Focused Concept Formation. - John H. Gennari (ML, 1989)

Models of Incremental Concept Formation. - John H. Gennari; Pat Langley; Douglas H. Fisher (Artif. Intell., 1989)

Learning Spatial Relations from Images. - Kazuo Hiraki; John H. Gennari; Yoshinobu Yamamoto; Yuichiro Anzai (ML, 1991)

Model-Based Automated Generation of User Interfaces. - Angel R. Puerta; Henrik Eriksson; John H. Gennari; Mark A. Musen (AAAI, 1994)

Beyond Data Models for Automated User Interface Generation. - Angel R. Puerta; Henrik Eriksson; John H. Gennari; Mark A. Musen (BCS HCI, 1994)

Mapping domains to methods in support of reuse. - John H. Gennari; Samson W. Tu; Thomas E. Rothenfluh; Mark A. Musen (Int. J. Hum. Comput. Stud., 1994)

Reuse with PROTÉgÉ-II: From Elevators to Ribosomes. - John H. Gennari; Russ B. Altman; Mark A. Musen (SSR, 1995)

Ontology-based configuration of problem-solving methods and generation of knowledge-acquisition tools: application of PROTEGE-II to protocol-based decision support. - Samson W. Tu; Henrik Eriksson; John H. Gennari; Yuval Shahar; Mark A. Musen (Artif. Intell. Medicine, 1995)

Reusable ontologies, knowledge-acquisition tools, and performance systems: PROTÉGÉ-II solutions to Sisyphus-2. - Thomas E. Rothenfluh; John H. Gennari; Henrik Eriksson; Angel R. Puerta; Samson W. Tu; Mark A. Musen (Int. J. Hum. Comput. Stud., 1996)

Reuse, CORBA, and knowledge-based systems. - John H. Gennari; Heyning Cheng; Russ B. Altman; Mark A. Musen (Int. J. Hum. Comput. Stud., 1998)

Research Paper: The GuideLine Interchange Format: A Model for Representing Guidelines. - Lucila Ohno-Machado; John H. Gennari; Shawn N. Murphy; Nilesh L. Jain; Samson W. Tu; Diane E. Oliver; Edward Pattison-Gordon; Robert A. Greenes; Edward H. Shortliffe; G. Octo Barnett (J. Am. Medical Informatics Assoc., 1998)

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 (AMIA, 1999)

Participatory design and an eligibility screening tool. - John H. Gennari; Madhu C. Reddy (AMIA, 2000)

Knowledge representation and tool support for critiquing clinical trial protocols. - Daniel L. Rubin; John H. Gennari; Mark A. Musen (AMIA, 2000)

Cross-tool communication: from protocol authoring to eligibility determination. - John H. Gennari; David Sklar; John S. Silva (AMIA, 2001)

Temporal knowledge representation for scheduling tasks in clinical trial protocols. - Chunhua Weng; Michael G. Kahn; John H. Gennari (AMIA, 2002)

Scenario-based Participatory Design of A Collaborative Clinical Trial Protocol Authoring System. - Chunhua Weng; John H. Gennari; David W. McDonald (AMIA, 2003)

Interoperability of Protege 2.0 beta and OilEd 3.5 in the Domain Knowledge of Osteoporosis. - Franz Calvo; John H. Gennari (EON, 2003)

The evolution of Protégé: an environment for knowledge-based systems development. - John H. Gennari; Mark A. Musen; Ray W. Fergerson; William E. Grosso; Monica Crubézy; Henrik Eriksson; Natalya Fridman Noy; Samson W. Tu (Int. J. Hum. Comput. Stud., 2003)

The multiple views of inter-organizational authoring. - David W. McDonald; Chunhua Weng; John H. Gennari (CSCW, 2004)

Asynchronous collaborative writing through annotations. - Chunhua Weng; John H. Gennari (CSCW, 2004)

An Ethnographic Study of Collaborative Clinical Trial Protocol Writing. - John H. Gennari; Chunhua Weng; David W. McDonald; Jacqueline Benedetti; Stephanie Green (MedInfo, 2004)

