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John H. Gennari
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2020 – today
- 2023
- [j32]Woosub Shin, John H. Gennari, Joseph L. Hellerstein, Herbert M. Sauro:
An automated model annotation system (AMAS) for SBML models. Bioinform. 39(10) (2023) - [j31]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) - 2022
- [j30]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 B. 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 A. 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 Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. 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): 108-114 (2022) - [i1]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 B. 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 A. 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 Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. 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 abs/2203.06732 (2022) - 2021
- [j29]Ciaran M. Welsh, David P. Nickerson, Anand K. Rampadarath, Maxwell Lewis Neal, Herbert M. Sauro, John H. Gennari:
libOmexMeta: enabling semantic annotation of models to support FAIR principles. Bioinform. 37(24): 4898-4900 (2021) - [j28]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) - 2020
- [j27]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)
2010 – 2019
- 2019
- [j26]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): 540-550 (2019) - [j25]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): 1600-1602 (2019) - [j24]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): 11:1-11:11 (2019) - [j23]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): 457:1-457:10 (2019) - [j22]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) - [c43]Daniel L. Cook, John H. Gennari, Maxwell Lewis Neal:
The Ontology of Physics for Biology - A Companion to Basic Formal Ontology. ICBO 2019: 1-9 - 2018
- [j21]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) - [c42]Ahmad K. Aljadaan, Peter Tarczy-Hornoch, Adam B. Wilcox, Todd F. Dardas, John H. Gennari:
Counting Readmissions: Surprisingly difficult. AMIA 2018 - [c41]Lucy Lu Wang, John H. Gennari:
Quantifying the effects of gene entity disambiguation for GSEA. AMIA 2018 - 2017
- [c40]Daniel L. Cook, John H. Gennari, Maxwell Lewis Neal:
Extending the Ontology of Physics for Biology with Thermodynamics. ICBO 2017 - [c39]Lucy Lu Wang, John H. Gennari:
Similarity Metrics for Determining Overlap Among Biological Pathways. ICBO 2017 - 2016
- [j20]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) - [c38]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 - [c37]Lucy Lu Wang, John H. Gennari, Neil F. Abernethy:
Discovering representational differences between pathway knowledge bases for pathway resource merging. AMIA 2016 - [c36]Maxwell Lewis Neal, John H. Gennari, Daniel L. Cook:
Qualitative Causal Analyses of Biosimulation Models. ICBO/BioCreative 2016 - [c35]Lucy Lu Wang, John H. Gennari, Neil F. Abernethy:
An Analysis of Differences in Biological Pathway Resources. ICBO/BioCreative 2016 - 2015
- [j19]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) - [c34]Ahmad Aljadaan, John H. Gennari, Mark H. Phillips, Wade P. Smith:
Decision Analysis for Oropharyngeal Cancer in Radiotherapy. AMIA 2015 - 2014
- [j18]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) - 2013
- [j17]Deanna Petrochilos, Ali Shojaie, John H. Gennari, Neil F. Abernethy:
Using random walks to identify cancer-associated modules in expression data. BioData Min. 6: 17 (2013) - [j16]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: 41 (2013) - [j15]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): S2 (2013) - [c33]Nikhil Gopal, Michal Galdzicki, Bryan Bartley, Evren Sirin, John H. Gennari:
Identifying High-Risk Components in Synthetic Biology. AMIA 2013 - [c32]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: 16-21 - 2011
- [j14]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: 124 (2011) - [j13]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): 146-154 (2011) - [c31]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
2000 – 2009
- 2009
- [c30]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: 304-315 - 2008
- [j12]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): 620-626 (2008) - [c29]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 - [c28]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 - [c27]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: 414-425 - 2007
- [j11]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): S245-S251 (2007) - [j10]Chunhua Weng, John H. Gennari, Douglas B. Fridsma:
User-centered semantic harmonization: A case study. J. Biomed. Informatics 40(3): 353-364 (2007) - [c26]Xiang Li, John H. Gennari, James F. Brinkley:
XGI: A Graphical Interface for XQuery Creation. AMIA 2007 - [c25]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: 16-27 - 2006
- [c24]Alan Au, Xiang Li, John H. Gennari:
Differences Among Cell-structure Ontologies: FMA, GO, & CCO. AMIA 2006 - [c23]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 - [c22]Andrea Civan, John H. Gennari, Wanda Pratt:
Integrating Protocol Schedules with Patients' Personal Calendars. AMIA 2006 - [c21]Hao Li, John H. Gennari, James F. Brinkley:
Model Driven Laboratory Information Management Systems. AMIA 2006 - 2005
- [j9]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): 797-807 (2005) - [c20]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 - [c19]Ravensara S. Travillian, John H. Gennari, Linda G. Shapiro:
Of Mice and Men: Design of a Comparative Anatomy Information System. AMIA 2005 - [c18]John H. Gennari, Peter Mork, Hao Li:
Knowledge transformations between frame systems and RDB systems. K-CAP 2005: 197-198 - [c17]John H. Gennari, Adam Silberfein, Jesse C. Wiley:
Integrating Genomic Knowledge Sources Through an Anatomy Ontology. Pacific Symposium on Biocomputing 2005: 128-139 - 2004
- [j8]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): 128-137 (2004) - [c16]David W. McDonald, Chunhua Weng, John H. Gennari:
The multiple views of inter-organizational authoring. CSCW 2004: 564-573 - [c15]Chunhua Weng, John H. Gennari:
Asynchronous collaborative writing through annotations. CSCW 2004: 578-581 - [c14]John H. Gennari, Chunhua Weng, David W. McDonald, Jacqueline Benedetti, Stephanie Green:
An Ethnographic Study of Collaborative Clinical Trial Protocol Writing. MedInfo 2004: 1461-1465 - [c13]Chunhua Weng, John H. Gennari, David W. McDonald:
A Collaborative Clinical Trial Protocol Writing System. MedInfo 2004: 1481-1485 - 2003
- [j7]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): 89-123 (2003) - [c12]Chunhua Weng, John H. Gennari, David W. McDonald:
Scenario-based Participatory Design of A Collaborative Clinical Trial Protocol Authoring System. AMIA 2003 - [c11]Franz Calvo, John H. Gennari:
Interoperability of Protege 2.0 beta and OilEd 3.5 in the Domain Knowledge of Osteoporosis. EON 2003 - [e1]John H. Gennari, Bruce W. Porter, Yolanda Gil:
Proceedings of the 2nd International Conference on Knowledge Capture (K-CAP 2003), October 23-25, 2003, Sanibel Island, FL, USA. ACM 2003, ISBN 1-58113-583-1 [contents] - 2002
- [c10]Chunhua Weng, Michael G. Kahn, John H. Gennari:
Temporal knowledge representation for scheduling tasks in clinical trial protocols. AMIA 2002 - 2001
- [c9]John H. Gennari, David Sklar, John S. Silva:
Cross-tool communication: from protocol authoring to eligibility determination. AMIA 2001 - 2000
- [c8]John H. Gennari, Madhu C. Reddy:
Participatory design and an eligibility screening tool. AMIA 2000 - [c7]Daniel L. Rubin, John H. Gennari, Mark A. Musen:
Knowledge representation and tool support for critiquing clinical trial protocols. AMIA 2000
1990 – 1999
- 1999
- [c6]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 - 1998
- [j6]John H. Gennari, Heyning Cheng, Russ B. Altman, Mark A. Musen:
Reuse, CORBA, and knowledge-based systems. Int. J. Hum. Comput. Stud. 49(4): 523-546 (1998) - [j5]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): 357-372 (1998) - 1996
- [j4]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): 303-332 (1996) - 1995
- [j3]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): 257-289 (1995) - [c5]John H. Gennari, Russ B. Altman, Mark A. Musen:
Reuse with PROTÉgÉ-II: From Elevators to Ribosomes. SSR 1995: 72-80 - 1994
- [j2]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): 399-424 (1994) - [c4]Angel R. Puerta, Henrik Eriksson, John H. Gennari, Mark A. Musen:
Model-Based Automated Generation of User Interfaces. AAAI 1994: 471-477 - [c3]Angel R. Puerta, Henrik Eriksson, John H. Gennari, Mark A. Musen:
Beyond Data Models for Automated User Interface Generation. BCS HCI 1994: 353-366 - 1991
- [c2]Kazuo Hiraki, John H. Gennari, Yoshinobu Yamamoto, Yuichiro Anzai:
Learning Spatial Relations from Images. ML 1991: 407-411
1980 – 1989
- 1989
- [j1]John H. Gennari, Pat Langley, Douglas H. Fisher:
Models of Incremental Concept Formation. Artif. Intell. 40(1-3): 11-61 (1989) - [c1]John H. Gennari:
Focused Concept Formation. ML 1989: 379-382
Coauthor Index
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