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  • Huff SM, Rocha RA, McDonald CJ, De Moor GJ, Fiers T, Bidgood WD Jr, Forrey AW, Francis WG, Tracy WR, Leavelle D, Stalling f, Griffin B, Maloney P, Leland D, Charles L, Hutchins K, Baenziger J. Development of the Logical Observation Identifier Names and Codes (LOINC) vocabulary. J Am Med Inform Assoc. 1998 May-Jun;5(3):276-92.
  • Hume S, Aerts J, Sarnikar S, Huser V. Current applications and future directions for the CDISC Operational Data Model standard: A methodological review. J Biomed Inform. 2016 Apr;60:352-62. doi: 10.1016/j.jbi.2016.02.016. Epub 2016 Mar 2.
  • Hunt S, Cimino J, Koziol DE. A comparison of clinicians' access to online knowledge resources using two types of information retrieval applications in an academic hospital setting. J Med Libr Assoc. 2013 Jan;101(1):26-31. doi: 10.3163/1536-5050.101.1.005.
  • Huser V, Cimino J. Providing pharmacogenomics clinical decision support using whole genome sequencing data as input. AMIA Jt Summits Transl Sci Proc. 2013 Mar 18;2013:81. eCollection 2013.
  • Huser V, Shmueli-Blumberg D. Data sharing platforms for de-identified data from human clinical trials. Clin Trials. 2018 Apr 1:1740774518769655. doi: 10.1177/1740774518769655. [Epub ahead of print]
  • 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.
  • Huser V, Sastry C, Breymaier M, Idriss A, Cimino JJ. Standardizing data exchange for clinical research protocols and case report forms: An assessment of the suitability of the Clinical Data Interchange Standards Consortium (CDISC) Operational Data Model (ODM). J Biomed Inform. 2015 Oct;57:88-99. doi: 10.1016/j.jbi.2015.06.023. Epub 2015 Jul 15.
  • Huser V, Sincan M, Cimino JJ. Developing genomic knowledge bases and databases to support clinical management: current perspectives. Pharmgenomics Pers Med. 2014 Sep 9;7:275-83. doi: 10.2147/PGPM.S49904. eCollection 2014.
  • Huser V, Cimino JJ. Don't take your EHR to heaven, donate it to science: legal and research policies for EHR post mortem. J Am Med Inform Assoc. 2014 Jan-Feb;21(1):8-12. doi: 10.1136/amiajnl-2013-002061. Epub 2013 Aug 21.
  • Huser V, Cimino JJ. Linking ClinicalTrials.gov and PubMed to track results of interventional human clinical trials. PLoS One. 2013 Jul 9;8(7):e68409. doi: 10.1371/journal.pone.0068409. Print 2013.
  • Jing X, Kay S, Marley T, Hardiker NR, Cimino JJ. Incorporating personalized gene sequence variants, molecular genetics knowledge, and health knowledge into an EHR prototype based on the Continuity of Care Record standard. J Biomed Inform. 2012 Feb;45(1):82-92. doi: 10.1016/j.jbi.2011.09.001. Epub 2011 Sep 17.
  • Jing X, Kay S, Hardiker N, Marley T. Ontology-based knowledge base model construction-OntoKBCF. Stud Health Technol Inform. 2007;129(Pt 1):785-90.
  • Jing X, Kay S, Hardiker N. Designing a bio-health information assistant within an EHR. Healthcare Computing 2006: 325-326 (Harrogate, England).
  • Jing X, Kay S, Hardiker NR. Bio-health information: a preliminary review of on-line cystic fibrosis resources. Stud Health Technol Inform. 2005;116:21-6.
  • Kho AN, Lemmon L, Commiskey M, Wilson SJ, McDonald C. Use of a Regional Health Information Exchange to Detect Crossover of Patients with MRSA between Urban Hospitals J Am Med Inform Assoc. 2008 Mar-Apr;15(2):212-6. Epub 2007 Dec 20.
  • Kho AN, Dexter PR, Warvel JS, Belsito AW, Commiskey M, Wilson SJ, Hui SL, McDonald CJ. An Effective Computerized Reminder for Contact Isolation of Patients Colonized or Infected with Resistant Organisms Int J Med Inform. 2008 Mar;77(3):194-8. Epub 2007 Mar 29
  • 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.
  • Kroth PJ, Murray MD, McDonald CJ. Undertreatment of osteoporosis in women, based on detection of vertebral compression fractures on chest radiography. Am J Geriatr Pharmacother. 2004 Jun;2(2):112-8.
  • Kury F, Cimino JJ. Identifying Repetitive Institutional Review Board Stipulations by Natural Language Processing and Network Analysis. Stud Health Technol Inform. 2015;216:579-83.
  • Laflamme MR, Wilcox DC, Sullivan J, Schadow G, Lindbergh D, Warvel J, Buchanan H, Ising T, Abernathy G, Perkins SM, Daggy J, Frankel RM, Dexter P, McDonald CJ, Weiner M. A pilot study of usefulness of clinician-patient videoconferencing for making routine medical decisions in the nursing home. J Am Geriatr Soc. 2005 Aug;53(8):1380-5.
  • Lin MC, Vreeman DJ, McDonald CJ, Huff SM. Auditing consistency and usefulness of LOINC use among three large institutions - using version spaces for grouping LOINC codes. J Biomed Inform. 2012 Aug;45(4):658-66. doi: 10.1016/j.jbi.2012.01.008. Epub 2012 Jan 28.
