| 2003 | AMIA | Developing Quality Indicators and Auditing Protocols from Formal Guideline Models: Knowledge Representation and Transformations. | Aneel A. Advani, Mary K. Goldstein, Yuval Shahar, Mark A. Musen |
| 2002 | AMIA | A framework for evidence-adaptive quality assessment that unifies guideline-based and performance-indicator approaches. | Aneel A. Advani, Mary K. Goldstein, Mark A. Musen |
| 2001 | AMIA | Medical quality assessment by scoring adherence to guideline intentions. | Aneel A. Advani, Yuval Shahar, Mark A. Musen |
| 2001 | AMIA | Patient safety in guideline-based decision support for hypertension management: ATHENA DSS. | Mary K. Goldstein, Brian B. Hoffman, Robert W. Coleman, Samson W. Tu, Ravi D. Shankar, Martin J. O'Connor, Susana B. Martins, Aneel A. Advani, Mark A. Musen |
| 2001 | AMIA | A Client-Server Framework for Deploying a Decision-support System in a Resource-constrained Environment. | Martin J. O'Connor, Ravi D. Shankar, Samson W. Tu, Aneel A. Advani, Mary K. Goldstein, Robert W. Coleman, Mark A. Musen |
| 2000 | AMIA | Quality Assessment of Guideline-oriented Medical Care Using Recognition of Clinician Intentions. | Aneel A. Advani, Yuval Shahar, Mark A. Musen |
| 2000 | AMIA | Implementing clinical practice guidelines while taking account of changing evidence: ATHENA DSS, an easily modifiable decision-support system for managing hypertension in primary care. | Mary K. Goldstein, Brian B. Hoffman, Robert W. Coleman, Mark A. Musen, Samson W. Tu, Aneel A. Advani, Ravi D. Shankar, Martin J. O'Connor |
| 1999 | AMIA | Integrating a modern knowledge-based system architecture with a legacy VA database: the ATHENA and EON projects at Stanford. | Aneel A. Advani, Samson W. Tu, Martin J. O'Connor, Robert W. Coleman, Mary K. Goldstein, Mark A. Musen |
| 1999 | AMIA | EON 2.0: Enhanced Middleware for Automation of Protocol-Directed Therapy. | Mark A. Musen, Samson W. Tu, Ravi D. Shankar, Martin J. O'Connor, Aneel A. Advani |
| 1998 | AMIA | Intention-based critiquing of guideline-oriented medical care. | Aneel A. Advani, Kin-Koi Lo, Yuval Shahar |
| 1997 | AMIA | Domain Modeling with Integrated Ontologies: Principles for Reconciliation and Reuse. | Aneel A. Advani, Samson W. Tu, Mark A. Musen |
| 1997 | AMIA | Theater-Style Demonstration: EON: CORBA-Based Middleware for Automation of Protocol-Directed Therapy. | Mark A. Musen, Samson W. Tu, Aneel A. Advani, Amar K. Das, Zaki Hasan, John H. Nguyen, Yuval Shahar |