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  • 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.
  • Zolnoori M, Fung K, Patrick TB, Fontelo P, Kharrazi H, Faiola A, Wu YSS, Eldredge CE, Luo J, Conway M, Zhu J, Park SK, Xu K, Moayyed H, Goudarzvand S. A systematic approach for developing a corpus of patient reported adverse drug events: A case study for SSRI and SNRI medications. NCBINCBI Logo Skip to main content Skip to navigation Resources How To About NCBI Accesskeys PubMed US National Library of Medicine National Institutes of Health Search databaseSearch term 30611893[uid] Clear inputSearch Create RSSCreate alertAdvancedHelp Result Filters Format: AbstractSend to J Biomed Inform. 2019 Feb;90:103091. doi: 10.1016/j.jbi.2018.12.005. Epub 2019 Jan 4.
  • 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]
  • 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.
  • 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.
  • Lau JJ, Gayen S, Ben Abacha A, Demner-Fushman D. A dataset of clinically generated visual questions and answers about radiology images. Sci Data. 2018 Nov 20;5:180251. doi: 10.1038/sdata.2018.251.
  • Zolnoori M, Fung K, Fontelo P, Kharrazi H, Faiola A, Wu YSS, Stoffel V, Patrick T. Identifying the Underlying Factors Associated With Patients' Attitudes Toward Antidepressants: Qualitative and Quantitative Analysis of Patient Drug Reviews. JMIR Ment Health. 2018 Sep 30;5(4):e10726. doi: 10.2196/10726.
  • Fontelo P, Liu F. A review of recent publication trends from top publishing countries. Syst Rev. 2018 Sep 27;7(1):147. doi: 10.1186/s13643-018-0819-1.
  • Sylim P, Liu F, Marcelo A, Fontelo P. Blockchain Technology for Detecting Falsified and Substandard Drugs in Distribution: Pharmaceutical Supply Chain Intervention. JMIR Res Protoc. 2018 Sep 13;7(9):e10163. doi: 10.2196/10163.
  • 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.
  • Goss FR, Lai KH, Topaz M, Acker WW, Kowalski L, Plasek JM, Blumenthal KG, Seger DL, Slight SP, Fung KW, Chang FY, Bates DW, Zhou L. A value set for documenting adverse reactions in electronic health records. J Am Med Inform Assoc. 2018 Jun 1;25(6):661-669. doi: 10.1093/jamia/ocx139.
  • Vreeman DJ, Abhyankar S, McDonald CJ. Re: Unit conversions between LOINC codes Published June 19, 2017 [Letter]. J Am Med Inform Assoc. 2018 May 1;25(5):614-615. doi: 10.1093/jamia/ocx087.
  • 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]
  • Kilicoglu H, Ben Abacha A, Mrabet Y, Shooshan SE, Rodriguez L, Masterton K, Demner-Fushman D. Semantic annotation of consumer health questions. BMC Bioinformatics. 2018 Feb 6;19(1):34. doi: 10.1186/s12859-018-2045-1.
  • 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.
  • McDonald CJ. Top LOINC Codes – Orders and Observations
  • 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.
  • Sun H, Li J, Wu Y, Wang L, Fung K. Using an Ontology-Based Approach to Handle Author Affiliations in a Large Biomedical Citation Database. Stud Health Technol Inform. 2017;245:1338.
  • Abhyankar S, Vreeman DJ, Westra BL, Delaney CW. Comments on the Use of LOINC and SNOMED CT for Representing Nursing Data [Letter]. Int J Nurs Knowl. 2017 Aug 30. doi: 10.1111/2047-3095.12183. [Epub ahead of print]
  • 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.
  • 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.
  • Vreeman DJ, Abhyankar S, McDonald CJ. Unit conversions between LOINC codes Published June 19, 2017 [Letter]. Journal of the American Medical Informatics Association, 1–3. http://doi.org/10.1093/jamia/ocx087.
  • Bush R, Heierman E, Knafel A, Lardin L, McDonald CJ. LIVD – Digital Format for Publication of LOINC to Vendor IVD Test Results. . IVD Industry Connectivity Consortium. http://ivdconnectivity.org/livd/. Published June 1, 2017. Accessed August 9, 2017.
  • Chakrabarti S, Sen A, Huser V, Hruby GW, Rusanova A, Albers DJ, Weng C. An Interoperable Similarity-based Cohort Identification Method Using the OMOP Common Data Model version 5.0. J Healthc Inform Res. 2017 Jun;1(1):1-18. doi: 10.1007/s41666-017-0005-6. Epub 2017 Jun 8.
