Jonathan Nebeker

Jonathan Nebeker, MD, MS

Languages spoken: French, English

Academic Information

Departments Primary - Internal Medicine

Divisions: Geriatrics

Dr. Nebeker is Chief Medical Informatics Officer (CMIO) at Veterans Health Administration (VHA) central office and Professor of Medicine at the University of Utah. His degrees and training took place at Harvard and the University of Pennsylvania. He practices geriatrics at the Salt Lake City VA Medical Center.

He has been the clinical and/or informatics lead of all EHR-related and health IT modernization programs at VA from 2014 through present. He works with other federal agencies and industry associations on standards and best practices to help VHA participate in markets of health IT and content.

His research has three areas of focus: adverse drug events, human interface design, and analytical systems/advanced process analysis. His work concerning the characterization, epidemiology, and prevention of adverse drug events is widely cited. Much of this work concerns how EHRs help or don’t help prevent these events. From 2005 through 2015, he focused on translating basic science of cognitive and social psychology to medical informatics and EHR design. Randomized controlled trials of his novel user-interface designs have demonstrated increased accuracy of and decreased time to diagnosis of medical conditions. He incorporates these lessons into the design of VA’s EHR systems. In 2008, he established the scientific computing infrastructure for Veterans Health Administration. His research now focuses on machine learning and artificial intelligence for human and electronic process control in support of a highly reliable, learning health system.

Research Statement

Dr. Nebeker directs active research projects on translating theory from the cognitive and social sciences to guide the design of software for clinicians, for real-time surveillance of safe operation and safe use of EHR systems, and for design of information systems for real-time analytics.

Education History

Undergraduate Harvard University
 AB
Graduate Training University of Pennsylvania
 MS
Professional Medical University of Pennsylvania
 MD
Internship New England Deaconess Hospital
 Intern
Residency Beth Israel Deaconess Medical Center
 Resident
Fellowship University of Utah School of Medicine
 Fellow

