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N. de Silva, D. Dou, and J. Huang, “Ontology-based information extraction on PubMed abstracts using the OMIT ontology to discover inconsistencies,” (in press) Proc. 8th ACM International Conference on Bioinformatics and Computational Biology (BCB-17), Boston, MA, Aug. 2017.

J. Huang, G. Borchert, D. Dou, J. Huan, W. Lan, M. Tan, and B. Wu, editors, Bioinformatics in microRNA research, Springer series of Methods in Molecular Biology, Humana Press, 2017 (ISBN: 978-1-4939-7044-5; DOI: 10.1007/978-1-4939-7046-9). Link in Springer

L. Zhang, R. Li, J. He, Q. Yang, Y. Wu, J. Huang, and B. Wu, “Co-expression analysis among microRNAs, long non-coding RNAs, and messenger RNAs to understand the pathogenesis and progression of diabetic kidney disease at the genetic level,”  Methods. 2017 May 31. pii: S1046-2023(17)30046-4. doi: 10.1016/j.ymeth.2017.05.023. Available online May 31, 2017. PubMed PMID: 28577935.

J. Huang,  F. Gutierrez, H.J. 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.M. 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,” J Biomed Semantics., 2016 May 10;7:25. doi: 10.1186/s13326-016-0064-2. eCollection 2016. PubMed PMID: 27175225; PubMed Central PMCID: PMC4863347.[PDF] Link in Journal of Biomedical Semantics

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.J. Strachan, Y. He, S. Zhang, X. Wang, Z. Liu, G.M. Borchert, and M. Tan, “The Non-Coding RNA Ontology (NCRO): A comprehensive resource for the unification of non-coding RNA biology,” J Biomed Semantics., 2016 May 4;7:24. doi: 10.1186/s13326-016-0066-0. eCollection 2016. PubMed PMID: 27152146; PubMed Central PMCID: PMC4857245.[PDF] Link in Journal of Biomedical Semantics

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.J. Strachan, N. de Silva, M. Kasukurthi, V. Jha, Y. He, S. Zhang, X. Wang, Z. Liu, G.M. Borchert, and M. Tan, “The Development of Non-Coding RNA Ontology,” Int. J. Data Mining and Bioinformatics, 15(3):214-232, June 2016. doi: 10.1504/IJDMB.2016.077072. PubMed Central PMCID: PMC5156483; NIHMSID: NIHMS795655.[PDF] Link in NCBI PMC

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, 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, 2014 Jul 15;9(7):e100855. doi: 10.1371/journal.pone.0100855. eCollection 2014. PubMed PMID: 25025130; PubMed Central PMCID: PMC4099014.[PDF] Link in PLOS ONE.

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)