| 2018 | AMIA | Counting Readmissions: Surprisingly difficult. | Ahmad K. Aljadaan, Peter Tarczy-Hornoch, Adam B. Wilcox, Todd F. Dardas, John H. Gennari |
| 2018 | AMIA | Quantifying the effects of gene entity disambiguation for GSEA. | Lucy Lu Wang, John H. Gennari |
| 2016 | AMIA | Assessing patient and caregiver needs and challenges in information and symptom management: a study of primary brain tumors. | Rebecca J. Hazen, Amanda Lazar, John H. Gennari |
| 2016 | AMIA | Discovering representational differences between pathway knowledge bases for pathway resource merging. | Lucy Lu Wang, John H. Gennari, Neil F. Abernethy |
| 2015 | AMIA | Decision Analysis for Oropharyngeal Cancer in Radiotherapy. | Ahmad Aljadaan, John H. Gennari, Mark H. Phillips, Wade P. Smith |
| 2013 | AMIA | Identifying High-Risk Components in Synthetic Biology. | Nikhil Gopal, Michal Galdzicki, Bryan Bartley, Evren Sirin, John H. Gennari |
| 2009 | PSB | Advances in Semantic Representation for Multiscale Biosimulation: A Case Study in Merging Models. | Maxwell Lewis Neal, John H. Gennari, Theo Arts, Daniel L. Cook |
| 2008 | AMIA | Bridging Biological Ontologies and Biosimulation: The Ontology of Physics for Biology. | Daniel L. Cook, Jos L. V. Mejino Jr., Maxwell Lewis Neal, John H. Gennari |
| 2008 | AMIA | Building an Automated Problem List Based on Natural Language Processing: Lessons Learned in the Early Phase of Development. | Imre Solti, Barry Aaronson, Grant S. Fletcher, Magdolna Solti, John H. Gennari, Melissa Cooper, Thomas H. Payne |
| 2008 | PSB | Integration of Multi-Scale Biosimulation Models via Light-Weight Semantics. | John H. Gennari, Maxwell Lewis Neal, Brian E. Carlson, Daniel L. Cook |
| 2007 | AMIA | XGI: A Graphical Interface for XQuery Creation. | Xiang Li, John H. Gennari, James F. Brinkley |
| 2007 | PSB | Chalkboard: Ontology-Based Pathway Modeling And Qualitative Inference Of Disease Mechanisms. | Daniel L. Cook, Jesse C. Wiley, John H. Gennari |
| 2006 | AMIA | Differences Among Cell-structure Ontologies: FMA, GO, & CCO. | Alan Au, Xiang Li, John H. Gennari |
| 2006 | AMIA | A framework for using reference ontologies as a foundation for the semantic web. | James F. Brinkley, Dan Suciu, Landon Detwiler, John H. Gennari, Cornelius Rosse |
| 2006 | AMIA | Integrating Protocol Schedules with Patients' Personal Calendars. | Andrea Civan, John H. Gennari, Wanda Pratt |
| 2006 | AMIA | Model Driven Laboratory Information Management Systems. | Hao Li, John H. Gennari, James F. Brinkley |
| 2005 | AMIA | Approach for Analysis of Order Check Overrides in a Computerized Practitioner Order Entry System. | Ching-Ping Lin, W. Paul Nichol, Patty Hoey, Terry L. Roth, Curtis L. Anderson, John H. Gennari, Thomas H. Payne |
| 2005 | AMIA | Of Mice and Men: Design of a Comparative Anatomy Information System. | Ravensara S. Travillian, John H. Gennari, Linda G. Shapiro |
| 2005 | PSB | Integrating Genomic Knowledge Sources Through an Anatomy Ontology. | John H. Gennari, Adam Silberfein, Jesse C. Wiley |
| 2004 | CSCW | The multiple views of inter-organizational authoring. | David W. McDonald, Chunhua Weng, John H. Gennari |
| 2004 | CSCW | Asynchronous collaborative writing through annotations. | Chunhua Weng, John H. Gennari |
| 2003 | AMIA | Scenario-based Participatory Design of A Collaborative Clinical Trial Protocol Authoring System. | Chunhua Weng, John H. Gennari, David W. McDonald |
| 2002 | AMIA | Temporal knowledge representation for scheduling tasks in clinical trial protocols. | Chunhua Weng, Michael G. Kahn, John H. Gennari |
| 2001 | AMIA | Cross-tool communication: from protocol authoring to eligibility determination. | John H. Gennari, David Sklar, John S. Silva |
| 2000 | AMIA | Participatory design and an eligibility screening tool. | John H. Gennari, Madhu C. Reddy |
| 2000 | AMIA | Knowledge representation and tool support for critiquing clinical trial protocols. | Daniel L. Rubin, John H. Gennari, 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 |
| 1994 | AAAI | Model-Based Automated Generation of User Interfaces. | Angel R. Puerta, Henrik Eriksson, John H. Gennari, Mark A. Musen |
| 1991 | ICML | Learning Spatial Relations from Images. | Kazuo Hiraki, John H. Gennari, Yoshinobu Yamamoto, Yuichiro Anzai |
| 1989 | ICML | Focused Concept Formation. | John H. Gennari |