Jonathan Nebeker, M.D., M.S.

Research Interests

  • Adverse Drug Reaction Reporting Systems
  • Pharmacoepidemiology
  • Health Services Research
  • Drug Therapy, Computer-Assisted
  • Computerized Medical Decision Making

Languages

  • English
  • French

Academic Information

  • Departments: Internal Medicine - Professor
  • Divisions: Geriatrics

Board Certification

  • American Board of Internal Medicine (Internal Medicine)
  • American Board of Internal Medicine (Sub: Geriatric Medicine)
  • American Board of Preventive Medicine (Clinical Informatics)

Academic Office Information

  • (801) 582-1565 Ext 2458
  • VA - Building #2
    Research
    500 S Foothill Dr, Room: 1A47
    Salt Lake City, UT 84148

Academic Bio

Dr. Nebeker is a geriatrician, epidemiologist, and informatician at the Department of Veterans Affairs and University of Utah. His research has two main foci: adverse drug events (ADEs) and cognitive support for electronic health record (EHR) systems. He leads national programs for analytics infrastructure and EHR modernization.
His early interests involved the epidemiology of ADEs and development and evaluation of surveillance rules for ADE prevention and detection. One of his more controversial findings was that ADE rates were high in a setting of electronic prescribing and numerous safeguards ostensibly designed to prevent ADEs. The implication is that many of these safeguards have low value for preventing ADEs and that safeguards need to be focused on dose- dependent ADEs, which are most common. Subsequently, he developed electronic surveillance rules for ADEs in the VA and community Medicaid settings. These rules are based on epidemiological principles and are designed to be more sensitive and specific than previously published rules.
Dr. Nebeker is currently interested in translating theoretical frameworks from social and cognitive psychology to medicine for designing and evaluating user interfaces for EHRs. He led an AHRQ grant to translate the Contextual Control Model from a branch of Cognitive Systems Engineering. Guided by this translated model, his team developed a new paradigm for graphical user interfaces (GUIs) for EHRs. Instead of focusing on data, which is typical of current EHRs, the GUI focuses on thought- and workflow. The GUIs incorporate ideas from mindset, dual process, and communication theories. They featured information displays that are designed to reduce cognitive effort to understand what is going on with the patient. In a randomized controlled trial versus a widely used traditional interface, the new interfaces were significantly faster—despite minimal training in the unfamiliar interfaces.
Dr. Nebeker also has national leadership roles in VA. He is Director of VA Informatics and Computing Infrastructure (VINCI.) VINCI is a research & development program offering secure, powerful, virtualized computing environment with national clinical data back to 2000. Researchers and engineers at this center develop and deploy tools for advanced analysis including pipelines for transparent, reproducible analysis, data visualization, and natural language processing. He is also national Associate Chief Medical Informatics Officer and lead clinician for VA’s EHR modernization program called VistA Evolution.

Short General
Dr. Nebeker is a geriatrician, researcher, and manager at the Department of Veterans Affairs and University of Utah. At VA, he is national Associate Chief Medical Informatics Officer and the clinical lead for the VistA Evolution Program, which is developing VA’s next-generation EHR. In this role, he focuses on designing a user experience that promotes patient-centric, team-based, quality-driven healthcare. In the recent past he was the VA lead for the joint DoD-VA user experience. He also directs the VA Informatics and Computing Infrastructure (VINCI), which develops and hosts cloud-based tools for advanced analysis and research including for data visualization and natural language processing. His research has focused on the epidemiology of adverse drug events and EHR functional design. He has found that many computerized interventions to prevent adverse drug events still permit high rates of drug-related harm. For EHR design, he has translated theoretical frameworks from cognitive and social psychology to medical informatics. In randomized controlled trials, users of his interfaces have completed their work faster with more accurate assessments of patient status compared to traditional tab-based EHRs interfaces.

