| 2022 | AMIA | Ontologies in the Behavioral Sciences: Accelerating Research and the Accessibility and Use of Knowledge. | Mark A. Musen, Jiang Bian, Bruce Chorpita, Vimla L. Patel, Cui Tao |
| 2021 | AMIA | Randomized user testing of recommender system clinical decision support. | Andre Kumar, Rachael C. Aikens, Jason Horn, Lisa Shieh, Mark A. Musen, Michael T. M. Baiocchi, Russ B. Altman, Mary K. Goldstein, Steven M. Asch, Jonathan H. Chen |
| 2020 | AMIA | Toward a Harmonized WHO Family of International Classifications Content Model. | Samson W. Tu, Csongor Nyulas, Tania Tudorache, Mark A. Musen, Andrea Martinuzzi, Coen H. van Gool, Vincenzo Della Mea, Christopher G. Chute, Lucilla Frattura, Nicholas R. Hardiker, Huib ten Napel, Richard Madden, Ann-Helene Almborg, Jeewani Anupama Ginige, Catherine Sykes, Can elik, Robert Jakob |
| 2019 | AMIA | Unleashing the value of Common Data Elements through the CEDAR Workbench. | Martin J. O'Connor, Denise B. Warzel, Marcos Martnez Romero, Josef Hardi, Debra Willrett, Aras Efekhari, John B. Graybeal, Mark A. Musen |
| 2019 | WWW | HopRank: How Semantic Structure Influences Teleportation in PageRank (A Case Study on BioPortal). | Lisette Espn-Noboa, Florian Lemmerich, Simon Walk, Markus Strohmaier, Mark A. Musen |
| 2019 | WWW | WebProtg: A Cloud-Based Ontology Editor. | Matthew Horridge, Rafael S. Gonalves, Csongor I. Nyulas, Tania Tudorache, Mark A. Musen |
| 2018 | AMIA | How Sustainable are Biomedical Ontologies? | James Geller, Vipina Kuttichi Keloth, Mark A. Musen |
| 2018 | WWW | CEDAR: Semantic Web Technology to Support Open Science. | Mark A. Musen, Susanna-Assunta Sansone, Kei-Hoi Cheung, Steven H. Kleinstein, Morgan Crafts, Stephan C. Schrer, John B. Graybeal |
| 2017 | AMIA | Big Data to Knowledge (BD2K) and the Application of Metadata. | Guoqian Jiang, Walter S. Campbell, Timothy Clark, Cui Tao, Mark A. Musen |
| 2017 | AMIA | Mechanism-based Pharmacovigilance over the Life Sciences Linked Open Data Cloud. | Maulik R. Kamdar, Mark A. Musen |
| 2017 | AMIA | Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations. | Marcos Martnez Romero, Martin J. O'Connor, Ravi D. Shankar, Maryam Panahiazar, Debra Willrett, Attila Levente Egyedi, Olivier Gevaert, John B. Graybeal, Mark A. Musen |
| 2017 | WWW | PhLeGrA: Graph Analytics in Pharmacology over the Web of Life Sciences Linked Open Data. | Maulik R. Kamdar, Mark A. Musen |
| 2017 | WWW | How Users Explore Ontologies on the Web: A Study of NCBO's BioPortal Usage Logs. | Simon Walk, Lisette Espin Noboa, Denis Helic, Markus Strohmaier, Mark A. Musen |
| 2016 | AMIA | CEDAR: Better Data Sharing Through the Authoring of Better Metadata. | Mark A. Musen, Martin J. O'Connor, Marcos Martnez Romero, Attila Levente Egyedi, Debra Willrett, John B. Graybeal |
| 2016 | EKAW | An Open Repository Model for Acquiring Knowledge About Scientific Experiments. | Martin J. O'Connor, Marcos Martnez Romero, Attila L. Egyedi, Debra Willrett, John B. Graybeal, Mark A. Musen |
| 2015 | AMIA | A Method to Compare ICF and SNOMED CT for Coverage of U.S. Social Security Administration's Disability Listing Criteria. | Samson W. Tu, Csongor Nyulas, Tania Tudorache, Mark A. Musen |
| 2015 | CHI | Helping Users Bootstrap Ontologies: An Empirical Investigation. | Yuhao Zhang, Tania Tudorache, Matthew Horridge, Mark A. Musen |
| 2014 | AMIA | Reasoning Based Quality Assurance of Medical Ontologies: A Case Study. | Matthew Horridge, Bijan Parsia, Natasha F. Noy, Mark A. Musen |
