| The Ontology of Physics for Biology: Semantic Modeling of Multiscale, Multidomain Physiological Systems DL Cook, JH Gennari, ML Neal CRC Press, 2023 | 1 | 2023 |
| VSCode-Antimony: a source editor for building, analyzing, and translating antimony models S Ma, L Fan, SA Konanki, E Liu, JH Gennari, LP Smith, JL Hellerstein, ... Bioinformatics 39 (12), btad753, 2023 | | 2023 |
| An automated model annotation system (AMAS) for SBML models W Shin, JH Gennari, JL Hellerstein, HM Sauro Bioinformatics 39 (11), btad658, 2023 | | 2023 |
| BioSimulators: a central registry of simulation engines and services for recommending specific tools B Shaikh, LP Smith, D Vasilescu, G Marupilla, M Wilson, E Agmon, ... Nucleic acids research 50 (W1), W108-W114, 2022 | 16 | 2022 |
| NLIMED: Natural Language Interface for model entity discovery in biosimulation model repositories Y Munarko, DM Sarwar, A Rampadarath, K Atalag, JH Gennari, ML Neal, ... Frontiers in Physiology 13, 820683, 2022 | 4 | 2022 |
| Understanding the differences in cognitively defined subgroups in Alzheimer's disease HK Sohi, JH Gennari, PK Crane, EM Wijsman | | 2022 |
| libOmexMeta: enabling semantic annotation of models to support FAIR principles C Welsh, DP Nickerson, A Rampadarath, ML Neal, HM Sauro, JH Gennari Bioinformatics 37 (24), 4898-4900, 2021 | 7 | 2021 |
| OMEX metadata specification (version 1.2) JH Gennari, M König, G Misirli, ML Neal, DP Nickerson, D Waltemath Journal of integrative bioinformatics 18 (3), 20210020, 2021 | 9 | 2021 |
| OMEX metadata specification (version 1.2). DP Nickerson, D Waltemath, JH Gennari, M König, G Misirli, ML Neal Journal of integrative bioinformatics, 2021 | | 2021 |
| SBMate: A Framework for Evaluating Quality of Annotations in Systems Biology Models W Shin, JL Hellerstein, Y Munarko, ML Neal, DP Nickerson, ... bioRxiv, 2021.10. 09.463757, 2021 | 2 | 2021 |
| Practical resources for enhancing the reproducibility of mechanistic modeling in systems biology ML Blinov, JH Gennari, JR Karr, II Moraru, DP Nickerson, HM Sauro Current Opinion in Systems Biology 27, 100350, 2021 | 8 | 2021 |
| Open modeling and exchange (OMEX) metadata specification version 1.0 ML Neal, JH Gennari, D Waltemath, DP Nickerson, M König Journal of integrative bioinformatics 17 (2-3), 20200020, 2020 | 12 | 2020 |
| Deep phenotyping of cardiac function in heart transplant patients using cardiovascular system models AL Colunga, KG Kim, NP Woodall, TF Dardas, JH Gennari, MS Olufsen, ... The Journal of Physiology 598 (15), 3203-3222, 2020 | 16 | 2020 |
| OMEX Metadata Specification version 1.0 M Neal, J Gennari, D Waltemath, D Nickerson, M König | | 2020 |
| Everyone’s Variant Annotation Tool: EVAT Y Ma University of Washington, 2020 | | 2020 |
| Predicting instances of pathway ontology classes for pathway integration LL Wang, G Thomas Hayman, JR Smith, M Tutaj, ME Shimoyama, ... Journal of biomedical semantics 10, 1-11, 2019 | 1 | 2019 |
| Model annotation and discovery with the Physiome Model Repository DM Sarwar, R Kalbasi, JH Gennari, BE Carlson, ML Neal, B Bono, ... BMC bioinformatics 20, 1-10, 2019 | 24 | 2019 |
| P1‐361: REGIONAL DIFFERENCES IN CORTICAL THICKNESS ACROSS COGNITIVELY DEFINED ALZHEIMER'S DISEASE SUBGROUPS H Sohi, J Gennari, T Madhyastha, BE Lee, SL Risacher, C MacDonald, ... Alzheimer's & Dementia 15, P389-P390, 2019 | | 2019 |
| P1‐335: FUNCTIONAL CONNECTIVITY PATTERNS ACROSS COGNITIVELY‐DEFINED ALZHEIMER'S DISEASE SUBTYPES IN THE ALZHEIMER'S DISEASE NEUROIMAGING INITIATIVE BE Lee, PK Crane, SL Risacher, C Groot, J Mez, AJ Saykin, EH Trittschuh, ... Alzheimer's & Dementia 15, P374-P375, 2019 | | 2019 |
| Synthetic biology open language (SBOL) version 2.3 C Madsen, A Goñi Moreno, U P, Z Palchick, N Roehner, C Atallah, ... Journal of integrative bioinformatics 16 (2), 20190025, 2019 | 31 | 2019 |
