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  • Pan H, Tryka KA, Vreeman DJ, Huggins W, Phillips MJ, Mehta JP, Phillips JH, McDonald C, Junkins HA, Ramos EM, Hamilton CM. Using PhenX measures to identify opportunities for cross-study analysis. Hum Mutat. 2012 May;33(5):849-57. doi: 10.1002/humu.22074. Epub 2012 Apr 3.
  • 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.
  • Wang Y, Halper M, Wei D, Gu H, Perl Y, Xu J, Elhanan G, Chen Y, Spackman KA, Case JT, Hripcsak G. Auditing complex concepts of SNOMED using a refined hierarchical abstraction network. J Biomed Inform. 2012 Feb;45(1):1-14. doi: 10.1016/j.jbi.2011.08.016. Epub 2011 Sep 1.
  • Ross JS, Tse T, Zarin DA, Xu H, Zhou L, Krumholz HM. Publication of NIH funded trials registered in ClinicalTrials.gov: cross sectional analysis. BMJ. 2012 Jan 3;344:d7292. doi: 10.1136/bmj.d7292.
  • 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.
  • 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.
  • Stanley RJ, De S, Demner-Fushman D, Antani SK, Thoma GR. An image feature-based approach to automatically find images for application to clinical decision support. Comput Med Imaging Graph. 2011 Jul;35(5):365-72. doi: 10.1016/j.compmedimag.2010.11.008. Epub 2010 Dec 8.
  • 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.
  • 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.
  • Ripple AM, Mork JG, Humphreys BL, Knecht LS. A retrospective cohort study of structured abstracts in MEDLINE, 1992-2006. J Med Libr Assoc. 2011 Apr;99(2):160-3. doi: 10.3163/1536-5050.99.2.009.
  • Zarin DA, Tse T, Williams RJ, Califf RM, Ide NC. The ClinicalTrials.gov results database--update and key issues. N Engl J Med. 2011 Mar 3;364(9):852-60. doi: 10.1056/NEJMsa1012065.
  • 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.
  • 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.
  • 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.
  • Zarin DA, Califf R. Point Counterpoint: ClinicalTrials.gov: Bureaucratic Nuisance or Opportunity to Improve the Field? APOR 2010 Nov; 6 (2): 3-5
  • Fung KW, McDonald C, Srinivasan S. The UMLS-CORE project: a study of the problem list terminologies used in large healthcare institutions. J Am Med Inform Assoc. 2010 Nov-Dec;17(6):675-80. doi: 10.1136/jamia.2010.007047.
  • Willams RJ, Tse T, Harlan WR, Zarin DA. Registration of observational studies: is it time? CMAJ. 2010 Oct 19;182(15):1638-42. doi: 10.1503/cmaj.092252. Epub 2010 Jul 19.
  • Friedlin J, McDonald CJ. An evaluation of medical knowledge contained in Wikipedia and its use in the LOINC database. J Am Med Inform Assoc. 2010 May-Jun;17(3):283-7. doi: 10.1136/jamia.2009.001180.
  • Downs SM, van Dyck PC, Rinaldo P, McDonald CJ, Howell RR, Zuckerman A, Downing G. Improving newborn screening laboratory test ordering and result reporting using health information exchange. J Am Med Inform Assoc. 2010 Jan-Feb;17(1):13-8. doi: 10.1197/jamia.M3295.
  • Vreeman DJ, McDonald C, Huff SM. LOINC® - A Universal Catalog of Individual Clinical Observations and Uniform Representation of Enumerated Collections. Int J Funct Inform Personal Med. 2010;3(4):273-291. Epub 2011 May 23.
  • Baorto D, Li L, Cimino JJ. Practical Experience with the Maintenance of a Large Ontology for an Academic Medical Center Journal of Biomedical Informatics; 2009 Jun;42(3):494-503)
  • Demner-Fushman D, Simpson M, Antani S, Thoma GR. Annotation and retrieval of clinically relevant images. Int J Med Inform. 2009 Dec;78(12):e59-67. doi: 10.1016/j.ijmedinf.2009.05.003. Epub 2009 Jul 9.
  • Demner-Fushman D, Chapman WW, McDonald CJ. What can natural language processing do for clinical decision support? J Biomed Inform. 2009 Oct;42(5):760-72. doi: 10.1016/j.jbi.2009.08.007. Epub 2009 Aug 13.
  • Simonaitis L, McDonald CJ. Using National Drug Codes and drug knowledge bases to organize prescription records from multiple sources. Am J Health Syst Pharm. 2009 Oct 1;66(19):1743-53. doi: 10.2146/ajhp080221.
