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  • Winnenburg R, Bodenreider O. A framework for assessing the consistency of drug classes across sources. J Biomed Semantics. 2014 Jul 9;5:30. doi: 10.1186/2041-1480-5-30. eCollection 2014.
  • Bodenreider O, Peters LB. A graph-based approach to auditing RxNorm. J Biomed Inform. 2009 Jun;42(3):558-70. doi: 10.1016/j.jbi.2009.04.004. Epub 2009 Apr 24.
  • Cameron D, Bodenreider O, Yalamanchili H, Danh T, Vallabhaneni S, Thirunarayan K, Sheth AP, Rindflesch TC. A graph-based recovery and decomposition of Swanson's hypothesis using semantic predications. J Biomed Inform. 2013 Apr;46(2):238-51. doi: 10.1016/j.jbi.2012.09.004. Epub 2012 Sep 28.
  • Rance B, Doughty E, Demner-Fushman D, Kann MG, Bodenreider O. A mutation-centric approach to identifying pharmacogenomic relations in text. J Biomed Inform. 2012 Oct;45(5):835-41. doi: 10.1016/j.jbi.2012.05.003. Epub 2012 Jun 7.
  • Sorbello A, Ripple AM, Bodenreider O. A pilot study to support prospective detection of emerging adverse drug events [Poster]. AMIA Annu Symp Proc 2015:1699.
  • Sahoo SS, Nguyen V, Bodenreider O, Parikh P, Minning T, Sheth AP. A unified framework for managing provenance information in translational research. BMC Bioinformatics. 2011 Nov 29;12:461. doi: 10.1186/1471-2105-12-461.
  • Burgun A, Bodenreider O. Accessing and Integrating Data and Knowledge for Biomedical Research Yearb Med Inform. 2008:91-101
  • Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, Chen H, Doherty D, Forsberg K, Gao Y, Kashyap V, Kinoshita J, Luciano J, Marshall MS, Oqbuji C, Rees J, Stephens S, Wong GT, Wu E, Zaccaqnini D, Hongsermeier T, Neumann E, Herman I, Cheung KH. Advancing Translational Research with the Semantic Web BMC Bioinformatics. 2007 May 9;8 Suppl 3:S2
  • Schulz S, Beisswanger, van den Hoek L, Bodenreider O, van Mulligen EM. Alignment of the UMLS Semantic Network with BioTop: Methodology and Assessment Bioinformatics 2009;25(12):i69-i76
  • Peters L, Nguyen T, Bodenreider O. An application programming interface for NDF-RT AMIA Annu Symp Proc 2011:1922
  • Wang H, Azuaje F, Bodenreider O. An Ontology-Driven Clustering Method for Supporting Gene Expression Analysis CBMS’2005. 2005:389-394.
  • Mougin FL, Bodenreider O, Burgun A. Analyzing polysemous concepts from a clinical perspective: application to auditing concept categorization in the UMLS. J Biomed Inform. 2009 Jun;42(3):440-51. doi: 10.1016/j.jbi.2009.03.008. Epub 2009 Mar 18.
  • Mougin F, Bodenreider O. Approaches to Eliminating Cycles in the UMLS Metathesaurus: Naive vs. Formal AMIA Annu Symp Proc. 2005:550-4
  • Amini S, Kilicoglu H, Hooft L, ter Riet G. Are we expressing uncertainty of our claims enough? Towards automatic detection of overstatement of claims [Poster]. 2015. World Conference on Research Integrity (WCRI).
  • Vizenor LT, Bodenreider O, McCray AT. Auditing associative relations across two knowledge sources. J Biomed Inform. 2009 Jun;42(3):426-39. doi: 10.1016/j.jbi.2009.01.004.
  • Cui L, Bodenreider O, Shi J, Zhang GQ. Auditing SNOMED CT hierarchical relations based on lexical features of concepts in non-lattice subgraphs. Biomed Inform. 2018 Feb;78:177-184. doi: 10.1016/j.jbi.2017.12.010. Epub 2017 Dec 20.
