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   M. W. 09:00 AM - 10:30 AM

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 Publications

(*: Corresponding Author)

 Books

  

93) J. Huang*, G.M. 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]

92) 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]

91) 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

  

90) T.L. Phung*, C. Manganti, M.V. Kasukurthi, K. Hebert, and J. Huang, “Clinical Impact Of Targeted Genomic Profiling,” (accepted) The Journal of Molecular Diagnostics, Aug. 2022.

89) A.B. Coley, A.N. Stahly, M.V. Kasukurthi, A.A. Barchie, S.B. Hutcheson, D. Houserova, Y. Huang, B.C. Watters, V.M. King, M.A. Dean, J.T. Roberts, J.D. DeMeis, K.V. Amin, C.H. McInnis, N.L. Godang, R.M. Wright, D.F. Haider, N.B. Piracha, C.L. Brown, Z.M. Ijaz, S. Li, Y. Xi, O.G. McDonald, J. Huang, and G.M. Borchert*, “MicroRNA-like snoRNA-derived RNAs (sdRNAs) promote castration resistant prostate cancer,” (accepted) Cells. Apr 2022.

88) D. Houserova, Y. Huang, M.V. Kasukurthi, B.C. Watters, F.F. Khan, R.V. Mehta, N.Y. Chaudhary, J.T. Roberts, J.D. DeMeis, T.K. Hobbs, K.R. Ghee, C.H. McInnis, N.P. Johns, A.J. Kegler, A.B. Coley, C.L. Brown, J.L. Hewes, M.M. McElyea, M.N. Reeves, T.M. Tran, N.R. Bauer, J. Huang, J.P. Audia, J.W. Foster, and G.M. Borchert*, “Salmonella Outer Membrane Vesicles contain tRNA Fragments (tRFs) that Inhibit Bacteriophage P22 infection,” (under review) Nature Communications. Nov 2021.

87) A.B. Coley, A.N. Stahly, M.V. Kasukurthi, A.A. Barchie, S.B. Hutcheson, D. Houserova, Y. Huang, B.C. Watters, V.M. King, M.A. Dean, J.T. Roberts, J.D. DeMeis, K.V. Amin, C.H. McInnis, N.L. Godang, R.M. Wright, D.F. Haider, N.B. Piracha, C.L. Brown, Z.M. Ijaz, S. Li, Y. Xi, O.G. McDonald, J. Huang, and G.M. Borchert*, “snoRNAsdRNAs promote castration resistant prostate cancer,” bioRxiv. 2021 Dec 20; doi: 10.1101/2021.12.17.473174.

86) D. Houserova, Y. Huang, M.V. Kasukurthi, B.C. Watters, F.F. Khan, R.V. Mehta, N.Y. Chaudhary, J.T. Roberts, J.D. DeMeis, T.K. Hobbs, K.R. Ghee, C.H. McInnis, N.P. Johns, A.J. Kegler, A.B. Coley, C.L. Brown, J.L. Hewes, M.M. McElyea, M.N. Reeves, T.M. Tran, N.R. Bauer, J. Huang, J.P. Audia, J.W. Foster, and G.M. Borchert*, “Salmonella Outer Membrane Vesicles contain tRFs that Inhibit Bacteriophage P22 infection,” bioRxiv. 2021 Nov 09; doi: 10.1101/2021.11.09.467952.

85) F. Huang, X. Leng, M.V. Kasukurthi, Y. Huang, D. Li, S. Tan, G. Lu, J. Lu, R.G. Benton, G.M. Borchert, and J. Huang*, “Utilizing Machine-Learning Techniques to Predict the Efficacy of Aerobic Exercise Intervention on Young Hypertensive Patients based on Cardiopulmonary Exercise Testing,” Journal of Healthcare Engineering, 2021 Apr 21;2021:6633832. doi: 10.1155/2021/6633832. PubMed PMID: 33968353; PMID Central PMCID: PMC8084649. [Link in PubMed]

84) M.V. Kasukurthi, D. Houserova, Y. Huang, A.A. Barchie, J.T. Roberts, D. Li, B. Wu, J. Huang*, and G.M. Borchert*, “SALTS – SURFR (sncRNA) And LAGOOn (lncRNA) Transcriptomics Suite,” bioRxiv. 2021 Feb 09; doi: 10.1101/2021.02.08.430280.

83) D. Houserova, D.J. Dahmer, S.V. Amin, A. Crucello, V.M. King, E.C. Barnhill, Y. Huang, M.E. Zambrano, M.A. Dean, K.M. Aria, M.P. Spector, J. Huang, and G.M. Borchert*, “Characterization of 475 novel, putative small RNAs (sRNAs) in Carbon-starved Salmonella enterica serovar typhimurium,” bioRxiv. 2021 Jan 11; doi: 10.1101/2021.01.11.426214.

