Debra J. Knisley

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For a graphical property P and a graph G, we say that a subset S of the vertices of G is a P-set if the subgraph induced by S has the property P. Then the P-domination number of G is the minimum cardinality of a dominating P-set and the P-independence number the maximum cardinality of a P-set. We show that several properties of domination, independent(More)
Determining the secondary structure of RNA from the primary structure is a challenging computational problem. A number of algorithms have been developed to predict the secondary structure from the primary structure. It is agreed that there is still room for improvement in each of these approaches. In this work we build a predictive model for secondary RNA(More)
The PDZ domain of proteins mediates a protein-protein interaction by recognizing the hydrophobic C-terminal tail of the target protein. One of the challenges put forth by the DREAM (Discussions on Reverse Engineering Assessment and Methods) 2009 Challenge consists of predicting a position weight matrix (PWM) that describes the specificity profile of five(More)
BACKGROUND We represent the protein structure of scTIM with a graph-theoretic model. We construct a hierarchical graph with three layers - a top level, a midlevel and a bottom level. The top level graph is a representation of the protein in which its vertices each represent a substructure of the protein. In turn, each substructure of the protein is(More)
It has become increasingly apparent that a comprehensive database of RNA motifs is essential in order to achieve new goals in genomic and proteomic research. Secondary RNA structures have frequently been represented by various modeling methods as graph-theoretic trees. Using graph theory as a modeling tool allows the vast resources of graphical invariants(More)
The prediction of secondary RNA folds from primary sequences continues to be an important area of research given the significance of RNA molecules in biological processes such as gene regulation. To facilitate this effort, graph models of secondary structure have been developed to quantify and thereby characterize the topological properties of the secondary(More)
MACHINE LEARNING WAS APPLIED TO A CHALLENGING AND BIOLOGICALLY SIGNIFICANT PROTEIN CLASSIFICATION PROBLEM: the prediction of avonoid UGT acceptor regioselectivity from primary sequence. Novel indices characterizing graphical models of residues were proposed and found to be widely distributed among existing amino acid indices and to cluster residues(More)
We describe how a team approach that we developed as a mentoring strategy can be used to recruit, advance, and guide students to be more interested in the interdisciplinary field of mathematical biology, and lead to success in undergraduate research in this field. Students are introduced to research in their first semester via lab rotations. Their(More)