J Kyle Medley
J Kyle Medley
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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
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
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
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
Synthetic biology: engineering living systems from biophysical principles
BA Bartley, K Kim, JK Medley, HM Sauro
Biophysical journal 112 (6), 1050-1058, 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
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
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
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
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
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
Untargeted metabolomics of the cavefish Astyanax mexicanus reveals the basis of metabolic strategies in adaptation to extreme conditions
JK Medley, J Person, R Peuß, L Olsen, S Xiong, N Rohner
BioRxiv, 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
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
libsbmljs—Enabling web-based SBML tools
JK Medley, J Hellerstein, HM Sauro
Biosystems 195, 104150, 2020
Towards a Scalable, Future-Proof Platform for Dynamical Modeling in Biology
JK Medley
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
A portable library to support the SBML Layout Extension
JK Medley, K Choi, HM Sauro
bioRxiv, 035725, 2016
Accelerated Biochemical Kinetic Model Fitting via the Asynchronous, Generalized Island Method
JK Medley, S Asifullah, J Hellerstein, HM Sauro
bioRxiv, 660522, 2019
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