John H. Gennari

Publication Activity (10 Years)

Years Active: 1989-2023
Publications (10 Years): 23

Top Topics

Biological Systems

Similarity Metric

Computational Models

Top Venues

J. Integr. Bioinform.

Publications

Woosub Shin, John H. Gennari, Joseph L. Hellerstein, Herbert M. Sauro
An automated model annotation system (AMAS) for SBML models. Bioinform. 39 (10) (2023)
Steve Ma, Longxuan Fan, Sai Anish Konanki, Eva Liu, John H. Gennari, Lucian P. Smith, Joseph L. Hellerstein, Herbert M. Sauro
VSCode-Antimony: a source editor for building, analyzing, and translating antimony models. Bioinform. 39 (12) (2023)
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, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary Haiman, Jan Hasenauer, Joseph L. Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Rahuman S. Malik-Sheriff, Synchon Mandal, Robert McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali S. Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, James C. Schaff, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr
BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Res. 50 (W1) (2022)
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, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary Haiman, Joseph L. Hellerstein, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Synchon Mandal, Robert McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali S. Saglam, Dilawar Singh, Ankur Sinha, Jacky Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr
BioSimulators: a central registry of simulation engines and services for recommending specific tools. CoRR (2022)
Ciaran M. Welsh, David P. Nickerson, Anand Rampadarath, Maxwell Lewis Neal, Herbert M. Sauro, John H. Gennari
libOmexMeta: enabling semantic annotation of models to support FAIR principles. Bioinform. 37 (24) (2021)
John H. Gennari, Matthias König, Goksel Misirli, Maxwell Lewis Neal, David P. Nickerson, Dagmar Waltemath
OMEX metadata specification (version 1.2). J. Integr. Bioinform. 18 (3) (2021)
Maxwell Lewis Neal, John H. Gennari, Dagmar Waltemath, David P. Nickerson, Matthias König
Open modeling and exchange (OMEX) metadata specification version 1.0. J. Integr. Bioinform. 17 (2-3) (2020)
Daniel L. Cook, John H. Gennari, Maxwell Lewis Neal
The Ontology of Physics for Biology - A Companion to Basic Formal Ontology. ICBO (2019)
Maxwell Lewis Neal, Matthias König, 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, Samuel H. Friedman, Alan Garny, John H. Gennari, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nick S. Juty, Chris J. Myers, Brett G. Olivier, Herbert M. Sauro, Martin Scharm, Jacky L. Snoep, Vasundra Touré, Anil Wipat, Olaf Wolkenhauer, Dagmar Waltemath
Harmonizing semantic annotations for computational models in biology. Briefings Bioinform. 20 (2) (2019)
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
Model annotation and discovery with the Physiome Model Repository. BMC Bioinform. 20 (1) (2019)
Maxwell Lewis Neal, Christopher T. Thompson, Karam G. Kim, Ryan C. James, Daniel L. Cook, Brian E. Carlson, John H. Gennari
SemGen: a tool for semantics-based annotation and composition of biosimulation models. Bioinform. 35 (9) (2019)
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, James Alastair McLaughlin, Xianwei Meng, Tramy Nguyen, Matthew R. Pocock, Meher Samineni, James Scott-Brown, Ysis Tarter, Michael Zhang, Zhen Zhang, Zach Zundel, Jacob Beal, Michael Bissell, Kevin Clancy, John H. Gennari, Goksel Misirli, Chris J. Myers, Ernst Oberortner, Herbert M. Sauro, Anil Wipat
Synthetic Biology Open Language (SBOL) Version 2.3. J. Integr. Bioinform. 16 (2) (2019)