  • McDonald CJ, Maglott D, Abhyankar S, Goodwin R, Kanduru A, Lu S, Lynch P, Vreeman D, Wang Y, Wood G. HL7 Version 2.5.1 Implementation Guide: Lab Results Interface (LRI), Release 1, STU Release 4. US Realm, Chapter 5, Clinical Genomics Results Reporting. Published for May 2017 Ballot.
  • 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.
  • Fung K, Xu J, Amey F, Gutierrez AR, D'Have A. Leveraging Lexical Matching and Ontological Alignment to Map SNOMED CT Surgical Procedures to ICD-10-PCS. AMIA Annu Symp Proc. 2017 Feb 10;2016:570-579. eCollection 2016.
  • Cahan A, Cimino JJ. Improving precision medicine using individual patient data from trials. CMAJ. 2017 Feb 6;189(5):E204-E207. doi: 10.1503/cmaj.160267. Epub 2016 Aug 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.
  • 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.
  • Topaz M, Goss F, Blumenthal K, Lai K, Seger DL, Slight SP, Wickner PG, Robinson GA, Fung KW, McClure RC, Spiro S, Acker WW, Bates DW, Zhou L. Towards improved drug allergy alerts: Multidisciplinary expert recommendations. Int J Med Inform. 2017 Jan;97:353-355. doi: 10.1016/j.ijmedinf.2016.10.006. Epub 2016 Oct 6.
  • Cohen T, Roberts K, Gururaj AE, Chen X, Pournejati S, Alter G, Hersh WR, Demner-Fushman D, Ohno-Machado L, Lu H. A publicly available benchmark for biomedical dataset retrieval: the reference standard for the 2016 bioCADDIE dataset retrieval challenge. Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax061.
  • 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.
  • De Herrera A, Schaer R, Bromuri S, Müller H. Overview of the ImageCLEF 2016 Medical Task. CLEF working notes 2016, CEUR, 2016.
  • 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.
  • Driessen J, Baik SH, Zhang Y. Trends in Off-Label Use of Second-Generation Antipsychotics in the Medicare Population From 2006 to 2012. Psychiatr Serv. 2016 Aug 1;67(8):898-903. doi: 10.1176/appi.ps.201500316. Epub 2016 Apr 15.
  • Hripcsak G, Ryan PB, Duke JD, Shah NH, Park RW, Huser V, Suchard MA, Schuemie MJ, DeFalco FJ, Perotte A, Banda JM, Reich CG, Schilling LM, Matheny ME, Meeker D, Pratt N, Madigan D. Characterizing treatment pathways at scale using the OHDSI network. Proc Natl Acad Sci U S A. 2016 Jul 5;113(27):7329-36. doi: 10.1073/pnas.1510502113. Epub 2016 Jun 6.
  • Benedict SH, Hoffman K, Martel MK, Abernethy AP, Asher AL, Capala J, Chen RC, Chera B, Couch J, Deye J, Efstathiou JA, Ford E, Fraass BA, Gabriel PE, Huser V, Kavanagh BD, Khuntia D, Marks LB, Mayo C, McNutt T, Miller RS, Moore KL, Prior F, Roelofs E, Rosenstein BS, Sloan J, Theriault A, Vikram B. Overview of the American Society for Radiation Oncology-National Institutes of Health-American Association of Physicists in Medicine Workshop 2015: Exploring Opportunities for Radiation Oncology in the Era of Big Data. Int J Radiat Oncol Biol Phys. 2016 Jul 1;95(3):873-879. doi: 10.1016/j.ijrobp.2016.03.006.
  • 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.
  • Roberts K, Demner-Fushman D. Interactive use of online health resources: a comparison of consumer and professional questions. J Am Med Inform Assoc. 2016 Jul;23(4):802-11. doi: 10.1093/jamia/ocw024. Epub 2016 May 4.
  • Demner-Fushman D, Kilicoglu H. Dataset: CHQA Named Entity Dataset
  • 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
  • Fung KW, Richesson R, Smerek M, Pereira KC, Green BB, Patkar A, Clowse M, Bauck A, Bodenreider O. Preparing for the ICD-10-CM Transition: Automated Methods for Translating ICD Codes in Clinical Phenotype Definitions. EGEMS (Wash DC). 2016 Apr 12;4(1):1211. doi: 10.13063/2327-9214.1211. eCollection 2016.
