Penn State Clinical and Translational Science Institute (CTSI)

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  • 2008

    Striking similarities in diverse telomerase proteins revealed by combining structure prediction and machine learning approaches

    Lee, J. H., Hamilton, M., Gleeson, C., Caragea, C., Zaback, P., Sander, J. D., Li, X., Wu, F., Terribilini, M., Honavar, V. & Dobbs, D., 2008, Pacific Symposium on Biocomputing 2008, PSB 2008. p. 501-512 12 p. (Pacific Symposium on Biocomputing 2008, PSB 2008).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    6 Scopus citations
  • TCP-Compose* - A TCP-net based algorithm for efficient composition of web services using qualitative preferences

    Santhanam, G. R., Basu, S. & Honavar, V., 2008, Service-Oriented Computing - ICSOC 2008 - 6th International Conference, Proceedings. Springer Verlag, p. 453-467 15 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 5364 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    21 Scopus citations
  • Towards semantics-enabled distributed infrastructure for knowledge acquisition

    Honavar, V. & Caragea, D., Sep 30 2008, Semantic Scientific Knowledge Integration - Papers from the AAAI Spring Symposium, Technical Report. p. 29-35 7 p. (AAAI Spring Symposium - Technical Report; vol. SS-08-05).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • Unsupervised learning of probabilistic context-free grammar using iterative biclustering

    Tu, K. & Honavar, V., 2008, Grammatical Inference: Algorithms and Applications - 9th International Colloquium, ICGI 2008, Proceedings. p. 224-237 14 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 5278 LNAI).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    9 Scopus citations
  • Using global sequence similarity to enhance biological sequence labeling

    Caragea, C., Dobbs, D., Sinapov, J. & Honavar, V., 2008, Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008. p. 104-111 8 p. 4684880. (Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • Visual methods for examining SVM classifiers

    Caragea, D., Cook, D., Wickham, H. & Honavar, V., 2008, Visual Data Mining - Theory, Techniques and Tools for Visual Analytics. Simoff, S. J., Bohlen, M. H. & Mazeika, A. (eds.). p. 136-153 18 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4404 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    19 Scopus citations
  • 2007

    Analysis of protein protein dimeric interfaces

    Wu, F., Towfic, F., Dobbs, D. & Honavar, V., 2007, Proceedings - 2007 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2007. p. 35-41 7 p. 4413034. (Proceedings - 2007 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2007).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    7 Scopus citations
  • A semantic importing approach to knowledge reuse from multiple ontologies

    Bao, J., Slutzki, G. & Honavar, V., 2007, AAAI-07/IAAI-07 Proceedings: 22nd AAAI Conference on Artificial Intelligence and the 19th Innovative Applications of Artificial Intelligence Conference. p. 1304-1309 6 p. (Proceedings of the National Conference on Artificial Intelligence; vol. 2).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    25 Scopus citations
  • A service-oriented architecture for electric power transmission system asset management

    Pathak, J., Li, Y., Honavar, V. & McCalley, J., 2007, Service-Oriented Computing ICSOC 2006 - 4th International Conference, Workshops Proceedings. Springer Verlag, p. 26-37 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4652 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    18 Scopus citations
  • Assessing the performance of macromolecular sequence classifiers

    Caragea, C., Sinapov, J., Honavar, V. & Dobbs, D., Dec 1 2007, Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE. p. 320-326 7 p. 4375583. (Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    14 Scopus citations
  • Designing a simulation center to test acoustical criteria for healthcare facilities

    Carballeira, A., Solet, J., Buxton, O. M. & Sykes, D., 2007, Institute of Noise Control Engineering of the USA - 22nd National Conference on Noise Control Engineering, NOISE-CON 2007. Vol. 3. p. 1545-1555 11 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • Gender diversity in engineering design teams: Investigating emergent states, team processes, and performance

    Okudan, G. E. & Mohammed, S., 2007, Proceedings of the Inaugural International Conference on Research in Engineering Education, ICREE.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • Integrated decision algorithms for auto-steered electric transmission system asset management

    McCalley, J., Honavar, V., Ryan, S., Meeker, W., Qiao, D., Roberts, R., Li, Y., Pathak, J., Ye, M. & Hong, Y., 2007, Computational Science - ICCS 2007 - 7th International Conference, Proceedings, Part I. Springer Verlag, p. 1066-1073 8 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4487 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    Open Access
    3 Scopus citations
  • On context-specific substitutability of Web services

