Applying reduction mappings in designing genomic regulatory networks

Ivan Ivanov, Ranadip Pal, Edward Dougherty

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations

Abstract

Probabilistic Boolean Networks (PBNs) represent a class of nonlinear models of genetic regulatory networks incorporating the indeterminacy owing to latent variables external to the model that have biological interaction with genes in the model. Besides being used to model biological phenomena, such as cellular state dynamics and the switch-like behavior of certain genes, PBNs have served as the main model for the application of intervention methods, including optimal control strategies, to favorably effect system dynamics. An obstacle in applying PBNs to large-scale networks is the computational complexity of the model. It is sometimes necessary to construct computationally tractable sub-networks while still carrying sufficient structure for the application at hand. Hence, there is a need for size reducing mappings. Such mappings can be used not only to render computationally manageable sub-networks but they can also play an important role in the process of designing PBNs from microarray data. The process of inferring PBNs from data is known to be a one-to-many mapping, and one needs a biologically sound constraints when selecting the PBN that is optimal with respect the given data. This paper proposes such a constraint based on the recently introduced DIRE reduction algorithm.

Original languageEnglish
Title of host publication2006 IEEE/NLM Life Science Systems and Applications Workshop, LiSA 2006
DOIs
StatePublished - 2006
Event2006 IEEE/NLM Life Science Systems and Applications Workshop, LiSA 2006 - Bethesda, MD, United States
Duration: Jul 13 2006Jul 14 2006

Publication series

Name2006 IEEE/NLM Life Science Systems and Applications Workshop, LiSA 2006

Conference

Conference2006 IEEE/NLM Life Science Systems and Applications Workshop, LiSA 2006
CountryUnited States
CityBethesda, MD
Period07/13/0607/14/06

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    Ivanov, I., Pal, R., & Dougherty, E. (2006). Applying reduction mappings in designing genomic regulatory networks. In 2006 IEEE/NLM Life Science Systems and Applications Workshop, LiSA 2006 [4015782] (2006 IEEE/NLM Life Science Systems and Applications Workshop, LiSA 2006). https://doi.org/10.1109/LSSA.2006.250381