82) B. Ma, Z. Wu, S. Li, R. Benton, D. Li, Y. Huang, M.V. Kasukurthi, J. Lin, G.M. Borchert, S. Tan, M. Yang*, and J. Huang*, “Development of a Support Vector Machine Learning and Smart Phone Internet of Things-based Architecture for Real-time Sleep Apnea Diagnosis,” BMC Medical Informatics and Decision Making, 2020 Dec 15;20(Suppl 14):298. doi: 10.1186/s12911-020-01329-1. PubMed PMID: 33323112; PMID Central PMCID: PMC7739462. [Link in PubMed]

81) J. Li, Z. Zhang, S. Li, R. Benton, Y. Huang, M.V. Kasukurthi, D. Li, J. Lin, G.M. Borchert, S. Tan, B. Ma*, M. Yang*, and J. Huang*, “A Partial Encryption Algorithm for Medical Images Based on Quick Response Code and Reversible Data Hiding Technology,” BMC Medical Informatics and Decision Making, 2020 Dec 15;20(Suppl 14):297. doi: 10.1186/s12911-020-01328-2. PubMed PMID: 33323108; PMID Central PMCID: PMC7739464. [Link in PubMed]

80) J.D. Williams, D. Houserova, B.R. Johnson, B. Dyniewski, A. Berroyer, H. French, A.A. Barchie, D.D. Bilbrey, J.D. Demeis, K.R. Ghee, A.G. Hughes, N.W. Kreitz, C.H. Mclnnis, S.C. Pudner, M.N. Reeves, A.N. Stahly, A. Turcu, B.C. Watters, G.T. Daly, R.J. Langley, M.N. Gillespie, A. Prakash, E.D. Larson, M.V. Kasukurthi, J. Huang, S. Jinks-Robertson, and G.M. Borchert*, “Characterization of long G4-rich enhancer-associated genomic regions engaging in a novel loop:loop 'G4 Kissing' interaction,” Nucleic Acids Research. May 2020. doi: 10.1093/nar/gkaa357. [Link in Oxford Academic]

79) Y. Qiu, Y. Huang, S. Tan, D. Li, A. van der Zijp-Tan, G.M. Borchert, H. Jiang*, and J. Huang*, “Exploring observability of attractor cycles in boolean networks for biomarker detection,” IEEE Access. September 2019;7(1):127745-127753. doi: 10.1109/ACCESS.2019.2937133. [Link in DBLP]

78) R. Renner, S. Li, Y. Huang, A. van der Zijp-Tan, S. Tan, D. Li, M.V. Kasukurthi, R. Benton, G.M. Borchert, J. Huang*, and G. Jiang*, “Using an artificial neural network to map cancer common data elements to the biomedical research integrated domain group model in a semi-automated manner,” BMC Medical Informatics and Decision Making, 2019 Dec 23;19(Suppl 7):276. doi: 10.1186/s12911-019-0979-5. PubMed PMID: 31865899, PMID Central PMCID: PMC6927104. [Link in PubMed]

77) B. Ma, C. Li, Z. Wu, Y. Huang, A. van der Zijp-Tan, S. Tan, D. Li, A. Fong, C. Basetty, G.M. Borchert, R. Benton, B. Wu*, and J. Huang*, “Muscle fatigue detection and treatment system driven by Internet of Things,” BMC Medical Informatics and Decision Making, 2019 Dec 23;19(Suppl 7):275. doi: 10.1186/s12911-019-0982-x. PubMed PMID: 31865898, PMID Central PMCID: PMC6927109. [Link in PubMed]

76) B. Wu*, J. Huang, L. Zhang, M.V. Kasukurthi, F. Huang, J. Bian, K. Fukuo, 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,” Methods. 2018 April 24; 145:60-66. doi: 10.1016/j.ymeth.2018.04.016. Available online April 24, 2018. PubMed PMID: 29702223, PMID Central PMCID: PMC6064666. [Link in PubMed]

75) L. Cai, J. Jiang, R. Datta, M. Zhu, H. Jiang, M. Du*, and J. Huang, “Sleep-disordered patient monitoring system based on the Internet of Things framework,” (under review) Journal of Cleaner Production. September 2019.

