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Agent-Based Models Predict Emergent Behavior of Heterogeneous Cell Populations in Dynamic Microenvironments
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June 2020 |
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Repulsive expansion dynamics in colony growth and gene expression
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March 2021 |
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Extinction, coexistence, and localized patterns of a bacterial population with contact-dependent inhibition
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February 2014 |
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A New Improved and Extended Version of the Multicell Bacterial Simulator gro
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May 2017 |
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Chemotaxis as a navigation strategy to boost range expansion
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November 2019 |
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Weak synchronization and large-scale collective oscillation in dense bacterial suspensions
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January 2017 |
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SediFoam: A general-purpose, open-source CFD–DEM solver for particle-laden flow with emphasis on sediment transport
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April 2016 |
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A framework for multidimensional modelling of activity and structure of multispecies biofilms
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April 2005 |
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Phenotypic variability of growing cellular populations
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November 2007 |
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BSim 2.0: An Advanced Agent-Based Cell Simulator
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June 2017 |
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Growth dependence of conjugation explains limited plasmid invasion in biofilms: an individual‐based modelling study
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September 2011 |
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Validated In Silico Model for Biofilm Formation in Escherichia coli
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January 2022 |
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Modeling chemotaxis of adhesive cells: stochastic lattice approach and continuum description
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February 2014 |
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Cooperative self-organization of microorganisms
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June 2000 |
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Spatiotemporal establishment of dense bacterial colonies growing on hard agar
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March 2019 |
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Genetic drift at expanding frontiers promotes gene segregation
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December 2007 |
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Quantitative Modeling of Escherichia coli Chemotactic Motion in Environments Varying in Space and Time
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April 2010 |
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AgentCell: a digital single-cell assay for bacterial chemotaxis
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March 2005 |
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Agent-based modelling in synthetic biology
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November 2016 |
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Individual Based Model Links Thermodynamics, Chemical Speciation and Environmental Conditions to Microbial Growth
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August 2019 |
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Mechanically-driven phase separation in a growing bacterial colony
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April 2015 |
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Reactive-transport modelling of Enterococcus faecalis JH2-2 passage through water saturated sediment columns
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July 2021 |
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Individual-Based Modeling of Spatial Dynamics of Chemotactic Microbial Populations
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November 2022 |
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Biomechanical ordering of dense cell populations
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October 2008 |
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Development and Validation of Primary, Secondary, and Tertiary Models for Growth of Salmonella Typhimurium on Sterile Chicken
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December 2005 |
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Particle-Based Multidimensional Multispecies Biofilm Model
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May 2004 |
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Mechanically Driven Growth of Quasi-Two-Dimensional Microbial Colonies
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October 2013 |
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Effect of EPS on biofilm structure and function as revealed by an individual-based model of biofilm growth
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March 2001 |
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Gaussian process emulation of an individual-based model simulation of microbial communities
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September 2017 |
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Emergent genetic oscillations in a synthetic microbial consortium
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August 2015 |
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Individual-based Modelling: An Essential Tool for Microbiology
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April 2008 |
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Cell morphology drives spatial patterning in microbial communities
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December 2016 |
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Logarithmic Sensing in Escherichia coli Bacterial Chemotaxis
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March 2009 |
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Advancing microbial sciences by individual-based modelling
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June 2016 |
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A heterogeneous microbial consortium producing short-chain fatty acids from lignocellulose
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August 2020 |
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Cell Polarity-Driven Instability Generates Self-Organized, Fractal Patterning of Cell Layers
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June 2013 |
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Synthetic microbial communities
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April 2014 |
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Dynamic cellular finite-element method for modelling large-scale cell migration and proliferation under the control of mechanical and biochemical cues: a study of re-epithelialization
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April 2017 |
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Bacterially Speaking
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April 2006 |
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Three-dimensional biofilm model with individual cells and continuum EPS matrix
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January 2006 |
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Microbial interactions: from networks to models
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July 2012 |
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Three-dimensional simulations of biofilm growth in porous media
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February 2009 |
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Evaluating heterotrophic growth in a nitrifying biofilm reactor using fluorescence in situ hybridization and mathematical modeling
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October 2005 |
