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 Office Hours:

   M. W. 09:00 AM - 11:00 AM

   or By Appointment


 Publications

 Books

  

61) 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]

60) J. Huang, Towards Mutual Understanding among Ontologies: Rule-Based and Learning-Based Matching Algorithms for Ontologies, ISBN: 978-3-639-11556-7, Verlag Dr. Müller (VDM), Germany, 2008. [Link in Amazon.com]

59) J. Huang, R. Kowalczyk, Z. Maamar, D. Martin, I. Müller, S. Stoutenburg, and K.P. Sycara, editors, Service-Oriented Computing: Agents, Semantics, and Engineering, Springer-Verlag, vol. LNCS 4504, Berlin, 2007. [URL] [Front Matter]

  

 Journal Papers

  

58) 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.

57) J. Huang, D. Dou, J. She, L. Guo, M. Kasukurthi, P. Yang, A.H. Limper, and Y. Yang, “An innovative approach combining genome-wide study, semantic analysis, and biological validation to investigate microRNA::mRNA regulatory interactions in chronic obstructive pulmonary disease and lung cancer,” (under review), Int. J. Mol. Sci. 2017.

56) J. Huang, B. Liu, Y. Liu, M. Kasukurthi, and J. Chen, “Explore microRNA regulation mechanisms in osteoarthritis with an ontology-driven analytical software tool,” (under review), Int. J. Mol. Sci. 2017.

55) B. Wu, J. Huang, M. Kasukurthi, J. Bian, K. Fukuo, K. Suzuki, G. Yoshino, and T. Kazumi, “An integrative approach to investigate the association among high-sensitive C-reactive protein, body fat mass distribution, and other cardiometabolic risk factors in young healthy women,” (under review), Int. J. Mol. Sci. 2017.

54) 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].

53) 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].

52) 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].

51) Z. Liu, K. Smith, H.T. Khong, J. Huang, E.Y. Erin Ahn, M. Zhou, and M. Tan, “miR-125b regulates differentiation and metabolic reprogramming of T cell acute lymphoblastic leukemia through directly targeting A20,” Journal of Oncotarget, 2016 Nov 29;7(48):78667-78679. doi: 10.18632/oncotarget.12018. PubMed PMID: 27637078; PubMed Central PMCID: PMC5346668.

50) Y. Liu, X. Li, N. Liu, J. Huang, and Y. Lin, “MIAGO: a curated RDF/OWL resource of microRNAs and respective targets in aging studies,” (under review) Database Journal, Oct. 2016.

49) B. Wu, J. Huang, K. Fukuo, K. Suzuki, G. Yoshino, and T. Kazumi, “Phenotypic Characteristics of Normal-Weight Obesity in Japanese Sedentary and Endurance Trained Young Women,” (under review)Journal of Atherosclerosis and Thrombosis, Dec. 2016.

48) B. Wu, J. Huang, K. Fukuo, K. Suzuki, G. Yoshino, and T. Kazumi, “Different Associations of Trunk and Leg Fat Mass with Cardiometabolic Risk Factors between Healthy, Middle-Aged Men and Women,” (under review) Journal of Atherosclerosis and Thrombosis, Dec. 2016.

47) 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]

46) M. Zhu, W. Wang, and J. Huang, “Improved Initial Cluster Center Selection in K-Means Clustering,” Engineering Computations, 2013 November 03; 31(8):1661-1667. doi: 10.1108/EC-11-2012-0288. [Link in Engineering Computations]

45) M. Zhu, W. Wang, B. Liu, and J. Huang, “Efficient Video Panoramic Image Stitching based on an Improved Selection of Harris Corners and a Multiple-Constraint Corner Matching,” PLOS ONE, 2013 Dec 4;8(12):e81182. doi: 10.1371/journal.pone.0081182. eCollection 2013. PubMed PMID: 24324675; PubMed Central PMCID: PMC3852024. [Link in PLOS ONE]

44) M. Zhu, W. Wang, B. Liu, and J. Huang, “Improved Prototype Selection in Synergetic Pattern Recognition to Recognize Human Face Expressions,” Journal of Algorithms and Computational Technology, 2013 December 15; 7(4):541-552. doi: 10.1260/1748-3018.7.4.541. [Link in Multi Science Publishing]