  • 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.
  • 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.
  • Baik SH, Hernandez I, Zhang Y. Evaluating the Initiation of Novel Oral Anticoagulants in Medicare Beneficiaries. J Manag Care Spec Pharm. 2016 Mar;22(3):281-92. doi: 10.18553/jmcp.2016.22.3.281.
  • Demner-Fushman D, Kohli MD, Rosenman MB, Shooshan SE, Rodriguez L, Antani S, Thoma GR, McDonald CJ. Preparing a collection of radiology examinations for distribution and retrieval. J Am Med Inform Assoc. 2016 Mar;23(2):304-10. doi: 10.1093/jamia/ocv080. Epub 2015 Jul 1.
  • 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.
  • Demner-Fushman D, Roberts K. Dataset: Question Decomposition Data
  • Demner-Fushman D, Roberts K. Dataset: Question Type Data
  • 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.
  • 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.
  • Payne TH, Corley S, Cullen TA, Gandhi TK, Harrington L, Kuperman GJ, Makar E, Mattison JE, McCallie DP, McDonald CJ, Tang PC, Tierney WM, Weaver C, Weir CR, Zaroukian MH. Report of the AMIA EHR-2020 Task Force on the status and future direction of EHRs J Am Med Inform Assoc. 2015 Sep;22(5):1102-10. doi: 10.1093/jamia/ocv066. Epub 2015 May 28.
  • Roberts K, Simpson M, Demner-Fushman D, Voorhees E, Hersh W. State-of-the-art in biomedical literature retrieval for clinical cases: A survey of the TREC 2014 CDS Track. Inf Retrieval J. 2015.
  • Gartrell K, Trinkoff AM, Storr CL, Wilson ML. Electronic Personal Health Record Use Among Nurses in the Nursing Informatics Community. Comput Inform Nurs. 2015 Jul;33(7):306-14. doi: 10.1097/CIN.0000000000000163.
  • Ayvas S, Horn J, Hassanzadeh O, Zhu Q, Stan J, Tatonetti NP, Vilar S, Brochhausen M8, Samwald M, Rastegar-Mojarad M, Dumontier M, Boyce RD. Toward a complete dataset of drug-drug interaction information from publicly available sources. J Biomed Inform. 2015 Jun;55:206-17. doi: 10.1016/j.jbi.2015.04.006. Epub 2015 Apr 24.
  • 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.
  • Fung KW, Xu J. An exploration of the properties of the CORE problem list subset and how it facilitates the implementation of SNOMED CT. J Am Med Inform Assoc. 2015 May;22(3):649-58. doi: 10.1093/jamia/ocu022. Epub 2015 Feb 26.
  • Gartrell K, Storr CL, Trinkoff AM, Wilson ML, Gurses AP. Electronic personal health record use among registered nurses. Nurs Outlook. 2015 May-Jun;63(3):278-87. doi: 10.1016/j.outlook.2014.11.013. Epub 2014 Nov 28.
  • 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.
  • Gartrell K, Trinkoff AM, Storr CL, Wilson ML, Gurses AP. Testing the Electronic Personal Health Record Acceptance Model by Nurses for Managing Their Own Health: A Cross-sectional Survey. Appl Clin Inform. 2015 Apr 8;6(2):224-47. doi: 10.4338/ACI-2014-11-RA-0107. eCollection 2015.
  • Abhyankar S, Goodwin RM, Sontag M, Yusuf C, Ojodu J, McDonald CJ. An update on the use of health information technology in newborn screening. Semin Perinatol. 2015 Apr;39(3):188-93. doi: 10.1053/j.semperi.2015.03.003. Epub 2015 Apr 29.
  • Zhu X, Cimino JJ. Clinicians' evaluation of computer-assisted medication summarization of electronic medical records. Comput Biol Med. 2015 Apr;59:221-31. doi: 10.1016/j.compbiomed.2013.12.006. Epub 2013 Dec 19.
  • Winnenburg R, Mortensen JM, Bodenreider O. Using description logics to evaluate the consistency of drug-class membership relations in NDF-RT. J Biomed Semantics. 2015 Mar 28;6:13. doi: 10.1186/s13326-015-0007-3. eCollection 2015.
  • 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.