Selected Publications

Journal Article

  1. 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. (Read full article)
  2. 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. (Read full article)
  3. Bennett CL, Nebeker JR, Yarnold PR, Tigue CC, Dorr DA, McKoy JM, Edwards BJ, Hurdle JF, West DP, Lau DT, Angelotta C, Weitzman SA, Belknap SM, Djulbegovic B, Tallman MS, Kuzel TM, Benson AB, Evens A, Trifilio SM, Courtney DM, Raisch DW (2007). Evaluation of serious adverse drug reactions: a proactive pharmacovigilance program (RADAR) vs safety activities conducted by the Food and Drug Administration and pharmaceutical manufacturers. Arch Intern Med, 167(10), 1041-9. (Read full article)
  4. 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. (Read full article)
  5. Harris CP, Alderson K, Nebeker J, Holds JB, Anderson RL (1991). Histologic features of human orbicularis oculi treated with botulinum A toxin. Arch Ophthalmol, 109(10), 393-5.
  6. Harris CP, Alderson K, Nebeker J, Holds JB, Anderson RL (1991). Histologic features of human orbicularis oculi treated with botulinum A toxin. Arch Ophthalmol, 109(3), 393-5. (Read full article)
  7. Burningham Z, He T, Teng CC, Zhou X, Nebeker J, Sauer BC (2017). Evaluation of the Case-Crossover (CCO) Study Design for Adverse Drug Event Detection. Drug Saf, 40(9), 789-798. (Read full article)
  8. 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. (Read full article)
  9. 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. (Read full article)
  10. LaFleur J, Steenhoek CL, Horne J, Meier J, Nebeker JR, Mambourg S, Swislocki A, Carmichael J (2015). Comparing fracture absolute risk assessment (FARA) tools: an osteoporosis clinical informatics tool to improve identification and care of men at high risk of first fracture. Ann Pharmacother, 49(5), 506-14. (Read full article)
  11. 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. (Read full article)
  12. 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.
  13. 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. (Read full article)
  14. Gundlapalli AV, Redd D, Gibson BS, Carter M, Korhonen C, Nebeker J, Samore MH, Zeng-Treitler Q (2015). Maximizing clinical cohort size using free text queries. Comput Biol Med, 60, 1-7. (Read full article)
  15. 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. (Read full article)
  16. Ladewski LA, Belknap SM, Nebeker JR, Sartor O, Lyons EA, Kuzel TC, Tallman MS, Raisch DW, Auerbach AR, Schumock GT, Kwaan HC, Bennett CL (2003). Dissemination of information on potentially fatal adverse drug reactions for cancer drugs from 2000 to 2002: first results from the research on adverse drug events and reports project. J Clin Oncol, 21(20), 3859-66. (Read full article)
  17. Richey EA, Lyons EA, Nebeker JR, Shankaran V, McKoy JM, Luu TH, Nonzee N, Trifilio S, Sartor O, Benson AB 3rd, Carson KR, Edwards BJ, Gilchrist-Scott D, Kuzel TM, Raisch DW, Tallman MS, West DP, Hirschfeld S, Grillo-Lopez AJ, Bennett CL (2009). Accelerated approval of cancer drugs: improved access to therapeutic breakthroughs or early release of unsafe and ineffective drugs? J Clin Oncol, 27(26), 4398-405. (Read full article)
  18. Legler A, Price M, Parikh M, Nebeker JR, Ward MC, Wedemeyer L, Pizer SD (2019). Effect on VA Patient Satisfaction of Provider's Use of an Integrated Viewer of Multiple Electronic Health Records. J Gen Intern Med, 34(1), 132-136. (Read full article)
  19. 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. (Read full article)
  20. 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. (Read full article)
  21. 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. (Read full article)
  22. 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. (Read full article)
  23. 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. (Read full article)
  24. Olola CH, Rowan B, Narus S, Smith M, Hastings T, Poynton M, Nebeker J, Hales J, Evans RS (2009). Implementation of an emergency medical card and a continuity of care report using continuity of care standard. Methods Inf Med, 48(6), 519-30. (Read full article)