43) M. Zhu, W. Wang, B. Liu, and J. Huang, “A Fast Image Stitching Algorithm via Multiple-Constraint Corner Matching,” Mathematical Problems in Engineering, 2013 September 07; 2013:1-6. doi: 10.1155/2013/157847. [Link in Mathematical Problems in Engineering]

42) 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,” World J Biol Chem., 2012 Feb 26;3(2):27-33. doi: 10.4331/wjbc.v3.i2.27. PubMed PMID: 22371823; PubMed Central PMCID: PMC3286791. [PDF]

41) J. Huang, C. Townsend, D. Dou, H. Liu, and M. Tan, “OMIT: A Domain-Specific Knowledge Base for MicroRNA Target Prediction,” Pharm Res., 2011 Dec;28(12):3101-3104. doi: 10.1007/s11095-011-0573-8. Epub 2011 Aug 31. PubMed PMID: 21879385. [PDF][Link in Springer]

40) J. Huang, L. He, and G.V. Davidson-Shivers, “Educational Assessment via a Web-Based Intelligent System,” US-China Education Review, 2011 May 05; 8(5):666-674. [Link in ERIC]

39) J. Huang, J. Dang, M.N. Huhns, and W.J. Zheng, “Use Artificial Neural Network to Align Biological Ontologies,” BMC Genomics., 2008 Sep 16;9 Suppl 2:S16. doi: 10.1186/1471-2164-9-S2-S16. PubMed PMID: 18831781; PubMed Central PMCID: PMC2559880. [PDF] [Link in BMC Genomics Website]

38) J. Huang, J. Dang, and M.N. Huhns, “Ontology Alignment as a Basis for Mobile Service Integration and Invocation,” International Journal of Pervasive Computing and Communications, 2007; 3(2):138-158. doi: 10.1108/17427370710847282. [PDF]

  


 Book Chapters

  

37) J. Huang and J. Dang, “Context-Sensitive Ontology Matching in Electronic Business,” Electronic Business Interoperability: Concepts, Opportunities and Challenges. Ejub Kajan, editor, IGI Global, 2010, pp. 279-301. [PDF]

36) J. Huang, J. Dang, and M.N. Huhns, “Ontology-Based Partner Selection in Business Interaction,” Handbook of Ontologies for Business Interaction. Peter Rittgen, editor, IGI Global, 2007, pp. 364-380. [PDF]

35) J. Huang, R. Zavala, B. Mendoza, and M.N. Huhns, “Reconciling Agent Ontologies for Web Service Applications,” Multiagent System Technologies: Third German Conference (MATES-05). Torsten Eymann, Franziska Klügl, Winfried Lamersdorf, Matthias Klusch, and Michael N. Huhns, editors, Springer Verlag, Vol. LNAI 3550, Berlin, 2005, pp. 106-117. [PDF]

  

 Conference and Workshop Papers

  

34) 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.

33) J. Huang, D. Dou, J. She, A.H. Limper, Y. Yang, and P. Yang, “A comprehensive (biological and computational) investigation on the role of microRNA::mRNA regulations performed in chronic obstructive pulmonary disease and lung cancer,” Proc. 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM-16), pp. 1067-1072, IEEE Computer Society Press, Shenzhen, China, Dec. 2016. [PDF]

32) L. Zhang, R. Li, Q. Yang, Y. Wu, J. Huang, and B. Wu, “Innovative microRNA-lncRNA-mRNA co-expression analysis to understand the pathogenesis and progression of diabetic kidney disease,” Proc. 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM-16), pp. 688-693, IEEE Computer Society Press, Shenzhen, China, Dec. 2016. [PDF]

31) J. Huang, B. Liu, Y. Liu, and J. Chen, “The utilization of the OmniSearch semantic search tool to explore various microRNA regulation mechanisms in osteoarthritis,” Proc. 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM-16), pp. 1073-1078, IEEE Computer Society Press, Shenzhen, China, Dec. 2016. [PDF]

30) F. Sheldon, D. Manz, J. Huang, T. Morris, R. Abercrombie, D. Wei, and D. Fetzer, “Intrinsically Resilient Energy Control Systems: Cybersecurity Challenges for Critical Public Infrastructures,” (under review) The 2016 IEEE Symposium Series on Computational Intelligence (IEEE SSCI 2016), Athens, Greece, Dec. 2016.