  • Zarin D, Tse T, Sheehan J. The proposed rule for U.S. clinical trial registration and results submission. N Engl J Med. 2015 Jan 8;372(2):174-80. doi: 10.1056/NEJMsr1414226. Epub 2014 Dec 24.
  • 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.
  • 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.
  • 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.
  • 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.
  • Cimino JJ, Ayres EJ, Remennik L, Rath S, Freedman R, Beri A, Chen Y, Huser V. The National Institutes of Health's Biomedical Translational Research Information System (BTRIS): design, contents, functionality and experience to date. J Biomed Inform. 2014 Dec;52:11-27. doi: 10.1016/j.jbi.2013.11.004. Epub 2013 Nov 19.
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  • Kim I, Le DX, Thoma GR. Automated method for extracting "citation sentences" from online biomedical articles using SVM-based text summarization technique. Proc. the 2014 IEEE Int'l Conf. on Systems, Man, and Cybernetics (SMC 2014), pp. 2006-2011, San Diego, October, 2014
  • 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.
  • Boyce RD, Ryan PB, Noren GN, Schuemie MJ, Reich C, Duke J, Tatonetti NP, Trifiro G, Harpaz R, Overhage JM, Hartzema AG, Kayter M, Voss EA, Lambert CG, Huser V, Dumontier M. Bridging islands of information to establish an integrated knowledge base of drugs and health outcomes of interest. Drug Saf. 2014 Aug;37(8):557-67. doi: 10.1007/s40264-014-0189-0.
  • Hess CN, Roe MT, Gibson CM, Temple RJ, Pencina MJ, Zarin DA, Anstrom KJ, Alexander JH, Sherman RE, Fiedorek FT, Mahaffey KW, Lee KL, Chow SC, Armstrong PW, Califf RM. Independent data monitoring committees: preparing a path for the future. Am Heart J. 2014 Aug;168(2):135-41.e1. doi: 10.1016/j.ahj.2014.05.003. Epub 2014 May 15.
  • 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.
  • Roberts K, Kilicoglu H, Fiszman M, Demner-Fushman D. Decomposing consumer health questions. BioNLP 2014.
  • 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.
  • Bekhuis T, Tseytlin E, Mitchell KJ, Demner-Fushman D. Feature engineering and a proposed decision-support system for systematic reviewers of medical evidence. PLoS One. 2014 Jan 27;9(1):e86277. doi: 10.1371/journal.pone.0086277. 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.
  • 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.
  • 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.
  • Fung K, Kayaalp M, Callaghan FM, McDonald CJ. Comparison of electronic pharmacy prescription records with manually collected medication histories in an emergency department. Ann Emerg Med. 2013 Sep;62(3):205-11. doi: 10.1016/j.annemergmed.2013.04.014. Epub 2013 May 18.
  • Hersh WR, Weiner MG, Embi PJ, Logan JR, Payne PR, Bernstam EV, Lehmann HP, Hripcsak G, Hartzog TH, Cimino J, Saltz JH. Caveats for the use of operational electronic health record data in comparative effectiveness research. Med Care. 2013 Aug;51(8 Suppl 3):S30-7. doi: 10.1097/MLR.0b013e31829b1dbd.
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  • 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.
  • Zarin D, Tse T. Trust but verify: trial registration and determining fidelity to the protocol [Letter]. Ann Intern Med. 2013 Jul 2;159(1):65-7. doi: 10.7326/0003-4819-159-1-201307020-00011.
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  • Fung KW, Jao CS, Demner-Fushman D. Extracting drug indication information from structured product labels using natural language processing. J Am Med Inform Assoc. 2013 May 1;20(3):482-8. doi: 10.1136/amiajnl-2012-001291. Epub 2013 Mar 9.
  • Zarin D, Tse T. Clarification about ClinicalTrials.gov [Letter]. IRB. 2013 May-Jun;35(3):19.
  • Abhyankar S, McDonald CJ. Overweight, obesity, and all-cause mortality [Letter]. JAMA. 2013 Apr 24;309(16):1680-1. doi: 10.1001/jama.2013.3092.
  • McDonald CJ, Vreeman DJ, Abhyankar S. Comment on "time to integrate clinical and research informatics" [Letter]. Sci Transl Med. 2013 Apr 3;5(179):179le1. doi: 10.1126/scitranslmed.3005700.
  • 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. Tutorial: meeting data access and reporting requirements with the NIH’s Biomedical Translational Research Information System (BTRIS).
  • 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.
  • 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.
