Publications |

- (with S. Koshy) From chaos to permanence using control theory. (PDF). Submitted.
- (with S. Ha, D. Altarawy, H. Hosamadine, D. Deb, R. Hilmer, M. Ansariola, M. Megraw, J. Setubal, F. Katagiri, J. Glazebrook, B. Tyler, J. McDowell, S. Hoops, R. Laubenbacher) PlantSimLab - A Modeling and Simulation Web Tool for Plant Biologists. (PDF). Submitted.
- (with Caromile, L.A., Laubenbacher, R., Shapiro, L.) The innate immune response to ischemic injury: a multiscale modeling perspective. BMC Systems Biology, 12:50.

- (with He, Q., Robbiano, L., Stigler, B.) Small Gröbner fans of ideals of points. Submitted.
- Discrete-Time Dynamical Systems. In “Handbook of Discrete and Combinatorial Mathematics,” 2nd Ed, Ed. Douglas Shier. CRC Press.
- (with Laubenbacher, R.) Boolean models in immunology. In “System Immunology: An Introduction to Modeling Methods for Scientists,” Eds. Das, J. and Jayaprakash, C. Taylor & Francis Group.

- (with Murrugarra, D) Molecular network control through Boolean canalization. (PDF). EURASIP Journal on Bioinformatics and Systems Biology, 2015:9.
- (with Matache, D. and Yordanov, O.) A difference equation for tracking perturbations in systems of Boolean nested canalyzing functions. (PDF).
*Physical Review Letters E*, 91(6), 062812.

- (with Le Pape, S., Hannaert, P., Konovalov, A.,Volmer, R., Ron, D., Thuillier, R., Hauet, H.) Polynomial algebra as a tool to identify potential therapeutic targets: an application to ischemia-reperfusion injury.
*FEBS Letters*, 588(17), pp. 3062-7. - (with Stigler, B.) Inferring the Topology of Gene Regulatory Networks: An Algebraic Approach to Reverse Engineering. (PDF).
*Bulleting of Mathematical Biology*, October 2014.

- (with Stigler, B.) Data Identification and Characterization for Improving Gene Network Inference. In Mathematical Concepts and Methods in Modern Biology, Eds. Hodge, T. and Robeva, R. Elsevier.

- (with Layne, L. and Macauley, M.) Nested canalyzing depth and network stability (PDF).
*Bulletin of Mathematical Biology*. 74(2), pp. 422-433.

- (with A. Jarrah and I. Mitra) Probabilistic polynomial dynamical systems for reverse engineering of gene regulatory networks.
*EURASIP J. on Bioinformatics and Systems Biology*. 2011:1, pp. 1-33. - (with L.D. Garcia-Puente, F. Hinkelmann, A. Jarrah, R. Laubenbacher, B. Stigler, M. Stillman, P. Vera-Licona) Parameter Estimation for Boolean Models of Biological Networks (PDF).
*Journal of Theoretical Computer Science*, 412(2011), pp. 2816-2826.

- Estimating the relative volumes of the cones in a Groebner fan (PDF).
*Special issue of Mathematics in Computer Science: Advances in Combinatorual Algorithms II,* - (with M.P. Vera Licona, J. McGee, and R. Laubenbacher) Discretization of Time Series Data (PDF).
*Journal of Computational Biology*17, pp. 1-17.

- (with R. Laubenbacher, A. Jarrah, B. Stigler, P. Vera-Licona) System Identification for Discrete Polynomial Models of Gene Regulatory Networks (PDF).
*15th IFAC Symposium on System Identification (SYSID 2009)*, Volume 15, Part 1, pp. 11-17.

- (with A. Zardecki) Forecasting Polynomial Dynamics (PDF).
*Applied Mathematics and Computation*, 204(1), pp. 233-239.

- (with A. Jarrah, R. Laubenbacher, and B. Stigler) A Groebner Fan Method for Biochemical Network Modeling.
*ISSAC Proceedings*: 122-126.

- Polynomial Models for Systems Biology: Data Discretization and Term Order Effect on Dynamics.
*Virginia Tech Digital Library and Archives*. Ph.D. Dissertation. 2006.

- (with O. Yordanov) Statistics of Some Low-dimensional Chaotic Flows (PDF).
*International Journal of Bifurcation and Chaos*, 11(10), pp. 2675-2682.

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