  • Lin MC, Vreeman DJ, McDonald CJ, Huff SM. A characterization of local LOINC mapping for laboratory tests in three large institutions. Methods Inf Med. 2011;50(2):105-14. doi: 10.3414/ME09-01-0072. Epub 2010 Aug 20.
  • 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.
  • Manning JD, Marciano BE, Cimino J. Visualizing the data - using lifelines2 to gain insights from data drawn from a clinical data repository. AMIA Jt Summits Transl Sci Proc. 2013 Mar 18;2013:168-72. eCollection 2013.
  • Marino-Ramirez L, Bodenreider O, Kantz N, Jordan IK. Co-evolutionary Rates of Functionally Related Yeast Genes Evolutionary Bioinformatics Online 2006;2:295-300.
  • 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.
  • McDonald CJ, Callaghan FM, Weissman A, Goodwin RM, Mundkur M, Kuhn T. Use of internist's free time by ambulatory care Electronic Medical Record systems. JAMA Intern Med. 2014 Nov;174(11):1860-3. doi: 10.1001/jamainternmed.2014.4506.
  • McDonald CJ. Toward electronic medical record alerts that consume less physician time. JAMA Intern Med. 2013 Oct 14;173(18):1755-6. doi: 10.1001/jamainternmed.2013.9332.
  • McDonald CJ, Abhyankar S. Clinical decision support and rich clinical repositories: a symbiotic relationship: comment on "Electronic health records and clinical decision support systems". Arch Intern Med. 2011 May 23;171(10):903-5. doi: 10.1001/archinternmed.2010.518. Epub 2011 Jan 24.
  • McDonald CJ. Protecting Patients In Health Information Exchange: A Defense Of The HIPAA Privacy Rule. Health Aff (Millwood). 2009 Mar-Apr;28(2):447-9. doi: 10.1377/hlthaff.28.2.447.
  • McDonald CJ. Computerization can create safety hazards: a bar-coding near miss. Ann Intern Med. 2006 Apr 4;144(7):510-6.
  • McDonald CJ, Overhage JM, Barnes M, Schadow G, Blevins L, Dexter PR, Mamlin BW. The Indiana network for patient care: a working local health information infrastructure. An example of a working infrastructure collaboration that links data from five health systems and hundreds of millions of entries. Health Aff (Millwood). 2005 Sep-Oct;24(5):1214-20.
  • McDonald CJ, Huff SM, Suico JG, Hill G, Leavelle D, Aller R, Forrey A, Mercer K, DeMoor G, Hook J, Williams W, Case J, Maloney P. LOINC, a universal standard for identifying laboratory observations: a 5-year update. Clin Chem. 2003 Apr;49(4):624-33.
  • McDonald CJ, Shadow G, Barnes M, Dexter P, Overhage M, Mamlin B, McCoy J. Open source software in medical informatics—why, how and what. Int J Med Inform 2003 vol: 69 (2-3) pp: 175-184.
  • McDonald CJ. Hickam 2000: the maturation of, and linkages between, medical informatics and bioinformatics. J Lab Clin Med. 2001 Dec;138(6):359-66.
  • McDonald CJ, Schadow G, Suico J, Overhage JM. Data standards in health care. Ann Emerg Med. 2001 Sep;38(3):303-11.
  • McDonald CJ, Overhage JM, Tierney WM, Dexter PR, Martin DK, Suico JG, Zafar A, Schadow G, Blevins L, Glazener T, Meeks-Johnson J, Lemmon L, Warvel J, Porterfield B, Cassidy P, Lindbergh D, Belsito A, Tucker M, Williams B, Wodniak C. The Regenstrief Medical Record System: a quarter century experience. Int J Med Inform. 1999 Jun;54(3):225-53.
  • McDonald CJ, Overhage JM, Dexter P, Takesue B, Suico JG. What is done, what is needed and what is realistic to expect from medical informatics standards. Int J Med Inform. 1998 Feb;48(1-3):5-12.
  • McDonald CJ, Park BH, Blevins L. Grocers, Physicians, and Electronic Data Processing. AMA Cont Med Ed Newsl. 1983;12:5-8.
  • McGowan JJ, Overhage JM, Barnes M, McDonald CJ. Indianapolis I3: the third generation Integrated Advanced Information Management Systems. J Med Libr Assoc. 2004 Apr;92(2):179-87.
  • 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.
  • Murray MD, Harris LE, Overhage JM, Zhou XH, Eckert GJ, Smith FE, Buchanan NN, Wolinsky FD, McDonald CJ, Tierney WM. Failure of computerized treatment suggestions to improve health outcomes of outpatients with uncomplicated hypertension: results of a randomized controlled trial. Pharmacotherapy. 2004 Mar;24(3):324-37.
  • Murray MD, Smith FE, Fox J, Teal EY, Kesterson JG, Stiffler TA, Ambuehl RJ, Wang J, Dibble M, Benge DO, Betley LJ, Tierney WM, McDonald CJ. Structure, functions, and activities of a research support informatics section. J Am Med Inform Assoc. 2003 Jul-Aug;10(4):389-98. Epub 2003 Mar 28.
  • 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.
  • Olesen H, Ibsen I, Bruunshuus I, Kenny D, Dybkaer R, Fuentes-Arderiu X, Hill G, Soares de Araujo P, McDonald CJ. Properties and Units in the Clinical Laboratory Sciences. Part X. Pure Appl Chem 2000 vol: 72 (5) pp: 889-962.

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