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- Wayne Goddard, Teresa W. Haynes, Debra J. Knisley
- Discussiones Mathematicae Graph Theory
- 2004

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)

- Denise R. Koessler, Debra J. Knisley, Jeff Knisley, Teresa W. Haynes
- BMC Bioinformatics
- 2010

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)

- Debra J. Knisley, Jeff Knisley
- Computational Biology and Chemistry
- 2011

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)

- Debra J. Knisley, Jeff Knisley
- BMC proceedings
- 2014

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)

- Teresa W. Haynes, Debra J. Knisley, Edith Seier, Yue Zou
- BMC Bioinformatics
- 2005

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)

- Odile Favaron, Teresa W. Haynes, Stephen T. Hedetniemi, Michael A. Henning, Debra J. Knisley
- Discrete Mathematics
- 2002

A set S of vertices in a graph G is called a total irredundant set if, for each vertex v in G; v or one of its neighbors has no neighbor in S −{v}. We investigate the minimum and maximum cardinalities of maximal total irredundant sets. c © 2002 Elsevier Science B.V. All rights reserved.

- Debra J. Knisley, Jeff Knisley, Chelsea Ross, Alissa Rockney
- ISRN bioinformatics
- 2012

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)

- Arthur Rhydon Jackson, Debra J. Knisley, Cecilia McIntosh, Phillip Pfeiffer
- Adv. Bioinformatics
- 2011

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)

- Debra J. Knisley, Jeff Knisley, Leonard Roberts
- BCBGC
- 2008

Each of the twenty amino acids are represented by a graph-theoretic tree. Biomolecular descriptors are defined by graphical invariants and are used to determine similarity based on the corresponding Euclidean distances. The results verify that graph-theoretic measures independent of biochemical and biophysical descriptors are valid measures of similarity of… (More)

- István Karsai, Jeff Knisley, Debra J. Knisley, Lev Y Yampolsky, Anant P. Godbole
- CBE life sciences education
- 2011

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)