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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Assessing patient and caregiver needs and challenges in information and symptom management: a study of primary brain tumors. - Hazen, Rebecca J.; Lazar, Amanda; Gennari, John H. (2016)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Building an Automated Problem List Based on Natural Language Processing: Lessons Learned in the Early Phase of Development. - Solti, Imre; Aaronson, Barry; Fletcher, Grant S.; Solti, Magdolna; Gennari, John H.; Cooper, Melissa; Payne, Thomas H. (2008)

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

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

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

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

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

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

A framework for using reference ontologies as a foundation for the semantic web. - Brinkley, James F.; Suciu, Dan; Detwiler, Landon; Gennari, John H.; Rosse, Cornelius (2006)

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

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

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

Approach for Analysis of Order Check Overrides in a Computerized Practitioner Order Entry System. - Lin, Ching-Ping; Nichol, W. Paul; Hoey, Patty; Roth, Terry L.; Anderson, Curtis L.; Gennari, John H.; Payne, Thomas H. (2005)

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

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

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

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

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

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

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

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

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

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

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

Proceedings of the 2nd International Conference on Knowledge Capture (K-CAP 2003), October 23-25, 2003, Sanibel Island, FL, USA (ACM, 2003)

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

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

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

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

Tool support for authoring eligibility criteria for cancer trials. - Rubin, Daniel L.; Gennari, John H.; Srinivas, Sandra; Yuen, Allen; Kaizer, Herbert; Musen, Mark A.; Silva, John S. (1999)

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

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

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

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

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

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

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

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

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

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

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