| 2014 | AMIA | Automating Identification of Multiple Chronic Conditions in Clinical Practice Guidelines. | Tiffany I. Leung, Hawre Jalal, Donna M. Zulman, Douglas K. Owens, Mark A. Musen, Michel Dumontier, Mary K. Goldstein |
| 2014 | AMIA | Crowdsourcing ICD-11 Sanctioning Rules. | Vincent Lou, Samson W. Tu, Csongor Nyulas, Tania Tudorache, Robert J. G. Chalmers, Mark A. Musen |
| 2014 | AMIA | An empirically derived taxonomy of errors in SNOMED CT. | Jonathan M. Mortensen, Mark A. Musen, Natasha F. Noy |
| 2014 | KSEM | Investigating Collaboration Dynamics in Different Ontology Development Environments. | Marco Rospocher, Tania Tudorache, Mark A. Musen |
| 2013 | AMIA | Crowdsourcing the Verification of Relationships in Biomedical Ontologies. | Jonathan Mortensen, Mark A. Musen, Natasha F. Noy |
| 2013 | HCOMP | Ontology Quality Assurance with the Crowd. | Jonathan Mortensen, Mark A. Musen, Natalya Fridman Noy |
| 2012 | AMIA | Application of Preference-Oriented Decision Making to Multimorbidity for Computerized Decision Support: Decision Analysis and Analytic Hierarchy. | Joshua Goldner, Samson W. Tu, Mary K. Goldstein, Susana B. Martins, Pamela Kum, Csongor Nyulas, Mark A. Musen |
| 2012 | AMIA | Opportunities to Support Complex Medical Decisions Through Informatics. | Mary K. Goldstein, Donna M. Zulman, Mark A. Musen, Roberto A. Rocha |
| 2012 | AMIA | Applications of Ontology Design Patterns in Biomedical Ontologies. | Jonathan Mortensen, Matthew Horridge, Mark A. Musen, Natalya Fridman Noy |
| 2012 | AMIA | Deriving an Abstraction Network to Support Quality Assurance in OCRe. | Christopher Ochs, Ankur Agrawal, Yehoshua Perl, Michael Halper, Samson W. Tu, Simona Carini, Ida Sim, Natalya Fridman Noy, Mark A. Musen, James Geller |
| 2011 | IUI | A knowledge base driven user interface for collaborative ontology development. | Tania Tudorache, Natalya Fridman Noy, Sean M. Falconer, Mark A. Musen |
| 2010 | EKAW | Ontology Development for the Masses: Creating ICD-11 in WebProtg. | Tania Tudorache, Sean M. Falconer, Natalya Fridman Noy, Csongor Nyulas, Tevfik Bedirhan stn, Margaret-Anne D. Storey, Mark A. Musen |
| 2010 | SERVICES | DataStorm. | Tomasz Wiktor Wlodarczyk, Chunming Rong, Baodong Jia, Laurentiu Cocanu, Csongor Nyulas, Mark A. Musen |
| 2009 | AMIA | Creating Mappings For Ontologies in Biomedicine: Simple Methods Work. | Amir Ghazvinian, Natalya Fridman Noy, Mark A. Musen |
| 2009 | AMIA | A Bayesian Network Model for Analysis of Detection Performance in Surveillance Systems. | Masoumeh T. Izadi, David L. Buckeridge, Anna Okhmatovskaia, Samson W. Tu, Martin J. O'Connor, Csongor Nyulas, Mark A. Musen |
| 2008 | AMIA | Predicting Outbreak Detection in Public Health Surveillance: Quantitative Analysis to Enable Evidence-Based Method Selection. | David L. Buckeridge, Anna Okhmatovskaia, Samson W. Tu, Martin J. O'Connor, Csongor Nyulas, Mark A. Musen |
| 2008 | AMIA | Comparison of Ontology-based Semantic-Similarity Measures. | Wei-Nchih Lee, Nigam Shah, Karanjot Sundlass, Mark A. Musen |
| 2008 | AMIA | Developing Biomedical Ontologies Collaboratively. | Natalya Fridman Noy, Tania Tudorache, Sherri de Coronado, Mark A. Musen |
| 2008 | AMIA | UMLS-Query: A Perl Module for Querying the UMLS. | Nigam H. Shah, Mark A. Musen |
| 2008 | EKAW | A Generic Ontology for Collaborative Ontology-Development Workflows. | Abraham Sebastian, Natalya Fridman Noy, Tania Tudorache, Mark A. Musen |
| 2007 | AIME | Using Semantic Web Technologies for Knowledge-Driven Querying of Biomedical Data. | Martin J. O'Connor, Ravi D. Shankar, Samson W. Tu, Csongor Nyulas, Dave Parrish, Mark A. Musen, Amar K. Das |
