Optimising time-series experimental design for modelling of circadian rhythms: the value of transient data

Laurent Mombaerts, Alexandre Mauroy, Jorge Gonçalves

Research output: Contribution in Book/Catalog/Report/Conference proceedingConference contribution

Abstract

Circadian clocks consist of complex networks that coordinate the daily cycle of most organisms. In light/dark cycles, the clock is synchronized (or entrained) by the environment, which corresponds to a constant rephasing of the oscillations and leads to a steady state regime. Some circadian clocks are endogenous oscillators with rhythms of about 24-hours that persist in constant light or constant darkness. This operating mechanism with and without entrainment provides flexibility and robustness to the clock against perturbations. Most of the clock-oriented experiments are performed under constant photoperiodic regime, overlooking the transitory regime that takes place between light/dark cycles and constant light or darkness. This paper provides a comparative analysis of the informative potential of the transient time-series data with the other regimes for clock modelling. Realistic data were simulated from 2 experimentally validated plant circadian clock models and sliced into several time windows. These windows represent the different regimes that take place before, meanwhile and after the switch to constant light. Then, a network inference tool was used over each window and its capability of retrieving the ground-truth of the network was compared for each window. The results suggest that including the transient data to the network inference technique significally improves its performance.

Original languageEnglish
Title of host publicationProceedings of the 6th IFAC Conference on Foundations of Systems Biology in Engineering
Pages109-113
Number of pages5
Volume49
Edition26
DOIs
Publication statusPublished - 2016
Externally publishedYes

Publication series

NameIFAC-PapersOnLine
PublisherIFAC Secretariat

Fingerprint

Design of experiments
Clocks
Time series
Complex networks
Switches
Experiments

Keywords

  • Circadian rhythms
  • Dynamics and control
  • Modelling
  • Network inference
  • Systems Medicine

Cite this

Mombaerts, L., Mauroy, A., & Gonçalves, J. (2016). Optimising time-series experimental design for modelling of circadian rhythms: the value of transient data. In Proceedings of the 6th IFAC Conference on Foundations of Systems Biology in Engineering (26 ed., Vol. 49, pp. 109-113). (IFAC-PapersOnLine). https://doi.org/10.1016/j.ifacol.2016.12.111
Mombaerts, Laurent ; Mauroy, Alexandre ; Gonçalves, Jorge. / Optimising time-series experimental design for modelling of circadian rhythms : the value of transient data. Proceedings of the 6th IFAC Conference on Foundations of Systems Biology in Engineering. Vol. 49 26. ed. 2016. pp. 109-113 (IFAC-PapersOnLine).
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Mombaerts, L, Mauroy, A & Gonçalves, J 2016, Optimising time-series experimental design for modelling of circadian rhythms: the value of transient data. in Proceedings of the 6th IFAC Conference on Foundations of Systems Biology in Engineering. 26 edn, vol. 49, IFAC-PapersOnLine, pp. 109-113. https://doi.org/10.1016/j.ifacol.2016.12.111

Optimising time-series experimental design for modelling of circadian rhythms : the value of transient data. / Mombaerts, Laurent; Mauroy, Alexandre; Gonçalves, Jorge.

Proceedings of the 6th IFAC Conference on Foundations of Systems Biology in Engineering. Vol. 49 26. ed. 2016. p. 109-113 (IFAC-PapersOnLine).

Research output: Contribution in Book/Catalog/Report/Conference proceedingConference contribution

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Mombaerts L, Mauroy A, Gonçalves J. Optimising time-series experimental design for modelling of circadian rhythms: the value of transient data. In Proceedings of the 6th IFAC Conference on Foundations of Systems Biology in Engineering. 26 ed. Vol. 49. 2016. p. 109-113. (IFAC-PapersOnLine). https://doi.org/10.1016/j.ifacol.2016.12.111