Agent-based modeling of host–pathogen systems: The successes and challenges

@article{Bauer2009AgentbasedMO,
  title={Agent-based modeling of host–pathogen systems: The successes and challenges},
  author={Amy L. Bauer and Catherine A. A. Beauchemin and Alan S. Perelson},
  journal={Information Sciences},
  year={2009},
  volume={179},
  pages={1379 - 1389}
}

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References

SHOWING 1-10 OF 137 REFERENCES

An enhanced agent based model of the immune system response.

Modeling Influenza Viral Dynamics in Tissue

The agent-based modeling component of this program is described and preliminary results from both the in vitro and in silico experiments are reported, indicating the potential for iteratively predicting the virulence of new Influenza strains.

Modeling Intercellular Interactions in Early Mycobacterium Infection

A model of early Mycobacterium infection using the CyCells simulator, which was designed to capture these effects, is described and related to several experimental observations of individual components of the response to Mtb.

In silico experiments of existing and hypothetical cytokine-directed clinical trials using agent-based modeling*

  • G. An
  • Medicine
    Critical care medicine
  • 2004
ABM may provide a synthetic, analytical platform to integrate basic science data on the IIR, thus eventually aiding in formulating and testing future mediator-directed therapies for SIRS/MOF before clinical trials, and it may provide insights into directions of future research.

Computer immunology

A body of work on computational immune systems that behave analogously to the natural immune system are described, which have several strengths that can complement wet lab immunology.

Concepts for developing a collaborative in silico model of the acute inflammatory response using agent-based modeling.

  • G. An
  • Computer Science
    Journal of critical care
  • 2006

Homeostasis of peripheral immune effectors

SIMMUNE, a tool for simulating and analyzing immune system behavior

The principles of SIMMUNE's multiscale analysis of emergent structure within the simulated immune system that allow the identification of immunological contexts using minimal a priori assumptions about the higher level organization of the immune system are outlined.

Agent-based modelling: a case study in HIV epidemic

This research presents an agent-based, bottom-up modelling approach to develop a simulation tool for estimating and predicting the spread of the human immunodeficiency virus (HIV) in a given population and investigates the performance of the tool and presents the first results obtained.
...