CITATION.cff

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cff-version: 1.2.0
title: cell_cycle_petab
message: >-
  If you use this software, please cite the preferred-citation in this file.
preferred-citation:
  type: article
  authors:
  - given-names: Paul
    name-particle: F
    family-names: Lang
    email: plang@deeporigin.com
    affiliation: Deep Origin
    orcid: 'https://orcid.org/0000-0002-6388-2405'
  - given-names: David
    name-particle: R
    family-names: Penas
    affiliation: Computational Biology Lab, MBG-CSIC (Spanish National Research Council), Pontevedra, Spain
    orcid: 'https://orcid.org/0000-0002-7256-3094'
  - given-names: Julio
    name-particle: R
    family-names: Banga
    affiliation: Computational Biology Lab, MBG-CSIC (Spanish National Research Council), Pontevedra, Spain
    orcid: 'https://orcid.org/0000-0002-4245-0320'
  - given-names: Daniel
    family-names: Weindl
    affiliation: Computational Health Center, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
    orcid: 'https://orcid.org/0000-0001-9963-6057'
  - given-names: Bela
    family-names: Novak
    affiliation: Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    orcid: 'https://orcid.org/0000-0002-6961-1366'

  doi: "10.1371/journal.pcbi.1011151"
  journal: "PLOS Computational Biology"
  month: 1
  title: "Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells"
  year: 2024
  keywords:
    - Cell Cycle
    - Parameter Estimation
  license: CC-BY-4.0
  repository-code: >-
    https://github.com/paulflang/cell_cycle_petab
  abstract: >-
    The mammalian cell cycle is regulated by a well-studied but complex biochemical reaction system.
    Computational models provide a particularly systematic and systemic description of the
    mechanisms governing mammalian cell cycle control. By combining both state-of-the-art
    multiplexed experimental methods and powerful computational tools, this work aims at improving
    on these models along four dimensions: model structure, validation data, validation methodology
    and model reusability.

    We developed a comprehensive model structure of the full cell cycle that qualitatively explains
    the behaviour of human retinal pigment epithelial-1 cells. To estimate the model parameters, time
    courses of eight cell cycle regulators in two compartments were reconstructed from single cell
    snapshot measurements. After optimisation with a parallel global optimisation metaheuristic we
    obtained excellent agreements between simulations and measurements. The PEtab specification of the
    optimisation problem facilitates reuse of model, data and/or optimisation results.

    Future perturbation experiments will improve parameter identifiability and allow for testing model
    predictive power. Such a predictive model may aid in drug discovery for cell cycle-related disorders.