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Frequency spectra and the color of cellular noise

Author

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  • Ankit Gupta

    (ETH Zürich)

  • Mustafa Khammash

    (ETH Zürich)

Abstract

The invention of the Fourier integral in the 19th century laid the foundation for modern spectral analysis methods. This integral decomposes a temporal signal into its frequency components, providing deep insights into its generating process. While this idea has precipitated several scientific and technological advances, its impact has been fairly limited in cell biology, largely due to the difficulties in connecting the underlying noisy intracellular networks to the frequency content of observed single-cell trajectories. Here we develop a spectral theory and computational methodologies tailored specifically to the computation and analysis of frequency spectra of noisy intracellular networks. Specifically, we develop a method to compute the frequency spectrum for general nonlinear networks, and for linear networks we present a decomposition that expresses the frequency spectrum in terms of its sources. Several examples are presented to illustrate how our results provide frequency-based methods for the design and analysis of noisy intracellular networks.

Suggested Citation

  • Ankit Gupta & Mustafa Khammash, 2022. "Frequency spectra and the color of cellular noise," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31263-x
    DOI: 10.1038/s41467-022-31263-x
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    References listed on IDEAS

    as
    1. Sant Kumar & Marc Rullan & Mustafa Khammash, 2021. "Rapid prototyping and design of cybergenetic single-cell controllers," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    2. Kurtz, Thomas G., 1978. "Strong approximation theorems for density dependent Markov chains," Stochastic Processes and their Applications, Elsevier, vol. 6(3), pages 223-240, February.
    3. Ankit Gupta & Corentin Briat & Mustafa Khammash, 2014. "A Scalable Computational Framework for Establishing Long-Term Behavior of Stochastic Reaction Networks," PLOS Computational Biology, Public Library of Science, vol. 10(6), pages 1-16, June.
    4. Dirk Benzinger & Mustafa Khammash, 2018. "Pulsatile inputs achieve tunable attenuation of gene expression variability and graded multi-gene regulation," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
    5. Zhixing Cao & Ramon Grima, 2018. "Linear mapping approximation of gene regulatory networks with stochastic dynamics," Nature Communications, Nature, vol. 9(1), pages 1-15, December.
    6. Laurent Potvin-Trottier & Nathan D. Lord & Glenn Vinnicombe & Johan Paulsson, 2016. "Synchronous long-term oscillations in a synthetic gene circuit," Nature, Nature, vol. 538(7626), pages 514-517, October.
    7. Hsin-Ho Huang & Yili Qian & Domitilla Del Vecchio, 2018. "A quasi-integral controller for adaptation of genetic modules to variable ribosome demand," Nature Communications, Nature, vol. 9(1), pages 1-12, December.
    8. Matthias Kaiser & Florian Jug & Thomas Julou & Siddharth Deshpande & Thomas Pfohl & Olin K. Silander & Gene Myers & Erik van Nimwegen, 2018. "Monitoring single-cell gene regulation under dynamically controllable conditions with integrated microfluidics and software," Nature Communications, Nature, vol. 9(1), pages 1-16, December.
    9. Christopher V. Rao & Denise M. Wolf & Adam P. Arkin, 2002. "Control, exploitation and tolerance of intracellular noise," Nature, Nature, vol. 420(6912), pages 231-237, November.
    10. Michael B. Elowitz & Stanislas Leibler, 2000. "A synthetic oscillatory network of transcriptional regulators," Nature, Nature, vol. 403(6767), pages 335-338, January.
    11. Thomas M. Norman & Nathan D. Lord & Johan Paulsson & Richard Losick, 2013. "Memory and modularity in cell-fate decision making," Nature, Nature, vol. 503(7477), pages 481-486, November.
    12. Deepak K. Agrawal & Ryan Marshall & Vincent Noireaux & Eduardo D Sontag, 2019. "In vitro implementation of robust gene regulation in a synthetic biomolecular integral controller," Nature Communications, Nature, vol. 10(1), pages 1-12, December.
    13. Stephanie K. Aoki & Gabriele Lillacci & Ankit Gupta & Armin Baumschlager & David Schweingruber & Mustafa Khammash, 2019. "A universal biomolecular integral feedback controller for robust perfect adaptation," Nature, Nature, vol. 570(7762), pages 533-537, June.
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    Cited by:

    1. Zhou Fang & Ankit Gupta & Sant Kumar & Mustafa Khammash, 2024. "Advanced methods for gene network identification and noise decomposition from single-cell data," Nature Communications, Nature, vol. 15(1), pages 1-19, December.

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