  25. 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. (Read full article)
  26. Nebeker JR, Hurdle JF, Bair B (2003). Future history: medical informatics in geriatrics. The journals of gerontology. Series A, Biological sciences and medical sciences, 58(9), M820-5. (Read full article)
  27. Phansalkar S, Hoffman JM, Nebeker JR, Hurdle J (2007). Pharmacists versus nonpharmacists in adverse drug event detection: a meta-analysis and systematic review. American journal of health-system pharmacy, 64(8), 842-9. (Read full article)
  28. Olola CH, Narus S, Poynton M, Nebeker J, Hales J, Rowan B, Smith M, Evans R (2011). Patient-perceived usefulness of an emergency medical card and a continuity-of-care report in enhancing the quality of care. International journal for quality in health care, 23(1), 60-7. (Read full article)
  29. Weir CR, Nebeker JJ, Hicken BL, Campo R, Drews F, Lebar (2007). A cognitive task analysis of information management strategies in a computerized provider order entry environment. Journal of the American Medical Informatics Association, 14(1), 65-75. (Read full article)
  30. Ohno-Machado L, Agha Z, Bell DS, Dahm L, Day ME, Doctor JN, Gabriel D, Kahlon MK, Kim KK, Hogarth M, Matheny ME, Meeker D, Nebeker JR, pSCANNER team (2014). pSCANNER: patient-centered Scalable National Network for Effectiveness Research. Journal of the American Medical Informatics Association, 21(4), 621-6. (Read full article)
  31. Boockvar KS, Ho W, Pruskowski J, DiPalo KE, Wong JJ, Patel J, Nebeker JR, Kaushal R, Hung (2017). Effect of health information exchange on recognition of medication discrepancies is interrupted when data charges are introduced: results of a cluster-randomized controlled trial. Journal of the American Medical Informatics Association, 24(6), 1095-1101. (Read full article)
  32. Nebeker JR, Hurdle JF, Hoffman JM, Roth B, Weir CR, Samroe M (2002). Developing a taxonomy for research in adverse drug events: potholes and signposts. Journal of the American Medical Informatics Association, 9(6 Suppl), S80-5.
  33. LaFleur J, Nelson RE, Sauer BC, Nebeker J (2011). Overestimation of the effects of adherence on outcomes: a case study in healthy user bias and hypertension. Heart (British Cardiac Society), 97(22), 1862-9. (Read full article)
  34. 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 R (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. International journal of medical informatics, 80(6), 412-20. (Read full article)
  35. Nelson RE, Nebeker JR, Hayden C, Reimer L, Kone K, LaFleur (2013). Comparing adherence to two different HIV antiretroviral regimens: an instrumental variable analysis. AIDS and behavior, 17(1), 160-7. (Read full article)
  36. Nelson RE, Nebeker JR, Hayden C, Reimer L, Kone K, LaFleur (2012). Comparing adherence to two different HIV antiretroviral regimens: an instrumental variable analysis. AIDS and behavior, 17(1), 160-7.
  37. 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. AMIA Symposium, 493-7. (Read full article)
  38. LaFleur J, McAdam-Marx C, Alder SS, Sheng X, Asche CV, Nebeker J, Brixner DI, Silverman S (2011). Clinical risk factors for fracture among postmenopausal patients at risk for fracture: a historical cohort study using electronic medical record data. Journal of bone and mineral metabolism, 29(2), 193-200. (Read full article)
  39. Kushniruk AW, Santos SL, Pourakis G, Nebeker JR, Boockvar K (2011). Cognitive analysis of a medication reconciliation tool: applying laboratory and naturalistic approaches to system evaluation. Studies in health technology and informatics, 164, 203-7. (Read full article)
  40. DuVall SL, Matheny ME, Ibragimov IR, Oats TD, Tucker JN, South BR, Turano A, Saoudian H, Kangas C, Hofmann K, Funk W, Nichols C, Bonnema A, Ferrucci L, Nebeker J (2019). A Tale of Two Databases: The DoD and VA Infrastructure for Clinical Intelligence (DaVINCI). Studies in health technology and informatics, 264, 1660-1661. (Read full article)
  41. Leecaster MK, Weir CR, Drews FA, Hellewell JL, Bolton D, Jones MM, Nebeker J (2017). Translation of Contextual Control Model to chronic disease management: A paradigm to guide design of cognitive support systems. Journal of biomedical informatics, 71S, S60-S67. (Read full article)
