A.I.

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Department of Computer Science

Center for Computational Intelligence, Learning, and Discovery

Artificial Intelligence Research Laboratory

Publications

Books

Honavar, V. and Caragea, D. (2007). Knowledge Acquisition from Autonomous, Semantically Disparate, Distributed Data Sources. Berlin: Springer, In press.

Honavar, V. and Slutzki, G. (1998) (Ed.). Proceedings of the Fourth International Colloquium on Grammatical Inference. (LNCS Vol. 1433). Berlin: Springer-Verlag.

Patel, M., Honavar, V., and Balakrishnan, K. (2001) (Ed.) Evolutionary Synthesis of Intelligent Agents. Boston, MA: MIT Press.

Honavar, V. and Uhr, L. (1994) (Ed). Artificial Intelligence and Neural Networks: Steps Toward Principled Integration. New York, NY: Academic Press.

Refereed Journal and Conference Publications

Bao, J., Voutsadakis, G., Slutzki, G., and Honavar, V. On the Decidability of Role Mappings between Modular Ontologies. In: Proceedings of the 23nd Conference on Artificial Intelligence (AAAI-2008), Chicago, USA, AAAI, In press.

Dunn-Thomas, T., Dobbs, D.L., Sakaguchi, D. Young, M.J. Honavar, V. Greenlee, H. M. W. (2008). Proteomic Differentiation Between Murine Retinal and Brain Derived Progenitor Cells. Stem Cells and Development. 17:119-131.

El-Manzalawy, Y., Dobbs, D., and Honavar, V. (2008) Predicting linear B-cell epitopes using string kernels. Journal of Molecular Recognition, In press, 2008.

Hecker, L., Alcon, T., Honavar, V., and Greenlee, H. Analysis and Interpretation of Large-Scale Gene Expression Data Sets Using a Seed Network. Journal of Bioinformatics and Biology Insights. Vol. 2. pp. 91-102, 2008.

Hughes, LaRon, Bao, J., Honavar, V., and Reecy, J. (2008). Animal Trait Ontology (ATO): the importance and usefulness of a unified trait vocabulary for animal species. Journal of Animal Science, In press.

Lee. J-H., Hamilton, M., Gleeson, C., Caragea, C., Zaback, P., Sander, J., Lee, X., Wu, F., Terribilini, M., Honavar, V. and Dobbs, D. Striking Similarities in Diverse Telomerase Proteins Revealed by Combining Structure Prediction and Machine Learning Approaches.. In Proceedings of the Pacific Symposium on Biocomputing (PSB 2008). Vol. 13. pp. 501-512, 2008.

Pathak, J., Basu, S., and Honavar, V. (2008). Composing Web Services through Automatic Reformulation of Service Specifications. IEEE International Conference on Services Computing, IEEE. Vol. In press.

Pathak, J., Basu, S., Lutz, R., and Honavar, V. (2008). MoSCoE: An Approach for Composing Web Services through Iterative Reformulation of Functional Specifications. International Journal of Artificial Intelligence Tools, Vol. 17. No. 1. pp. 109-138, 2008.

Pathak, J., Basu, S., and Honavar, V. (2008). Composing Web Services through Automatic Reformulation of Service Specifications. IEEE International Conference on Services Computing, IEEE. Vol. In press.

Towfic, F., Caragea, C., Dobbs, D., and Honavar, V. (2008). Struct-NB: Predicting protein-RNA binding sites using structural features. International Journal of Data Mining and Bioinformatics, In press.

Andorf, C., Dobbs, D. and Honavar, V. (2007). Exploring Inconsistencies in Genome Wide Protein Function Annotations: A Machine Learning Approach. BMC Bioinformatics 8:284 doi:10.1186/1471-2105-8-284

Bao, J., Slutzki, G., and Honavar, V. (2007). Distributed Reasoning with Modular ALC Ontologies (ALCP). Web Intelligence and Agent Systems. In press.

Bao, J., Slutzki, G., and Honavar, V. (2007). A Semantic Importing Approach to Knowledge Reuse from Multiple Ontologies.. In: Proceedings of the 22nd Conference on Artificial Intelligence (AAAI-2007). Vancouver, Canada. Semantic Importing Approach to Knowledge Reuse from Multiple Ontologies. pp. 1304-1309. AAAI Press.

Bao, J., Slutzki, G., and Honavar, V. (2007). Privacy-Preserving Reasoning on the Semantic Web. IEEE/WIC/ACM Conference on Web Intelligence. IEEE. pp. 791-797

Caragea, C., Sinapov, J., Dobbs, D., and Honavar, V. (2007). Assessing the Performance of Macromolecular Sequence Classifiers, In: Proceedings of the IEEE Conference on Bioinformatics and Bioengineering (BIBE 2007). pp. 320-326, 2007.

Caragea, C., Sinapov, J., Silvescu, A., Dobbs, D. And Honavar, V. (2007). Glycosylation Site Prediction Using Ensembles of Support Vector Machine Classifiers. BMC Bioinformatics. doi:10.1186/1471-2105-8-438.

Helmer, G., Wong, J., Slagell, M., Honavar, V., Miller, L., Wang, Y., Wang, X., and Stakhanova, N. (2007). Software Fault Tree and Colored Petri Net Based Specification, Design, and Implementation of Agent-Based Intrusion Detection Systems. International Journal of Information and Computer Security. Vol. 1. No. 1/2. pp. 109-142, 2007

J. McCalley, V. Honavar, S. Ryan, W. Meeker, D. Qiao, R. Roberts, Y. Li, J. Pathak, M. Ye, Y. Hong (2007). Integrated Decision Algorithms for Auto-steered Electric Transmission System Asset Management. 7th Intl. Conference on Computational Science, Berlin: Springer-Verlag. Vol. 4487. pp. 1066-1073.

Pathak, J., Basu, S., and Honavar, V. (2007). On Context-Specific Substitutability of Web Services. In: Proceedings of the IEEE International Conference on Web Services. pp. 192-199. IEEE Press.

Pathak, J., Li, Y., Honavar, V., McCalley , J. (2007). A Service-Oriented Architecture for Electric Power Transmission System Asset Management. Second International Workshop on Engineering Service-Oriented Applications: Design and Composition, Lecture Notes in Computer Science, Berlin: Springer-Verlag, 2007.

Terribilini, M., Sander, J.D., Lee, J-H., Zaback, P., Jernigan, R.L., Honavar, V. and Dobbs, D. (2007). RNABindR: A Server for Analyzing and Predicting RNA Binding Sites in Proteins. Nucleic Acids Research. doi:10.1093/nar/gkm294

Towfic, F., Gemperline, D.C., Caragea, C., Wu, F., Dobbs, D., and Honavar, V. (2007). Structural Characterization of RNA-Binding Sites of Proteins: Preliminary Results. In: Computational Structural Bioinformatics Workshop, IEEE International Conference on Bioinformatics and Biomedicine.

Wu, F., Towfic, F., Dobbs, D. and Honavar, V. (2007). Analysis of Protein Protein Dimeric Interfaces. IEEE International Conference on Bioinformatics and Biomedicine.

Yan, C., Dobbs, D., Jernigan, R., and Honavar, V. (2007). Characterization of Protein-Protein Interfaces. The Protein journal. doi:10.1007/s10930-007-9108-x

Bao, J., Caragea, D., and Honavar, V.