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Our objective is to create a suite of software solutions that enable the complex tasks in which life science professionals and biomedical researchers engage towards the discovery and evaluation of new treatments, our research efforts yielded highly innovative techniques which is evidenced in the form of peer-reviewed publications and posters:

Patents

  • US Patent US 20140046894 A1 awarded for "Resource community topic modeling with spreading activation". December 10, 2014

  • US Patent US 20140067793 A1 awarded for "Query Optimization for SPARQL". March 6, 2014

  • US Patent US 20130275345 A1 awarded for "Automated verification of hypotheses using ontologies". October 17, 2013

  • US Patent US 20130275354 A1 awarded for "Hypothesis verification using ontologies". October 17, 2013

Publications

  • Menze, Bjoern, Andras Jakab, Stefan Bauer, Jayashree Kalpathy-Cramer, Keyvan Farahani, Justin Kirby, Yuliya Burren, et al. "The Multimodal Brain Tumor Image Segmentation Benchmark (BRATS)." IEEE Transactions on Medical Imaging (January 27, 2014). http://hal.inria.fr/hal-00935640.

  • Buendia, Patricia, Thomas Taylor, Michael Ryan, and Nigel John. “A Grouping Artificial Immune Network for Segmentation of Tumor Images.” Proceedings of NCI-MICCAI BRATS 2013 (September 22, 2013).

  • Taylor, Thomas, Nigel John, Patricia Buendia, and Michael Ryan. “Map-Reduce Enabled Hidden Markov Models for High Throughput Multimodal Brain Tumor Segmentation.” Proc. NCI-MICCAI BRATS 2013 (Sept 22, 2013).

  • Wang, Z., Sagotsky, J., Taylor, T., Shironoshita, P., and Deisboeck, T. S. (2013). Accelerating cancer systems biology research through Semantic Web technology. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 5(2), 135-151.

  • Buendia, P., Tyree, J., Loredo, R., and Hsu, S. (2012): Identification of conserved splicing motifs in mutually exclusive exons of 15 insect species. BMC Genomics, 13:S1

  • E. Shironoshita, Y. Jean-Mary, R. Bradley, P. Buendia, and M. Kabuka, "Cancer Data Integration and Querying with GeneTegra," presented at the Data Integration for the Life Sciences (DILS) 2012, College Park, MD, USA.

  • Yves R. Jean-Mary, E. Patrick Shironoshita, Mansur R. Kabuka: "ASMOV: Results for OAEI 2010," 5th International Workshop on Ontology Matching (OM 2010), Shanghai, China.

  • T. J. Taylor, R. M. Bradley, J. Sagotsky, E. P. Shironoshita, Z. Wang, P. Vazquez, T. S. Deisboeck, M.R. Kabuka, "Grid-based cancer model simulation with CViT’s Computational Model Execution Framework", caBIG© 2010 Annual Meeting

  • Yves R. Jean-Mary, E. Patrick Shironoshita, Mansur R. Kabuka: "ASMOV: Results for OAEI 2009," 4th International Workshop on Ontology Matching (OM 2009), Chantilly, VA, USA.

  • Yves R. Jean-Mary, E. Patrick Shironoshita, Mansur R. Kabuka: "Ontology matching with semantic verification," Journal of Web Semantics, vol. 7, no. 3, pp 235-251, September 2009, doi:10.1016/j.websem.2009.04.001.

  • E. Patrick Shironoshita, Yves R. Jean-Mary, Ray M. Bradley, Mansur R. Kabuka, "semQA: SPARQL with Idempotent Disjunction," IEEE Transactions on Knowledge and Data Engineering, vol. 21, no. 3, pp. 401-414, March 2009, doi:10.1109/TKDE.2008.91.

  • E. Patrick Shironoshita, Yves R. Jean-Mary , Ray M. Bradley and Mansur R. Kabuka: "semCDI: a query formulation for semantic data integration in caBIG". Journal of the American Medical Informatics Association (JAMIA), vol. 15, no. 4, pp 559-568, July-August 2008, doi:10.1197/jamia.M2732.

  • E. Patrick Shironoshita, Ray M. Bradley, Yves R. Jean-Mary, Thomas J. Taylor, Michael T. Ryan, Mansur R. Kabuka: "Semantic Representation and Querying of caBIG Data Services," Data Integration in the Life Sciences, Springer Berlin/Heidelberg, June 2008, pp 108-115, doi:10.1007/978-3-540-69828-9_10.

  • Yves R. Jean-Mary, Mansur R. Kabuka: "ASMOV: Results for OAEI 2008," 3rd International Workshop on Ontology Matching (OM 2008), Karlsruhe, Germany.

  • E. Patrick Shironoshita, Michael T. Ryan, Mansur R. Kabuka: "Cardinality estimation for the optimization of queries on ontologies," ACM SIGMOD Record, vol. 36, no. 2, pp 13-18, June 2007, doi:10.1145/1328854.1328856.

  • Yves R. Jean-Mary, Mansur R. Kabuka. "ASMOV: Ontology Alignment with Semantic Validation". Joint SWDB-ODBIS Workshop, September 2007, Vienna, Austria, 15-20.

  • Yves R. Jean-Mary, E. Patrick Shironoshita, Thomas J. Taylor, Michael T. Ryan, Ray M. Bradley , Mansur R. Kabuka: "Ontology Alignment with Semantic Validation: A Comparison using UMLS Metathesaurus and WordNet". IEEE 7th International Symposium on Bioinformatics and Bioengineering, 2007.

  • Yves R. Jean-Mary, Mansur R. Kabuka: "ASMOV: Results for OAEI 2007," 2nd International Workshop on Ontology Matching (OM 2007), Busan, Korea.

  • Thomas J. Taylor, Mansur R. Kabuka, E. Patrick Shironoshita, Michael T. Ryan, Akmal A. Younis, Nigel M. John, John R. McQuaid, M. H. Trivedi, G. W. Currier, R. A. McKinney, B. D. Grannemann, C. Claassen: "Viability of Mental Health Assessment Software in Diverse Settings". 45th Annual NCDEU (New Clinical Drug Evaluation Unit), Boca Raton, Florida, June 6-9, 2005.

Conference Participation

International Semantic Web Conference (ISWC 07-90)

Cancer Biomedical Informatics Grid (caBIG 2009)

Data Integration in the Life Sciences (DILS 2008)

Very Large Data Bases Conference (VLDB 2007)

IEEE International Conference on BioInformatics & BioEngineering (BIBE 2007)

New Research Approaches for Mental Health Interventions (NCDEU 2005)

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