Department of Computer Science

Artificial Intelligence Research Laboratory

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Publications: By Type | By Year

Ph.D. Thesis:

Caragea, C. Abstraction-based Probabilistic Models for Sequence Classification. (2009)

Journal Papers:

Caragea, C., Caragea, D., Silvescu, A., and Honavar, V. Semi-Supervised Prediction of Protein Subcellular Localization Using Abstraction Augmented Markov Models., BMC Bioinformatics, Special Issue on Machine Learning in Computational Biology (MLCB), 2010.

Caragea, C., Sinapov, J., Dobbs, D., and Honavar, V. Mixture of experts models to exploit global sequence similarity on biomolecular sequence labeling., BMC Bioinformatics 2009, doi:10.1186/1471-2105-10-S4-S4.

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

Caragea, C., Sinapov, J., Silvescu, A., Dobbs, D., and Honavar, V. Glycosylation site prediction using ensembles of Support Vector Machine classifiers., BMC Bioinformatics 2007, 8:438.

Conference Papers:

Caragea, C., Silvescu, A., Caragea, D., and Honavar, V. Semi-Supervised Sequence Classification Using Abstraction Augmented Markov Models., In: Proceedings of the ACM Conference on Bioinformatics and Computational Biology (ACM-BCB 2010), Niagara Falls, New York, USA, 2010.

Silvescu, A., Caragea, C., and Honavar, V. Combining Super-Structuring and Abstraction on Sequence Classication., In: Proceedings of the IEEE International Conference on Data Mining (ICDM 2009), Miami, Florida, USA, 2009.

Caragea, C., Caragea, D., and Honavar, V. Learning Link-Based Classifiers from Ontology-Extended Textual Data., In: Proceedings of the 21st International Conference on Tools with Artificial Intelligence (ICTAI 2009), Newark, New Jersey, USA, 2009.

Caragea, C., Caragea, D., and Honavar, V. Learning Link-Based Naive Bayes Classifiers from Ontology-Extended Distributed Data., In: Proceedings of the 8th International Conference on Ontologies, DataBases, and Applications of Semantics (ODBASE 2009), Vilamoura, Algarve-Portugal, 2009.

Koul, N., Bahirwani, V., Caragea, C., Caragea, D., and Honavar, V. Learning Classifiers from Large Databases Using Statistical Queries., In: Proceedings of the International Conference on Web Intelligence (WI 2008), Sydney, Australia, 2008.

Caragea, C., Sinapov, J., Dobbs, D., and Honavar, V. Using Global Sequence Similarity to Enhance Biological Sequence Labeling., In: Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2008), Philadelphia, PA, USA, pp. 104-111, 2008.

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), The Big Island of Hawaii, Vol. 13., pp. 501-512, 2008.

Caragea, C., Sinapov, J, Dobbs, D., and Honavar, V. Assessing the Performance of Macromolecular Sequence Classifiers., In: Proceedings of IEEE 7th International Conference on Bioinformatics and Bioengineering (BIBE 2007), Boston, MA, USA, pp. 320-326, 2007.

Workshop Papers:

Caragea, C., Silvescu, A., Caragea, D., and Honavar, V. Abstraction Augmented Markov Models., In: Machine Learning in Computational Biology Workshop, Co-located with NIPS. (NIPS WS 2009), Vancouver, BC, Canada, 2009.

Caragea, C., Silvescu, A., and Honavar, V. Designing Abstract Features for Sequence Classication Tasks., In: Workshop for Women in Machine Learning, Co-located with NIPS (NIPS WS 2009), Vancouver, BC, Canada, 2009.

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

Book Chapters:

Caragea, C. and Honavar, V. Machine Learning in Computational Biology, In: Encyclopedia of Database Systems, 2008.

Student Abstracts and Poster Programs:

Silvescu, A., Caragea, C., and Honavar, V. Combining Abstraction and Super-Structuring on Macromolecular Sequence Classication. The 13^th Annual International Conference on Research in Computational Molecular Biology, Poster Program, Tucson, AZ (RECOMB 2009). [poster]

Silvescu, A., Caragea, C., and Honavar, V. Predicting Protein Subcellular Localization Using Abstract Sequential Features. The 17^th Annual International Conference on Intelligent Systems For Molecular Biology, Poster Program, Stockholm, Sweden (ISMB 2009).