  42. Pfaff MS, Eris O, Weir C, Anganes A, Crotty T, Rahman M, Ward M, Nebeker JR (2020). Analysis of the cognitive demands of electronic health record use. Journal of biomedical informatics, 113,
  43. Pfaff MS, Eris O, Weir C, Anganes A, Crotty T, Rahman M, Ward M, Nebeker J (2021). Analysis of the cognitive demands of electronic health record use. Journal of biomedical informatics, 113, 103633. (Read full article)
  44. Boockvar KS, Liu S, Goldstein N, Nebeker J, Siu A, Fried (2009). Prescribing discrepancies likely to cause adverse drug events after patient transfer. Quality & safety in health care, 18(1), 32-6. (Read full article)
  45. Kaafarani HM, Rosen AK, Nebeker JR, Shimada S, Mull HJ, Rivard PE, Savitz L, Helwig A, Shin MH, Itani K (2010). Development of trigger tools for surveillance of adverse events in ambulatory surgery. Quality & safety in health care, 19(5), 425-9. (Read full article)
  46. Boockvar KS, Livote EE, Goldstein N, Nebeker JR, Siu A, Fried (2010). Electronic health records and adverse drug events after patient transfer. Quality & safety in health care, 19(5), e16. (Read full article)
  47. Hurdle JF, Weir CR, Roth B, Hoffman J, Nebeker J (2003). Critical gaps in the world's largest electronic medical record: Ad Hoc nursing narratives and invisible adverse drug events. AMIA ... Annual Symposium proceedings. AMIA Symposium, 309-12. (Read full article)
  48. Weir CR, Nebeker J (2007). Critical issues in an electronic documentation system. AMIA ... Annual Symposium proceedings. AMIA Symposium, 786-90. (Read full article)
  49. Mull HJ, Nebeker J (2008). Informatics tools for the development of action-oriented triggers for outpatient adverse drug events. AMIA ... Annual Symposium proceedings. AMIA Symposium, 505-9. (Read full article)
  50. Weir C, Drews FA, Leecaster MK, Barrus RJ, Hellewell JL, Nebeker J (2012). The orderly and effective visit: impact of the electronic health record on modes of cognitive control. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2012, 979-87. (Read full article)
  51. Zeng QT, Redd D, Rindflesch T, Nebeker (2012). Synonym, topic model and predicate-based query expansion for retrieving clinical documents. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2012, 1050-9. (Read full article)
  52. Weir C, Drews FA, Butler J, Barrus RJ, Jones ML, Nebeker J (2013). Support for contextual control in primary care: a qualitative analysis. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2013, 1463-71. (Read full article)
  53. Divita G, Zeng QT, Gundlapalli AV, Duvall S, Nebeker J, Samore M (2014). Sophia: A Expedient UMLS Concept Extraction Annotator. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2014, 467-76. (Read full article)
  54. Bouhaddou O, Davis M, Donahue M, Mallia A, Griffin S, Teal J, Nebeker (2016). Automated Detection of Privacy Sensitive Conditions in C-CDAs: Security Labeling Services at the Department of Veterans Affairs. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2016, 332-341. (Read full article)
  55. D'Amore J, Bouhaddou O, Mitchell S, Li C, Leftwich R, Turner T, Rahn M, Donahue M, Nebeker (2018). Interoperability Progress and Remaining Data Quality Barriers of Certified Health Information Technologies. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2018, 358-367. (Read full article)
  56. Donahue M, Bouhaddou O, Hsing N, Turner T, Crandall G, Nelson J, Nebeker (2018). Veterans Health Information Exchange: Successes and Challenges of Nationwide Interoperability. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2018, 385-394. (Read full article)
  57. Brown SH, Stevenson L, Territo DJ, Kilbourne J, Nebeker JR, Miller H, Lincoln M (2020). One-Way and Round-Trip Analysis Demonstrates Surprising Limitations of Standards-Based Terminology Maps. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2019, 258-266. (Read full article)