74) H. Chen, D. Zhang, G. Zhang, X. Li, Y. Liang, M.V. Kasukurthi, S. Li, G.M. Borchert, and J. Huang*, “A semantics-oriented computational approach to investigate microRNA regulation on glucocorticoid resistance in pediatric acute lymphoblastic,” BMC Medical Informatics and Decision Making, Jul 23;18(Suppl 2):57. doi: 10.1186/s12911-018-0637-3. PubMed PMID: 30066657, PMID Central PMCID: PMC6069764. [Link in PubMed]

73) B. Wu*, J. Huang, M.V. Kasukurthi, J. Bian, K. Fukuo, K. Suzuki, G. Yoshino, and T. Kazumi, “Different associations of trunk and lower-body fat mass distribution with cardiometabolic risk factors between healthy middle-aged men and women,” International Journal of Endocrinology, vol. 2018, Article ID 1289485, 2018. doi: 10.1155/2018/1289485. Available online April 24, 2018. PubMed PMID: 29531527, PMID Central PMCID: PMC5817354. [Link in PubMed]

72) 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; 124:46-56. pii: S1046-2023(17)30046-4. doi: 10.1016/j.ymeth.2017.05.023. Available online May 31, 2017. PubMed PMID: 28577935, PMID Central PMCID: PMC5540768. [Link in PubMed]

71) N. de Silva, D. Dou*, and J. Huang, “Discovering inconsistencies and similarities in PubMed abstracts through ontology-based information extraction,” (under review) Journal of Biomedical Informatics, 2017.

70) 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].

69) 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].

68) 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.V. 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 PMID: 27990175, PubMed Central PMCID: PMC5156483, NIHMSID: NIHMS795655. [PDF][Link in NCBI PMC].

67) 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.

66) 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]

65) 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]

64) 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]

63) 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]

62) 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]

61) 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]

60) J. Huang*, C. Townsend, D. Dou, H. Liu, and M. Tan, “OMIT: A domain-specific knowledge kase 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]

59) 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]

58) 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]

57) 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

  

56) 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]

55) 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]

54) 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

  

53) T.L. Phung*, C. Manganti, M.V. Kasukurthi, K. Hebert, and J. Huang, “Clinical Impact Of Targeted Genomic Profiling (Solid Tumors, short version),” (accepted) Annual Meeting & Expo(AMP 2022), Aug. 2022.

52) S. Li, Y. Huang, M.V. Kasukurthi, J. Yang, D. Li, G. Yang, J. Lin, S. Tan, D. Bourrie, B. Ma, G.M. Borchert, and J. Huang*, “A New Classification Algorithm and a New Oversampling Method of Mapping Common Data Elements to the BRIDG Model,” Proc. 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM-21), pp. 2788-2795, Houston, TX, Dec. 2021.

51) M.V. Kasukurthi, D. Houserova, Y. Huang, S. Li, D. Li, J. Lin, G. Yang, S. Tan, D. Bourrie, B. Ma, G.M. Borchert, and J. Huang*, “SURFR: A Real-Time Platform for Non-Coding RNA Fragmentation Analysis Using Wavelets,” Proc. 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM-21), pp. 2720-2727, Houston, TX, Dec. 2021.

50) Y. Guan, J. Huang, S. Huang, M.V. Kasukurthi, Y. Huang, D. Li, S. Tan, S. Wang, X. Nian, J. Lin, G.M. Borchert, and B. Wu*, “FGF21 mediates corticosteroid-related bone mass loss through PPAR-γ,” Proc. 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM-19), pp. 1915-1919, San Diego, CA, Nov. 2019.

49) M.V. Kasukurthi, D. Zhang, M. Housevera, Y. Huang, S. Tan, B. Ma, D. Li, R. Benton, J. Lin, S. Li, G.M. Borchert, and J. Huang*, “SURFr: Algorithm for identification and analysis of ncRNA-derived RNAs,” Proc. 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM-19), pp. 1504-1507, San Diego, CA, Nov. 2019.

48) B. Ma, Z. Wu, S. Li, R. Benton, D. Li, Y. Huang, M.V. Kasukurthi, J. Lin, G.M. Borchert, S. Tan, M. Yang*, and J. Huang*, “A SVM-based algorithm to diagnose sleep apnea,” Proc. 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM-19), pp. 1556-1560, San Diego, CA, Nov. 2019.

47) J. Li, Z. Zhang, S. Li, R. Benton, Y. Huang, M.V. Kasukurthi, D. Li, J. Lin, G.M. Borchert, S. Tan, B. Ma*, M. Yang*, and J. Huang*, “Reversible data hiding based key region protection method in medical images,” Proc. 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM-19), pp. 1526-1530, San Diego, CA, Nov. 2019.

46) L. Cai, R. Datta, J. Huang*, S. Dong, and M. Du*, “Sleep disorder data stream classification based on classifiers ensemble and active learning,” Proc. 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM-19), pp. 1432-1435, San Diego, CA, Nov. 2019.

