Global Optimization in Systems Biology and Bioinformatics

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.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Chemical Engineering

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2015

Author dc:creator

• Chang, Youngjung

Contributors dc:contributor

• Sahinidis, Nikolaos V.

• Biology, Bioinformatics

Language dc:language

eng

Identifier

(MiAaPQ)AAI3250223

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/82390