  • Apostolova E, You D, Xue Z, Antani SK, Demner-Fushman D, Thoma GR. Image Retrieval From Scientific Publications: Text and Image Content Processing To Separate Multipanel Figures. JASIST (Journal of the American Society for Information Science and Technology), 64(5):893–908, 2013.
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  • Del Fiol G, Curtis C, Cimino J, Iskander A, Kalluri AS, Jing X, Hulse NC, Long J, Overby CL, Schardt C, Douglas DM. Disseminating context-specific access to online knowledge resources within electronic health record systems. Stud Health Technol Inform. 2013;192:672-6.
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  • 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.
  • Montufar-Rueda C, Rodriguez L, Jarquin JD, Barboza A, Bustillo MC, Marin F, Ortiz G, Estrada F. Severe postpartum hemorrhage from uterine atony: a multicentric study. J Pregnancy. 2013;2013:525914. doi: 10.1155/2013/525914. Epub 2013 Dec 2.
  • 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.
  • 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.
  • Winnenburg R, Bodenreider O. Exploring pharmacoepidemiologic groupings of drugs from a clinical perspective. Stud Health Technol Inform. 2013;192:827-31.
  • Bodenreider O. API: Prescribable
  • 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.
  • 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.
  • Abhyankar S, Demner-Fushman D, McDonald CJ. Standardizing clinical laboratory data for secondary use. J Biomed Inform. 2012 Aug;45(4):642-50. doi: 10.1016/j.jbi.2012.04.012. Epub 2012 May 3.
  • 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.
  • Vreeman D, Chiaravalloti MT, Hook J, McDonald CJ. Enabling international adoption of LOINC through translation. J Biomed Inform. 2012 Aug;45(4):667-73. doi: 10.1016/j.jbi.2012.01.005. Epub 2012 Jan 21.
  • Bekhuis T, Demner-Fushman D. Screening nonrandomized studies for medical systematic reviews: a comparative study of classifiers. Artif Intell Med. 2012 Jul;55(3):197-207. doi: 10.1016/j.artmed.2012.05.002. Epub 2012 Jun 5.
  • Fung K. Dataset: SNOMED CT to ICD-10-CM Map
  • McDonald CJ, Vreeman D, Goodwin RM. Dataset: LOINC Top 2000+ Lab Observations and Mapper's Guide
  • Demner-Fushman D, Antani SK, Simpson M, Thoma GR. Design and Development of a Multimodal Biomedical Information Retrieval System JCSE. June 2012;6(2):168-177.
  • Bodenreider O. Web Interface: RxMix
  • McDonald CJ, Tierney WM. The effect of electronic health records on test ordering [Letter}. Health Aff (Millwood). 2012 Jun;31(6):1365; author reply 1366. doi: 10.1377/hlthaff.2012.0471.
  • 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.
  • Fung KW. Dataset: ICD-9-CM to SNOMED CT Map
  • 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.
  • Zarin D. Factual Errors about ClinicalTrials.gov and other federal mandates in special report by Shuster [Letter]. Clin Transl Sci. 2012 Apr;5(2):217; author reply 217. doi: 10.1111/j.1752-8062.2012.00410.x.
  • Fung KW. Web Interface: I-Magic SNOMED-CT to ICD-10-CM code mapping tool.
  • McDonald CJ, McDonald MH. Electronic medical records and preserving primary care physicians' time: comment on "electronic health record-based messages to primary care providers" [Letter]. Arch Intern Med. 2012 Feb 13;172(3):285-7. doi: 10.1001/archinternmed.2011.1678.
  • 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.
  • Abhyankar S, Goodwin RM, Zuckerman A, McDonald CJ. Dataset: newborn screening results annotated example HL7 electronic message guidance (v 5.2).
  • 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.
  • Abhyankar S, Goodwin RM, Zuckerman AE, McDonald CJ. Dataset: Newborn screening LOINC panel.
  • Abhyankar S, Goodwin RM, Zuckerman AE, McDonald CJ. Dataset: newborn screening LOINC codes (AHIC panel).
  • Altemus AR. Mobile App: Native Voices: Native Peoples' Concepts of Health and Illness
  • McDonald CJ, Abhyankar S, Taft L. Dataset: common units of measure - subset of the Unified Code for Units of Measure.
  • 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 C, Vreeman D, Goodwin RM. Dataset: LOINC Top 300+ Lab Orders
  • 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.