29) 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 Computer Society Press, Washington D.C., Nov. 2015. [PDF]

28) 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. 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM-15), pp. 975-982, IEEE Computer Society Press, Washington D.C., Nov. 2015. [PDF]

27) B. Wu, J. Huang, K. Fukuo, K. Suzuki, G. Yoshino, and T. Kazumi, “Associations between C Reactive Protein and Body Fat Mass Distribution, Adipokines, Oxidative Stress Index, and Arterial Stiffness and Thickness in Healthy Young Women,” Proc. The 19th Scientific Meeting of the Chinese Diabetes Society, Aug. 2015.

26) 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), pp. 526-529, IEEE Computer Society Press, Shanghai, China, Dec. 2013. [PDF]

25) J. Huang, J. Huan, A. Tropsha, J. Dang, H. Zhang, and M. Xiong, “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), pp. 608-611, IEEE Computer Society Press, Shanghai, China, Dec. 2013. [PDF]

24) F. Sheldon, J. Huang, J. Dang, D. Fetzer, S. Goose, J. Kirsch, D. Manz, T. Morris, and D. Wei, “Intrinsically Resilient Energy Control Systems,” Proc. 8th Annual Cyber Security and Information Intelligence Research Workshop (CSIIRW-12), Oak Ridge, TN, Jan. 2013. [PDF]

23) F. Sheldon, J. Huang, J. Dang, D. Fetzer, D. Manz, T. Morris, D. Wei, J. Kirsch, and S. Goose, “Using Semantic Web Technologies to Develop Intrinsically Resilient Energy Control Systems,” Proc. 7th International Conference on Semantic Technologies for Intelligence, Defense, and Security (STIDS-12), Fairfax, VA, Oct. 2012. [PDF]

22) 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. 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM-12), pp. 16-23, IEEE Computer Society Press, Philadelphia, PA, Oct. 2012. [PDF]

21) C. Townsend, J. Huang, D. Dou, H. Liu, L. He, P.J. Hayes, R. Rudnick, H. Shah, D. Fell, and W. Liu, “NeuMORE: Ontology in Stroke Recovery,” Proc. 2010 IEEE International Conference on Bioinformatics & Biomedicine (BIBM-10), IEEE Computer Society Press, Hong Kong, China, Dec. 2010. [PDF]

20) C. Townsend, J. Huang, D. Dou, H. Liu, L. He, P.J. Hayes, R. Rudnick, H. Shah, D. Fell, and W. Liu, “Ontology-Based Knowledge Acquisition for Neuromotor Functional Recovery in Stroke,” Proc. 2010 IEEE International Conference on Bioinformatics & Biomedicine (BIBM-10), IEEE Computer Society Press, Hong Kong, China, Dec. 2010. [PDF]

19) 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. 9th International Conference on Ontologies, DataBases, and Applications of Semantics (ODBASE-10), pp. 1162-1169, Springer-Verlag, Crete, Greece, Oct. 2010. [PDF]

18) J. Huang, M. Tan, D. Dou, L. He, C. Townsend, R. Rudnick, and P.J. Hayes, “MiRNA Ontology for Target Prediction in Human Cancer,” Proc. 1st ACM International Conference on Bioinformatics and Computational Biology (BCB-10), pp. 472-474, ACM Press, Niagara Falls, NY, Aug. 2010 (doi: 10.1145/1854776.1854861). [PDF]

17) 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. 7th International Conference on Fuzzy Systems and Knowledge Discovery (FSKD-10), Yantai, China, Aug. 2010. [PDF]

16) J. Huang, A. Yasinsac, and P. Hayes, “Knowledge Sharing and Reuse in Digital Forensics,” Proc. 4th International IEEE Workshop on Systematic Approaches to Digital Forensic Engineering (SADFE-10), Oakland, CA, May 2010. [PDF]

15) J. Huang, L. He, and G.V. Davidson-Shivers, “IWAS: Intelligent Web-Based Assessment System,” Proc. Society for Information Technology & Teacher Education (SITE-10), San Diego, CA, Mar. 2010. [Link in LearnTechLib]