  • Bodenreider O, Stevens R. Bio-ontologies: Current Trends and Future Directions Brief Bioinform. 2006 Sep;7(3):256-74. Epub 2006 Aug 9
  • Kilicoglu H, Demner-Fushman D. Bio-SCoRes: A Smorgasbord Architecture for Coreference Resolution in Biomedical Text. PLoS One. 2016 Mar 2;11(3):e0148538. doi: 10.1371/journal.pone.0148538. eCollection 2016.
  • Zheng S, Mork P, Bodenreider O, Bernstein PA. Comparing Two Approaches for Aligning Representations of Anatomy Artif Intell Med. 2007 Mar;39(3):227-36. Epub 2007 Jan 23
  • Fung K, Kapusnik-Uner J, Cunningham J, Higby-Baker S, Bodenreider O. Comparison of three commercial knowledge bases for detection of drug-drug interactions in clinical decision support. J Am Med Inform Assoc. 2017 Jul 1;24(4):806-812. doi: 10.1093/jamia/ocx010.
  • Kilicoglu H, Peng Z, Tafreshi S, Tran T, Rosemblat G, Schneider J. Confirm or Refute?: A Comparative Study on Citation Sentiment Classification in Clinical Research Publications. J Biomed Inform. 2019 Feb 9:103123. doi: 10.1016/j.jbi.2019.103123.
  • Mougin F, Burgun A, Bodenreider O. Data Integration Through Data Elements: Mapping Data Elements to Terminological Resources BMC Bioinformatics. 2006 Nov 24;7 Suppl 3:S6.
  • Peters L, Nguyen T, Bodenreider O. Displaying drug classes in RxNav [Poster]. AMIA Annu Symp Proc, 2013: p. 1134.
  • Peters L, Mortensen J, Nguyen T, Bodenreider O. Enabling complex queries to drug information sources through functional composition. Stud Health Technol Inform. 2013;192:692-6.
  • Peters LB, Bahr N, Bodenreider O. Evaluating drug-drug interaction information in NDF-RT and DrugBank. J Biomed Semantics. 2015 May 11;6:19. doi: 10.1186/s13326-015-0018-0. eCollection 2015.
  • Scarton LA, Wang L, Kilicoglu H, Jahries M, Del Fiol M. Expanding vocabularies for complementary and alternative medicine therapies. Int J Med Inform. 2019 Jan;121:64-74. doi: 10.1016/j.ijmedinf.2018.11.009. Epub 2018 Nov 22.
  • Zhang S, Bodenreider O. Experience in Aligning Anatomical Ontologies Int J Semant Web Inf Syst. 2007;3(2):1-26
  • Winnenburg R, Sorbello A, Bodenreider O. Exploring adverse drug events at the class level. J Biomed Semantics. 2015 May 1;6:18. doi: 10.1186/s13326-015-0017-1. eCollection 2015.
  • Zeng QT, Tse T. Exploring and Developing Consumer Health Vocabularies J Am Med Inform Assoc. 2006 Jan-Feb;13(1):24-9. Epub 2005 Oct 12
  • Rance B, Demner-Fushman D, Rindflesch TC, Bodenreider O. Exploring Automatic Approaches to Extracting Pharmacogenomic Information from the Biomedical Literature Proceedings of the 2011 PSB Workshop on Mining the Pharmacogenomics Literature 2011
  • Winnenburg R, Bodenreider O. Exploring pharmacoepidemiologic groupings of drugs from a clinical perspective. Stud Health Technol Inform. 2013;192:827-31.
  • Bodenreider O, McCray AT. Exploring Semantic Groups Through Visual Approaches J Biomed Inform. 2003 Dec;36(6):414-432.
  • Dhombres F, Winnenburg R, Case JT, Bodenreider O. Extending the coverage of phenotypes in SNOMED CT through post-coordination. Stud Health Technol Inform. 2015;216:795-9.
  • Rance B, Le T, Bodenreider O. Fingerprinting Biomedical Terminologies--Automatic Classification and Visualization of Biomedical Vocabularies through UMLS Semantic Group Profiles. Stud Health Technol Inform. 2015;216:771-5.
  • Schulz S, Balkanyi L, Cornet R, Bodenreider O. From concept representations to ontologies: a paradigm shift in health informatics? Healthc Inform Res. 2013 Dec;19(4):235-42. doi: 10.4258/hir.2013.19.4.235. Epub 2013 Dec 31.