  • Fung KW. Dataset: Nursing Problem List Subset of SNOMED CT
  • 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.
  • Zarin D, Tse T. The effect of funding source on outcome reporting among drug trials [Letter]. Ann Intern Med. 2011 Jan 18;154(2):137-8; author reply 138. doi: 10.7326/0003-4819-154-2-201101180-00020.
  • 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.
  • Fung KW. API: RxTerms
  • Fung KW. Dataset: SNOMED CT route of administration subset.
  • Thoma GR, Ford G, Antani SK, Demner-Fushman D, Chung M, Simpson M. Interactive Publication: The document as a research tool. Web Semant. 2010 Jul 1;8(2-3):145-150.
  • Zou J, Le DX, Thoma GR. Locating and parsing bibliographic references in HTML medical articles. Int J Doc Anal Recognit. 2010 Jun 1;13(2):107-119.
  • 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.
  • Ackerman MJ, Siegel, E, Wood, F. Interactive Science Publishing: A joint OSA-NLM project. Information Services & Use. 2010 Jan-Feb;30:39-50. DOI: 10.3233/ISU-2010-0612.
  • 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.
  • Fung KW. Dataset: CORE problem list of SNOMED CT.
  • 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
  • Demner-Fushman D, Antani SK, Simpson M. Web Interface: Open-I
  • 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.
  • Zarin DA, Tse T. Tracking health services research studies [Letter]. JAMA. 2008 Nov 19;300(19):2252; author reply 2252. doi: 10.1001/jama.2008.612.
  • 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.
  • Thoma GR, Ford G, Demner-Fushman D, Antani SK, Chung M. Software: Panorama
  • 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
  • Zarin DA, Tse T. Moving Towards Transparency of Clinical Trials Science. 2008 Mar 7;319(5868):1340-2.
  • Overhage JM, Grannis S, McDonald CJ. A comparison of the completeness and timeliness of automated electronic laboritory reporting and spontaneous reporting of notifiable conditions. Am J Public Health. 2008 Feb;98(2):344-50. Epub 2008 Jan 2
  • McDonald C. Dataset: LOINC Panels and Forms file
  • Hsu W, Long LR, Antani SK. SPIRS: A Framework for Content-based Image Retrieval from Large Biomedical Databases Stud Health Technol Inform. 2007;129(Pt 1):188-92.
  • Logan RA, Tse T. A Multidiscipline Conceptual Framework for Consumer Health Informatics Stud Health Technol Inform. 2007;129(Pt 2):1169-73
  • Zhang S, Bodenreider O. Experience in Aligning Anatomical Ontologies Int J Semant Web Inf Syst. 2007;3(2):1-26
  • Bennett A, Liu J, Van Ryk D, Bliss D, Arthos J, Henderson RM, Subramaniam S. Cryoelectron Tomographic Analysis of an HIV-neutralizing Protein and Its Complex with Native Viral gp120 J Biol Chem. 2007 Sep 21;282(38):27754-9. Epub 2007 Jun 28
  • Drake TA, Braun J, Marchevsky A, Kohan IS, Fletcher C, Chueh H, Beckwith B, Berkowicz D, Kuo F, Zeng QT, Balis U, Holzbach A, McMurry A, Gee CE, McDonald C, Schadow G, Davis M, Hattab EM, Blevins L, Hook J, Becich M, Crowley RS, Taube SE, Berman J. A System for Sharing Routine Surgical Pathology Specimens Across Institutions: The Shared Pathology Informatics Network Hum Pathol. 2007 Aug;38(8):1212-25. Epub 2007 May 8
  • 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.
  • Ide NC, Loane RF, Demner-Fushman D. Essie: A Concept-based Search Engine for Structured BiomedicalText J Am Med Inform Assoc. 2007 May-Jun;14(3):253-63. Epub 2007 Feb 28
  • Zarin DA, Ide NC, Tse T, Harlan WR, West JC, Lindberg DA. Issues in the registration of clinical trials. JAMA. 2007 May 16;297(19):2112-20
  • 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
  • Drazen JM, Zarin DA. Salvation by Registration N Engl J Med 356;2
  • 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
  • Zarin DA, Keselman A. Registering a Clinical Trial in ClinicalTrials.gov Chest. 2007 Mar;131(3):909-12. Epub 2007 Feb 15
  • 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
  • Zeng QT, Tse T, Divita G, Keselman A, Crowell J, Browne AC, Goryachev S, Ngo L. Term Identification Methods for Consumer Health Vocabulary Development J Med Internet Res. 2007 Feb 28;9(1):e4.
