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Title: Reconstruction of gene regulatory networks from postgenomic data
Author: Werhli, Adriano Velasque
ISNI:       0000 0004 2726 5236
Awarding Body: University of Edinburgh
Current Institution: University of Edinburgh
Date of Award: 2007
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An important problem in systems biology is the inference of biochemical pathways and regulatory networks from postgenomic data. The recent substantial increase in the availability of such data has stimulated the interest in inferring the networks and pathways from the data themselves. The main interests of this thesis are the application, evaluation and the improvement of machine learning methods applied to the reverse engineering of biochemical pathways and networks. The thesis starts with the application of an established method to newly available gene expression data related to the interferon pathway of the human immune system in order to identify active subpathways under di erent experimental conditions. The thesis continues with the comparative evaluation of various machine learning methods (Relevance networks, Graphical Gaussian Models, Bayesian networks) using observational and interventional data from cytometry experiments as well as simulated data from a gold-standard network. The thesis also extends and improves existing methods to include biological prior knowledge under the Bayesian approach in order to increase the accuracy of the predicted networks and it quanti es to what extent the reconstruction accuracy can be improved in this way.
Supervisor: Armstrong, Douglas. ; Husmeier, Dirk. Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available
Keywords: Informatics ; Institute for Adaptive and Neural Computation ; Bayesian networks ; machine learning