Department of Computer Science

Journal Papers:

• 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, In press.

• 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:

• Koul, N., Bahirwani, V., Caragea, C., Caragea, D., and Honavar, V. Learning from Large Autonomous Data Sources using Sufficient Statistics, In: Proceedings of the International Conference on Web Intelligence (WI 2008) 2008 (.ppt (soon))

• 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) 2008 (.ppt (soon))

• 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.

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

Workshop Papers:

• 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)

Book Chapters:

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

      Student Abstracts and Poster Programs:

• Caragea, C., Terribilini, M., Sinapov, J., Lee, J.H., Towfic, F., Dobbs, D., and Honavar, V. Predicting Protein-RNA Binding Sites Using Structural Information. Accepted to The 16^th Annual International Conference On Intelligent Systems For Molecular Biology & 6^th, Poster Program, Toronto, Canada  (ISMB 2008) (.ppt)

• 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. Accepted to The 16^th Annual International Conference On Intelligent Systems For Molecular Biology & 6^th, Poster Program, Toronto, Canada  (ISMB 2008) (.ppt)

• Sinapov, J., Caragea, C., Dobbs, D., and Honavar, V. Using Global Sequence Similarity Improves Biological Site-Specific Classifiers. Accepted to The 16^th Annual International Conference On Intelligent Systems For Molecular Biology & 6^th, Poster Program, Toronto, Canada  (ISMB 2008) (.ppt)

• 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. Accepted to The 5^th Annual Rocky Mountain Bioinformatics Conference (Rocky 2007), Poster Program, Aspen/Snowmass, Colorado

• 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. First 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. First Annual Midwest Symposium on Computational Biology and Bioinformatics Chicago, Illinois (MSCBB 2007)

• 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 16th Annual Growth Factor and Signal Transduction Conferences, Ames, Iowa (GFST 2007)

• Caragea, C., Sinapov, J., Terribilini, M., Dobbs, D., and Honavar, V. Assessing the Performance of Macromolecular Sequence Classifiers. Accepted to The 15^th Annual International Conference On Intelligent Systems For Molecular Biology & 6^th European Conference on Computational Biology, Poster Program, Vienna, Austria  (ISMB/ECCB 2007) (.ppt)

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

• Caragea, C., Sinapov, J., Silvescu, A., Dobbs, D., and Honavar, V. Glycosylation Site Prediction using Machine Learning Approaches. Accepted to The Eleventh Annual International Conference on Research in Computational Molecular Biology, Poster Program, Oakland, California  (RECOMB2007) (.ppt)

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

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

• El-Manzalawy, Y., Caragea, C., Dobbs, D., Honavar, V. Machine Learning versus Profile-Based Methods for Protein Phosphorylation Site Prediction, Accepted to The Sixth Annual Joint Bioinformatics Symposium, Student Abstract and Poster Program, Ames, Iowa, 2006

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