Education History

Type School Degree
Fellowship University of Utah School of Medicine
Geriatrics
Fellow
Residency Beth Israel Deaconess Medical Center
Internal Medicine
Resident
Internship New England Deaconess Hospital
Internal Medicine
Intern
Professional Medical University of Pennsylvania
Medicine
M.D.
Graduate Training University of Pennsylvania
Education
M.S.
Undergraduate Harvard University
History and Science
A.B.

Selected Publications

Journal Article

  1. Support for contextual control in primary care: a qualitative analysis.Weir C, Drews FA, Butler J, Barrus RJ, Jones ML, Nebeker JR (2013). Support for contextual control in primary care: a qualitative analysis. AMIA Annu Symp Proc, 2013, 1463-71.
  2. Comparing adherence to two different HIV antiretroviral regimens: an instrumental variable analysis.Nelson RE, Nebeker JR, Hayden C, Reimer L, Kone K, LaFleur J (2013). Comparing adherence to two different HIV antiretroviral regimens: an instrumental variable analysis. AIDS Behav, 17(1), 160-7.
  3. Nelson RE, Nebeker JR, Hayden C, Reimer L, Kone K, LaFleur J (2013). Comparing adherence to two different HIV antiretroviral regimens: an instrumental variable analysis. AIDS Behav, 17(1), 160-7.
  4. The orderly and effective visit: impact of the electronic health record on modes of cognitive control.Weir C, Drews FA, Leecaster MK, Barrus RJ, Hellewell JL, Nebeker JR (2012). The orderly and effective visit: impact of the electronic health record on modes of cognitive control. AMIA Annu Symp Proc, 2012, 979-87.
  5. Synonym, topic model and predicate-based query expansion for retrieving clinical documents.Zeng QT, Redd D, Rindflesch T, Nebeker J (2012). Synonym, topic model and predicate-based query expansion for retrieving clinical documents. AMIA Annu Symp Proc, 2012, 1050-9.
  6. Mergenhagen KA, Blum SS, Kugler A, Livote EE, Nebeker JR, Ott MC, Signor D, Sung S, Yeh J, Boockvar K (2012). Pharmacist- versus physician-initiated admission medication reconciliation: impact on adverse drug events. Am J Geriatr Pharmacother, 10(4), 242-50.
  7. Factors associated with screening or treatment initiation among male United States veterans at risk for osteoporosis fracture.Nelson RE, Nebeker JR, Sauer BC, LaFleur J (2012). Factors associated with screening or treatment initiation among male United States veterans at risk for osteoporosis fracture. Bone, 50(4), 983-8.
  8. Validated risk rule using computerized data to identify males at high risk for fracture.LaFleur J, Nelson RE, Yao Y, Adler RA, Nebeker JR (2012). Validated risk rule using computerized data to identify males at high risk for fracture. Osteoporos Int, 23(3), 1017-27.
  9. LaFleur J, Nelson RE, Yao Y, Adler RA, Nebeker JR (2011). Validated risk rule using computerized data to identify males at high risk for fracture. Osteoporos Int.
  10. Qing T Zeng, Doug Redd, Guy Divita, SamahJarad, Cynthia Brandt, Jonathan R Nebeker (12/26/2011). Characterizing Clinical Text and Sublanguage: A Case Study of the VA Clinical Notes. J Health Med Informat.
  11. The perception of medical professionals and medical students on the usefulness of an emergency medical card and a continuity of care report in enhancing continuity of care.Olola CH, Narus S, Nebeker J, Poynton M, Hales J, Rowan B, LeSieur H, Zumbrennen C, Edwards AA, Crawford R, Amundsen S, Kabir Y, Atkin J, Newberry C, Young J, Hanifi T, Risenmay B, Sorensen T, Evans RS (2011). The perception of medical professionals and medical students on the usefulness of an emergency medical card and a continuity of care report in enhancing continuity of care. Int J Med Inform, 80(6), 412-20.
