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Jennifer Chang, Ph.D. Thesis Defense

Jun 26, 2017 - 12:00 PM
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The Ph.D. Defense seminar for Jennifer Chang, a Department of Genetics, Development and Cell Biology graduate student, will be held on Monday, June 26, at noon the Carver Co-Lab Conference Room.

Title: Developing an integrated system for biological network exploration

Abstract: Network analysis and visualization have been used in systems biology to extract biological insight from complex datasets. Many existing network analysis tools either focus on visualization but have limited scalability, or focus on analysis with limited visualizations. The separation of analysis from visualizing the analysis results causes systems biologists to jump between forming a question, building a massive network, identifying a subnetwork for visualization, and using the visualization as feedback and inspiration for the next question. This iterative process can take several days, making it difficult for researchers to maintain the mental map of the questions queried. In addition, biological data is stored in different formats and has annotations, thus systems biologists often run into hurdles when merging large or heterogeneous networks. The polymorphic nature of the datasets makes it difficult for researchers to integrate data to answer biological questions.  A more systematic method for merging data, resolving data conflict, and analyzing subnetworks may improve the efficiency and scalability of heterogeneous multi-network analysis.

Towards improving and pushing forward multi-network analysis where a researcher can easily combine multiple heterogeneous biological data networks to answer biological questions, this dissertation has several goals: (i) provide a set of standard multi-network operations; (ii) provide standard merging rules for heterogeneous networks; (iii) provide standard methods to reproduce network analyses; (iv) provide these functionalities all within a single integrated software environment that also allows users to visualize and explore the network analysis results and (v) present several examples applying these methods  in biological analysis. These efforts culminating in three academic publications.