| 2007 | AIME | Document-Oriented Views of Guideline Knowledge Bases. | Samson W. Tu, Shantha Condamoor, Tim Mather, Richard W. Hall, Neill Jones, Mark A. Musen |
| 2007 | AMIA | Interpretation Errors related to the GO Annotation File Format. | Dilvan A. Moreira, Nigam H. Shah, Mark A. Musen |
| 2006 | AMIA | Identifying Barriers to Hypertension Guideline Adherence Using Clinician Feedback at the Point of Care. | N. D. Lin, Susana B. Martins, Albert Chan, Robert W. Coleman, Hayden B. Bosworth, Eugene Oddone, Ravi D. Shankar, Mark A. Musen, Brian B. Hoffman, Mary K. Goldstein |
| 2006 | AMIA | Ontology-Based Representation of Simulation Models of Physiology. | Daniel L. Rubin, David Grossman, Maxwell Lewis Neal, Daniel L. Cook, James B. Bassingthwaighte, Mark A. Musen |
| 2006 | AMIA | Ontology-based Annotation and Query of Tissue Microarray Data. | Nigam H. Shah, Daniel L. Rubin, Kaustubh S. Supekar, Mark A. Musen |
| 2006 | AMIA | Use of Declarative Statements in Creating and Maintaining Computer-Interpretable Knowledge Bases for Guideline-Based Care. | Samson W. Tu, Karen M. Hrabak, James R. Campbell, Julie Glasgow, Mark A. Nyman, Robert C. McClure, James C. McClay, Robert M. Abarbanel, James G. Mansfield, Susana B. Martins, Mary K. Goldstein, Mark A. Musen |
| 2006 | WWW | Topic-Specific Trust and Open Rating Systems: An Approach for Ontology Evaluation. | Holger Lewen, Kaustubh Supekar, Natalya Fridman Noy, Mark A. Musen |
| 2005 | AMIA | Challenges in Converting Frame-Based Ontology into OWL: the Foundational Model of Anatomy Case-Study. | Olivier Dameron, Daniel L. Rubin, Mark A. Musen |
| 2005 | AMIA | Semantic Clinical Guideline Documents. | Henrik Eriksson, Samson W. Tu, Mark A. Musen |
| 2005 | AMIA | Use of Description Logic Classification to Reason about Consequences of Penetrating Injuries. | Daniel L. Rubin, Olivier Dameron, Mark A. Musen |
| 2005 | AMIA | Protg-OWL: Creating Ontology-Driven Reasoning Applications with the Web Ontology Language. | Daniel L. Rubin, Holger Knublauch, Ray W. Fergerson, Olivier Dameron, Mark A. Musen |
| 2005 | AMIA | Ontology Metadata to Support the Building of a Library of Biomedical Ontologies. | Kaustubh Supekar, Mark A. Musen |
| 2004 | IKE | A Knowledge-Based Framework for Deploying Surveillance Problem Solvers. | David L. Buckeridge, Martin J. O'Connor, Haobo Xu, Mark A. Musen |
| 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 |
| 2003 | AMIA | An Analytic Framework for Space-Time Aberrancy Detection in Public Health Surveillance Data. | David L. Buckeridge, Mark A. Musen, Paul Switzer, Monica Crubzy |
| 2003 | AMIA | Protg-2000: An Open-Source Ontology-Development and Knowledge-Acquisition Environment: AMIA 2003 Open Source Expo. | Natalya Fridman Noy, Monica Crubzy, Ray W. Fergerson, Holger Knublauch, Samson W. Tu, Jennifer Vendetti, Mark A. Musen |
| 2003 | AMIA | BioSTORM: A System for Automated Surveillance of Diverse Data Sources. | Martin J. O'Connor, David L. Buckeridge, Michael Choy, Monica Crubzy, Zachary Pincus, Mark A. Musen |
| 2003 | AMIA | Contextualizing Heterogeneous Data for Integration and Inference. | Zachary Pincus, Mark A. Musen |
| 2003 | AMIA | A Knowledge-Acquisition Wizard to Encode Guidelines. | Ravi D. Shankar, Samson W. Tu, Mark A. Musen |
| 2003 | AMIA | The Structure of Guideline Recommendations: A Synthesis. | Samson W. Tu, James R. Campbell, Mark A. Musen |
