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dc.contributor.authorViksna, J-
dc.contributor.authorGilbert, D-
dc.identifier.citationBaltic Journal of Modern Computing, 4(4): pp. 876–895, (2016)en_US
dc.description.abstractIn this paper we study evolution of gene regulatory networks from the graph-theoretic perspective. We consider two gene duplication models that are based on those studied before, but are more general and/or mathematically more precise than previously published schemes. Our aims are to assess the biological appropriateness of the proposed models and to study the possibilities of reconstruction of the evolution history of networks solely on the basis of network topology. For one of the proposed models, which is fully deterministic, we provide an exact algorithm for reconstruction of evolutionary history of the network. The algorithm is applicable in real time to networks with up to 200 genes, which is comparable to sizes of real biological networks. The other proposed model involves random deletions of gene interactions. In this case a heuristic modification of the algorithm can be used to identify a large subset of genes that have been duplicated during the last duplication event. The methods have been tested for analysis of yeast gene regulatory network and have been able to identify several biologically confirmed pairs of duplicated genes. Similarity between inferred pairs of gene duplicates is shown to be above average, thus indicating that traces from gene duplications, which have occurred long time ago, can still be detected from the network topology alone.en_US
dc.description.sponsorshipThe work was supported by Latvian Council of Science grant 258/2012 and Latvian State Research programme project NexIT (2014-2017).en_US
dc.publisherVilnius University, University of Latviaen_US
dc.subjectGene regulatory networksen_US
dc.subjectEvolution of biological networksen_US
dc.subjectGraph algorithmsen_US
dc.titleGene Duplication Models and Reconstruction of Gene Regulatory Network Evolution from Network Structureen_US
dc.relation.isPartOfBaltic Journal of Modern Computing-
Appears in Collections:Dept of Computer Science Research Papers

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