Overview
The focus of my scholarship is the integration and effective use of information from complex systems such as metabolic networks and computer networks. My work combines fuzzy logic, signal processing, and data science with biological systems to create innovative data resources and analysis methods. I integrate this research into the classroom using innovative teaching/outreach methods such as serious games and integrative laboratory assignments.
Systems Biology Regulatory Network Analysis
- Time-based correlation networks combined with partial correlation network pruning for analyzing timing in gene regulatory networks.
- Top-down network analysis methods for genome-wide regulatory networks.
- Pipeline developed for determining the change in function and phenomics due to mutations in directed evolution experiments.
Alternative Splicing Quantification and Occurrence
- Improved methods for alternative splicing detection and quantification in RNA-seq data sets.
- Created machine learning methods for assigning function to alternatively spliced transcripts.