Lucy Lu Wang, G. Thomas Hayman, Jennifer R. Smith, Monika Tutaj, Mary Shimoyama, John H. Gennari
Predicting instances of pathway ontology classes for pathway integration. J. Biomed. Semant. 10 (1) (2019)
Lucy Lu Wang, John H. Gennari
Quantifying the effects of gene entity disambiguation for GSEA. AMIA (2018)
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, Goksel Misirli, Ernst Oberortner, Matthew R. Pocock, Meher Samineni, Michael Zhang, Zhen Zhang, Zach Zundel, John H. Gennari, Chris J. Myers, Herbert M. Sauro, Anil Wipat
Synthetic Biology Open Language (SBOL) Version 2.2.0. J. Integr. Bioinform. 15 (1) (2018)
Ahmad K. Aljadaan, Peter Tarczy-Hornoch, Adam B. Wilcox, Todd F. Dardas, John H. Gennari
Counting Readmissions: Surprisingly difficult. AMIA (2018)
Daniel L. Cook, John H. Gennari, Maxwell Lewis Neal
Extending the Ontology of Physics for Biology with Thermodynamics. ICBO (2017)
Lucy Lu Wang, John H. Gennari
Similarity Metrics for Determining Overlap Among Biological Pathways. ICBO (2017)
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, Ernst Oberortner, Matthew R. Pocock, Nicholas Roehner, Meher Samineni, Michael Zhang, Zhen Zhang, Zach Zundel, John H. Gennari, Chris J. Myers, Herbert M. Sauro, Anil Wipat
Synthetic Biology Open Language (SBOL) Version 2.1.0. J. Integr. Bioinform. 13 (3) (2016)
Maxwell Lewis Neal, John H. Gennari, Daniel L. Cook
Qualitative Causal Analyses of Biosimulation Models. ICBO/BioCreative (2016)
Rebecca J. Hazen, Amanda Lazar, John H. Gennari
Assessing patient and caregiver needs and challenges in information and symptom management: a study of primary brain tumors. AMIA (2016)
Lucy Lu Wang, John H. Gennari, Neil F. Abernethy
Discovering representational differences between pathway knowledge bases for pathway resource merging. AMIA (2016)
Lucy Lu Wang, John H. Gennari, Neil F. Abernethy
An Analysis of Differences in Biological Pathway Resources. ICBO/BioCreative (2016)
Bryan Bartley, Jacob Beal, Kevin Clancy, Goksel Misirli, Nicholas Roehner, Ernst Oberortner, Matthew R. Pocock, Michael Bissell, Curtis Madsen, Tramy Nguyen, Zhen Zhang, John H. Gennari, Chris J. Myers, Anil Wipat, Herbert M. Sauro
Synthetic Biology Open Language (SBOL) Version 2.0.0. J. Integr. Bioinform. 12 (2) (2015)
Ahmad Aljadaan, John H. Gennari, Mark H. Phillips, Wade P. Smith
Decision Analysis for Oropharyngeal Cancer in Radiotherapy. AMIA (2015)
Maxwell Lewis Neal, Michael T. Cooling, Lucian P. Smith, Christopher T. Thompson, Herbert M. Sauro, Brian E. Carlson, Daniel L. Cook, John H. Gennari
A Reappraisal of How to Build Modular, Reusable Models of Biological Systems. PLoS Comput. Biol. 10 (10) (2014)
Deanna Petrochilos, Ali Shojaie, John H. Gennari, Neil F. Abernethy
Using random walks to identify cancer-associated modules in expression data. BioData Min. 6 (2013)
Daniel L. Cook, Maxwell Lewis Neal, Fred L. Bookstein, John H. Gennari
Ontology of physics for biology: representing physical dependencies as a basis for biological processes. J. Biomed. Semant. 4 (2013)
Nikhil Gopal, Michal Galdzicki, Bryan Bartley, Evren Sirin, John H. Gennari
Identifying High-Risk Components in Synthetic Biology. AMIA (2013)
Maxwell Lewis Neal, Daniel L. Cook, John H. Gennari
An OWL knowledge base for classifying and querying collections of physiological models: A prototype human physiome. ICBO (2013)
Daniel L. Cook, Maxwell Lewis Neal, Robert Hoehndorf, Georgios V. Gkoutos, John H. Gennari
Representing physiological processes and their participants with PhysioMaps. J. Biomed. Semant. 4 (S-1) (2013)
Daniel L. Cook, Michal Galdzicki, Maxwell Lewis Neal, José L. V. Mejino Jr., John H. Gennari