  12. Cognitive analysis of a medication reconciliation tool: applying laboratory and naturalistic approaches to system evaluation.Kushniruk AW, Santos SL, Pourakis G, Nebeker JR, Boockvar KS (2011). Cognitive analysis of a medication reconciliation tool: applying laboratory and naturalistic approaches to system evaluation. Stud Health Technol Inform, 164, 203-7.
  13. Applying Trigger Tools to Detect Adverse Events Associated With Outpatient Surgery.Rosen AK, Mull HJ, Kaafarani H, Nebeker J, Shimada S, Helwig A, Nordberg B, Long B, Savitz LA, Shanahan CW, Itani K (2011). Applying Trigger Tools to Detect Adverse Events Associated With Outpatient Surgery. J Patient Saf, 7(1), 45-59.
  14. Medication reconciliation: Barriers and facilitators from the perspectives of resident physicians and pharmacists.Boockvar KS, Santos SL, Kushniruk A, Johnson C, Nebeker JR (2011). Medication reconciliation: Barriers and facilitators from the perspectives of resident physicians and pharmacists. J Hosp Med, 6(6), 329-37.
  15. Effect of admission medication reconciliation on adverse drug events from admission medication changes.Boockvar KS, Blum S, Kugler A, Livote E, Mergenhagen KA, Nebeker JR, Signor D, Sung S, Yeh J (2011). Effect of admission medication reconciliation on adverse drug events from admission medication changes. Arch Intern Med, 171(9), 860-1.
  16. Overestimation of the effects of adherence on outcomes: a case study in healthy user bias and hypertension.LaFleur J, Nelson RE, Sauer BC, Nebeker JR (2011). Overestimation of the effects of adherence on outcomes: a case study in healthy user bias and hypertension. Heart, 97(22), 1862-9.
  17. Consensus building for development of outpatient adverse drug event triggers.Mull HJ, Nebeker JR, Shimada SL, Kaafarani HM, Rivard PE, Rosen AK (2011). Consensus building for development of outpatient adverse drug event triggers. J Patient Saf, 7(2), 66-71.
  18. Clinical risk factors for fracture among postmenopausal patients at risk for fracture: a historical cohort study using electronic medical record data.LaFleur J, McAdam-Marx C, Alder SS, Sheng X, Asche CV, Nebeker J, Brixner DI, Silverman SL (2011). Clinical risk factors for fracture among postmenopausal patients at risk for fracture: a historical cohort study using electronic medical record data. J Bone Miner Metab, 29(2), 193-200.
  19. A simulation-based evaluation of methods to estimate the impact of an adverse event on hospital length of stay.Samore MH, Shen S, Greene T, Stoddard G, Sauer B, Shinogle J, Nebeker J, Harbarth S (2007). A simulation-based evaluation of methods to estimate the impact of an adverse event on hospital length of stay. Med Care, 45(10 Supl 2), S108-15.
  20. Critical issues in an electronic documentation system.Weir CR, Nebeker JR (2007). Critical issues in an electronic documentation system. AMIA Annu Symp Proc, 786-90.
  21. Out-of-pocket pharmacy expenditures for veterans under medicare part D.Rupper RW, Bair BD, Sauer BC, Nebeker JR, Shinogle J, Samore M (2007). Out-of-pocket pharmacy expenditures for veterans under medicare part D. Med Care, 45(10 Supl 2), S77-80.
  22. Developing indicators of inpatient adverse drug events through nonlinear analysis using administrative data.Nebeker JR, Yarnold PR, Soltysik RC, Sauer BC, Sims SA, Samore MH, Rupper RW, Swanson KM, Savitz LA, Shinogle J, Xu W (2007). Developing indicators of inpatient adverse drug events through nonlinear analysis using administrative data. Med Care, 45(10 Supl 2), S81-8.
  23. A cognitive task analysis of information management strategies in a computerized provider order entry environment.Weir CR, Nebeker JJ, Hicken BL, Campo R, Drews F, Lebar B (2007). A cognitive task analysis of information management strategies in a computerized provider order entry environment. J Am Med Inform Assoc, 14(1), 65-75.
