| Year |
Citation |
Score |
| 2024 |
Li LX, Aguilar B, Gennari JH, Qin G. Merging logical models: An application in Acute Myeloid Leukemia modeling. Biorxiv : the Preprint Server For Biology. PMID 39345612 DOI: 10.1101/2024.09.13.612961 |
0.353 |
|
| 2023 |
Ma S, Fan L, Konanki SA, Liu E, Gennari JH, Smith LP, Hellerstein JL, Sauro HM. VSCode-Antimony: A Source Editor for Building, Analyzing, and Translating Antimony Models. Bioinformatics (Oxford, England). PMID 38096590 DOI: 10.1093/bioinformatics/btad753 |
0.658 |
|
| 2023 |
Shin W, Gennari JH, Hellerstein JL, Sauro HM. An automated model annotation system (AMAS) for SBML models. Bioinformatics (Oxford, England). 39. PMID 37882737 DOI: 10.1093/bioinformatics/btad658 |
0.635 |
|
| 2023 |
Shin W, Gennari JH, Hellerstein JL, Sauro HM. An Automated Model Annotation System (AMAS) for SBML Models. Biorxiv : the Preprint Server For Biology. PMID 37503075 DOI: 10.1101/2023.07.19.549722 |
0.635 |
|
| 2022 |
Shaikh B, Smith LP, Vasilescu D, Marupilla G, Wilson M, Agmon E, Agnew H, Andrews SS, Anwar A, Beber ME, Bergmann FT, Brooks D, Brusch L, Calzone L, Choi K, ... ... Gennari JH, et al. BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Research. PMID 35524558 DOI: 10.1093/nar/gkac331 |
0.566 |
|
| 2022 |
Munarko Y, Sarwar DM, Rampadarath A, Atalag K, Gennari JH, Neal ML, Nickerson DP. NLIMED: Natural Language Interface for Model Entity Discovery in Biosimulation Model Repositories. Frontiers in Physiology. 13: 820683. PMID 35283794 DOI: 10.3389/fphys.2022.820683 |
0.697 |
|
| 2021 |
Gennari JH, König M, Misirli G, Neal ML, Nickerson DP, Waltemath D. OMEX metadata specification (version 1.2). Journal of Integrative Bioinformatics. 18. PMID 34668356 DOI: 10.1515/jib-2021-0020 |
0.729 |
|
| 2021 |
Welsh C, Nickerson DP, Rampadarath A, Neal ML, Sauro HM, Gennari JH. libOmexMeta: Enabling semantic annotation of models to support FAIR principles. Bioinformatics (Oxford, England). PMID 34132740 DOI: 10.1093/bioinformatics/btab445 |
0.778 |
|
| 2020 |
Neal ML, Gennari JH, Waltemath D, Nickerson DP, König M. Open modeling and exchange (OMEX) metadata specification version 1.0. Journal of Integrative Bioinformatics. PMID 32589606 DOI: 10.1515/Jib-2020-0020 |
0.744 |
|
| 2019 |
Sarwar DM, Kalbasi R, Gennari JH, Carlson BE, Neal ML, Bono B, Atalag K, Hunter PJ, Nickerson DP. Model annotation and discovery with the Physiome Model Repository. Bmc Bioinformatics. 20: 457. PMID 31492098 DOI: 10.1186/S12859-019-2987-Y |
0.733 |
|
| 2019 |
Madsen C, Goñi Moreno A, P U, Palchick Z, Roehner N, Atallah C, Bartley B, Choi K, Cox RS, Gorochowski T, Grünberg R, Macklin C, McLaughlin J, Meng X, Nguyen T, ... ... Gennari JH, et al. Synthetic Biology Open Language (SBOL) Version 2.3. Journal of Integrative Bioinformatics. PMID 31199770 DOI: 10.1515/Jib-2019-0025 |
0.65 |
|
| 2019 |
Misirli G, Taylor R, Goñi-Moreno A, Mclaughlin JA, Myers CJ, Gennari J, Lord P, Wipat A. SBOL-OWL: An ontological approach for formal and semantic representation of synthetic biology information. Acs Synthetic Biology. PMID 31059645 DOI: 10.1021/Acssynbio.8B00532 |
0.436 |
|
| 2018 |
Neal ML, König M, Nickerson D, Misirli G, Kalbasi R, Dräger A, Atalag K, Chelliah V, Cooling MT, Cook DL, Crook S, de Alba M, Friedman SH, Garny A, Gennari JH, et al. Harmonizing semantic annotations for computational models in biology. Briefings in Bioinformatics. PMID 30462164 DOI: 10.1093/Bib/Bby087 |