  58. Mergenhagen KA, Blum SS, Kugler A, Livote EE, Nebeker JR, Ott MC, Signor D, Sung S, Yeh J, Boockvar (2012). Pharmacist- versus physician-initiated admission medication reconciliation: impact on adverse drug events. The American journal of geriatric pharmacotherapy, 10(4), 242-50.
  59. 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. The American journal of geriatric pharmacotherapy, 10(4), 242-50. (Read full article)
  60. Boockvar KS, Santos SL, Kushniruk A, Johnson C, Nebeker J (2011). Medication reconciliation: barriers and facilitators from the perspectives of resident physicians and pharmacists. Journal of hospital medicine, 6(6), 329-37. (Read full article)
  61. Mull HJ, Nebeker JR, Shimada SL, Kaafarani HM, Rivard PE, Rosen A (2011). Consensus building for development of outpatient adverse drug event triggers. Journal of patient safety, 7(2), 66-71. (Read full article)
  62. Rosen AK, Mull HJ, Kaafarani H, Nebeker J, Shimada S, Helwig A, Nordberg B, Long B, Savitz LA, Shanahan CW, Itani (2011). Applying trigger tools to detect adverse events associated with outpatient surgery. Journal of patient safety, 7(1), 45-59. (Read full article)
  63. Moore C, Li J, Hung CC, Downs J, Nebeker J (2009). Predictive value of alert triggers for identification of developing adverse drug events. Journal of patient safety, 5(4), 223-8. (Read full article)
  64. Ozmen O, Klasky HB, Omitaomu OA, Olama M, Kuruganti T, Ward M, Scott JM, Laurio A, Drews F, Nebeker J (2020). Feature Engineering and Process Mining to Enable Hazard Detection in Health Information Technology. AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science, 2020, 469-476. (Read full article)
  65. Sauer B, Nebeker J, Shen S, Rupper R, West S, Shinogle JA, Xu W, Lohr KN, Samore (2014). Methodological framework to identify possible adverse drug reactions using population-based administrative data. F1000Research, 3, 258. (Read full article)
  66. Sauer B, Nebeker JR, Shen S, West S, Shinogle JA , Xu W , Rupper R, Lohr KN, Samore (2014). Methodological framework to identify possible adverse drug reactions using population-based administrative data. F1000Research, 3(258),
  67. Olufemi A. Omitaomu, Ozgur Ozmen, Mohammed M. Olama, Laura L. Pullum, Teja Kuruganti, James Nutaro, Hilda B. Klasky, Helia Zandi, Aneel Advani, Angela L. Laurio, Merry Ward, Jeanie Scott, Jonathan R. Nebeke (2019). Real-Time Automated Hazard Detection Framework for Health Information Technology Systems, Health Systems. Health systems (Basingstoke, England),
  68. Olufemi A Omitaomu, Ozgur Ozmen, Mohammed M Olama, Laura L Pullum, Teja Kuruganti, James Nutaro, Hilda B Klasky, Helia Zandi, Aneel Advani, Angela L Laurio, Merry Ward, Jeanie Scott, Jonathan R Nebeke (2019). Real-Time Automated Hazard Detection Framework for Health Information Technology Systems. Health systems (Basingstoke, England), 1-13.
  69. Omitaomu OA, Ozmen O, Olama MM, Pullum LL, Kuruganti T, Nutaro J, Klasky HB, Zandi H, Advani A, Laurio AL, Ward M, Scott J, Nebeker J (2019). Real-Time Automated Hazard Detection Framework for Health Information Technology Systems. Health systems (Basingstoke, England), 8(3), 190-202. (Read full article)
  70. Mull HJ, Rosen AK, Shimada SL, Rivard PE, Nordberg B, Long B, Hoffman JM, Leecaster M, Savitz LA, Shanahan CW, Helwig A, Nebeker J (2015). Assessing the potential adoption and usefulness of concurrent, action-oriented, electronic adverse drug event triggers designed for the outpatient setting. EGEMS (Washington, DC), 3(1), 1116. (Read full article)
  71. Qing T. Zeng, Doug Redd, Guy Divita, SamahJarad, Cynthia Brandt, Jonathan R. Nebeke (2011). Characterizing Clinical Text and Sublanguage: A Case Study of the VA Clinical Notes. Journal of health & medical informatics,
  72. Butler JM, Gibson B, Lewis L, Reiber G, Kramer H, Rupper R, Herout J, Long B, Massaro D, Nebeker (2020). Patient-centered care and the electronic health record: exploring functionality and gaps. JAMIA open, 3(3), 360-368. (Read full article)
  73. Xu W, Pickard S, Silver MP, Hougland P, Mashter C, Donnely S, Nebeker J, Samore M, Williams S (2006). Patient Safety Events in Utah, 2001.
