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Estimating cell cycle model parameters using systems identification

View ORCID ProfileEdwin Juarez, View ORCID ProfileAhmadreza Ghaffarizadeh, View ORCID ProfileSamuel H. Friedman, View ORCID ProfileEdmond Jonckheere, View ORCID ProfilePaul Macklin
doi: https://doi.org/10.1101/035766
Edwin Juarez
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Ahmadreza Ghaffarizadeh
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Samuel H. Friedman
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Edmond Jonckheere
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Paul Macklin
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Abstract

A current challenge in data-driven mathematical modeling of cancer is identifying biologically-relevant parameters of mathematical models from sparse and often noisy experimental data of mixed types. We describe a cell cycle model and outline how to use the Optimization Toolbox in Matlab to estimate its timescale parameters, given flow cytometry and cell viability (synthetic) data, and illustrate the technique with simulated data. This technique can be similarly applied to a variety of cell cycle models, particularly as more laboratories begin to use high-content, quantitative cell screening and imaging platforms. An advanced version of this work (CellPD: cell line phenotype digitizer) will be released as open source in early 2016 at MultiCellDS.org.

Footnotes

  • Research supported by The Breast Cancer Research Foundation, USC James H. Zumberge Research & Innovation Fund, and USC Provost’s PhD Fellowship.

  • E. Juarez, A. Ghaffarizadeh, S. H. Friedman, and P. Macklin are with the Center for Applied Molecular Medicine, Department of Medicine, University of Southern California, 2250 Alcazar St., HSC-CSC 240, Los Angeles, Ca 90033–9075, USA. E-mail: [juarezro{at}usc.edu, aghaffar{at}usc.edu, samuelf{at}usc.edu, paul.macklin{at}usc.edu.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted December 31, 2015.
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Estimating cell cycle model parameters using systems identification
Edwin Juarez, Ahmadreza Ghaffarizadeh, Samuel H. Friedman, Edmond Jonckheere, Paul Macklin
bioRxiv 035766; doi: https://doi.org/10.1101/035766
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Estimating cell cycle model parameters using systems identification
Edwin Juarez, Ahmadreza Ghaffarizadeh, Samuel H. Friedman, Edmond Jonckheere, Paul Macklin
bioRxiv 035766; doi: https://doi.org/10.1101/035766

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