    Pathak, J., Basu, S. & Honavar, V., Dec 1 2007, Proceedings - 2007 IEEE International Conference on Web Services, ICWS 2007. p. 192-199 8 p. 4279599. (Proceedings - 2007 IEEE International Conference on Web Services, ICWS 2007).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    44 Scopus citations
  • Privacy-preserving reasoning on the semantic Web

    Bao, J., Slutzki, G. & Honavar, V., 2007, Proceedings of the IEEE/WIC/ACM International Conference on Web Intelligence, WI 2007. p. 791-797 7 p. 4427191. (Proceedings of the IEEE/WIC/ACM International Conference on Web Intelligence, WI 2007).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    25 Scopus citations
  • Query translation for ontology-extended data sources

    Bao, J., Caragea, D. & Honavar, V., 2007, Semantic e-Science - Papers from the 2007 AAAI Workshop, Technical Report. p. 9-16 8 p. (AAAI Workshop - Technical Report; vol. WS-07-11).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    4 Scopus citations
  • Structural characterization of RNA-binding sites of proteins: Preliminary results

    Towfic, F., Caragea, C., Dobbs, D., Gemperline, D. C., Wu, F. & Honavar, V., 2007, Proceedings - 2007 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW. p. 60-66 7 p. 4425401. (Proceedings - 2007 IEEE International Conference on Bioinformaticsand Biomedicine Workshops, BIBMW).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    3 Scopus citations
  • 2006

    A general strategy for knowledge acquisition from semantically heterogeneous data sources

    Caragea, D., Bao, J. & Honavar, V., 2006, Semantic Web for Collaborative Knowledge Acquisition - Papers from the AAAI Fall Symposium, Technical Report. p. 1-8 8 p. (AAAI Fall Symposium - Technical Report; vol. FS-06-06).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • A risk-based model predictive control approach to adaptive interventions in behavioral health

    Zafra-Cabeza, A., Rivera, D. E., Collins, L. M., Ridao, M. A. & Camacho, E. F., 2006, Proceedings of the 45th IEEE Conference on Decision and Control 2006, CDC. Institute of Electrical and Electronics Engineers Inc., p. 673-678 6 p. 4177533. (Proceedings of the IEEE Conference on Decision and Control).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • A tableau-based federated reasoning algorithm for modular ontologies

    Bao, J., Caragea, D. & Honavar, V., Jan 1 2006, Proceedings - 2006 IEEE/WIC/ACM International Conference on Web Intelligence (WI 2006 Main Conference Proceedings), WI'06. Institute of Electrical and Electronics Engineers Inc., p. 404-410 7 p. 4061404. (Proceedings - 2006 IEEE/WIC/ACM International Conference on Web Intelligence (WI 2006 Main Conference Proceedings), WI'06).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    20 Scopus citations
  • A tool for collaborative construction of large biological ontologie

    Bao, J., Hu, Z., Caragea, D., Reecy, J. & Honavar, V. G., 2006, Proceedings - 17th International Conference on Database and Expert Systems Applications, DEXA 2006. p. 191-195 5 p. 1698333. (Proceedings - International Workshop on Database and Expert Systems Applications, DEXA).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    12 Scopus citations
  • Auto-steered information-decision processes for electric system asset management

    McCalley, J. D., Honavar, V. G., Ryan, S. M., Meeker, W. Q., Roberts, R. A., Qiao, D. & Li, Y., 2006, Computational Science - ICCS 2006: 6th International Conference, Proceedings. Springer Verlag, p. 440-447 8 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 3993 LNCS - III).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    4 Scopus citations
  • Collaborative knowledge acquisition from semantically disparate, distributed data sources

    Honavar, V. & Caragea, D., Dec 22 2006, Proceedings of the 2006 International Symposium on Collaborative Technologies and Systems, CTS 2006. 1644105. (Proceedings of the 2006 International Symposium on Collaborative Technologies and Systems, CTS 2006; vol. 2006).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • Comparing kernels for predicting protein binding sites from amino acid sequence

    Wu, F., Olson, B., Dobbs, D. & Honavar, V., Dec 1 2006, International Joint Conference on Neural Networks 2006, IJCNN '06. p. 1612-1616 5 p. 1716299. (IEEE International Conference on Neural Networks - Conference Proceedings).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    8 Scopus citations
  • Condition data aggregation with application to failure rate calculation of power transformers

    Pathak, J., Jiang, Y., Honavar, V. & McCalley, J., Oct 17 2006, Proceedings of the 39th Annual Hawaii International Conference on System Sciences, HICSS'06. 1579787. (Proceedings of the Annual Hawaii International Conference on System Sciences; vol. 10).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    34 Scopus citations
  • Efficient Markov network structure discovery using independence tests

