Automatic Reconstruction of the Building Blocks of Molecular Interaction Networks
Rivera, Corban G.
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High-throughput whole-genome biological assays are highly intricate and difficult to interpret. The molecular interaction networks generated from evaluation of those experiments suggest that cellular functions are carried out by modules of interacting molecules. Reverse-engineering the modular structure of cellular interaction networks has the promise of significantly easing their analysis. We hypothesize that:
- cellular wiring diagrams can be decomposed into overlapping modules, where each module is a set of coherently-interacting molecules and
- a cell responds to a stress or a stimulus by appropriately modulating the activities of a subset of these modules.
- Given a wiring diagram and genome-wide gene expression data measured after the application of a stress or in a disease state, compute the active network of molecular interactions perturbed by the stress or the disease.
- Given the active networks for multiple stresses, stimuli, or diseases, compute a set of network legos, which are molecular modules with the property that each active network can be expressed as an appropriate combination of a subset of modules.
- Doctoral Dissertations