations and Microbial Ecosystem Modeling: A Practical Guide
inferred← citeshttps://doi.org/10.1146/annurev-marine-032123-033718openalex-snapshot
Metabolic Flux Modeling in Marine Ecosystems
inferred← citeshttps://doi.org/10.1186/s12866-024-03566-0openalex-snapshot
Bacterial community dynamics as a result of growth-yield trade-off and multispecies metabolic interactions toward understanding the gut biofilm niche
inferred← citeshttps://doi.org/10.1371/journal.pbio.2001457openalex-snapshot
Effects of stochasticity and division of labor in toxin production on two-strain bacterial competition in Escherichia coli
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1006815openalex-snapshot
Bacterial surface colonization, preferential attachment and fitness under periodic stress
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1007125openalex-snapshot
NUFEB: A massively parallel simulator for individual-based modelling of microbial communities
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1009777openalex-snapshot
McComedy: A user-friendly tool for next-generation individual-based modeling of microbial consumer-resource systems
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1010533openalex-snapshot
Calibrating spatiotemporal models of microbial communities to microscopy data: A review
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1010807openalex-snapshot
Environmental and ecological controls of the spatial distribution of microbial populations in aggregates
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1011303openalex-snapshot
Is it selfish to be filamentous in biofilms? Individual-based modeling links microbial growth strategies with morphology using the new and modular iDynoMiCS 2.0
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1012605openalex-snapshot
An off-lattice discrete model to characterise filamentous yeast colony morphology
inferred← citeshttps://doi.org/10.1371/journal.pone.0173249openalex-snapshot
MI-Sim: A MATLAB package for the numerical analysis of microbial ecological interactions
inferred← citeshttps://doi.org/10.1371/journal.pone.0251643openalex-snapshot
Combining SIMS and mechanistic modelling to reveal nutrient kinetics in an algal-bacterial mutualism
inferred← citeshttps://doi.org/10.1371/journal.ppat.1007888openalex-snapshot
Bacteriophages benefit from generalized transduction
inferred← citeshttps://doi.org/10.1515/9781501512001-010openalex-snapshot
9. Microbial Controls on the Biogeochemical Dynamics in the Subsurface
inferred← citeshttps://doi.org/10.18307/2021.0103openalex-snapshot
Lake eutrophication responses modeling and watershed management optimization algorithm: A review
inferred← citeshttps://doi.org/10.18699/vjgb-26-21openalex-snapshot
Mathematical and computational modeling of biosystems at different levels of organization
inferred← citeshttps://doi.org/10.20868/upm.thesis.48812openalex-snapshot
A new agent-based platform for simulating multicellular biocircuits with conjugative plasmids
inferred← citeshttps://doi.org/10.20868/upm.thesis.52613openalex-snapshot
Modelling bacterial ecological strategies using an individual-based simulator
inferred← citeshttps://doi.org/10.21105/joss.04207openalex-snapshot
PlanktonIndividuals.jl: A GPU supported individual-based phytoplankton life cycle model
inferred← citeshttps://doi.org/10.2138/rmg.2019.85.9openalex-snapshot
Microbial Controls on the Biogeochemical Dynamics in the Subsurface
inferred← citeshttps://doi.org/10.23919/eusipco.2017.8081537openalex-snapshot
Reconstructing the forest of lineage trees of diverse bacterial communities using bio-inspired image analysis
inferred← citeshttps://doi.org/10.31223/osf.io/srdh3openalex-snapshot
Considering the role of adaptive evolution in models of the ocean and climate system
inferred← citeshttps://doi.org/10.33619/10.33619/2414-2948/60/09openalex-snapshot
