| libRoadRunner: a high performance SBML simulation and analysis library ET Somogyi, JM Bouteiller, JA Glazier, M König, JK Medley, MH Swat, ... Bioinformatics 31 (20), 3315-3321, 2015 | 149 | 2015 |
| Tellurium: an extensible python-based modeling environment for systems and synthetic biology K Choi, JK Medley, M König, K Stocking, L Smith, S Gu, HM Sauro Biosystems 171, 74-79, 2018 | 137 | 2018 |
| Toward community standards and software for whole-cell modeling D Waltemath, JR Karr, FT Bergmann, V Chelliah, M Hucka, M Krantz, ... IEEE Transactions on Biomedical Engineering 63 (10), 2007-2014, 2016 | 64 | 2016 |
| Tellurium notebooks—an environment for reproducible dynamical modeling in systems biology JK Medley, K Choi, M König, L Smith, S Gu, J Hellerstein, SC Sealfon, ... PLoS computational biology 14 (6), e1006220, 2018 | 61 | 2018 |
| Synthetic biology: engineering living systems from biophysical principles BA Bartley, K Kim, JK Medley, HM Sauro Biophysical journal 112 (6), 1050-1058, 2017 | 45 | 2017 |
| Guidelines for reproducibly building and simulating systems biology models JK Medley, AP Goldberg, JR Karr IEEE Transactions on Biomedical Engineering 63 (10), 2015-2020, 2016 | 32 | 2016 |
| Metabolic reprogramming underlies cavefish muscular endurance despite loss of muscle mass and contractility L Olsen, M Levy, JK Medley, H Hassan, B Miller, R Alexander, E Wilcock, ... Proceedings of the National Academy of Sciences 120 (5), e2204427120, 2023 | 22 | 2023 |
| Tellurium: A python based modeling and reproducibility platform for systems biology K Choi, JK Medley, C Cannistra, M König, L Smith, K Stocking, HM Sauro BioRxiv, 054601, 2016 | 22 | 2016 |
| phraSED-ML: A paraphrased, human-readable adaptation of SED-ML K Choi, LP Smith, JK Medley, HM Sauro Journal of bioinformatics and computational biology 14 (06), 1650035, 2016 | 18 | 2016 |
| 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 | 17 | 2022 |
| The metabolome of Mexican cavefish shows a convergent signature highlighting sugar, antioxidant, and Ageing-Related metabolites JK Medley, J Persons, T Biswas, L Olsen, R Peuß, J Krishnan, S Xiong, ... Elife 11, e74539, 2022 | 16 | 2022 |
| A compiler for biological networks on silicon chips JK Medley, J Teo, SS Woo, J Hellerstein, R Sarpeshkar, HM Sauro PLoS computational biology 16 (9), e1008063, 2020 | 7 | 2020 |
| Untargeted metabolomics of the cavefish Astyanax mexicanus reveals the basis of metabolic strategies in adaptation to extreme conditions JK Medley, J Persons, R Peuß, L Olsen, S Xiong, N Rohner BioRxiv, 2020 | 6* | 2020 |
| Tellurium: a python based modeling and reproducibility platform for systems biology. bioRxiv, 054601 K Choi, JK Medley, C Cannistra, M Konig, L Smith, K Stocking, HM Sauro | 5 | 2016 |
| libsbmljs—Enabling web-based SBML tools JK Medley, J Hellerstein, HM Sauro Biosystems 195, 104150, 2020 | 3 | 2020 |
| Towards a Scalable, Future-Proof Platform for Dynamical Modeling in Biology JK Medley | 1 | 2019 |
| Tellurium notebooks-an environment for dynamical model development, reproducibility, and reuse JK Medley, K Choi, M König, L Smith, S Gu, J Hellerstein, SC Sealfon, ... bioRxiv, 239004, 2017 | 1 | 2017 |
| A portable library to support the SBML Layout Extension JK Medley, K Choi, HM Sauro bioRxiv, 035725, 2016 | 1 | 2016 |
| Accelerated Biochemical Kinetic Model Fitting via the Asynchronous, Generalized Island Method JK Medley, S Asifullah, J Hellerstein, HM Sauro bioRxiv, 660522, 2019 | | 2019 |