    Bromberg, F., Margaritis, D. & Honavar, V., 2006, Proceedings of the Sixth SIAM International Conference on Data Mining. Society for Industrial and Applied Mathematics, p. 141-152 12 p. (Proceedings of the Sixth SIAM International Conference on Data Mining; vol. 2006).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    Open Access
    20 Scopus citations
  • Experimental comparison of feature subset selection using G A and AGO algorithm

    Lee, K., Joo, J., Yang, J. & Honavar, V., 2006, Advanced Data Mining and Applications - Second International Conference, ADMA 2006, Proceedings. Li, X., Zaïane, O. R. & Li, Z. (eds.). Springer Verlag, p. 465-472 8 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4093 LNAI).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    11 Scopus citations
  • Identifying interaction sites in "Recalcitrant" proteins: Predicted protein and RNA binding sites in REV proteins of HIV-1 and EIAV agree with experimental data

    Terribllini, M., Lee, J. H., Yan, C., Jernigan, R. L., Carpenter, S., Honavar, V. & Dobbs, D., 2006, Proceedings of the Pacific Symposium on Biocomputing 2006, PSB 2006. p. 415-426 12 p. (Proceedings of the Pacific Symposium on Biocomputing 2006, PSB 2006).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    10 Scopus citations
  • Independence, Decomposability and functions which take values into an Abelian Group

    Silvescu, A. & Honavar, V., 2006, 9th International Symposium on Artificial Intelligence and Mathematics, ISAIM 2006.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • Learning classifiers from distributed, ontology-extended data sources

    Caragea, D., Zhang, J., Pathak, J. & Honavar, V., 2006, Data Warehousing and Knowledge Discovery - 8th International Conference, DaWaK 2006, Proceedings. Springer Verlag, p. 363-373 11 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4081 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • Modeling Web service composition using symbolic transition systems

    Pathak, J., Basu, S. & Honavar, V., Dec 1 2006, AI-Driven Technologies for Services-Oriented Computing - Papers from the AAAI Workshop, Technical Report. p. 44-51 8 p. (AAAI Workshop - Technical Report; vol. WS-06-01).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    13 Scopus citations
  • Modeling Web services by iterative reformulation of functional and non-functional requirements

    Pathak, J., Basu, S. & Honavar, V., 2006, Service-Oriented Computing - ICSOC 2006 - 4th International Conference, Proceedings. p. 314-326 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4294 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    24 Scopus citations
  • Modular ontologies - A formal investigation of semantics and expressivity

    Bao, J., Caragea, D. & Honavar, V. G., 2006, The Semantic Web - ASWC 2006 - First Asian Semantic Web Conference, Proceedings. Springer Verlag, p. 616-631 16 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4185 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    23 Scopus citations
  • MoSCoE: A framework for modeling web service composition and execution

    Pathak, J., Basu, S., Lutz, R. & Honavar, V., Jan 1 2006, ICDEW 2006 - Proceedings of the 22nd International Conference on Data Engineering Workshops. Zhou, X. & Barga, R. S. (eds.). Institute of Electrical and Electronics Engineers Inc., 1623939. (ICDEW 2006 - Proceedings of the 22nd International Conference on Data Engineering Workshops).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    16 Scopus citations
  • On the semantics of linking and importing in modular ontologies

    Bao, J., Caragea, D. & Honavar, V. G., 2006, The Semantic Web - ISWC 2006 - 5th International Semantic Web Conference, ISWC 2006, Proceedings. Springer Verlag, p. 72-86 15 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4273 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    Open Access
    30 Scopus citations
  • Package-based description logics - Preliminary results

    Bao, J., Caragea, D. & Honavar, V. G., 2006, The Semantic Web - ISWC 2006 - 5th International Semantic Web Conference, ISWC 2006, Proceedings. Springer Verlag, p. 967-969 3 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4273 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    Open Access
    4 Scopus citations
  • Parallel Web service composition in MoSCoE: A choreography-based approach

    Pathak, J., Basu, S., Lutz, R. & Honavar, V., Dec 1 2006, Proceedings of ECOWS 2006: Fourth European Conference on Web Services. p. 3-12 10 p. 4031145. (Proceedings of ECOWS 2006: Fourth European Conference on Web Services).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    24 Scopus citations
  • Representing and reasoning with modular ontologies

    Bao, J. & Honavar, V., 2006, Semantic Web for Collaborative Knowledge Acquisition - Papers from the AAAI Fall Symposium, Technical Report. p. 86-89 4 p. (AAAI Fall Symposium - Technical Report; vol. FS-06-06).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    2 Scopus citations
  • RNBL-MN: A recursive Naive Bayes learner for sequence classification