  24. Xu W, Pickard S, Silver MP, Hougland P, Mashter C, Donnely S, Nebeker J, Samore M, Williams SD (2006). Patient Safety Events in Utah, 2001. Utah's Health: An Annual Review.
  25. Hypersensitivity cases associated with drug-eluting coronary stents: a review of available cases from the Research on Adverse Drug Events and Reports (RADAR) project.Nebeker JR, Virmani R, Bennett CL, Hoffman JM, Samore MH, Alvarez J, Davidson CJ, McKoy JM, Raisch DW, Whisenant BK, Yarnold PR, Belknap SM, West DP, Gage JE, Morse RE, Gligoric G, Davidson L, Feldman MD (2006). Hypersensitivity cases associated with drug-eluting coronary stents: a review of available cases from the Research on Adverse Drug Events and Reports (RADAR) project. J Am Coll Cardiol, 47(1), 175-81.
  26. Crossing the quality chasm: the role of information technology departments.Weir CR, Hicken BL, Rappaport HS, Nebeker JR (2006). Crossing the quality chasm: the role of information technology departments. Am J Med Qual, 21(6), 382-93.
  27. Risk factors for adverse drug events: a 10-year analysis.Evans RS, Lloyd JF, Stoddard GJ, Nebeker JR, Samore MH (2005). Risk factors for adverse drug events: a 10-year analysis. Ann Pharmacother, 39(7-8), 1161-8.
  28. High rates of adverse drug events in a highly computerized hospital.Nebeker JR, Hoffman JM, Weir CR, Bennett CL, Hurdle JF (2005). High rates of adverse drug events in a highly computerized hospital. Arch Intern Med, 165(10), 1111-6.
  29. Nurse's role in tracking adverse drug events: the impact of provider order entry.Weir C, Hoffman J, Nebeker JR, Hurdle JF (2005). Nurse's role in tracking adverse drug events: the impact of provider order entry. Nurs Adm Q, 29(1), 39-44.
  30. The Research on Adverse Drug Events and Reports (RADAR) project.Bennett CL, Nebeker JR, Lyons EA, Samore MH, Feldman MD, McKoy JM, Carson KR, Belknap SM, Trifilio SM, Schumock GT, Yarnold PR, Davidson CJ, Evens AM, Kuzel TM, Parada JP, Cournoyer D, West DP, Sartor O, Tallman MS, Raisch DW (2005). The Research on Adverse Drug Events and Reports (RADAR) project. JAMA, 293(17), 2131-40.
  31. Clarifying adverse drug events: a clinician's guide to terminology, documentation, and reporting.Nebeker JR, Barach P, Samore MH (2004). Clarifying adverse drug events: a clinician's guide to terminology, documentation, and reporting. Ann Intern Med, 140(10), 795-801.
  32. Direct text entry in electronic progress notes. An evaluation of input errors.Weir CR, Hurdle JF, Felgar MA, Hoffman JM, Roth B, Nebeker JR (2003). Direct text entry in electronic progress notes. An evaluation of input errors. Methods Inf Med, 42(1), 61-7.
  33. Critical gaps in the world's largest electronic medical record: Ad Hoc nursing narratives and invisible adverse drug events.Hurdle JF, Weir CR, Roth B, Hoffman J, Nebeker JR (2003). Critical gaps in the world's largest electronic medical record: Ad Hoc nursing narratives and invisible adverse drug events. AMIA Annu Symp Proc, 309-12.
  34. Nebeker JR, Hurdle JF, Hoffman JM, Roth B, Weir CR, Samroe MH (2002). Developing a taxonomy for research in adverse drug events: potholes and signposts. J Am Med Inform Assoc, 9(6 Suppl), S80-5.
  35. Developing a taxonomy for research in adverse drug events: potholes and signposts.Nebeker JR, Hurdle JF, Hoffman J, Roth B, Weir CR, Samore MH (2001). Developing a taxonomy for research in adverse drug events: potholes and signposts. Proc AMIA Symp, 493-7.
  36. Gundlapalli AV, Redd D, Gibson B, Carter M, Korhonen C, Nebeker J, Samore M, Zeng-Treiltler Q (In Press). Exploring the Value of Free Text Queries for Patient Cohort Identification Using Electronic Medical Records. BMC Health Serv Res.