0.796 |
|
| 2018 |
Neal ML, Thompson CT, Kim KG, James RC, Cook DL, Carlson BE, Gennari JH. SemGen: a tool for semantics-based annotation and composition of biosimulation models. Bioinformatics (Oxford, England). PMID 30256901 DOI: 10.1093/Bioinformatics/Bty829 |
0.746 |
|
| 2018 |
Cox RS, Madsen C, McLaughlin JA, Nguyen T, Roehner N, Bartley B, Beal J, Bissell M, Choi K, Clancy K, Grünberg R, Macklin C, Misirli G, Oberortner E, Pocock M, ... ... Gennari JH, et al. Synthetic Biology Open Language (SBOL) Version 2.2.0. Journal of Integrative Bioinformatics. PMID 29605823 DOI: 10.1515/Jib-2018-0001 |
0.633 |
|
| 2017 |
Kalet AM, Doctor JN, Gennari JH, Phillips MH. Developing Bayesian networks from a dependency-layered ontology: a proof-of-concept in radiation oncology. Medical Physics. PMID 28500765 DOI: 10.1002/Mp.12340 |
0.377 |
|
| 2016 |
Beal J, Cox RS, Grünberg R, McLaughlin J, Nguyen T, Bartley B, Bissell M, Choi K, Clancy K, Macklin C, Madsen C, Misirli G, Oberortner E, Pocock M, Roehner N, ... ... Gennari JH, et al. Synthetic Biology Open Language (SBOL) Version 2.1.0. Journal of Integrative Bioinformatics. 13: 30-132. PMID 29215992 DOI: 10.1515/jib-2016-291 |
0.606 |
|
| 2016 |
Neal ML, Gennari JH, Cook DL. Qualitative causal analyses of biosimulation models. Ceur Workshop Proceedings. 1747. PMID 28804276 |
0.72 |
|
| 2016 |
Beal J, Cox RS, Grünberg R, McLaughlin J, Nguyen T, Bartley B, Bissell M, Choi K, Clancy K, Macklin C, Madsen C, Misirli G, Oberortner E, Pocock M, Roehner N, ... ... Gennari J, et al. Synthetic Biology Open Language (SBOL) Version 2.1.0. Journal of Integrative Bioinformatics. 13: 291. PMID 28187407 DOI: 10.2390/biecoll-jib-2016-291 |
0.606 |
|
| 2016 |
Roehner N, Beal J, Clancy K, Bartley B, Misirli G, Gruenberg R, Oberortner E, Pocock M, Bissell M, Madsen C, Nguyen T, Zhang M, Zhang Z, Zundel Z, Densmore D, ... Gennari J, et al. Sharing Structure and Function in Biological Design with SBOL 2.0. Acs Synthetic Biology. PMID 27111421 DOI: 10.1021/Acssynbio.5B00215 |
0.639 |
|
| 2015 |
Bartley B, Beal J, Clancy K, Misirli G, Roehner N, Oberortner E, Pocock M, Bissell M, Madsen C, Nguyen T, Zhang Z, Gennari JH, Myers C, Wipat A, Sauro H. Synthetic Biology Open Language (SBOL) Version 2.0.0. Journal of Integrative Bioinformatics. 12: 902-991. PMID 29220967 DOI: 10.1515/jib-2015-272 |
0.636 |
|
| 2015 |
Neal ML, Carlson BE, Thompson CT, James RC, Kim KG, Tran K, Crampin EJ, Cook DL, Gennari JH. Semantics-Based Composition of Integrated Cardiomyocyte Models Motivated by Real-World Use Cases. Plos One. 10: e0145621. PMID 26716837 DOI: 10.1371/Journal.Pone.0145621 |
0.717 |
|
| 2015 |
Bartley B, Beal J, Clancy K, Misirli G, Roehner N, Oberortner E, Pocock M, Bissell M, Madsen C, Nguyen T, Zhang Z, Gennari JH, Myers C, Wipat A, Sauro H. Synthetic Biology Open Language (SBOL) Version 2.0.0. Journal of Integrative Bioinformatics. 12: 272. PMID 26528570 DOI: 10.1515/Jib-2016-291 |
0.669 |
|
| 2015 |
Kalet AM, Gennari JH, Ford EC, Phillips MH. Bayesian network models for error detection in radiotherapy plans. Physics in Medicine and Biology. 60: 2735-49. PMID 25768885 DOI: 10.1088/0031-9155/60/7/2735 |
0.306 |
|
| 2014 |