  • Chen Y, Gu H, Perl Y, Halper M, Xu J. Expanding the extent of a UMLS semantic type via group neighborhood auditing. J Am Med Inform Assoc. 2009 Sep-Oct;16(5):746-57. doi: 10.1197/jamia.M2951. Epub 2009 Jun 30.
  • Dawson L, Zarin DA, Emanuel EJ, Friedman LM, Chaudhari B, Goodman SN. Considering usual medical care in clinical trial design. PLoS Med. 2009 Sep;6(9):e1000111. doi: 10.1371/journal.pmed.1000111. Epub 2009 Sep 29.
  • Tse T, Williams RJ, Zarin DA. Reporting "basic results" in ClinicalTrials.gov. Chest. 2009 Jul;136(1):295-303. doi: 10.1378/chest.08-3022.
  • Tse T, Williams RJ, Zarin DA. Update on Registration of Clinical Trials in ClinicalTrials.gov. Chest. 2009 Jul;136(1):304-5. doi: 10.1378/chest.09-1219.
  • Zarin DA. Clinical trials registry expands. Interview by Bridget M. Kuehn. JAMA. 2009 Jul 1;302(1):22. doi: 10.1001/jama.2009.891.
  • 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.
  • 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.
  • 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.
  • 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.
  • Zhu X, Fan JW, Baort D, Weng C, Cimino JJ. A review of auditing methods applied to the content of controlled biomedical terminologies. J Biomed Inform. 2009 Jun;42(3):413-25. doi: 10.1016/j.jbi.2009.03.003. Epub 2009 Mar 12.
  • Deserno TM, Antani S, Long LR. Ontology of gaps in content-based image retrieval. J Digit Imaging. 2009 Apr;22(2):202-15. doi: 10.1007/s10278-007-9092-x. Epub 2008 Feb 1.
  • Hsu W, Antani SK, Long LR, Neve L, Thoma GR. SPIRS: a Web-based image retrieval system for large biomedical databases. Int J Med Inform. 2009 Apr;78 Suppl 1:S13-24. doi: 10.1016/j.ijmedinf.2008.09.006. Epub 2008 Nov 8.
  • 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.
  • Collins SA, Currie LM, Bakken S, Cimino JJ. Information needs, infobutton manager use, and satisfaction by clinician type: a case study. J Am Med Inform Assoc. 2009 Jan-Feb;16(1):140-2. Epub 2008 Oct 24.
  • Lee DJ, Antani S, Chang Y, Long LR, Christensen P, Jeronimo J. CBIR of Spine X-ray Images On Inter-vertebral Disc Space and Shape Profiles Using Feature Ranking and Voting Consensus. Data & Knowledge Engineering, Special Issue on Knowledge Discovery in Medicine. 2009.
  • 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.
  • 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
  • Tse T, Zarin DA. Clinical Trial Registration and Results Reporting: ClinicalTrials.gov and FDAAA FDLI Update. 2009 Jan/Feb;1:18-22
  • Deserno TM, Antani S, Long LR. Content-based image retrieval for scientific literature access. Methods Inf Med. 2009;48(4):371-80. doi: 10.3414/ME0561. Epub 2009 Jul 20.
  • Pontet F, Magdal Petersen U, Fuentes-Arderiu X, Nordin G, Bruunshuus I, Ihalainen J, Karlsson D, Forsum U, Dybkaer R, Schadow G, Kuelpmann W, Ferard G, Kang D, McDonald C, Hill G. Clinical laboratory sciences data transmission: the NPU coding system. Stud Health Technol Inform. 2009;150:265-9.
  • Burgun A, Bodenreider O. Accessing and Integrating Data and Knowledge for Biomedical Research Yearb Med Inform. 2008:91-101
  • Huang KC, Geller J, Halper M, Perl Y, Xu J. Using WordNet synonym substitution to enhance UMLS source integration. Artif Intell Med. June 2009;46(2):97-109. doi: 10.1016/j.artmed.2008.11.008. Epub 2008 Dec 30.
  • Hansen RA, Wanzhu T, Wang J, Ambuehl R, McDonald CJ, Murray MD. Risk of adverse gastrointestinal events from inhaled corticosteroids. 2008 Nov;28(11):1325-34.
  • Demner-Fushman D, Ananiadou S, Cohen KB, Pestian J, Tsujii J, Webber B. Themes in biomedical natural language processing: BioNLP08 BMC Bioinformatics. 2008 Nov 19;9 Suppl 11:S1.
  • Richesson RL, Fung KW, Krischer JP. Heterogeneous but 'Standard' Coding Systems for Adverse Events: Issues in Achieving Interoperability Between Apples and Oranges Contemp Clin Trials. 2008 Sep;29(5):635-45. Epub 2008 Mar 5
  • 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.

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