List of publications

Refereed (conference, journal and workshop)

Andorf, C., Dobbs, D., and Honavar, V. (2004). Discovering Protein Function Classification Rules from Reduced Alphabet Representations of Protein Sequences. Information Sciences. In press.

Andorf, C., Silvescu, A., Dobbs, D. and Honavar, V. Learning Classifiers for Assigning Protein Sequences to Gene Ontology Functional Families. In: Proceedings of the Fifth International Conference on Knowledge Based Computer Systems (KBCS 2004), India.

Andorf, C., Dobbs, D., and Honavar, V. (2002). Discovering Protein Function Classification Rules from Reduced Alphabet Representations of Protein Sequences. In: Proceedings of the Conference on Computational Biology and Genome Informatics. Durham, North Carolina.

Honavar, V., Andorf, C., Caragea, D., Silvescu, A., Reinoso-Castillo, J., and Dobbs, D. (2001). Ontology-Driven Information Extraction and Knowledge Acquisition from Heterogeneous, Distributed Biological Data Sources. In: Proceedings of the IJCAI-2001 Workshop on Knowledge Discovery from Heterogeneous, Distributed, Autonomous, Dynamic Data and Knowledge Sources.

Caragea, D., Silvescu, A., Pathak, J., Bao, J., Andorf, C., Dobbs, D., and Honavar, V. (2005) Information Integration and Knowledge Acquisition from Semantically Heterogeneous Biological Data Sources. Data Integration in Life Sciences (DILS 2005), San Diego, Berlin: Springer-Verlag. Lecture Notes in Computer Science. In press, 2005.

Caragea, D., Bao, J., Pathak, J., Andorf, C, Dobbs, D., and Honavar, V. (2005). Information Integration from Semantically Heterogeneous Biological Data Sources. Proceedings of the Third International Workshop on Biological Data Management (BIDM 2005), Copenhagen, IEEE Computer Society, In press, 2005.

Silvescu, A., Reinoso-Castillo, J., Andorf, C., Honavar, V., and Dobbs, D. (2001). Ontology-Driven Information Extraction and Knowledge Acquisition from Heterogeneous, Distributed Biological Data Sources. In: Proceedings of the IJCAI-2001 Workshop on Knowledge Discovery from Heterogeneous, Distributed, Autonomous, Dynamic Data and Knowledge Sources.

Refereed Extended Abstracts in Conferences

Andorf, C., Dobbs, D., Honavar, V. (2006) Learning Classifiers for Assigning Protein Sequences to Subcellular Localization Families. In: Proceedings of the Annual Meeting of the International Society for Computational Biology (ISMB 2006), Poster Program, Fortaleza, Brazil.

Andorf, C., Dobbs, D., Honavar, V. (2005) Learning Classifiers for Assigning Protein Sequences to Gene Ontology Functional Families. In: Proceedings of the Annual Meeting of the International Society for Computational Biology (ISMB 2005), Poster Program, Detroit, Michigan.

Caragea, D., Silvescu, A., Pathak, J., Bao, J., Andorf, C., Yan, C., Dobbs, D. and Honavar, V. (2005). Knowledge Acquisition from Autonomous, Distributed, Semantically Heterogeneous Data Sources. In: Proceedings of the Annual Meeting of the International Society for Computational Biology (ISMB 2005), Poster Program, Detroit, Michigan.

Pathak, J., Bao, J., Caragea, D., Silvescu, A., Andorf, C., Yan, C., Dobbs, D. and Honavar, V. (2005). INDUS: A System for Information Integration and Knowledge Acquisition from Autonomous, Distributed, and Semantically Heterogeneous Data Sources. In: The Program of the Annual Meeting of the International Society for Computational Biology (ISMB 2005), Demo Program, Detroit, Michigan.

Caragea, D., Pathak, J., Bao, J., Silvescu, A., Andorf, C., Dobbs, D., and Honavar, V. (2005). Information Integration from Semantically Heterogeneous Biological Data Sources. In: Proceedings of the 3rd International Workshop on Biological Data Management (BIDM 2005), DEXA Workshops 2005, Copenhagen, Denmark. Pp. 580-584. IEEE Computer Society.

In preperation

Andorf, C., Dobbs, D. and Honavar, V. (2006) Genome-Wide Protein Function Annotations: Errors and What to Do About Them . Submitted: Nature Biotechnology.

Andorf, C., Silvescu, A., Dobbs, D. and Honavar, V. (2006) Learning Classifiers for Assigning Protein Sequences to Gene Ontology Functional Families. To be submitted: International Journal of Bioinformatics Research and Applications.

Andorf, C., Silvescu, A., Dobbs, D. and Honavar, V. (2006) Learning Classifiers for Assigning Protein Sequences to Subcellular Localization Families. To be submitted: BMC Bioinformatics.

Andorf, C., A., Dobbs, D. and Honavar, V. (2006) The effects of information gain in random alphabets in classification accuracy of protein sequences.