Neal ML, Cooling MT, Smith LP, Thompson CT, Sauro HM, Carlson BE, Cook DL, Gennari JH. A reappraisal of how to build modular, reusable models of biological systems. Plos Computational Biology. 10: e1003849. PMID 25275523 DOI: 10.1371/Journal.Pcbi.1003849 |
0.678 |
|
| 2014 |
Galdzicki M, Clancy KP, Oberortner E, Pocock M, Quinn JY, Rodriguez CA, Roehner N, Wilson ML, Adam L, Anderson JC, Bartley BA, Beal J, Chandran D, Chen J, Densmore D, ... ... Gennari JH, et al. The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. Nature Biotechnology. 32: 545-50. PMID 24911500 DOI: 10.1038/Nbt.2891 |
0.784 |
|
| 2014 |
Kalet A, Phillips M, Gennari J. SU-E-T-51: Bayesian Network Models for Radiotherapy Error Detection Medical Physics. 41: 233-233. DOI: 10.1118/1.4888381 |
0.355 |
|
| 2013 |
Cook DL, Neal ML, Bookstein FL, Gennari JH. Ontology of physics for biology: representing physical dependencies as a basis for biological processes. Journal of Biomedical Semantics. 4: 41. PMID 24295137 DOI: 10.1186/2041-1480-4-41 |
0.66 |
|
| 2013 |
Cook DL, Neal ML, Hoehndorf R, Gkoutos GV, Gennari JH. Representing physiological processes and their participants with PhysioMaps. Journal of Biomedical Semantics. 4: S2. PMID 23735231 DOI: 10.1186/2041-1480-4-S1-S2 |
0.704 |
|
| 2013 |
Neal ML, Cook DL, Gennari JH. An OWL knowledge base for classifying and querying collections of physiological models: A prototype human physiome Ceur Workshop Proceedings. 1060: 16-21. |
0.659 |
|
| 2011 |
Cook DL, Bookstein FL, Gennari JH. Physical properties of biological entities: an introduction to the ontology of physics for biology. Plos One. 6: e28708. PMID 22216106 DOI: 10.1371/Journal.Pone.0028708 |
0.462 |
|
| 2011 |
Lin CP, Gennari JH. Understanding the work of pediatric inpatient medicine teams: implications for information system requirements. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 2011: 455-64. PMID 22195099 |
0.476 |
|
| 2011 |
Hoehndorf R, Dumontier M, Gennari JH, Wimalaratne S, de Bono B, Cook DL, Gkoutos GV. Integrating systems biology models and biomedical ontologies. Bmc Systems Biology. 5: 124. PMID 21835028 DOI: 10.1186/1752-0509-5-124 |
0.489 |
|
| 2011 |
Galdzicki M, Rodriguez C, Chandran D, Sauro HM, Gennari JH. Standard biological parts knowledgebase. Plos One. 6: e17005. PMID 21390321 DOI: 10.1371/Journal.Pone.0017005 |
0.787 |
|
| 2011 |
Gennari JH, Neal ML, Galdzicki M, Cook DL. Multiple ontologies in action: composite annotations for biosimulation models. Journal of Biomedical Informatics. 44: 146-54. PMID 20601121 DOI: 10.1016/J.Jbi.2010.06.007 |
0.801 |
|
| 2011 |
Cook DL, Galdzicki M, Neal ML, Mejino JLV, Gennari JH. HeartCyc, a cardiac cycle process ontology based in the ontology of physics for biology Ceur Workshop Proceedings. 833: 41-46. |
0.742 |
|
| 2010 |
Lin CP, Black RA, Laplante J, Keppel GA, Tuzzio L, Berg AO, Whitener RJ, Buchwald DS, Baldwin LM, Fishman PA, Greene SM, Gennari JH, Tarczy-Hornoch P, Stephens KA. Facilitating health data sharing across diverse practices and communities. Amia Joint Summits On Translational Science Proceedings Amia Summit On Translational Science. 2010: 16-20. PMID 21347138 |
0.477 |
|
| 2009 |
Cook DL, Mejino JL, Neal ML, Gennari JH. Composite annotations: requirements for mapping multiscale data and models to biomedical ontologies. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2009: 2791-4. PMID 19964601 DOI: 10.1109/IEMBS.2009.5333830 |