Genetic-Mathematical Modeling of Population Interaction, New Psychoneuroimmunoendocrinology and Psychoneuroimmunology
inferred← citeshttps://doi.org/10.3389/fagro.2020.00008openalex-snapshot
Rhizosphere Spatiotemporal Organization–A Key to Rhizosphere Functions
inferred← citeshttps://doi.org/10.3389/fbioe.2020.00705openalex-snapshot
Toward Engineering Biosystems With Emergent Collective Functions
inferred← citeshttps://doi.org/10.3389/fevo.2020.00021openalex-snapshot
Prospects for Integrating Disturbances, Biodiversity and Ecosystem Functioning Using Microbial Systems
inferred← citeshttps://doi.org/10.3389/fevo.2020.00053openalex-snapshot
Physical, Chemical and Biological Effects on Soil Bacterial Dynamics in Microscale Models
inferred← citeshttps://doi.org/10.3389/fevo.2021.739047openalex-snapshot
Symbiosis in Digital Evolution: Past, Present, and Future
inferred← citeshttps://doi.org/10.3389/fgene.2017.00088openalex-snapshot
Perspectives and Challenges in Microbial Communities Metabolic Modeling
inferred← citeshttps://doi.org/10.3389/fmars.2021.636699openalex-snapshot
Transcriptomic Responses of Four Pelagophytes to Nutrient (N, P) and Light Stress
inferred← citeshttps://doi.org/10.3389/fmars.2022.975414openalex-snapshot
Modelling approaches for capturing plankton diversity (MODIV), their societal applications and data needs
inferred← citeshttps://doi.org/10.3389/fmicb.2016.02040openalex-snapshot
Microscale Insight into Microbial Seed Banks
inferred← citeshttps://doi.org/10.3389/fmicb.2017.01364openalex-snapshot
Spatial Organization Plasticity as an Adaptive Driver of Surface Microbial Communities
inferred← citeshttps://doi.org/10.3389/fmicb.2017.01813openalex-snapshot
Heterogeneity in Pure Microbial Systems: Experimental Measurements and Modeling
inferred← citeshttps://doi.org/10.3389/fmicb.2017.02299openalex-snapshot
From Genes to Ecosystems in Microbiology: Modeling Approaches and the Importance of Individuality
inferred← citeshttps://doi.org/10.3389/fmicb.2017.02628openalex-snapshot
Digital Image Analysis of Yeast Single Cells Growing in Two Different Oxygen Concentrations to Analyze the Population Growth and to Assist Individual-Based Modeling
inferred← citeshttps://doi.org/10.3389/fmicb.2018.01637openalex-snapshot
Dynamic Modeling of Streptococcus pneumoniae Competence Provides Regulatory Mechanistic Insights Into Its Tight Temporal Regulation
inferred← citeshttps://doi.org/10.3389/fmicb.2018.01929openalex-snapshot
Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain
inferred← citeshttps://doi.org/10.3389/fmicb.2019.01871openalex-snapshot
Individual Based Model Links Thermodynamics, Chemical Speciation and Environmental Conditions to Microbial Growth
inferred← citeshttps://doi.org/10.3389/fmicb.2020.00808openalex-snapshot
Alternative Strategies for Microbial Remediation of Pollutants via Synthetic Biology
inferred← citeshttps://doi.org/10.3389/fmicb.2021.606396openalex-snapshot
Mathematical Models of Plasmid Population Dynamics
inferred← citeshttps://doi.org/10.3389/fmicb.2021.717809openalex-snapshot
A Review on Occurrence and Spread of Antibiotic Resistance in Wastewaters and in Wastewater Treatment Plants: Mechanisms and Perspectives
inferred← citeshttps://doi.org/10.3389/fmicb.2021.726409openalex-snapshot
Application of Machine Learning Techniques to an Agent-Based Model of Pantoea
inferred← citeshttps://doi.org/10.3389/fmicb.2022.1004488openalex-snapshot
Do microbes have a memory? History-dependent behavior in the adaptation to variable environments
inferred← citeshttps://doi.org/10.3389/fphys.2018.00304openalex-snapshot
High-Performance Agent-Based Modeling Applied to Vocal Fold Inflammation and Repair
inferred← citeshttps://doi.org/10.3390/computation4040039openalex-snapshot
A Multi-Compartment Hybrid Computational Model Predicts Key Roles for Dendritic Cells in Tuberculosis Infection