    Kang, D. K., Silvescu, A. & Honavar, V., 2006, Advances in Knowledge Discovery and Data Mining - 10th Pacific-Asia Conference, PAKDD 2006, Proceedings. Springer Verlag, p. 45-54 10 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 3918 LNAI).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    3 Scopus citations
  • Selecting and composing web services through iterative reformulation of functional specifications

    Pathak, J., Basu, S., Lutz, R. & Honavar, V., Dec 1 2006, Procedings - 18th IEEE International Conference on Tools with Artificial Intelligence, ICTAI 2006. p. 445-454 10 p. 4031930. (Proceedings - International Conference on Tools with Artificial Intelligence, ICTAI).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    9 Scopus citations
  • Towards collaborative environments for ontology construction and sharing

    Bao, J., Caragea, D. & Honavar, V., 2006, Proceedings of the 2006 International Symposium on Collaborative Technologies and Systems, CTS 2006. p. 99-108 10 p. 1644121. (Proceedings of the 2006 International Symposium on Collaborative Technologies and Systems, CTS 2006; vol. 2006).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    35 Scopus citations
  • TRIPPER: Rule learning using taxonomies

    Vasile, F., Silvescu, A., Kang, D. K. & Honavar, V., Jul 14 2006, Advances in Knowledge Discovery and Data Mining - 10th Pacific-Asia Conference, PAKDD 2006, Proceedings. p. 55-59 5 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 3918 LNAI).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    5 Scopus citations
  • 2005

    A comprehensive investigation on industry-sponsored design projects' effectiveness at the first-year level: Phase I

    Okudan, G. E., Mohammed, S., Ogot, M. & Wu, X., 2005, 2005 ASEE Annual Conference and Exposition, Conference Proceedings. p. 2049-2062 14 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • A framework for Semantic Web services discovery

    Pathak, J., Koul, N., Caragea, D. & Honavar, V. G., 2005, WIDM 2005 - Proceedings of the 7th ACM International Workshop on Web Information and Data Management, Co-located with CIKM 2005. p. 45-50 6 p. (Proceedings of the Interntational Workshop on Web Information and Data Management WIDM).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    72 Scopus citations
  • Algorithms and software for collaborative discovery from autonomous, semantically heterogeneous, distributed information sources

    Caragea, D., Zhang, J., Bao, J., Pathak, J. & Honavar, V., 2005, Discovery Science - 8th International Conference, DS 2005, Proceedings. p. 14 1 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 3735 LNAI).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    3 Scopus citations
  • Algorithms and software for collaborative discovery from autonomous, semantically heterogeneous, distributed information sources

    Caragea, D., Zhang, J., Bao, J., Pathak, J. & Honavar, V., 2005, Algorithmic Learning Theory - 16th International Conference, ALT 2005, Proceedings. p. 13-44 32 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 3734 LNAI).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    14 Scopus citations
  • Discriminatively trained markov model for sequence classification

    Yakhnenko, O., Silvescu, A. & Honavar, V., 2005, Proceedings - Fifth IEEE International Conference on Data Mining, ICDM 2005. p. 498-505 8 p. 1565717. (Proceedings - IEEE International Conference on Data Mining, ICDM).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    51 Scopus citations
  • Effective design project management with a spreadsheet based approach

    Ogot, M. M., Okudan, G. E., Mohammed, S. & Wu, X., 2005, Proceedings ICED 05, the 15th International Conference on Engineering Design. (Proceedings ICED 05, the 15th International Conference on Engineering Design; vol. DS 35).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • Information integration from semantically heterogeneous biological data sources

    Caragea, D., Bao, J., Pathak, J., Silvescu, A., Andorf, C., Dobbs, D. & Honavar, V., 2005, Proceedings - Sixteenth International Workshop on Database and Expert Systems Applications, DEXA 2005. p. 580-584 5 p. 1508335. (Proceedings - International Workshop on Database and Expert Systems Applications, DEXA; vol. 2006).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    6 Scopus citations
  • Learning classifiers for misuse and anomaly detection using a bag of system calls representation

    Kang, D. K., Fuller, D. & Honavar, V., 2005, Proceedings from the Sixth Annual IEEE System, Man and Cybernetics Information Assurance Workshop, SMC 2005. p. 118-125 8 p. 1495942. (Proceedings from the 6th Annual IEEE System, Man and Cybernetics Information Assurance Workshop, SMC 2005; vol. 2005).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    87 Scopus citations