  74. Feyman Y, Figueroa SM, Yuan Y, Price ME, Kabdiyeva A, Nebeker JR, Ward MC, Shafer PR, Pizer SD, Strombotne K (2023). Effect of mental health staffing inputs on suicide-related events. Health services research, 58(2), 375-382. (Read full article)
  75. Falls Z, Brown SH, Shah N, LeHouillier F, Badwal R, Hall K, Franklin G, Kelly WH, Holdaway A, Montella D, Wedemeyer L, Keni S, Rose E, Nebeker JR, Elkin P (2022). CDS-Compare: A Web Application for Machine Learning Assisted Curation of Clinical Order Sets. Studies in health technology and informatics, 294, 465-469. (Read full article)
  76. Yuan Y, Price M, Schmidt DF, Ward M, Nebeker J, Pizer (2022). Integrated Health Record Viewers and Reduction in Duplicate Medical Imaging: Retrospective Observational Analysis. JMIR medical informatics, 10(5), e32168. (Read full article)
  77. Niu H, Omitaomu OA, Langston MA, Olama M, Ozmen O, Klasky HB, Laurio A, Sauer B, Ward M, Nebeker (2022). Detecting anomalous sequences in electronic health records using higher-order tensor networks. Journal of biomedical informatics, 135, 104219. (Read full article)
  78. Omitaomu OA, Klasky HB, Olama M, Ozmen O, Pullum L, Malviya Thakur A, Kuruganti T, Scott JM, Laurio A, Drews F, Sauer BC, Ward M, Nebeker J (2021). A new methodological framework for hazard detection models in health information technology systems. Journal of biomedical informatics, 124, 103937. (Read full article)
  79. Shafer PR, Yuan Y, Feyman Y, Price ME, Kabdiyeva A, Figueroa SM, Shen YJ, Nebeker JR, Ward MC, Strombotne KL, Pizer S (2024). Effect of mental health staffing inputs on initiation of care among recently separated Veterans. Health services research, (Read full article)
  80. Rush E, Ozmen O, Kim M, Ortegon ER, Jones M, Park BH, Pizer S, Trafton J, Brenner LA, Ward M, Nebeker J (2024). A framework for inferring and analyzing pharmacotherapy treatment patterns. BMC medical informatics and decision making, 24(1), 68. (Read full article)
  81. Resendez S, Brown SH, Ruiz Ayala HS, Rangan P, Nebeker J, Montella D, Elkin P (2024). Defining the Subtypes of Long COVID and Risk Factors for Prolonged Disease: Population-Based Case-Crossover Study. JMIR public health and surveillance, 10, e49841. (Read full article)
  82. Niu H, Omitaomu OA, Langston MA, Olama M, Ozmen O, Klasky HB, Laurio A, Ward M, Nebeker (2024). EHR-BERT: A BERT-based model for effective anomaly detection in electronic health records. Journal of biomedical informatics, 150, 104605. (Read full article)
  83. Ozmen O, Rush E, Park BH, Jones M, Trafton J, Brenner L, Rupper RW, Ward M, Nebeker JR, Pizer S (2025). Combining Machine Learning and Comparative Effectiveness Methodology to Study Primary Care Pharmacotherapy Pathways for Veterans With Depression. Medical care, 63(6), 422-429. (Read full article)
  84. Resnick M, Elkin A, Tiosano S, Koppel R, Franklin G, Piracha MU, Taylor K, Tung K, Brown S, Nebeker J, Elkin (2025). The Semantic Clinical Artificial Intelligence (SCAI) Chatbot: Preliminary Usability Testing. Studies in health technology and informatics, 326, 22-26. (Read full article)
  85. Elkin PL, Mehta G, LeHouillier F, Koppel R, Elkin AN, Nebeker J, Brown S (2025). Retrieval Augmented Generation: What Works and Lessons Learned. Studies in health technology and informatics, 326, 2-6. (Read full article)
  86. Niu H, Omitaomu OA, Langston MA, Grady SK, Olama M, Ozmen O, Klasky HB, Laurio A, Ward M, Nebeker (2025). Anomaly Detection in Electronic Health Records Across Hospital Networks: Integrating Machine Learning With Graph Algorithms. IEEE journal of biomedical and health informatics, 29(5), 3723-3735. (Read full article)
  87. Elkin PL, Mehta G, LeHouillier F, Resnick M, Mullin S, Tomlin C, Resendez S, Liu J, Nebeker JR, Brown S (2025). Semantic Clinical Artificial Intelligence vs Native Large Language Model Performance on the USMLE. JAMA network open, 8(4), e256359. (Read full article)
  88. Resnick MP, Hitt J, McCray W, Hall K, LeHouillier F, Brown SH, Campbell KE, Montella D, Nebeker J, Elkin P (2025). Semantic Relations: Extending SNOMED CT and Solor. Applied clinical informatics, 16(4), 1263-1270. (Read full article)