  • Demner-Fushman D, Lin J. Answering Clinical Questions with Knowledge-based and Statistical Techniques Computational Linguistics. 2007 Jan;33(1):63-103
  • 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
  • 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.
  • 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
  • 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
  • Siegel ER, Wood FB, Dutcher GA, Ruffin A, Logan RA, Scott J. Assessment of the National Library of Medicine's Health Disparities Plan: A Focus on Native American Outreach J Med Libr Assoc. 2005 Oct;93(4 Suppl):S10-20
  • Wood FB, Siegel ER, Dutcher GA, Ruffin A, Logan RA. The National Library of Medicine's Native American Outreach Portfolio: A Descriptive Overview J Med Libr Assoc. 2005 Oct;93(4 Suppl):S21-34
  • Morrison SM. Web Interface: Genetics Home Reference
  • Bodenreider O, Stevens R. Bio-ontologies: Current Trends and Future Directions Brief Bioinform. 2006 Sep;7(3):256-74. Epub 2006 Aug 9
  • 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
  • Mitchell JA, Fomous C, Fun J. Challenges and strategies of the Genetics Home Reference J Med Libr Assoc. 2006 Jul;94(3):336-42
  • Marino-Ramirez L, Bodenreider O, Kantz N, Jordan IK. Co-evolutionary Rates of Functionally Related Yeast Genes Evolutionary Bioinformatics Online 2006;2:295-300.
  • McDonald CJ. Computerization can create safety hazards: a bar-coding near miss. Ann Intern Med. 2006 Apr 4;144(7):510-6.
  • Demner-Fushman D, Few B, Hauser SE, Thoma GR. Automatically Identifying Health Outcome Information in MEDLINE Records J Am Med Inform Assoc. 2006 Jan-Feb;13(1):52-60. Epub 2005 Oct 12.
  • 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
  • Jing X, Kay S, Hardiker N. Designing a bio-health information assistant within an EHR. Healthcare Computing 2006: 325-326 (Harrogate, England).
  • Zarin DA, Tse T, Ide NC. Trial Registration at ClinicalTrials.gov between May and October 2005 N Engl J Med. 2005 Dec 29;353(26):2779-87
  • 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
  • Mougin F, Bodenreider O. Approaches to Eliminating Cycles in the UMLS Metathesaurus: Naive vs. Formal AMIA Annu Symp Proc. 2005:550-4
  • Wang H, Azuaje F, Bodenreider O. An Ontology-Driven Clustering Method for Supporting Gene Expression Analysis CBMS’2005. 2005:389-394.
  • 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.
  • Sears C, Prescott V, McDonald CJ. The Indiana Network for Patient Care: A Case Study of a Successful Healthcare Data Sharing Agreement. Am Bar Assoc Health eSource. Sept 2005; 2(1), p1-15.
  • 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.
  • 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.
  • Weiner M, Stump TE, Callahan CM, Lweis JN, McDonald CJ. Pursuing integration of performance measures into electronic medical records: beta-adrenergic receptor antagonist medications. Qual Saf Health Care. 2005 Apr;14(2):99-106.
  • Thoma GR. Mobile App: Turning the Pages
  • Dexter PR, Perkins SM, Maharry KS, Jones K, McDonald CJ. Inpatient computer-based standing orders vs physician reminders to increase influenza and pneumococcal vaccination rates: a randomized trial. JAMA. 2004 Nov 17;292(19):2366-71.
  • Bodenreider O, Nelson SJ. RxNav: A Semantic Navigation Tool for Clinical Drugs Medinfo. 2004 Sept.;2004: 1530.
  • Bodenreider O. Web Interface: RxNav
  • Zafar A, Mamlin B, Perkins S, Belsito AM, Overhage JM, McDonald CJ. A simple error classification system for understanding sources of error in automatic speech recognition and human transcription. Int J Med Inform. 2004 Sep;73(9-10):719-30.
  • 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.
  • Bodenreider O, McCray AT. Exploring Semantic Groups Through Visual Approaches J Biomed Inform. 2003 Dec;36(6):414-432.
  • 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.
  • McDonald CJ, Overhage JM, Mamlin BW, Dexter PD, Tierney WM. Physicians, information technology, and health care systems: a journey, not a destination [Letter]. J Am Med Inform Assoc. 2004 Mar-Apr;11(2):121-4.
