| 2020 | AMIA | Normalizing Clinical Document Titles to LOINC Document Ontology: an Initial Study. | Xu Zuo, Jianfu Li, Bo Zhao, Yujia Zhou, Xiao Dong, Jon D. Duke, Karthik Natarajan, George Hripcsak, Nigam Shah, Juan M. Banda, Ruth M. Reeves, Hua Xu |
| 2018 | AMIA | Using HL7 FHIR to Improve Standardization and Interoperability of Common Data Models for Clinical and Translational Research. | Guoqian Jiang, Jon D. Duke, Daniella Meeker, Mitra Rocca, Harold R. Solbrig, Shawn N. Murphy |
| 2017 | AMIA | From Large-Scale Network Analytics to Clinical Solutions in OHDSI. | Jon D. Duke, George Hripcsak, Patrick B. Ryan, Nigam Shah |
| 2016 | AMIA | Methods to Measure and Improve the Quality of Large Scale Health Data: An Application in Public Health Surveillance. | Brian E. Dixon, Jon D. Duke, Shaun J. Grannis |
| 2016 | AMIA | Ensuring Reproducibility in Observational Research: Building and Sharing Knowledge Resources in the OHDSI Network. | Jon D. Duke, Nigam H. Shah, George Hripcsak, Patrick B. Ryan |
| 2016 | CHI | Endorsement, Prior Action, and Language: Modeling Trusted Advice in Computerized Clinical Alerts. | Debaleena Chattopadhyay, Jon D. Duke, Davide Bolchini |
| 2015 | AMIA | An Interactive User Interface for Drug Labeling to Improve Readability and Decision-Making. | Hamed Abedtash, Jon D. Duke |
| 2015 | AMIA | OHDSI: An Open-Source Platform for Observational Data Analytics and Collaborative Research. | Jon D. Duke, Frank J. DeFalco, Chris Knoll, Vojtech Huser, Richard D. Boyce, Patrick B. Ryan |
| 2015 | AMIA | The Value of an Open-Source Observational Research Collaboratory: Results from the OHDSI Initiative. | Jon D. Duke, George Hripcsak, Nigam Shah, Patrick B. Ryan |
| 2015 | AMIA | Regenstrief ePRO: A Rule-Based Platform for Capturing Targeted Patient-Reported Outcomes. | Jon D. Duke, Daniel J. Vreeman, Jeremy Leventhal, Chen Wen, Katie Allen, David A. Haggstrom |
| 2015 | AMIA | Supporting Clinical Cognition: A Human-Centered Approach to a Novel ICU Information Visualization Dashboard. | Anthony Faiola, Preethi Srinivas, Jon D. Duke |
| 2014 | AMIA | An EMR Designed for Teaching and Educational Research Based on Regenstrief Institute's Gopher System. | Blaine Y. Takesue, John T. Finnell, Jon D. Duke |
| 2014 | AMIA | Challenges in Quantifying Narcotic Use from Drug Dispensing Records. | Jianmin Wu, Jon D. Duke, John T. Finnell |
| 2013 | AMIA | Regenstrief Institute's Gopher Order Entry System: Advances in Provider Collaboration and Clinical Decision Support. | Jon D. Duke, Douglas K. Martin, Burke W. Mamlin |
| 2012 | AMIA | Regenstrief Institute's Next-Generation Clinical Decision Support System. | Jon D. Duke, Burke W. Mamlin, Douglas K. Martin |
| 2012 | AMIA | Development of Beers' Criteria Clinical Decision Support System for Potentially a Computerized Order Entry System. | Brittany Melton, Alissa L. Russ, Bruce Carlstedt, Jon D. Duke, Alan J. Zillich |
| 2009 | HCI | A Novel Visualization Tool for Evaluating Medication Side-Effects in Multi-drug Regimens. | Jon D. Duke, Anthony Faiola, Hadi Kharrazi |