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  • 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
  • Bergun A, Bodenreider O, Jacquelinet C. Issues in the Classification of Disease Instances with Ontologies Stud Health Technol Inform 2005;116:695-700
  • Bodenreider O, Cornet R, Vreeman DJ. Recent Developments in Clinical Terminologies - SNOMED CT, LOINC, and RxNorm. Yearb Med Inform. 2018 Aug;27(1):129-139. doi: 10.1055/s-0038-1667077. Epub 2018 Aug 29.
  • Bodenreider O. Web Interface: RxMix
  • Bodenreider O, Peters L, Nguyen T. RxNav: Browser and Application Programming Interfaces for Drug Information Sources [Abstract]. AMIA Annu Symp Proc 2011:2129
  • 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.
  • Bodenreider O. Semantic Web for Translational Biomedicine: Two Pilot Experiments [Abstract]. Proc. MIA Summit on Translational Bioinformatics 2008:141
  • 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
  • Bodenreider O, Stevens R. Bio-ontologies: Current Trends and Future Directions Brief Bioinform. 2006 Sep;7(3):256-74. Epub 2006 Aug 9
  • Bodenreider O, Nelson SJ. RxNav: A Semantic Navigation Tool for Clinical Drugs Medinfo. 2004 Sept.;2004: 1530.
  • Bodenreider O. Web Interface: RxNav
  • Bodenreider O, McCray AT. Exploring Semantic Groups Through Visual Approaches J Biomed Inform. 2003 Dec;36(6):414-432.
  • Burgun A, Bodenreider O. Accessing and Integrating Data and Knowledge for Biomedical Research Yearb Med Inform. 2008:91-101
  • 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.
  • Cimino JJ, Hayamizu TF, Bodenreider O, Davis B, Stafford GA, Ringwald M. The caBIG terminology review process. J Biomed Inform. 2009 Jun;42(3):571-80. doi: 10.1016/j.jbi.2008.12.003. Epub 2008 Dec 25.
  • 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.
  • Cui L, Zhu W, Tao S, Case JT, Bodenreider O, Zhang GQ. Mining non-lattice subgraphs for detecting missing hierarchical relations and concepts in SNOMED CT. J Am Med Inform Assoc. 2017 Jul 1;24(4):788-798. doi: 10.1093/jamia/ocw175.
  • 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.
  • 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.
  • 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.
  • Doughty E, Kertesz-Farkas A, Bodenreider O, Thompson G, Adadey A, Peterson T, Kann MG. Toward an automatic method for extracting cancer- and other disease-related point mutations from the biomedical literature. Bioinformatics. 2011 Feb 1;27(3):408-15. doi: 10.1093/bioinformatics/btq667. Epub 2010 Dec 7.
  • Fomous C, Miller N. The Role of the National Library of Medicine Web Sites in Newborn Screening Education Ment Retard Dev Disabil Res Rev. 2006;12(4):305-12
  • 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.
  • Harpaz R, DuMouchel W, Schuemie M, Bodenreider O, Friedman C, Horvitz E, Ripple A, Sorbello A, White RW, Winnenburg R, Shah NH. Toward multimodal signal detection of adverse drug reactions. J Biomed Inform. 2017 Dec;76:41-49. doi: 10.1016/j.jbi.2017.10.013. Epub 2017 Nov 1.
  • Hripcsak G, Duke JD, Shah NH, Reich CG, Huser V, Schuemie MJ, Suchard MA, Park RW, Wong IC, Rijnbeek PR, van der Lei J, Pratt N, Norén GN, Li YC, Stang PE, Madigan D, Ryan PB. Observational Health Data Sciences and Informatics (OHDSI): Opportunities for Observational Researchers. Stud Health Technol Inform. 2015;216:574-8.
  • Huser V, DeFalco FJ, Schuemie M, Ryan PB, Shang N, Velez M, Park RW, Boyce RD, Duke J, Khare R, Utidjian L, Bailey L. Multisite Evaluation of a Data Quality Tool for Patient-Level Clinical Data Sets. EGEMS (Wash DC). 2016 Nov 30;4(1):1239. doi: 10.13063/2327-9214.1239. eCollection 2016.
  • 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.
  • 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.
  • 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.
  • Luciano JS, Andersson B, Batchelor C, Bodenreider O, Clark T, Denny CK, Domarew C, Gambet T, Harland L, Jentzsch A, Kashyap V, Kos P, Kozlovsky J, Lebo T, Marshall SM, McCusker JP, McGuinness DL, Ogbuji C, Pichler E, Powers RL, Prud'hommeaux E, Samwald M, Schrimi L, Tonellato PJ, Wjetzel JZ, Stephens S, Dumontier M. The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside. J Biomed Semantics. 2011 May 17;2 Suppl 2:S1. doi: 10.1186/2041-1480-2-S2-S1.
  • 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.
  • 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.
  • 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
  • Mougin F, Bodenreider O. Approaches to Eliminating Cycles in the UMLS Metathesaurus: Naive vs. Formal AMIA Annu Symp Proc. 2005:550-4
  • 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.
  • Oellrich A, Collier N, Groza T, Rebholz-Schuhmann D, Shah N, Bodenreider O, Borlan MR, Georgiev I, Liu H, Livingston K, Luna A, Mallon AM, Manda P, Robinson PM, Rustici G, Simonn M, Wang L, Winnenburg R, Dumontier M. The digital revolution in phenotyping. Brief Bioinform. 2016 Sep;17(5):819-30. doi: 10.1093/bib/bbv083. Epub 2015 Sep 29.
  • Peters L, Nguyen T, Bodenreider O. Terminology Status APIs - Mapping Obsolete Codes to Current RxNorm, SNOMED CT, and LOINC Concepts. Stud Health Technol Inform. 2017;245:1333.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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
  • 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.
  • 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.
  • 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.
  • 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
  • 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.
  • 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.

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