• 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

  Abstract | pub2005035.pdf

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• Beaudoin DE, Longo N, Logan RA, Jones JP, Mitchell JA. Using information prescriptions to refer patients with metabolic conditions to the Genetics Home Reference website. J Med Libr Assoc. 2011 Jan;99(1):70-6. doi: 10.3163/1536-5050.99.1.012.

  Abstract | pub2011004.pdf | PMID:  21243058 | PMCID:  PMC3016649

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• Bergun A, Bodenreider O, Jacquelinet C. Issues in the Classification of Disease Instances with Ontologies Stud Health Technol Inform 2005;116:695-700

  Abstract | pub2005029.pdf | PMID:  16160339 | PMCID:  PMC1784521

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• 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.

  Abstract | PMID:  30157516

  Abstract
• Bodenreider O. Web Interface: RxMix

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• Bodenreider O, Peters L, Nguyen T. RxNav: Browser and Application Programming Interfaces for Drug Information Sources [Abstract]. AMIA Annu Symp Proc 2011:2129

  Abstract | pub2011018.pdf

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• 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.

  Abstract | PMID:  19394440 | PMCID:  PMC2722378

  Abstract
• Bodenreider O. Semantic Web for Translational Biomedicine: Two Pilot Experiments [Abstract]. Proc. MIA Summit on Translational Bioinformatics 2008:141

  Abstract | pub2008025.pdf

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• 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

  Abstract | pub2007011.pdf | PMID:  17241777 | PMCID:  PMC2442845

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• Bodenreider O, Stevens R. Bio-ontologies: Current Trends and Future Directions Brief Bioinform. 2006 Sep;7(3):256-74. Epub 2006 Aug 9

  Abstract | pub2006053.pdf | PMID:  16899495 | PMCID:  PMC1847325

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• Bodenreider O, Nelson SJ. RxNav: A Semantic Navigation Tool for Clinical Drugs Medinfo. 2004 Sept.;2004: 1530.

  Abstract | pub2004037.pdf

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• Bodenreider O. Web Interface: RxNav

  Abstract

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• Bodenreider O, McCray AT. Exploring Semantic Groups Through Visual Approaches J Biomed Inform. 2003 Dec;36(6):414-432.

  Abstract | pub2003065.pdf | PMID:  14759816 | PMCID:  PMC1997308

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• Burgun A, Bodenreider O. Accessing and Integrating Data and Knowledge for Biomedical Research Yearb Med Inform. 2008:91-101

  Abstract | pub2008027.pdf | PMID:  18660883 | PMCID:  PMC2553094

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• Califf RM, Zarin DA, Kramer JM, Sherman RE, Aberle LH, Tasneem A. Characteristics of clinical trials registered in ClinicalTrials.gov, 2007-2010. JAMA. 2012 May 2;307(17):1838-47. doi: 10.1001/jama.2012.3424.

  Abstract | PMID:  22550198 | URL:  http://jama.jamanetwork.com/article.aspx?articleid=1150093

  AbstractExternal link
• 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.

  Abstract | PMID:  23026233 | PMCID:  PMC4031661

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• 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.

  Abstract | PMID:  19154797 | PMCID:  PMC2729758

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• Collins H, Calvo SC, Greenberg K, Forman, NL, Morrison SM. Information Needs in the Precision Medicine Era: How Genetics Home Reference Can Help. Interact J Med Res 2016;5(2):e13 DOI: 10.2196/ijmr.5199

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• 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.

  Abstract | PMID:  29274386 | PMCID:  PMC5835197

  Abstract
• 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.

  Abstract | PMID:  28339775 | PMCID:  PMC6080685

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• Deardorff A, Masterton K, Roberts K, Kilicoglu H, Demner-Fushman D. A protocol-driven approach to automatically finding authoritative answers to consumer health questions in online resources. JASIST, 68(7): 1724-1736. doi: 10.1002/asi.23806.

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• 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.

  Abstract | PMID:  22226933 | PMCID:  PMC3334468

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• 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.

  Abstract | PMID:  26865946 | PMCID:  PMC4748471

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• 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.

  Abstract | PMID:  26262161

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• 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.