A Collaborative Clinical Trial Protocol Writing System. - Chunhua Weng; John H. Gennari; David W. McDonald (MedInfo, 2004)

Incorporating ideas from computer-supported cooperative work. - Wanda Pratt; Madhu C. Reddy; David W. McDonald; Peter Tarczy-Hornoch; John H. Gennari (J. Biomed. Informatics, 2004)

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 (AMIA, 2005)

Of Mice and Men: Design of a Comparative Anatomy Information System. - Ravensara S. Travillian; John H. Gennari; Linda G. Shapiro (AMIA, 2005)

Knowledge transformations between frame systems and RDB systems. - John H. Gennari; Peter Mork; Hao Li (K-CAP, 2005)

Integrating Genomic Knowledge Sources Through an Anatomy Ontology. - John H. Gennari; Adam Silberfein; Jesse C. Wiley (Pacific Symposium on Biocomputing, 2005)

Asynchronous communication among clinical researchers: A study for systems design. - John H. Gennari; Chunhua Weng; Jacqueline Benedetti; David W. McDonald (Int. J. Medical Informatics, 2005)

Differences Among Cell-structure Ontologies: FMA, GO, & CCO. - Alan Au; Xiang Li; John H. Gennari (AMIA, 2006)

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 (AMIA, 2006)

Integrating Protocol Schedules with Patients' Personal Calendars. - Andrea Civan; John H. Gennari; Wanda Pratt (AMIA, 2006)

Model Driven Laboratory Information Management Systems. - Hao Li; John H. Gennari; James F. Brinkley (AMIA, 2006)

XGI: A Graphical Interface for XQuery Creation. - Xiang Li; John H. Gennari; James F. Brinkley (AMIA, 2007)

Chalkboard: Ontology-Based Pathway Modeling And Qualitative Inference Of Disease Mechanisms. - Daniel L. Cook; Jesse C. Wiley; John H. Gennari (Pacific Symposium on Biocomputing, 2007)

Participatory design of a collaborative clinical trial protocol writing system. - Chunhua Weng; David W. McDonald; Dana Sparks; Jason McCoy; John H. Gennari (Int. J. Medical Informatics, 2007)

User-centered semantic harmonization: A case study. - Chunhua Weng; John H. Gennari; Douglas B. Fridsma (J. Biomed. Informatics, 2007)

Bridging Biological Ontologies and Biosimulation: The Ontology of Physics for Biology. - Daniel L. Cook; José L. V. Mejino Jr.; Maxwell Lewis Neal; John H. Gennari (AMIA, 2008)

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 (AMIA, 2008)

Integration of Multi-Scale Biosimulation Models via Light-Weight Semantics. - John H. Gennari; Maxwell Lewis Neal; Brian E. Carlson; Daniel L. Cook (Pacific Symposium on Biocomputing, 2008)

Research Paper: Evaluating Clinical Decision Support Systems: Monitoring CPOE Order Check Override Rates in the Department of Veterans Affairs' Computerized Patient Record System. - Ching-Ping Lin; Thomas H. Payne; W. Paul Nichol; Patricia J. Hoey; Curtis L. Anderson; John H. Gennari (J. Am. Medical Informatics Assoc., 2008)

Advances in Semantic Representation for Multiscale Biosimulation: A Case Study in Merging Models. - Maxwell Lewis Neal; John H. Gennari; Theo Arts; Daniel L. Cook (Pacific Symposium on Biocomputing, 2009)

HeartCyc: A Cardiac Cycle Process Ontology Based in the Ontology of Physics for Biology. - Daniel L. Cook; Michal Galdzicki; Maxwell Lewis Neal; José L. V. Mejino Jr.; John H. Gennari (ICBO, 2011)

Integrating systems biology models and biomedical ontologies. - Robert Hoehndorf; Michel Dumontier; John H. Gennari; Sarala M. Wimalaratne; Bernard de Bono; Daniel L. Cook; Georgios V. Gkoutos (BMC Syst. Biol., 2011)

