Applied Machine Learning and Combinatorial Challenges in Gene Regulatory Circuit Identification
Monday, November 19, 2012 - 4:00pm - 4:50pm KEC 1001 Molly Megraw Assistant Professor Botany & Plant Pathology Oregon State University Abstract: My laboratory is broadly interested in understanding how certain important small RNAs known as "microRNAs" and important protein-coding genes known as "Transcription Factors" work together in living cells. As a part of these studies, we need to identify (1) which RNAs and genes interact, and (2) which interactions form circuits that play key roles in physiological processes. My recent work in these areas has given rise to two challenges which may interest EECS graduate students, postdocs, or other collaborators. In the first portion of the talk I will demonstrate how a machine learning model can suggest sets of gene interactions which have the potential to "turn on" a particular gene, and briefly discuss one possible approach for dissecting which of those sets are optimal predictors of gene up-regulation. In the second portion of the talk I will present a new method for identifying over-represented gene circuits, explain why this method has properties which rule out many fal! se positives as compared with existing methods, and finally point out where further study leading to rigorous proofs would greatly advance the field of network motif discovery.Speaker Biography: Molly Megraw received her doctoral degree in Genomics and Computational Biology from the University of Pennsylvania. During her post-doctoral work at Duke University, she developed a machine learning model which demonstrates that highly accurate gene and microRNA transcription start site prediction can be achieved using DNA sequence information alone. Her current work combines computational analysis of gene regulatory network topology with experimental methods for TSS-Seq library generation to identify over-represented regulatory circuits in the Arabidopsis thaliana root system. This September she began a faculty position in Systems Biology within the Center for Genome Research and Biocomputing at Oregon State University, the departmental home for her laboratory is Botany & Plant Pathology.
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