  • Tsaparas P, Marino-Ramirez L, Bodenreider O. Global Similarity and Local Divergence in Human and Mouse Gene Co-expression Networks BMC Evol Biol. 2006 Sep 12;6:70
  • Sorbello A, Ripple AM, Tonning J, Munoz M, Hasan R, Ly T, Francis H, Bodenreider O. Harnessing scientific literature reports for pharmacovigilance. Prototype software analytical tool development and usability testing. Appl Clin Inform. 2017 Mar 22;8(1):291-305. doi: 10.4338/ACI-2016-11-RA-0188.
  • Mariño-Ramírez L, Tharakaraman K, Bodenreider O, Spounge J, Landsman D. Identification of cis-regulatory Elements in Gene Co-expression Networks Using A-GLAM. Methods Mol Biol. 2009;541:1-22.
  • Huser V, Cimino JJ. Impending Challenges for the Use of Big Data. Int J Radiat Oncol Biol Phys. 2016 Jul 1;95(3):890-894. doi: 10.1016/j.ijrobp.2015.10.060. Epub 2015 Nov 5.
  • Del Fiol G, Huser V, Strasberg HR, Maviglia SM, Curtis C, Cimino JJ. Implementations of the HL7 Context-Aware Knowledge Retrieval ("Infobutton") Standard: challenges, strengths, limitations, and uptake. J Biomed Inform. 2012 Aug;45(4):726-35. doi: 10.1016/j.jbi.2011.12.006.. Epub 2012 Jan 2.
  • Siegel ER, Logan RA, Harnsberger RL, Cravedi K, Krause JA, Lyon B, Hajarian K, Uhl J, Ruffin A, Lindberg DA. Information Rx: Evaluation of a New Informatics Tool for Physicians, Patients, and Libraries Inf Serv Use. 2006;26(1):1-10.
  • Zeng K, Bodenreider O. Integrating the UMLS into an RDF-Based Biomedical Knowledge Repository AMIA Annu Symp Proc. 2007 Oct 11:1170.
  • Dhombres F, Bodenreider O. Interoperability between phenotypes in research and healthcare terminologies--Investigating partial mappings between HPO and SNOMED CT. J Biomed Semantics. 2016 Feb 9;7:3. doi: 10.1186/s13326-016-0047-3. eCollection 2016.
  • Bodenreider O, Smith B, Kumar A, Burgun A. Investigating Subsumption in SNOMED CT: An Exploration into Large Description Logic-based Biomedical Terminologies Artif Intell Med. 2007 Mar;39(3):183-95. Epub 2007 Jan 22
  • Rindflesch TC, Blake CL, Cairelli MJ, Fiszman M, Zeiss CJ, Kilicoglu H. Investigating the role of interleukin-1 beta and glutamate in inflammatory bowel disease and epilepsy using discovery browsing. J Biomed Semantics. 2018 Dec 27;9(1):25. doi: 10.1186/s13326-018-0192-y.
  • Bergun A, Bodenreider O, Jacquelinet C. Issues in the Classification of Disease Instances with Ontologies Stud Health Technol Inform 2005;116:695-700
  • Backer A, Bodenreider O, Karp P, Kelly H, Loranger S, Musen M, Sriram R, Wroe C. Knowledge Integration for Bio-Threat Response Los Alamos White Paper
  • Winnenburg R, Sorbello A, Ripple AM, Harpaz R, Tonning J, Szarfman A, Francis H, Bodenreider O. Leveraging MEDLINE indexing for pharmacovigilance - Inherent limitations and mitigation strategies. J Biomed Inform. 2015 Oct;57:425-35. doi: 10.1016/j.jbi.2015.08.022. Epub 2015 Sep 2.
  • Rance B, Snyder M, Lewis J, Bodenreider O. Leveraging terminological resources for mapping between rare disease information sources. Stud Health Technol Inform. 2013;192:529-33.
  • Mougin F, Burgun A, Bodenreider O. Mapping Data Elements to Terminological Resources for Integrating Biomedical Data Sourcse BMC Bioinformatics. 2006 Nov 24;7 Suppl 3:S6

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