Multiple ontologies in action: Composite annotations for biosimulation models. - John H. Gennari; Maxwell Lewis Neal; Michal Galdzicki; Daniel L. Cook (J. Biomed. Informatics, 2011)

Identifying High-Risk Components in Synthetic Biology. - Nikhil Gopal; Michal Galdzicki; Bryan Bartley; Evren Sirin; John H. Gennari (AMIA, 2013)

An OWL knowledge base for classifying and querying collections of physiological models: A prototype human physiome. - Maxwell Lewis Neal; Daniel L. Cook; John H. Gennari (ICBO, 2013)

Using random walks to identify cancer-associated modules in expression data. - Deanna Petrochilos; Ali Shojaie; John H. Gennari; Neil F. Abernethy (BioData Min., 2013)

Ontology of physics for biology: representing physical dependencies as a basis for biological processes. - Daniel L. Cook; Maxwell Lewis Neal; Fred L. Bookstein; John H. Gennari (J. Biomed. Semant., 2013)

Representing physiological processes and their participants with PhysioMaps. - Daniel L. Cook; Maxwell Lewis Neal; Robert Hoehndorf; Georgios V. Gkoutos; John H. Gennari (J. Biomed. Semant., 2013)

A Reappraisal of How to Build Modular, Reusable Models of Biological Systems. - Maxwell Lewis Neal; Michael T. Cooling; Lucian P. Smith; Christopher T. Thompson; Herbert M. Sauro; Brian E. Carlson; Daniel L. Cook; John H. Gennari (PLoS Comput. Biol., 2014)

Decision Analysis for Oropharyngeal Cancer in Radiotherapy. - Ahmad Aljadaan; John H. Gennari; Mark H. Phillips; Wade P. Smith (AMIA, 2015)

Synthetic Biology Open Language (SBOL) Version 2.0.0. - Bryan Bartley; Jacob Beal; Kevin Clancy; Goksel Misirli; Nicholas Roehner; Ernst Oberortner; Matthew R. Pocock; Michael Bissell; Curtis Madsen; Tramy Nguyen; Zhen Zhang 006; John H. Gennari; et al. (J. Integr. Bioinform., 2015)

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 (AMIA, 2016)

Discovering representational differences between pathway knowledge bases for pathway resource merging. - Lucy Lu Wang; John H. Gennari; Neil F. Abernethy (AMIA, 2016)

Qualitative Causal Analyses of Biosimulation Models. - Maxwell Lewis Neal; John H. Gennari; Daniel L. Cook (ICBO/BioCreative, 2016)

An Analysis of Differences in Biological Pathway Resources. - Lucy Lu Wang; John H. Gennari; Neil F. Abernethy (ICBO/BioCreative, 2016)

Synthetic Biology Open Language (SBOL) Version 2.1.0. - Jacob Beal; Robert Sidney Cox III; Raik Grünberg; James Alastair McLaughlin; Tramy Nguyen; Bryan Bartley; Michael Bissell; Kiri Choi; Kevin Clancy; Chris Macklin; Curtis Madsen; Goksel Misirli; et al. (J. Integr. Bioinform., 2016)

Extending the Ontology of Physics for Biology with Thermodynamics. - Daniel L. Cook; John H. Gennari; Maxwell Lewis Neal (ICBO, 2017)

Similarity Metrics for Determining Overlap Among Biological Pathways. - Lucy Lu Wang; John H. Gennari (ICBO, 2017)

Counting Readmissions: Surprisingly difficult. - Ahmad K. Aljadaan; Peter Tarczy-Hornoch; Adam B. Wilcox; Todd F. Dardas; John H. Gennari (AMIA, 2018)

Quantifying the effects of gene entity disambiguation for GSEA. - Lucy Lu Wang; John H. Gennari (AMIA, 2018)

Synthetic Biology Open Language (SBOL) Version 2.2.0. - Robert Sidney Cox III; Curtis Madsen; James Alastair McLaughlin; Tramy Nguyen; Nicholas Roehner; Bryan Bartley; Jacob Beal; Michael Bissell; Kiri Choi; Kevin Clancy; Raik Grünberg; Chris Macklin; et al. (J. Integr. Bioinform., 2018)