HeartCyc: A Cardiac Cycle Process Ontology Based in the Ontology of Physics for Biology. ICBO (2011)
John H. Gennari, Maxwell Lewis Neal, Michal Galdzicki, Daniel L. Cook
Multiple ontologies in action: Composite annotations for biosimulation models. J. Biomed. Informatics 44 (1) (2011)
Robert Hoehndorf, Michel Dumontier, John H. Gennari, Sarala M. Wimalaratne, Bernard de Bono, Daniel L. Cook, Georgios V. Gkoutos
Integrating systems biology models and biomedical ontologies. BMC Syst. Biol. 5 (2011)
Maxwell Lewis Neal, John H. Gennari, Theo Arts, Daniel L. Cook
Advances in Semantic Representation for Multiscale Biosimulation: A Case Study in Merging Models. Pacific Symposium on Biocomputing (2009)
Ching-Ping Lin, Thomas H. Payne, W. Paul Nichol, Patricia J. Hoey, Curtis L. Anderson, John H. Gennari
Research Paper: Evaluating Clinical Decision Support Systems: Monitoring CPOE Order Check Override Rates in the Department of Veterans Affairs' Computerized Patient Record System. J. Am. Medical Informatics Assoc. 15 (5) (2008)
John H. Gennari, Maxwell Lewis Neal, Brian E. Carlson, Daniel L. Cook
Integration of Multi-Scale Biosimulation Models via Light-Weight Semantics. Pacific Symposium on Biocomputing (2008)
Imre Solti, Barry Aaronson, Grant S. Fletcher, Magdolna Solti, John H. Gennari, Melissa Cooper, Thomas H. Payne
Building an Automated Problem List Based on Natural Language Processing: Lessons Learned in the Early Phase of Development. AMIA (2008)
Daniel L. Cook, José L. V. Mejino Jr., Maxwell Lewis Neal, John H. Gennari
Bridging Biological Ontologies and Biosimulation: The Ontology of Physics for Biology. AMIA (2008)
Chunhua Weng, John H. Gennari, Douglas B. Fridsma
User-centered semantic harmonization: A case study. J. Biomed. Informatics 40 (3) (2007)
Xiang Li, John H. Gennari, James F. Brinkley
XGI: A Graphical Interface for XQuery Creation. AMIA (2007)
Chunhua Weng, David W. McDonald, Dana Sparks, Jason McCoy, John H. Gennari
Participatory design of a collaborative clinical trial protocol writing system. Int. J. Medical Informatics 76 (S1) (2007)
Daniel L. Cook, Jesse C. Wiley, John H. Gennari
Chalkboard: Ontology-Based Pathway Modeling And Qualitative Inference Of Disease Mechanisms. Pacific Symposium on Biocomputing (2007)
Hao Li, John H. Gennari, James F. Brinkley
Model Driven Laboratory Information Management Systems. AMIA (2006)
Andrea Civan, John H. Gennari, Wanda Pratt
Integrating Protocol Schedules with Patients' Personal Calendars. AMIA (2006)
Alan Au, Xiang Li, John H. Gennari
Differences Among Cell-structure Ontologies: FMA, GO, & CCO. AMIA (2006)
James F. Brinkley, Dan Suciu, Landon Detwiler, John H. Gennari, Cornelius Rosse
A framework for using reference ontologies as a foundation for the semantic web. AMIA (2006)
John H. Gennari, Adam Silberfein, Jesse C. Wiley
Integrating Genomic Knowledge Sources Through an Anatomy Ontology. Pacific Symposium on Biocomputing (2005)
John H. Gennari, Chunhua Weng, Jacqueline Benedetti, David W. McDonald
Asynchronous communication among clinical researchers: A study for systems design. Int. J. Medical Informatics 74 (10) (2005)
Ravensara S. Travillian, John H. Gennari, Linda G. Shapiro
Of Mice and Men: Design of a Comparative Anatomy Information System. AMIA (2005)
John H. Gennari, Peter Mork, Hao Li
Knowledge transformations between frame systems and RDB systems. K-CAP (2005)
Ching-Ping Lin, W. Paul Nichol, Patty Hoey, Terry L. Roth, Curtis L. Anderson, John H. Gennari, Thomas H. Payne
Approach for Analysis of Order Check Overrides in a Computerized Practitioner Order Entry System. AMIA (2005)
