Global Optimization in Systems Biology and Bioinformatics
Chang, Youngjung
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https://hdl.handle.net/2142/82390
Description
Title
Global Optimization in Systems Biology and Bioinformatics
Author(s)
Chang, Youngjung
Issue Date
2006
Doctoral Committee Chair(s)
Sahinidis, Nikolaos V.
Department of Study
Chemical Engineering
Discipline
Chemical Engineering
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
Biology, Bioinformatics
Language
eng
Abstract
Identification of transcription factor binding motif and sites is a crucial effort to elucidate gene regulatory networks and its combinatorial problem is NP -hard. In this thesis, the problem is modeled as an integer linear program with weak assumptions on the binding pattern. A computationally efficient formulation and linearization scheme is developed and the resulting problem is solved to global optimality. The proposed formulation successfully solved the CRP problem to identify its binding motif and sites simultaneously.
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