The Ontology of Physics for Biology - A Companion to Basic Formal Ontology. - Daniel L. Cook; John H. Gennari; Maxwell Lewis Neal (ICBO, 2019)

Harmonizing semantic annotations for computational models in biology. - Maxwell Lewis Neal; Matthias König 003; David P. Nickerson; Goksel Misirli; Reza Kalbasi; Andreas Dräger; Koray Atalag; Vijayalakshmi Chelliah; Michael T. Cooling; Daniel L. Cook; Sharon M. Crook; Miguel de Alba; et al. (Briefings Bioinform., 2019)

SemGen: a tool for semantics-based annotation and composition of biosimulation models. - Maxwell Lewis Neal; Christopher T. Thompson; Karam G. Kim; Ryan C. James; Daniel L. Cook; Brian E. Carlson; John H. Gennari (Bioinform., 2019)

Predicting instances of pathway ontology classes for pathway integration. - Lucy Lu Wang; G. Thomas Hayman; Jennifer R. Smith; Monika Tutaj; Mary Shimoyama; John H. Gennari (J. Biomed. Semant., 2019)

Model annotation and discovery with the Physiome Model Repository. - Dewan M. Sarwar; Reza Kalbasi; John H. Gennari; Brian E. Carlson; Maxwell Lewis Neal; Bernard de Bono; Koray Atalag; Peter J. Hunter; David P. Nickerson (BMC Bioinform., 2019)

Synthetic Biology Open Language (SBOL) Version 2.3. - Curtis Madsen; Ángel Goñi-Moreno; Umesh P; Zachary Palchick; Nicholas Roehner; Christian Atallah; Bryan Bartley; Kiri Choi; Robert Sidney Cox III; Thomas E. Gorochowski; Raik Grünberg; Chris Macklin; et al. (J. Integr. Bioinform., 2019)

Open modeling and exchange (OMEX) metadata specification version 1.0. - Maxwell Lewis Neal; John H. Gennari; Dagmar Waltemath; David P. Nickerson; Matthias König 003 (J. Integr. Bioinform., 2020)

libOmexMeta: enabling semantic annotation of models to support FAIR principles. - Ciaran M. Welsh; David P. Nickerson; Anand K. Rampadarath; Maxwell Lewis Neal; Herbert M. Sauro; John H. Gennari (Bioinform., 2021)

OMEX metadata specification (version 1.2). - John H. Gennari; Matthias König 003; Goksel Misirli; Maxwell Lewis Neal; David P. Nickerson; Dagmar Waltemath (J. Integr. Bioinform., 2021)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - Bilal Shaikh; Lucian P. Smith; Dan Vasilescu; Gnaneswara Marupilla; Michael Wilson; Eran Agmon; Henry Agnew; Steven S. Andrews; Azraf Anwar; Moritz E. Beber; Frank T. Bergmann; David Brooks 006; et al. (CoRR, 2022)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - Bilal Shaikh; Lucian P. Smith; Dan Vasilescu; Gnaneswara Marupilla; Michael Wilson; Eran Agmon; Henry Agnew; Steven S. Andrews; Azraf Anwar; Moritz E. Beber; Frank T. Bergmann; David Brooks 006; et al. (Nucleic Acids Res., 2022)

An automated model annotation system (AMAS) for SBML models. - Woosub Shin; John H. Gennari; Joseph L. Hellerstein; Herbert M. Sauro (Bioinform., 2023)

VSCode-Antimony: a source editor for building, analyzing, and translating antimony models. - Steve Ma; Longxuan Fan; Sai Anish Konanki; Eva Liu; John H. Gennari; Lucian P. Smith; Joseph L. Hellerstein; Herbert M. Sauro (Bioinform., 2023)

LM-Merger: a workflow for merging logical models with an application to gene regulatory network models. - Luna Xingyu Li; Boris Aguilar; John H. Gennari; Guangrong Qin (BMC Bioinform., 2025)