inferred← citeshttps://doi.org/10.3390/environments8020016openalex-snapshot
Microbial Communities in Methane Cycle: Modern Molecular Methods Gain Insights into Their Global Ecology
inferred← citeshttps://doi.org/10.3390/foods10092119openalex-snapshot
The Inclusion of the Food Microstructural Influence in Predictive Microbiology: State-of-the-Art
inferred← citeshttps://doi.org/10.3390/genes14010154openalex-snapshot
Novel Ground-Up 3D Multicellular Simulators for Synthetic Biology CAD Integrating Stochastic Gillespie Simulations Benchmarked with Topologically Variable SBML Models
inferred← citeshttps://doi.org/10.3390/math11122783openalex-snapshot
A New Visualization and Analysis Method for a Convolved Representation of Mass Computational Experiments with Biological Models
inferred← citeshttps://doi.org/10.3390/membranes12070678openalex-snapshot
A Self-Controlled and Self-Healing Model of Bacterial Cells
inferred← citeshttps://doi.org/10.3390/microorganisms9020417openalex-snapshot
Agent Based Models of Polymicrobial Biofilms and the Microbiome—A Review
inferred← citeshttps://doi.org/10.3390/microorganisms9091931openalex-snapshot
Assessment of Bacillus subtilis Plasmid pLS20 Conjugation in the Absence of Quorum Sensing Repression
inferred← citeshttps://doi.org/10.3390/pr12071446openalex-snapshot
Modeling and Optimizing Biocontrol in Wines: pH as a Modulator of Yeast Amensalism Interaction
inferred← citeshttps://doi.org/10.3390/pr5040053openalex-snapshot
Modeling Microbial Communities: A Call for Collaboration between Experimentalists and Theorists
inferred← citeshttps://doi.org/10.3390/su13147968openalex-snapshot
Lattice Boltzmann Method in Modeling Biofilm Formation, Growth and Detachment
inferred← citeshttps://doi.org/10.3410/f.732740136.793545412openalex-snapshot
Faculty Opinions recommendation of Spatial organization of bacterial populations in response to oxygen and carbon counter-gradients in pore networks.
inferred← citeshttps://doi.org/10.4018/979-8-2600-2998-5.ch009openalex-snapshot
The Future of Microbial Environmental Biotechnology
inferred← citeshttps://doi.org/10.4236/abb.2024.1510038openalex-snapshot
Advances in Research on Synthetic Microbial Communities
inferred← citeshttps://doi.org/10.4995/msel.2019.10975openalex-snapshot
Modelización basada en agentes: canibalismo microbiano
inferred← citeshttps://doi.org/10.69997/sct.102831openalex-snapshot
Optimizing Individual-based Modelling: A Grid-based Approach to Computationally Efficient Microbial Simulations
inferred← citeshttps://doi.org/10.70675/4bd6a8faz943az4318zbd61zfd5706ff9d70openalex-snapshot
Evolution et modélisation de processus biologiques : application à la régulation de la compétence naturelle pour la transformation génétique bactérienne chez les streptocoques
inferred← citeshttps://doi.org/10.70675/a601a3d1zb301z46c3zbf8fz9cca9bbbd2f9openalex-snapshot
Development of Chlorella vulgaris and Saccharomyces cerevisiae in immobilized cultures
inferred← citeshttps://doi.org/10.70675/fc1722e4z6066z40f0z8fdaz93eab2f9c461openalex-snapshot
Fine-scale modelling of the dynamics of phytoplankton communities
inferred← citeshttps://doi.org/10.7287/peerj.preprints.1469v1openalex-snapshot
simplex: An individual-based platform for ecological modeling
inferred← citeshttps://doi.org/10.7554/elife.21855openalex-snapshot
Flow environment and matrix structure interact to determine spatial competition in Pseudomonas aeruginosa biofilms
inferred← citeshttps://doi.org/10.7554/elife.65355openalex-snapshot
Matrix-trapped viruses can prevent invasion of bacterial biofilms by colonizing cells
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Science and Advanced Computing — runs a structured editorial panel for researchers
publishing outside journals, and publishes on CiteStamp rails. Submission is free
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