| 2002 | AAAI | PROMPTDIFF: A Fixed-Point Algorithm for Comparing Ontology Versions. | Natalya Fridman Noy, 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 |
| 2002 | AMIA | Standards-based Sharable Active Guideline Environment (SAGE): A Project to Develop a Universal Framework for Encoding and Disseminating Electronic Clinical Practice Guidelines. | Nick Beard, James R. Campbell, Stanley M. Huff, Mauricio Leon, James G. Mansfield, Eric Mays, James C. McClay, David N. Mohr, Mark A. Musen, David O'Brien, Roberto A. Rocha, Anne Saulovich, Sidna M. Scheitel, Samson W. Tu |
| 2002 | AMIA | Knowledge-based bioterrorism surveillance. | David L. Buckeridge, Justin Graham, Martin J. O'Connor, Michael Choy, Samson W. Tu, Mark A. Musen |
| 2002 | AMIA | SYNCHRONUS: a reusable software module for temporal integration. | Amar K. Das, Mark A. Musen |
| 2002 | AMIA | Conceptual Heterogeneity Complicates Automated Syndromic Surveillance for Bioterrorism. | Justin Graham, David L. Buckeridge, Michael Choy, Mark A. Musen |
| 2002 | AMIA | Protocol Design Patterns: Domain-oriented Abstractions to Support the Authoring of Computer-executable Clinical Trials. | John H. Nguyen, Michael G. Kahn, Carol A. Broverman, Mark A. Musen |
| 2002 | AMIA | The Chronus II temporal database mediator. | Martin J. O'Connor, Samson W. Tu, Mark A. Musen |
| 2002 | AMIA | Use of Protg-2000 to Encode Clinical Guidelines. | Ravi D. Shankar, Samson W. Tu, Mark A. Musen |
| 2002 | AMIA | A Typology for Modeling Processes in Clinical Guidelines and Protocols. | Samson W. Tu, Peter D. Johnson, Mark A. Musen |
| 2002 | CHI | SHriMP views: an interactive environment for information visualization and navigation. | Margaret-Anne D. Storey, Casey Best, Jeff Michaud, Derek Rayside, Marin Litoiu, Mark A. Musen |
| 2002 | IUI | Jambalaya: an interactive environment for exploring ontologies. | Margaret-Anne D. Storey, Natasha F. Noy, Mark A. Musen, Casey Best, Ray W. Fergerson, Neil A. Ernst |
| 2001 | AMIA | Medical quality assessment by scoring adherence to guideline intentions. | Aneel A. Advani, Yuval Shahar, Mark A. Musen |
| 2001 | AMIA | A formal method to resolve temporal mismatches in clinical databases. | Amar K. Das, 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 virtual medical record for guideline-based decision support. | Peter D. Johnson, Samson W. Tu, Mark A. Musen, Ian N. Purves |
| 2001 | AMIA | Representation of Structural Relationships in the Foundational Model of Anatomy. | Jos L. V. Mejino Jr., Natalya Fridman Noy, Mark A. Musen, James F. Brinkley, Cornelius Rosse |
| 2001 | AMIA | Protege-2000: A Plug-in Architecture to Support Knowledge Acquisition, Knowledge Visualization, and the Semantic Web. | Mark A. Musen, Ray W. Fergerson, Natalya Fridman Noy, Monica Crubzy |
| 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 |
| 2001 | AMIA | Integration of textual guideline documents with formal guideline knowledge bases. | Ravi D. Shankar, Samson W. Tu, Susana B. Martins, Lawrence M. Fagan, Mary K. Goldstein, Mark A. Musen |
| 2001 | IJCAI | Anchor-PROMPT: Using Non-Local Context for Semantic Matching. | Natalya Fridman Noy, Mark A. Musen |
| 2000 | AAAI | PROMPT: Algorithm and Tool for Automated Ontology Merging and Alignment. | Natalya Fridman Noy, 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 |
| 2000 | AMIA | Representation of Nursing Guidelines Using the EON Guideline Model. | Zhen Lin, Samson W. Tu, Mark A. Musen |
| 2000 | AMIA | Ontology acquisition from on-line knowledge sources. | Qi Li, Philip Shilane, Natalya Fridman Noy, Mark A. Musen |