45) G. Yang, X. Leng, F. Huang, M.V. Kasukurthi, Y. Huang, D. Li, J. Lin, S. Tan, G. Lu, R. Benton, G.M. Borchert, B. Ma, and J. Huang*, “Use CPET data to predict the intervention effect of aerobic exercise on young hypertensive patients,” Proc. 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM-19), pp. 1699-1702, San Diego, CA, Nov. 2019.

44) L. Cai, J. Jiang, X. Liu, M. Zhu, K. Cheng, M. Du, R. Datta, J. Huang, D. Zhu, H. Jiang, D. Zhang, and J. Huang, “OSA patient monitoring system based on the Internet of Things framework,” Proc. The 4th International Conference on Smart and Sustainable Technologies (SpliTech-19), Split, Croatia, June 2019.

43) L. Cai, C. Chen, X. Wang, S. Lin, K. Cheng, J. Huang, J. Jiang, M. Zhu, M. Du, R. Datta, Y. Li, and J. Huang, “An Open Source Map Optimization Platform for efficient navigation,” Proc. The 22nd IEEE International Conference on Computational Science and Engineering (CSE-19), New York, August 2019.

42) R. Renner, S. Li, Y. Huang, S. Tan, D. Li, A. van der Zijp-Tan, R.  Benton, G.M. Borchert, J. Huang*, and G. Jiang*, “Mapping common data elements to a domain model using an artificial neural network,” Proc. 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM-18), pp. 1532-1535, Madrid, Spain, Nov. 2018.

41) J. Huang, K. Fukuo, G. Yoshino, T. Kazumi, C. Basetty, Y. Huang, S. Tan, D. Li, A. van der Zijp-Tan, A. Fong, G.M. Borchert, and B. Wu*, “Body composition and biochemical characteristics of normal weight obesity in Japanese young women with different physical activities,” Proc. 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM-18), pp. 1480-1483, Madrid, Spain, Nov. 2018.

40) B. Ma, C. Li, Z. Wu, Y. Huang, A. van der Zijp-Tan, S. Tan, D. Li, A. Fong, C. Basetty, G.M. Borchert, and J. Huang*, “A PWM-based muscle fatigue detection and recovery system,” Proc. 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM-18), pp. 1013-1016, Madrid, Spain, Nov. 2018.

39) Y. Qiu, Y. Huang, S. Tan, D. Li, A. van der Zijp-Tan, A. Fong, G.M. Borchert, and J. Huang*, “An efficient method for attractor observability in Boolean Networks,” Proc. 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM-18), pp. 1526-1531, Madrid, Spain, Nov. 2018.

38) B. Wu*, J. Huang*, M.V. Kasukurthi, F. Huang, J. Bian, K. Fukuo, K. Suzuki, G. Yoshino, and T. Kazumi, “Combine biological experiments, statistical analysis, and semantic search to discover association among high-sensitive C-reactive protein, body fat mass distribution, and other cardiometabolic risk factors in young healthy women,” Proc. 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM-17), pp. 457-462, Kansas City, MO, Nov. 2017.

37) H. Jin, Z. Yu, X. Wang, W. Chen, S. Guo, M.V. Kasukurthi, G.M. Borchert, and J. Huang*, “Computational analysis to discover microRNA biomarkers in glioblastoma,” Proc. 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM-17), pp. 1251-1252, Kansas City, MO, Nov. 2017.

36) H. Chen, D. Zhang, G. Zhang, X. Li, Y. Liang, M.V. Kasukurthi, G.M. Borchert, and J. Huang*, “MeSH term-based semantic analysis of microRNA regulation on glucocorticoid resistance in pediatric acute lymphoblastic leukemia,” Proc. 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM-17), pp. 1233-1234, Kansas City, MO, Nov. 2017.

35) J. Huang*, D. Dou, M. Tan, G.M. Borchert, K. Eilbeck, A. Ruttenberg, and P. Yang, “Semantics-oriented data science and computational life sciences: innovative application of semantic technologies in microRNA and lncRNA research,” Proc. The 7th  IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS-17), Orlando, FL, Oct. 2017. doi: 10.1109/ICCABS.2017.8114284.

34) N. de Silva, D. Dou*, and J. Huang, “Discovering inconsistencies in PubMed abstracts through ontology-based information extraction,” Proc. 8th ACM International Conference on Bioinformatics and Computational Biology (BCB-17), pp. 362-371, ACM Press, Boston, MA, Aug. 2017. doi: 10.1145/3107411.3107452.

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,” Proc. 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. C&O Workshop at National Conference on Artificial Intelligence (AAAI-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

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