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For the most current documentation refer to the "Netflux Documentation.docx" file found at (https://github.com/saucermanlab/Netflux).**
[1] M. J. Kraeutler, A. R. Soltis, and J. J. Saucerman, “Modeling cardiac β-adrenergic signaling with normalized-Hill differential equations: comparison with a biochemical model,” BMC Syst Biol, vol. 4, p. 157, Nov. 2010, doi: 10.1186/1752-0509-4-157.
[2] K. A. Ryall, D. O. Holland, K. A. Delaney, M. J. Kraeutler, A. J. Parker, and J. J. Saucerman, “Network reconstruction and systems analysis of cardiac myocyte hypertrophy signaling,” J Biol Chem, vol. 287, no. 50, pp. 42259–42268, Dec. 2012, doi: 10.1074/jbc.M112.382937.
[3] A. C. Zeigler, W. J. Richardson, J. W. Holmes, and J. J. Saucerman, “A computational model of cardiac fibroblast signaling predicts context-dependent drivers of myofibroblast differentiation,” J Mol Cell Cardiol, vol. 94, pp. 72–81, May 2016, doi: 10.1016/j.yjmcc.2016.03.008.
[4] P. M. Tan, K. S. Buchholz, J. H. Omens, A. D. McCulloch, and J. J. Saucerman, “Predictive model identifies key network regulators of cardiomyocyte mechano-signaling,” PLoS Comput Biol, vol. 13, no. 11, p. e1005854, Nov. 2017, doi: 10.1371/journal.pcbi.1005854.
[5] D. U. Frank, M. D. Sutcliffe, and J. J. Saucerman, “Network-based predictions of in vivo cardiac hypertrophy,” J Mol Cell Cardiol, vol. 121, pp. 180–189, Aug. 2018, doi: 10.1016/j.yjmcc.2018.07.243.
[6] S. M. Rikard et al., “Multiscale Coupling of an Agent-Based Model of Tissue Fibrosis and a Logic-Based Model of Intracellular Signaling,” Front Physiol, vol. 10, p. 1481, 2019, doi: 10.3389/fphys.2019.01481.
[7] S. Cao et al., “Quantification of model and data uncertainty in a network analysis of cardiac myocyte mechanosignalling,” Philos Trans A Math Phys Eng Sci, vol. 378, no. 2173, p. 20190336, Jun. 2020, doi: 10.1098/rsta.2019.0336.
[8] A. Khalilimeybodi, A. M. Paap, S. L. M. Christiansen, and J. J. Saucerman, “Context-specific network modeling identifies new crosstalk in β-adrenergic cardiac hypertrophy,” PLoS Comput Biol, vol. 16, no. 12, p. e1008490, Dec. 2020, doi: 10.1371/journal.pcbi.1008490.
[9] A. C. Zeigler, A. R. Nelson, A. S. Chandrabhatla, O. Brazhkina, J. W. Holmes, and J. J. Saucerman, “Computational model predicts paracrine and intracellular drivers of fibroblast phenotype after myocardial infarction,” Matrix Biol, vol. 91–92, pp. 136–151, Sep. 2020, doi: 10.1016/j.matbio.2020.03.007.
[10] A. C. Estrada, K. Yoshida, J. J. Saucerman, and J. W. Holmes, “A multiscale model of cardiac concentric hypertrophy incorporating both mechanical and hormonal drivers of growth,” Biomech Model Mechanobiol, vol. 20, no. 1, pp. 293–307, Feb. 2021, doi: 10.1007/s10237-020-01385-6.
[11] M. E. Grabowska, B. Chun, R. Moya, and J. J. Saucerman, “Computational model of cardiomyocyte apoptosis identifies mechanisms of tyrosine kinase inhibitor-induced cardiotoxicity,” J Mol Cell Cardiol, vol. 155, pp. 66–77, Jun. 2021, doi: 10.1016/j.yjmcc.2021.02.014.
[12] X. Liu, J. Zhang, A. C. Zeigler, A. R. Nelson, M. L. Lindsey, and J. J. Saucerman, “Network Analysis Reveals a Distinct Axis of Macrophage Activation in Response to Conflicting Inflammatory Cues,” J Immunol, vol. 206, no. 4, pp. 883–891, Feb. 2021, doi: 10.4049/jimmunol.1901444.
[13] J. D. Rogers, J. W. Holmes, J. J. Saucerman, and W. J. Richardson, “Mechano-chemo signaling interactions modulate matrix production by cardiac fibroblasts,” Matrix Biol Plus, vol. 10, p. 100055, Jun. 2021, doi: 10.1016/j.mbplus.2020.100055.
[14] A. C. Zeigler, A. S. Chandrabhatla, S. L. Christiansen, A. R. Nelson, J. W. Holmes, and J. J. Saucerman, “Network model-based screen for FDA-approved drugs affecting cardiac fibrosis,” CPT Pharmacometrics Syst Pharmacol, vol. 10, no. 4, pp. 377–388, Apr. 2021, doi: 10.1002/psp4.12599.
[15] C. M. Gorick, J. J. Saucerman, and R. J. Price, “Computational model of brain endothelial cell signaling pathways predicts therapeutic targets for cerebral pathologies,” J Mol Cell Cardiol, vol. 164, pp. 17–28, Mar. 2022, doi: 10.1016/j.yjmcc.2021.11.005.
[16] S. K. Hota et al., “Brahma safeguards canalization of cardiac mesoderm differentiation,” Nature, vol. 602, no. 7895, pp. 129–134, Feb. 2022, doi: 10.1038/s41586-021-04336-y.
[17] A. Khalilimeybodi et al., “Signaling network model of cardiomyocyte morphological changes in familial cardiomyopathy,” J Mol Cell Cardiol, vol. 174, pp. 1–14, Nov. 2022, doi: 10.1016/j.yjmcc.2022.10.006.
[18] K. Yoshida, J. J. Saucerman, and J. W. Holmes, “Multiscale model of heart growth during pregnancy: integrating mechanical and hormonal signaling,” Biomech Model Mechanobiol, vol. 21, no. 4, pp. 1267–1283, Aug. 2022, doi: 10.1007/s10237-022-01589-y.