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Methods Mol Biol. 2018;1819:385-402. doi: 10.1007/978-1-4939-8618-7_18.

Developing Network Models of Multiscale Host Responses Involved in Infections and Diseases.

Author information

1
Medical Scientist Training Program and Biophysics, Structural & Computational Biology graduate program, Rochester, NY, USA.
2
Departments of Microbiology and Immunology, Rochester, NY, USA. juilee_thakar@urmc.rochester.edu.

Abstract

Complex interactions involved in host response to infections and diseases require advanced analytical tools to infer drivers of the response in order to develop strategies for intervention. This chapter discusses approaches to assemble interactions ranging from molecular to cellular levels and their analysis to investigate the cross talk between immune pathways. Particularly, construction of immune networks by either data-driven or literature-driven methods is explained. Next, graph theoretic approaches for probing static network properties as well as visualization of networks are discussed. Finally, development of Boolean models for simulation of network dynamics to investigate cross talk and emergent properties are considered along with Boolean-like models that may compensate for some of the limitations encountered in Boolean simulations. In conclusion, the chapter will allow readers to construct and analyze multiscale networks involved in immune responses.

KEYWORDS:

Biological networks; Boolean modeling; Gene networks; Graph theory; Systems immunology

PMID:
30421414
DOI:
10.1007/978-1-4939-8618-7_18
[Indexed for MEDLINE]

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