0.63 |
|
| 2009 |
Neal ML, Gennari JH, Arts T, Cook DL. Advances in semantic representation for multiscale biosimulation: a case study in merging models. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 304-15. PMID 19209710 |
0.684 |
|
| 2008 |
Overby CL, Galdzicki M, Gennari JH. Analysis of simulation environments utilized in biomedical research. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 1077. PMID 18999224 |
0.748 |
|
| 2008 |
Cook DL, Mejino JL, Neal ML, Gennari JH. Bridging biological ontologies and biosimulation: the ontology of physics for biology. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 136-40. PMID 18999003 |
0.692 |
|
| 2008 |
Lin CP, Payne TH, Nichol WP, Hoey PJ, Anderson CL, Gennari JH. Evaluating clinical decision support systems: monitoring CPOE order check override rates in the Department of Veterans Affairs' Computerized Patient Record System. Journal of the American Medical Informatics Association : Jamia. 15: 620-6. PMID 18579840 DOI: 10.1197/Jamia.M2453 |
0.467 |
|
| 2008 |
Gennari JH, Neal ML, Carlson BE, Cook DL. Integration of multi-scale biosimulation models via light-weight semantics. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 414-25. PMID 18229704 |
0.69 |
|
| 2007 |
Lin CP, Gennari JH. Designing CPOE systems using an ecological approach. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 1033. PMID 18694131 |
0.479 |
|
| 2007 |
Weng C, Gennari JH, Fridsma DB. User-centered semantic harmonization: a case study. Journal of Biomedical Informatics. 40: 353-64. PMID 17452021 DOI: 10.1016/J.Jbi.2007.03.004 |
0.605 |
|
| 2007 |
Weng C, McDonald DW, Sparks D, McCoy J, Gennari JH. Participatory design of a collaborative clinical trial protocol writing system. International Journal of Medical Informatics. 76: S245-51. PMID 16798070 DOI: 10.1016/J.Ijmedinf.2006.05.035 |
0.53 |
|
| 2006 |
Li H, Gennari JH, Brinkley JF. Model driven laboratory information management systems. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 484-8. PMID 17238388 |
0.335 |
|
| 2006 |
Brinkley JF, Suciu D, Detwiler LT, Gennari JH, Rosse C. A framework for using reference ontologies as a foundation for the semantic web. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 96-100. PMID 17238310 |
0.338 |
|
| 2006 |
Au AP, Li X, Gennari JH. Differences among cell-structure ontologies: FMA, GO, & CCO. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 16-20. PMID 17238294 |
0.378 |
|
| 2005 |
Lin CP, Nichol WP, Hoey P, Roth TL, Anderson C, Gennari JH, Payne TH. Approach for analysis of order check overrides in a computerized practitioner order entry system. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 1033. PMID 16779320 |
0.408 |
|
| 2005 |
Gennari JH, Weng C, Benedetti J, McDonald DW. Asynchronous communication among clinical researchers: a study for systems design. International Journal of Medical Informatics. 74: 797-807. PMID 16023408 DOI: 10.1016/J.Ijmedinf.2005.03.019 |
0.512 |
|
| 2004 |
Weng C, Gennari JH, McDonald DW. A collaborative clinical trial protocol writing system. Studies in Health Technology and Informatics. 107: 1481-6. PMID 15361061 |
0.43 |
|
| 2004 |