14) J. Dang, J. Huang, and M.N. Huhns, “Workflow Coordination for Service-Oriented Multiagent Systems,” Proc. 6th International Conference on Autonomous Agents and Multiagent Systems (AAMAS-07), Honolulu, HI, May 2007. [PDF]

13) J. Huang, J. Dang, J.M. Vidal, and M.N. Huhns, “Ontology Matching Using an Artificial Neural Network to Learn Weights,” Proc. IJCAI Workshop on Semantic Web for Collaborative Knowledge Acquisition (SWeCKa-07), pp. 80-85, Hyderabad, India, Jan. 2007. [PDF]

12) J. Huang and M.N. Huhns, “Superconcept Formation System-An Ontology Matching Algorithm for Web Applications,” Supplemental Proc. 5th International Semantic Web Conference (ISWC-06), Athens, GA, Nov. 2006. [PDF]

11) J. Huang, J. Dang, and M.N. Huhns, “Ontology Reconciliation for Service-Oriented Computing,” Proc. 2006 IEEE International Conference on Services Computing (SCC-06), pp. 3-10, Chicago, IL, Sept. 2006 (2nd Place for Best Student Paper Award at SCC-06). [PDF]

10) J. Huang and M.N. Huhns, “An Ontology Matching Algorithm for Service Discovery,” Proc. Service Discovery on the WWW Workshop at 1st Asian Semantic Web Conference (ASWC-06), Beijing, China, Sept. 2006.

9) J. Huang, J. Dang, and M.N. Huhns, “Reconciling Ontologies for Coordination among E-business Agents,” Proc. BASeWEB Workshop at International Conference on Autonomous Agents and Multiagent Systems (AAMAS-06), pp. 62–69, Hakodate, Japan, May 2006. [PDF]

8) J. Huang, J. Dang, and M.N. Huhns, “Ontology Reconciliation in E-business Domain,” presented in International Student Workshop on Agents (ISWA-06), Kyoto, Japan, May 2006. [PDF]

7) J. Huang, R. Zavala, B. Mendoza, and M.N. Huhns, “A Schema-based Approach Combined with Inter-Ontology Reasoning to Construct Consensus Ontologies,” Proc. AAAI Workshop on Contexts and Ontologies (C&O-05), pp. 80-87, Pittsburgh, PA, July 2005.

6) J. Huang, R. Zavala, B. Mendoza, and M.N. Huhns, “Sharing Ontology Schema Information for Web Service Integration,” Proc. 5th International Conference on Computer and Information Technology (CIT-05), pp. 1056-1062, Shanghai, China, Sept. 2005. [PDF]

5) M.G. Valtorta, J. Huang, et al., “Extending Heuer's Analysis of Competing Hypotheses Method to Support Complex Decision Analysis,” Proc. 2005 International Conference on Intelligence Analysis Methods and Tools (IA-05), Washington D.C., May 2005. [PDF]

4) J. Cheng, J. Huang, et al., “OmniSeer: A Cognitive Framework for User Modeling, Reuse of Prior and Tacit Knowledge, and Collaborative Knowledge Services,” Proc. 38th Annual Hawaii International Conference on System Sciences (HICSS-38) - Track 9, Big Island, Hawaii, Jan. 2005. [PDF]

3) S. Xu, J. Huang, et al., “Security Issues in Privacy and Key Management Protocols of 802.16,” Proc. The Workshop of 2005 International Conference on Computational Intelligence and Security (CIS-05), Xi'an, China, Oct. 2005. [PDF]

  

 Technical Reports

  

2) M.G. Valtorta, J. Huang, et al., “Tutorial and Training Manual for the Prior and Tacit Knowledge System of OmniSeer,” Dec. 2003.

1) J. Cheng, J. Huang, et al., “OmniSeer Project Final Report,” Aug. 2004.

  

Dr. Jingshan Huang
School of Computing - Suite 2101, University of South Alabama

Office: (251) 460-7612, Fax: (251) 460-7274

Email: my last name in southalabama domain
© 2016 Dr. Jingshan Huang, All Rights Reserved.