| 2000 | AMIA | Representation of temporal indeterminacy in clinical databases. | Martin J. O'Connor, Samson W. Tu, Mark A. Musen |
| 2000 | AMIA | Knowledge representation and tool support for critiquing clinical trial protocols. | Daniel L. Rubin, John H. Gennari, Mark A. Musen |
| 2000 | AMIA | Explanations for a Hypertension Decision Support System. | Ravi D. Shankar, Samson W. Tu, Mary K. Goldstein, Mark A. Musen |
| 2000 | AMIA | The impact of displayed awards on the credibility and retention of Web site information. | John Shon, Jonathan Marshall, Mark A. Musen |
| 2000 | AMIA | From guideline modeling to guideline execution: defining guideline-based decision-support services. | Samson W. Tu, Mark A. Musen |
| 2000 | EKAW | The Knowledge Model of Protg-2000: Combining Interoperability and Flexibility. | Natalya Fridman Noy, Ray W. Fergerson, Mark A. Musen |
| 2000 | EKAW | A Case Study in Using Protg-2000 as a Tool for CommonKADS. | Guus Schreiber, Monica Crubzy, Mark A. Musen |
| 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 | Representing the Digital Anatomist Foundational Model as a Protege Ontology. | Jin S. Hahn, Elizabeth S. Burnside, James F. Brinkley, Cornelius Rosse, 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 |
| 1999 | AMIA | Applying temporal joins to clinical databases. | Martin J. O'Connor, Samson W. Tu, Mark A. Musen |
| 1999 | AMIA | Tool support for authoring eligibility criteria for cancer trials. | Daniel L. Rubin, John H. Gennari, Sandra Srinivas, Allen Yuen, Herbert Kaizer, Mark A. Musen, John S. Silva |
| 1999 | AMIA | Justification of automated decision-making: medical explanations as medical arguments. | Ravi D. Shankar, Mark A. Musen |
| 1999 | AMIA | The low availability of metadata elements for evaluating the quality of medical information on the World Wide Web. | John Shon, Mark A. Musen |
| 1999 | AMIA | Effects of Evidence-Based Explanations of Clinical Guideline Recommendations on Clinical Decision-Making. | John Shon, Mark A. Musen |
| 1999 | AMIA | A flexible approach to guideline modeling. | Samson W. Tu, Mark A. Musen |
| 1998 | AMIA | Modern architectures for intelligent systems: reusable ontologies and problem-solving methods. | Mark A. Musen |
| 1998 | AMIA | A declarative explanation framework that uses a collection of visualization agents. | Ravi D. Shankar, Samson W. Tu, Mark A. Musen |
| 1998 | AMIA | Therapy planning as constraint satisfaction: a computer-based antiretroviral therapy advisor for the management of HIV. | D. Scott Smith, John Y. Park, Mark A. Musen |
| 1997 | AMIA | Domain Modeling with Integrated Ontologies: Principles for Reconciliation and Reuse. | Aneel A. Advani, Samson W. Tu, Mark A. Musen |
| 1997 | AMIA | A foundational model of time for heterogeneous clinical databases. | Amar K. Das, 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 |
| 1997 | AMIA | A temporal database mediator for protocol-based decision support. | John H. Nguyen, Yuval Shahar, Samson W. Tu, Amar K. Das, Mark A. Musen |
| 1995 | AIME | A Component-Based Architecture for Automation of Protocol-Directed Therapy. | Mark A. Musen, Samson W. Tu, Amar K. Das, Yuval Shahar |
| 1994 | AAAI | Model-Based Automated Generation of User Interfaces. | Angel R. Puerta, Henrik Eriksson, John H. Gennari, Mark A. Musen |
| 1993 | UAI | Graph-Grammar Assistance for Automated Generation of Influence Diagrams. | John W. Egar, Mark A. Musen |
| 1992 | EKAW | Conceptual Models for Automatic Generation of Knowledge-Acquisition Tools. | Henrik Eriksson, Mark A. Musen |