  Abstract | pub2011001.pdf | PMID:  21138947 | PMCID:  PMC3031038

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• 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

  Abstract | pub2006062.pdf | PMID:  17183579

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• Fomous C, Mitchell JA, McCray A. Genetics Home Reference: Helping Patients Understand the Role of Genetics in Health and Disease Community Genet. 2006;9(4):274-8

  Abstract | pub2006027.pdf

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• 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.

  Abstract | PMID:  28339701 | PMCID:  PMC6080681

  Abstract
• Gopal AD, Desai NR, Tse T, Ross JS. Reporting of noninferiority trials in ClinicalTrials.gov and corresponding publications. JAMA. 2015 Mar 17;313(11):1163-5. doi: 10.1001/jama.2015.1697.

  Abstract | PMID:  25781447

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• 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.

  Abstract | PMID:  29081385

  Abstract
• Hartung DM, Zarin D, Guise JM, McDonagh M, Paynter R, Helfand M. Reporting discrepancies between the ClinicalTrials.gov results database and peer-reviewed publications. Ann Intern Med. 2014 Apr 1;160(7):477-83. doi: 10.7326/M13-0480.

  Abstract | PMID:  24687070 | PMCID:  PMC4617780

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• 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.

  Abstract | PMID:  26262116 | PMCID:  PMC4815923

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• 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.

  Abstract | PMID:  28154833 | PMCID:  PMC5226382

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• 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.

  Abstract | PMID:  26797535 | PMCID:  PMC4860172

  Abstract
• Huston M, Williams RJ, Bergeris A, Fun J, Tse T. New style and new content for ClinicalTrials.gov. NLM Tech Bull. 2012 Jul-Aug;(387):e5.

  Abstract | URL:  http://www.nlm.nih.gov/pubs/techbull/ja12/ja12_clinicaltrials.html

  AbstractExternal link
• 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.

  Abstract | PMID:  30753947

  Abstract
• Kilicoglu H. Dataset: Consumer Health Spelling Error Dataset

  Abstract | URL:  https://ceb.nlm.nih.gov/ridem/infobot_docs/CHQA_SpellCorrection_Dataset.zip

  AbstractExternal link
• 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.

  Abstract | PMID:  26934708 | PMCID:  PMC4774913

  Abstract
• Logan RA, Tse T. A Multidiscipline Conceptual Framework for Consumer Health Informatics Stud Health Technol Inform. 2007;129(Pt 2):1169-73

  Abstract | pub2007030.pdf | PMID:  17911899

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• Lu C, Aronson, AR, Shooshan SE, Demner-Fushman D. Spell checker for consumer language (CSpell). J Am Med Inform Assoc. 2019 Jan 21. doi: 10.1093/jamia/ocy171. [Epub ahead of print]

  Abstract | PMID:  30668712

  Abstract
• 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.

  Abstract | pub2011013.pdf | PMID:  21624155 | PMCID:  PMC3102889

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• 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.

  Abstract | PMID:  19381547 | PMCID:  PMC2719765

  Abstract
• McCray AT. Better access to information about clinical trials. Ann Intern Med. 2000 Oct 17;133(8):609-14.

  Abstract | pub2000020.pdf | PMID:  11033590

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• McCray AT, Ide NC. Design and implementation of a national clinical trials registry. J Am Med Inform Assoc. 2000 May-Jun;7(3):313-23.

  Abstract | pub2000019.pdf | PMID:  10833169 | PMCID:  PMC61435

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• Mitchell JA, Fomous C, Fun J. Challenges and strategies of the Genetics Home Reference J Med Libr Assoc. 2006 Jul;94(3):336-42

  Abstract | pub2006026.pdf | PMID:  16888669 | PMCID:  PMC1525308

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• Morrison SM. Web Interface: Genetics Home Reference

  Abstract

  Abstract
• 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.

  Abstract | pub2006019.pdf

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• 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

  Abstract | pub2006056.pdf | PMID:  17134479 | PMCID:  PMC1764450

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• Mougin F, Bodenreider O. Approaches to Eliminating Cycles in the UMLS Metathesaurus: Naive vs. Formal AMIA Annu Symp Proc. 2005:550-4

  Abstract | pub2005034.pdf | PMID:  16779100 | PMCID:  PMC1560864

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• 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.

  Abstract | PMID:  19303057

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