  • 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.
  • Grannis SJ, Overhage JM, McDonald CJ. Real world performance of approximate string comparators for use in patient matching. Stud Health Technol Inform. 2004;107(Pt 1):43-7.
  • Tierney VM, Overhage JM, Murray MD, Harris LE, Zhou XH, Eckert GJ, Smith FE, Nienaber N, McDonald CJ, Wolinsky FD. Effects of computerized guidelines for managing heart disease in primary care. J Gen Intern Med. 2003 Dec;18(12):967-76.
  • Weiner M, Callahan CM, Tierney WM, Overhage JM, Mamlin B, Dexter PR, McDonald CJ. Using information technology to improve the health care of older adults. Ann Intern Med. 2003 Sep 2;139(5 Pt 2):430-6.
  • Weiner M, Stump TE, Callahan CM, Lewis JN, McDonald CJ. A practical method of linking data from Medicare claims and a comprehensive electronic medical records system. Int J Med Inform. 2003 Aug;71(1):57-69.
  • 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.
  • 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.
  • Weinberger M, Murray MD, Marrero DG, Brewer N, Lykens M, Harris LE, Seshadri R, Caffrey H, Roesner JF, Smith F, Newell AJ, Collins JC, McDonald CJ, Tierney WM. Effectiveness of pharmacist care for patients with reactive airways disease: a randomized controlled trial. JAMA. 2002 Oct 2;288(13):1594-602.
  • Overhage JM, Dexter PR, Perkins SM, Cordell WH, McGoff J, McGrath R, McDonald CJ. A randomized, controlled trial of clinical information shared from another institution. Ann Emerg Med. 2002 Jan;39(1):14-23.
  • McDonald CJ. Hickam 2000: the maturation of, and linkages between, medical informatics and bioinformatics. J Lab Clin Med. 2001 Dec;138(6):359-66.
  • Schadow G, Russler DC, McDonald CJ. Conceptual alignment of electronic health record data with guideline and workflow knowledge. Int J Med Inform. 2001 Dec;64(2-3):259-74.
  • Overhage JM, Suico J, McDonald CJ. Electronic laboratory reporting: barriers, solutions and findings. J Public Health Manag Pract. 2001 Nov;7(6):60-6.
  • Dexter PR, Perkins S, Overhage JM, Maharry K, Kohler RB, McDonald CJ. A computerized reminder system to increase the use of preventive care for hospitalized patients. N Engl J Med. 2001 Sep 27;345(13):965-70.
  • McDonald CJ, Schadow G, Suico J, Overhage JM. Data standards in health care. Ann Emerg Med. 2001 Sep;38(3):303-11.
  • Overhage JM, Perkins S, Tierney WM, McDonald CJ. Controlled trial of direct physician order entry: effects on physicians' time utilization in ambulatory primary care internal medicine practices. J Am Med Inform Assoc. 2001 Jul-Aug;8(4):361-71.
  • McCray AT. Better access to information about clinical trials. Ann Intern Med. 2000 Oct 17;133(8):609-14.
  • 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.
  • 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.
  • Schadow G, Russler DC, McDonald CJ. Conceptual integration of guidelines and workflow into the electronic health record. Stud Health Technol Inform. 2000;77:807-11.
  • West RT. IAIMS: an interview with Dick West. Integrated Advanced Information Management Systems. Interview by Joan S Ash and Frances E Johnson. J Am Med Inform Assoc. 1999 Nov-Dec;6(6):447-56.
  • 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.
  • Overhage J, Tierney W, McDonald CJ. Clinical Decision Support in Ambulatory Care Tools, Trials, and Tribulations. J Health Manag 1999 vol: 13 (2) pp: 67-79.
  • Lingappa G, Thoma GR, Antani SK. Web Interface: MyMorph
  • Zafar A, Overhage JM, McDonald CJ. Continuous speech recognition for clinicians. J Am Med Inform Assoc. 1999 May-Jun;6(3):195-204.
  • Schadow G, McDonald CJ, Suico JG, Fohring U, Tolxdorff T. Units of measure in clinical information systems. J Am Med Inform Assoc. 1999 Mar-Apr;6(2):151-62.
  • Clark DO, Kroenke K, Callahan CM, McDonald CJ. Validity and utility of patient-reported health measures on hospital admission. J Clin Epidemiol. 1999 Jan;52(1):65-71.
  • 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.
  • 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.