Conference Proceedings

  1. Sauer BC, Nebeker JR, Shen S, Rupper R, Samore M (2014). Identification of possible adverse drug reactions using population-based administrative data. In Faculty of Pharmaceutical Sciences, Ubon Ratchathani University, Thailand (Eds.), Patient Safety Annu Symp, Ubon, Thailand: ISBN 978-974-523-265-5 (Thailand), Proc. 2011, 60-66.
  2. Redd D, Rindflesch T, Nebeker J, Zeng-Treitler Q (2013). Improve Retrieval Performance on Clinical Notes: A Comparison of Four Methods. The 46th Hawaii International International Conference onSystems Science (HICSS- 46 2013), 2389 - 2397.
  3. Sauer BC, Shen S, Nebeker J, Rupper R, Samore M (2011). Identification of Possible Adverse Drug Reactions using Population-based Administrative Data. Patient Safety Annu Symp Proc, Detroit, 1(1), 60-66.
  4. DuVall SL, South BR, DAvolio LW, Shen S, Boone KW, Gundlapalli AV, Nebeker JR, Samore MH (2011). Creating Reusable Annotated Corpora Using the Clinical Document Architecture. Hawaii International Conference on System Sciences (HICSS), Koloa, HI: IEEE Society.
  5. Weir CR, Nebeker JR (2007). Critical Issues in an Electronic Documentation System. Homer Warner Award for Best Paper at Fall AMIA 2007. AMIA Proceedings, Washington, DC.
  6. Nebeker JR, Hurdle JF, Hoffman J, Roth B, Weir CR, Samore M (2001). Developing a taxonomy for research in adverse drug events: potholes and signposts. Proceedings of the American Medical Informatics Association Annual Fall Symposium, 493-7.

Case Report

  1. Zeng QT, Redd D, Divita G, Jarad S, Brandt C, Nebeker JR (2011). Characterizing Clinical Text and Sublanguage: A Case Study of the VA Clinical Notes. J Health Med Informat, S3, 1-9.

Report

  1. Sauer BC, Shinogle JA, Xu W, Samore M, Nebeker J, Liu Z, Rupper R, Lux L, Amoozegar J, Lohr KN (August 2008). Improving Patient Safety and Pharmacovigilance: Methods Using Observational Data and Cohort Studies (Number 6). Agency for Healthcare Research and Quality.
  2. Sauer B, Shinogle JA, Xu W, Samore M, Nebeker J, Rupper R, Lux L, Amoozegar J, Lohr K (2006). Medicare Prescription Drug Data Development: Methods for Improving Patient Safety and Pharmacovigilance Using Observational Data, RTI International DEcIDE Center (HHSA29020050036I). Agency for Healthcare Research and Quality.
  3. Weir C, Nebeker J, Hicken B (2005). Evaluation of Care Management Software. VA National Office of Chief Information Office Internal Report.