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Selfishness driving reductive evolution shapes interdependent patterns in spatially structured microbial communities
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December 2020 |
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A stabilized microbial ecosystem of self-limiting bacteria using synthetic quorum-regulated lysis
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June 2017 |
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The biofilm matrix
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August 2010 |
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Efficient Modeling and Simulation of Bacteria-Based Nanonetworks with BNSim
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December 2013 |
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Individual-based modelling of biofilms
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November 2001 |
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Agent-based Models in Synthetic Biology: Tools for Simulation and Prospects
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March 2012 |
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iDynoMiCS: next-generation individual-based modelling of biofilms: iDynoMiCS for Biofilm Modelling
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March 2011 |
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Chemotactic behaviour of Escherichia coli at high cell density
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November 2019 |
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An Ecological Understanding of Quorum Sensing-Controlled Bacteriocin Synthesis
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May 2016 |
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Interaction variability shapes succession of synthetic microbial ecosystems
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January 2020 |
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Quantitative Investigation of the Role of Intra-/Intercellular Dynamics in Bacterial Quorum Sensing
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March 2018 |
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BSim: An Agent-Based Tool for Modeling Bacterial Populations in Systems and Synthetic Biology
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August 2012 |
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A Computational Multiagent Model of Bioluminescent Bacteria for the Emergence of Self-Sustainable and Self-Maintaining Artificial Wireless Networks
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September 2019 |
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Integrative Circuit-Host Modeling of a Genetic Switch in Varying Environments
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May 2020 |
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Contact-Dependent Inhibition of Growth in Escherichia coli
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August 2005 |
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Bacterial social interactions drive the emergence of differential spatial colony structures
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September 2015 |
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Persistence of antibiotic resistant bacteria
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October 2003 |
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Synthetic neural-like computing in microbial consortia for pattern recognition
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May 2021 |
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Spatial interference scale as a determinant of microbial range expansion
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November 2018 |
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Principles for designing synthetic microbial communities
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June 2016 |
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BacSim, a simulator for individual-based modelling of bacterial colony growth
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December 1998 |
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Extracellular Polymeric Substance Production and Aggregated Bacteria Colonization Influence the Competition of Microbes in Biofilms
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September 2017 |
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Modeling of Clostridium tyrobutyricum for Butyric Acid Selectivity in Continuous Fermentation
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April 2014 |
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Description of mechanical response including detachment using a novel particle model of biofilm/flow interaction
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April 2007 |
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Bacterial biofilms: from the Natural environment to infectious diseases
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February 2004 |
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A mechanistic Individual-based Model of microbial communities
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August 2017 |
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Mechanistic models of microbial community metabolism
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January 2021 |
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Toxin production spontaneously becomes regulated by local cell density in evolving bacterial populations
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August 2019 |
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Engineering microbial consortia: a new frontier in synthetic biology
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September 2008 |
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Fast Parallel Algorithms for Short-Range Molecular Dynamics
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March 1995 |
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Engineering microbial consortia with rationally designed cellular interactions
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August 2022 |
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Computational Modeling of Synthetic Microbial Biofilms
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July 2012 |
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Modeling microbial growth and dynamics
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August 2015 |
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Individual based modeling of Pseudomonas aeruginosa biofilm with three detachment mechanisms
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January 2015 |
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Drift and Behavior of E. coli Cells
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December 2017 |
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Effect of diffusive and convective substrate transport on biofilm structure formation: A two-dimensional modeling study
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January 2000 |
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Biofilms: an emergent form of bacterial life
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August 2016 |
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Challenges of biofilm control and utilization: lessons from mathematical modelling
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June 2019 |
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Recent advances in n-butanol and butyrate production using engineered Clostridium tyrobutyricum
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August 2020 |
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Biofilm-control strategies based on enzymic disruption of the extracellular polymeric substance matrix – a modelling study
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December 2005 |
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Hybrid Model of Bacterial Biofilm Growth
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February 2020 |
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Physiological heterogeneity in biofilms
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March 2008 |
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NUFEB: A massively parallel simulator for individual-based modelling of microbial communities
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December 2019 |
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Inferring directional relationships in microbial communities using signed Bayesian networks
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December 2020 |