Review

  1. Hougland P, Nebeker J, Pickard S, Van Tuinen M, Masheter C, Elder S, Williams S, Xu W, Henriksen K, Battles JB, Keyes MA, Grady M (2008). Using ICD-9-CM Codes in Hospital Claims Data to Detect Adverse Events in Patient Safety Surveillance. (Read full article)

Conference Proceedings

  1. Redd D, Rindflesch T, Nebeker J, Zeng-Treitler (2013). Improve Retrieval Performance on Clinical Notes: A Comparison of Four Methods. 2389 - 2397.
  2. Boockvar KS, Blum, SS, Kugler AJ, Livote E, Mergenhagen, KA, Nebeker J, Signor, D, Sung S, Yeh, (2011). Effect of Admission Medication Reconciliation on Adverse Drug Events in Hospitalized Veterans.
  3. Sauer, BC, He Tao, Nebeker JR (2013). SAS® Tools for Transparent and Reproducible Research: Medication History Estimator. 1-10.
  4. Sauer BC, Nebeker JR, Shen S, Rupper R, Samore (2014). Identification of possible adverse drug reactions using population-based administrative data. Proc. 2011, 60-66.
  5. DuVall SL, South BR, D'Avolio LW, Shen S, Boone KW, Gundlapalli AV, Nebeker JR, Samore M (2011). Creating Reusable Annotated Corpora Using the Clinical Document Architecture.
  6. Sauer BC, Shen S, Nebeker J, Rupper R, Samore (2011). Identification of Possible Adverse Drug Reactions using Population-based Administrative Data. 1(1), 60-66.
  7. Nebeker JR, Hurdle JF, Hoffman J, Roth B, Weir CR, Samore (2001). Developing a taxonomy for research in adverse drug events: potholes and signposts. 493-7.
  8. Weir CR, Nebeker J (2007). Critical Issues in an Electronic Documentation System. Homer Warner Award for Best Paper at Fall AMIA 2007.
  9. Weir CR, Nebeker J (2007). Critical Issues in an Electronic Documentation System. Homer Warner Award for Best Paper at Fall AMIA 2007.

Case Report

  1. Zeng QT, Redd D, Divita G, Jarad S, Brandt C, Nebeker J (2011). Characterizing Clinical Text and Sublanguage: A Case Study of the VA Clinical Notes. Journal of health & medical informatics, S3, 1-9.

Editorial

  1. Nebeker JR, Bennett CL (2005). Reducing adverse drug events in the outpatient chemotherapy setting: attention must be paid. Cancer, 104(11), 2289-91. (Read full article)
  2. Weir CR, Rubin MA, Nebeker J, Samore (2017). Modeling the mind: How do we design effective decision-support?. Journal of biomedical informatics, 71S, S1-S5. (Read full article)
  3. White PJ, Nebeker J (2023). Evidence Enlightens Electronic Health Record Modernization. Journal of general internal medicine, 38(Suppl 4), 937-939. (Read full article)

Letter

  1. Bennett CL, Nebeker JR (2010). Reply to M.L. Lanthier et al [Letter to the editor]. J Clin Oncol.

Abstract

  1. Kaafarani, Haytham, Savitz, Lucy, Shin, Marlena, Rosen, Amy, Shimada, Stephanie, Rivard, Peter, Long, Brenna, Mull, Hillary, Nebeker, Jonatha (2008). Feasibility and Development of Trigger Tools for Surveillance of Adverse Events in Ambulatory Surgery.
  2. Nebeker J (2013). Integrating Information Objects and Annotations in the Notional DoD-VA iEHR User Experience: Results from a randomized controlled trial on efficiency and accuracy of problem assessment and intervention specification.

Report

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

Video/Film/CD/Web/Podcast

  1. Nebeker J (2004). ConSenis: Mission critical, resident-management, and heath record database for assisted living.
  2. Nebeker J (1994). MechInfect, An interactive database of microbiology and basic infectious disease designed for medical students.
  3. Nebeker J (1994). An interactive model of membrane electrochemistry designed for medical students.