Defense Date

2013

Document Type

Thesis

Degree Name

Master of Science

Department

Computer Science

First Advisor

Preetam Jr Ghosh

Abstract

Understanding the underlying architecture of gene regulatory networks (GRNs) has been one of the major goals in systems biology and bioinformatics as it can provide insights in disease dynamics and drug development. Such GRNs are characterized by their scale-free degree distributions and existence of network motifs, which are small subgraphs of specific types and appear more abundantly in GRNs than in other randomized networks. In fact, such motifs are considered to be the building blocks of GRNs (and other complex networks) and they help achieve the underlying robustness demonstrated by most biological networks. The goal of this thesis is to design biological network (specifically, GRN) growing models. As the motif distribution in networks grown using preferential attachment based algorithms do not match that of the GRNs seen in model organisms like E. coli and yeast, we hypothesize that such models at a single node level may not properly reproduce the observed degree and motif distributions of biological networks. Hence, we propose a new network growing algorithm wherein the central idea is to grow the network one motif (specifically, we consider one downlink motif) at a time. The accuracy of our proposed algorithm was evaluated extensively and show much better performance than existing network growing models both in terms of degree and motif distributions. We also propose a complex network growing game that can identify important strategies behind motif interactions by exploiting human (i.e., gamer) intelligence. Our proposed gaming software can also help in educational purposes specifically designed for complex network studies.

Rights

© The Author

Is Part Of

VCU University Archives

Is Part Of

VCU Theses and Dissertations

Date of Submission

May 2013

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