Caragea, C., Terribilini, M., Sinapov, J., Lee, J.H., Towfic, F., Dobbs, D., and Honavar, V. Predicting Protein-RNA Binding Sites Using Structural Information. The 16^th Annual International Conference On Intelligent Systems For Molecular Biology, Poster Program, Toronto, Canada (ISMB 2008). [poster]

Terribilini, M., Caragea, C., Reyon, D., Sander, J., Lee, J.H., Jernigan, R.L., Honavar, V., and Dobbs, D. Comparing Sequence and Structure-based Classifiers for Predicting RNA Binding Sites in Specific Families of RNA Binding Proteins. The 16^th Annual International Conference On Intelligent Systems For Molecular Biology, Poster Program, Toronto, Canada (ISMB 2008).

Sinapov, J., Caragea, C., Dobbs, D., and Honavar, V. Using Global Sequence Similarity Improves Biological Site-Specific Classifiers. The 16^th Annual International Conference On Intelligent Systems For Molecular Biology, Poster Program, Toronto, Canada (ISMB 2008). [poster]

Reyon, D., Lewis, B., Lee, J-H., Gleeson, C., Hamilton, M., Caragea, C., Towfic, F., Terribilini, M., Honavar, V., and Dobbs, D. (2007) Combining Structural Modeling, Evolutionary Information, and Machine Learning to Improve Prediction of Nucleic Acid Binding Sites in Telomerase. The 5^th Annual Rocky Mountain Bioinformatics Conference, Poster Program, Aspen/Snowmass, Colorado (Rocky 2007).

Terribilini, M., Sander, J., Caragea, C., Lee, J-H., Jernigan, R.L., Honavar, V. and Dobbs, D. Comparing Sequence vs. Structure-based Predictions of RNA Binding Sites in Proteins.The 1^st Annual Midwest Symposium on Computational Biology and Bioinformatics, Chicago, Illinois (MSCBB 2007).

Towfic, F., Gemperline, D., Caragea, C., Wu, F., Dobbs, D., and Honavar, V. Prediction of RNA-Protein Interfaces Using Structural Features. The 1^st Annual Midwest Symposium on Computational Biology and Bioinformatics, Chicago, Illinois (MSCBB 2007). [poster]

Gleeson, C., Hamilton, M., Lee, J.-H., Caragea, C., Honavar, V., and Dobbs, D. Generating Models as a Platform for Comparing Functional and Structural Elements of Telomerase. The 16^th Annual Growth Factor and Signal Transduction Conferences, Ames, Iowa (GFST 2007). [poster]

Caragea, C., Sinapov, J., Terribilini, M., Dobbs, D., and Honavar, V. Assessing the Performance of Macromolecular Sequence Classifiers. The 15^th Annual International Conference On Intelligent Systems For Molecular Biology, Poster Program, Vienna, Austria (ISMB 2007). [poster]

Caragea, D., Caragea, C., Bao, J., and Honavar, V. Ontology-Based Information Integration Using INDUS: Intelligent Data Understanding System. Emerging Technologies Conference, Ames, Iowa (ETC 2007). [poster]

Caragea, C., Sinapov, J., Silvescu, A., Dobbs, D., and Honavar, V. Glycosylation Site Prediction using Machine Learning Approaches. The 11^th Annual International Conference on Research in Computational Molecular Biology, Poster Program, Oakland, California (RECOMB 2007). [poster]

Caragea, C., Sinapov, J., Silvescu, A., Dobbs, D., and Honavar, V. Learning Classifiers to Predict Glycosylation Sites in Proteins. The 4^th Annual Rocky Mountain Bioinformatics Conference, Poster Program, Aspen/Snowmass, Colorado (Rocky 2006). [poster]

El-Manzalawy, Y., Caragea, C., Dobbs, D., Honavar, V. On the Quality of Motifs for Protein Phosphorylation Site Prediction. The 14^th Annual International Conference On Intelligent Systems For Molecular Biology, Poster Program, Fortaleza, Brazil (ISMB 2006). [poster]

El-Manzalawy, Y., Caragea, C., Dobbs, D., Honavar, V. Machine Learning versus Profile-Based Methods for Protein Phosphorylation Site Prediction, The 6^th Annual Joint Bioinformatics Symposium, Poster Program, Ames, Iowa, 2006. [poster]

Caragea, C., Caragea, D. and Honavar, V. Learning Support Vector Machine Classifiers from Distributed Data Sources. In: Proceedings of the 20^th National Conference on Artificial Intelligence, Student Abstract and Poster Program, Pittsburgh, Pennsylvania. Pp. 1602-1603. AAAI Press (AAAI 2005). [poster]