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J. Huang, K. Eilbeck, B. Smith, J.A. Blake, D. Dou, W. Huang, D.A. Natale, A. Ruttenberg, J. Huan, M.T. Zimmermann, G. Jiang, Y. Lin, B. Wu, H. Strachan, Y. He, S. Zhang, X. Wang, Z. Liu, G. Borchert, and M. Tan, "The Non-Coding RNA Ontology (NCRO): A comprehensive resource for the unification of non-coding RNA biology," Journal of Biomedical Semantics, 7(24): 1-12, April 2016 (doi: 10.1186/s13326-016-0066-0). [PDF]


J. Huang, F. Gutierrez, H. Strachan, D. Dou, W. Huang, B. Smith, J.A. Blake, K. Eilbeck, D.A. Natale, Y. Lin, B. Wu, N. de Silva, X. Wang, Z. Liu, G. Borchert, M. Tan, and A. Ruttenberg, "OmniSearch: A semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data," (in press) Journal of Biomedical Semantics, April 2016.


J. Huang, K. Eilbeck, B. Smith, J.A. Blake, D. Dou, W. Huang, D.A. Natale, A. Ruttenberg, J. Huan, M.T., Zimmermann, G. Jiang, Y. Lin, B. Wu, H. Strachan, N. de Silva, M. Kasukurthi, V. Jha, Y. He, S. Zhang, X. Wang, Z. Liu, G. Borchert, and M. Tan, "The Development of Non-Coding RNA Ontology," (in press) International Journal of Data Mining and Bioinformatics, March 2016.


J. Huang, K. Eilbeck, J.A. Blake, D. Dou, D.A. Natale, A. Ruttenberg, B. Smith, M.T. Zimmermann, G. Jiang, Y. Lin, B. Wu, Y. He, S. Zhang, X. Wang, H. Zhang, Z. Liu, and M. Tan, "A domain ontology for the non-coding RNA field," Proc. 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM-15), pp. 621-624, IEEE, Washington D.C., Nov. 2015. [PDF]


J. Huang, F. Gutierrez, D. Dou, J.A. Blake, K. Eilbeck, D.A. Natale, B. Smith, Y. Lin, X. Wang, Z. Liu, M. Tan, and A. Ruttenberg, "A semantic approach for knowledge capture of microRNA-target gene interactions," Proc. BHI Workshop at 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM-15), pp. 975-982, IEEE, Washington D.C., Nov. 2015. [PDF]


J. Huang, G. Borchert, D. Dou, J. Huan, and M. Tan, editors, Bioinformatics in microRNA research: computational methods in exploring microRNAs' functions, (in-progress) Springer series of Methods in Molecular Biology, 2015.


J. Huang, J. Dang, G.M. Borchert, K. Eilbeck, H. Zhang, M. Xiong, W. Jiang, H. Wu, J.A. Blake, D.A. Natale, and M. Tan, "OMIT: Dynamic, Semi-Automated Ontology Development for the microRNA Domain," PLOS ONE, 9(7): 1-16, e100855, July 2014 (doi:10.1371/journal.pone.0100855). [PDF]


J. Huang, J. Dang, X. Lu, M. Xiong, W.T. Gerthoffer, and M. Tan, "Semi-Automated microRNA Ontology Development based on Artificial Neural Networks," Proc. 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM-13), Shanghai, China, Dec. 2013. [PDF]


J. Huang, J. Huan, A. Tropsha, J. Dang, M. Xiong, and W. Jiang, "Semantics-Driven Frequent Data Pattern Mining on Electronic Health Records for Effective Adverse Drug Event Monitoring," Proc. 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM-13), Shanghai, China, Dec. 2013. [PDF]


J. Huang, J. Dang, X. Lu, D. Dou, J.A. Blake, W.T. Gerthoffer, and M. Tan, "An Ontology-Based MicroRNA Knowledge Sharing and Acquisition Framework," Proc. BHI Workshop at 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM-12), Philadelphia, PA, Oct. 2012. [PDF]


J. Huang, D. Dou, J. Dang, J.H. Pardue, X. Qin, J. Huan, W.T. Gerthoffer, and M. Tan, "Knowledge Acquisition, Semantic Text Mining, and Security Risks in Health and Biomedical Informatics," Proc. World Journal of Biological Chemistry, 3(2): 27-33, Baishideng, Feb. 2012 (doi: 10.4331/wjbc.v3.i2.27). [PDF]



J. Huang, C. Townsend, D. Dou, H. Liu, and M. Tan, "OMIT: A Domain-Specific Knowledge Base for MicroRNA Target Prediction," Pharmaceutical Research, Springer, Aug. 2011 (doi:10.1007/s11095-011-0573-8). [PDF]


C. Townsend, J. Huang, D. Dou, S. Dalvi, P.J. Hayes, L. He, W. Lin, H. Liu, R. Rudnick, H. Shah, H. Sun, X. Wang, and M. Tan, "OMIT: Domain Ontology and Knowledge Acquisition in MicroRNA Target Prediction," Proc. Ninth International Conference on Ontologies, DataBases, and Applications of Semantics (ODBASE-10), Crete, Greece, Oct. 2010. [PDF]


J. Huang, M. Tan, D. Dou, L. He, J. Dang, and P. Hayes, "Ontology for MiRNA Target Prediction in Human Cancer," Proc. First ACM International Conference on Bioinformatics and Computational Biology (BCB-10), Niagara Falls, NY, Aug. 2010. [PDF]


J. Huang, D. Dou, L. He, J. Dang, and P. Hayes, "Ontology-Based Knowledge Discovery and Sharing in Bioinformatics and Medical Informatics: A Brief Survey," Proc. Seventh International Conference on Fuzzy Systems and Knowledge Discovery (FSKD-10), Yantai, China, Aug. 2010. [PDF]


J. Huang, J. Dang, M.N. Huhns, and W.J. Zheng, "Use Artificial Neural Network to Align Biological Ontologies," BMC Genomics 2008, 9 (Suppl 2): S16. [PDF] (An electronic version is available in BMC Genomics Website)