Poster

  1. Sauer BC, Porucznik C, Teng CC, Pickard SG, Johnson E, Nebeker J (4/2013). Evaluating the Impact of the Utah Clinical Guidelines on Prescribing Opioids for Treatment of Pain on Opioid Prescribing in Utah, 2002–2009. Poster session presented at American Academy of Pain Medicine's 29th Annual Meeting, Fort Lauderdale.
  2. Zeng QT, Divita G, DuVall SL, Samore MH, Nebeker JR (2012). V3NLP: Open Source NLP for Big Data. Poster session presented at National Library of Medicine (NLM) and National Institute of Biomedical Imaging and Bioengineering (NIBIB) workshop on Natural Language Processing: State of the Art, Future Directions and Applications for Enhancing Clinical Decision-Making, Bethesda, MD.
  3. DuVall SL, Patterson OV, Ginter T, Cornia R, Nebeker JR (2012). FLAP: Flying Towards Real-time Decision Support. National Library of Medicine (NLM) and National Institute of Biomedical Imaging and Bioengineering (NIBIB). Poster session presented at National Library of Medicine (NLM) and National Institute of Biomedical Imaging and Bioengineering (NIBIB) workshop on Natural Language Processing: State of the Art, Future Directions and Applications for Enhancing Clinical Decision-Making, Bethesda, MD.
  4. Forbush TB, Adams B, Shen S, South BR, Nebeker JR, DuVall SL (2012). CASPR: Friendly Annotation Management. Poster session presented at American Medical Informatics Association (AMIA) Annual Symposium, Chicago, IL.
  5. LaFleur J, Ginter T, Hayden C, DuVall SL, Adler R, Nebeker JR (2011). Bone Mineral Density Screening and Osteoporosis Rates in Veterans. Poster session presented at The American Society for Bone and Mineral Research (ASBMR) Annual Meeting, San Diego, CA.
  6. LaFleur J, Nelson RE, Hayden C, Reimer L, Kone K, Nebeker J (2011). Anaheim, California. Poster session presented at VA HSR&D National Meeting, Washington DC.
  7. LaFleur J, Nelson RE, Hayden C, Nebeker J (2010). Poor adherence to HIV antiretroviral drug regimens in veterans. Poster session presented at American Society of Health-System Pharmacists Midyear Clinical Meeting, Anaheim, California.
  8. Weir, C, Drews, F, Leecaster, M, Mallin, B, Barrus, R, amp Nebeker, J (June 2010). Usage patterns of an electronic health record and modes of cognitive control. Poster session presented at AHRQ Annual Health IT Grantee and Contractor Meeting, Washington, DC.
  9. Nebeker, J, Weir, C, Drews, F, Hellewell, J, Jones, M, amp Underwood, A (June 2010). Translating Contextual Control Model to use of health information technology. Poster session presented at AHRQ Annual Health IT Grantee and Contractor Meeting, Washington, DC.
  10. Drews, F, Weir, C, Nebeker, J, Hollnagel, E, Mallin, B, amp Barrus, R (June 2010). A theoretical perspective to develop a medication management system. Poster session presented at AHRQ Annual Health IT Grantee and Contractor Meeting, Washington, DC.
  11. Weir C, Nebeker J, Pepper G, Hoffman J, Drews F, Kinney, A, Buffum, M (2009). Identifying and understanding the barriers to effective collaboration in medication management. Poster session presented at Human-Computer Interaction International Annual Conference, San Diego, CA.
  12. Weir C, Nebeker J, Pepper G, Hoffman J, Drews F, Kinney A, Buffum M (2009). Stereotypes and scripts: Identifying and understanding the barriers to effective collaboration in medication management in the VA. Poster session presented at VA HSR&D National Meeting, Baltimore, MD.
  13. Nelson RE, LaFleur J, Pickard S, Nebeker J (2009). Predictors of bisphosphonate treatment in male United States veterans. Poster session presented at 2009 Western Pharmacoeconomics Conference, Pasadena, California.
  14. LaFleur J, Nelson R, Sauer B, Sheng X, Pickard S, Ong SH, Brixner D, Nebeker J (11/2009). Any-cause hospitalization outcomes associated with poor patient adherence to antihypertensives.
  15. LaFleur J, Nelson R, Pickard SG, Nebeker JR (2008). Recognition of male osteoporosis is low. Poster session presented at American Society for Bone Mineral Research 30th Annual Meeting, Montreal, Quebec, Canada.
  16. Tuteja, Ashok, Tolman, Keith, Talley, Nicholas, Samore, Matthew (2008). Post-Infectious Dyspepsia among Persian Gulf War Veterans. Luzerne, Switzerland.
  17. Sauer BC, Kapoor D, Nebeker J, Beddhu S, Samore MH (2006). Factors Associates with Serum Potassium Monitoring in Veterans using Renin-Angiotensin-Aldosterone inhibitors. Poster session presented at 24th HSR&D National Meeting, Crystal City, Arlington, VA.