Gennari JH, Weng C, McDonald DW, Benedetti J, Green S. An ethnographic study of collaborative clinical trial protocol writing. Studies in Health Technology and Informatics. 107: 1461-5. PMID 15361057 |
0.416 |
|
| 2004 |
Pratt W, Reddy MC, McDonald DW, Tarczy-Hornoch P, Gennari JH. Incorporating ideas from computer-supported cooperative work. Journal of Biomedical Informatics. 37: 128-37. PMID 15120659 DOI: 10.1016/J.Jbi.2004.04.001 |
0.35 |
|
| 2004 |
McDonald DW, Weng C, Gennari JH. The multiple views of inter-organizational authoring Proceedings of the Acm Conference On Computer Supported Cooperative Work, Cscw. 564-573. |
0.338 |
|
| 2004 |
Weng C, Gennari JH. Asynchronous collaborative writing through annotations Proceedings of the Acm Conference On Computer Supported Cooperative Work, Cscw. 578-581. |
0.442 |
|
| 2003 |
Weng C, Gennari JH, McDonald DW. Scenario-based participatory design of a collaborative clinical trial protocol authoring system. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 1051. PMID 14728554 |
0.429 |
|
| 2003 |
Gennari JH, Musen MA, Fergerson RW, Grosso WE, Crubezy M, Eriksson H, Noy NF, Tu SW. The evolution of Protégé: An environment for knowledge-based systems development International Journal of Human Computer Studies. 58: 89-123. DOI: 10.1016/S1071-5819(02)00127-1 |
0.436 |
|
| 2002 |
Weng C, Kahn M, Gennari J. Temporal knowledge representation for scheduling tasks in clinical trial protocols. Proceedings / Amia ... Annual Symposium. Amia Symposium. 879-83. PMID 12463951 |
0.392 |
|
| 2001 |
Gennari JH, Sklar D, Silva J. Cross-tool communication: from protocol authoring to eligibility determination. Proceedings / Amia ... Annual Symposium. Amia Symposium. 199-203. PMID 11825180 |
0.315 |
|
| 1998 |
Ohno-Machado L, Gennari JH, Murphy SN, Jain NL, Tu SW, Oliver DE, Pattison-Gordon E, Greenes RA, Shortliffe EH, Barnett GO. The guideline interchange format: a model for representing guidelines. Journal of the American Medical Informatics Association : Jamia. 5: 357-72. PMID 9670133 DOI: 10.1136/Jamia.1998.0050357 |
0.393 |
|
| 1998 |
Gennari JH, Cheng H, Altman RB, Musen MA. Reuse, CORBA, and knowledge-based systems International Journal of Human Computer Studies. 49: 523-546. DOI: 10.1006/Ijhc.1998.0217 |
0.369 |
|
| 1996 |
Rothenfluh TE, Gennari JH, Eriksson H, Puerta AR, Tu SW, Musen MA. Reusable ontologies, knowledge-acquisition tools, and performance systems: PROTE´GE´-II solutions to Sisyphus-2 International Journal of Human-Computer Studies \/ International Journal of Man-Machine Studies. 44: 303-332. DOI: 10.1006/Ijhc.1996.0017 |
0.354 |
|
| 1995 |
Tu SW, Eriksson H, Gennari JH, Shahar Y, Musen MA. Ontology-based configuration of problem-solving methods and generation of knowledge-acquisition tools: application of PROTEGE-II to protocol-based decision support. Artificial Intelligence in Medicine. 7: 257-89. PMID 7581625 DOI: 10.1016/0933-3657(95)00006-R |
0.353 |
|
| 1994 |
Gennari JH, Tu SW, Rothenfluh TE, Musen MA. Mapping domains to methods in support of reuse International Journal of Human - Computer Studies. 41: 399-424. DOI: 10.1006/Ijhc.1994.1066 |
0.304 |
|
| 1989 |
Gennari JH, Langley P, Fisher D. Models of incremental concept formation Artificial Intelligence. 40: 11-61. DOI: 10.1016/0004-3702(89)90046-5 |
0.402 |
|
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