Chunhua Weng, John H. Gennari, David W. McDonald
A Collaborative Clinical Trial Protocol Writing System. MedInfo (2004)
John H. Gennari, Chunhua Weng, David W. McDonald, Jacqueline Benedetti, Stephanie Green
An Ethnographic Study of Collaborative Clinical Trial Protocol Writing. MedInfo (2004)
Chunhua Weng, John H. Gennari
Asynchronous collaborative writing through annotations. CSCW (2004)
Wanda Pratt, Madhu C. Reddy, David W. McDonald, Peter Tarczy-Hornoch, John H. Gennari
Incorporating ideas from computer-supported cooperative work. J. Biomed. Informatics 37 (2) (2004)
David W. McDonald, Chunhua Weng, John H. Gennari
The multiple views of inter-organizational authoring. CSCW (2004)
John H. Gennari, Mark A. Musen, Ray W. Fergerson, William E. Grosso, Monica Crubézy, Henrik Eriksson, Natalya Fridman Noy, Samson W. Tu
The evolution of Protégé: an environment for knowledge-based systems development. Int. J. Hum. Comput. Stud. 58 (1) (2003)
Franz Calvo, John H. Gennari
Interoperability of Protege 2.0 beta and OilEd 3.5 in the Domain Knowledge of Osteoporosis. EON (2003)
Chunhua Weng, John H. Gennari, David W. McDonald
Scenario-based Participatory Design of A Collaborative Clinical Trial Protocol Authoring System. AMIA (2003)
Chunhua Weng, Michael G. Kahn, John H. Gennari
Temporal knowledge representation for scheduling tasks in clinical trial protocols. AMIA (2002)
John H. Gennari, David Sklar, John S. Silva
Cross-tool communication: from protocol authoring to eligibility determination. AMIA (2001)
John H. Gennari, Madhu C. Reddy
Participatory design and an eligibility screening tool. AMIA (2000)
Daniel L. Rubin, John H. Gennari, Mark A. Musen
Knowledge representation and tool support for critiquing clinical trial protocols. AMIA (2000)
Daniel L. Rubin, John H. Gennari, Sandra Srinivas, Allen Yuen, Herbert Kaizer, Mark A. Musen, John S. Silva
Tool support for authoring eligibility criteria for cancer trials. AMIA (1999)
John H. Gennari, Heyning Cheng, Russ B. Altman, Mark A. Musen
Reuse, CORBA, and knowledge-based systems. Int. J. Hum. Comput. Stud. 49 (4) (1998)
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
Research Paper: The GuideLine Interchange Format: A Model for Representing Guidelines. J. Am. Medical Informatics Assoc. 5 (4) (1998)
Thomas E. Rothenfluh, John H. Gennari, Henrik Eriksson, Angel R. Puerta, Samson W. Tu, Mark A. Musen
Reusable ontologies, knowledge-acquisition tools, and performance systems: PROTÉGÉ-II solutions to Sisyphus-2. Int. J. Hum. Comput. Stud. 44 (3-4) (1996)
Samson W. Tu, Henrik Eriksson, John H. Gennari, Yuval Shahar, Mark A. Musen
Ontology-based configuration of problem-solving methods and generation of knowledge-acquisition tools: application of PROTEGE-II to protocol-based decision support. Artif. Intell. Medicine 7 (3) (1995)
John H. Gennari, Russ B. Altman, Mark A. Musen
Reuse with PROTÉgÉ-II: From Elevators to Ribosomes. SSR (1995)
Angel R. Puerta, Henrik Eriksson, John H. Gennari, Mark A. Musen
Model-Based Automated Generation of User Interfaces. AAAI (1994)
John H. Gennari, Samson W. Tu, Thomas E. Rothenfluh, Mark A. Musen
Mapping domains to methods in support of reuse. Int. J. Hum. Comput. Stud. 41 (3) (1994)
Angel R. Puerta, Henrik Eriksson, John H. Gennari, Mark A. Musen
Beyond Data Models for Automated User Interface Generation. BCS HCI (1994)
Kazuo Hiraki, John H. Gennari, Yoshinobu Yamamoto, Yuichiro Anzai
Learning Spatial Relations from Images. ML (1991)
John H. Gennari
Focused Concept Formation. ML (1989)
John H. Gennari, Pat Langley, Douglas H. Fisher
Models of Incremental Concept Formation. Artif. Intell. 40 (1-3) (1989)