IDEAS home Printed from https://ideas.repec.org/a/eee/phsmap/v387y2008i8p2170-2186.html
   My bibliography  Save this article

Evolution of gene regulatory networks: Robustness as an emergent property of evolution

Author

Listed:
  • Krishnan, Arun
  • Tomita, Masaru
  • Giuliani, Alessandro

Abstract

Gene Regulatory Networks (GRNs) have become a major focus of interest in recent years. Although much work has been done in elucidating the transcriptional regulatory network, the underlying mechanisms that have possibly influenced the evolution of these GRNs are still debatable. We have developed a framework to analyze the effect of objective functions, input types and starting populations on the evolution of GRNs with a specific emphasis on the robustness of evolved GRNs.

Suggested Citation

  • Krishnan, Arun & Tomita, Masaru & Giuliani, Alessandro, 2008. "Evolution of gene regulatory networks: Robustness as an emergent property of evolution," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 387(8), pages 2170-2186.
    • Handle: RePEc:eee:phsmap:v:387:y:2008:i:8:p:2170-2186
    DOI: 10.1016/j.physa.2007.11.022
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0378437107012241
    Download Restriction: Full text for ScienceDirect subscribers only. Journal offers the option of making the article available online on Science direct for a fee of $3,000
    File URL: https://libkey.io/10.1016/j.physa.2007.11.022?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. William J. Blake & Mads KÆrn & Charles R. Cantor & J. J. Collins, 2003. "Noise in eukaryotic gene expression," Nature, Nature, vol. 422(6932), pages 633-637, April.
    2. Annie E. Tsong & Brian B. Tuch & Hao Li & Alexander D. Johnson, 2006. "Evolution of alternative transcriptional circuits with identical logic," Nature, Nature, vol. 443(7110), pages 415-420, September.
    3. Antonis Rokas, 2006. "Different paths to the same end," Nature, Nature, vol. 443(7110), pages 401-402, September.
    4. Stefano Ciliberti & Olivier C Martin & Andreas Wagner, 2007. "Robustness Can Evolve Gradually in Complex Regulatory Gene Networks with Varying Topology," PLOS Computational Biology, Public Library of Science, vol. 3(2), pages 1-10, February.
    5. Leland H. Hartwell & John J. Hopfield & Stanislas Leibler & Andrew W. Murray, 1999. "From molecular to modular cell biology," Nature, Nature, vol. 402(6761), pages 47-52, December.
    6. Aviv Bergman & Mark L. Siegal, 2003. "Evolutionary capacitance as a general feature of complex gene networks," Nature, Nature, vol. 424(6948), pages 549-552, July.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Tracy Chih-Ting Koubkova-Yu & Jung-Chi Chao & Jun-Yi Leu, 2018. "Heterologous Hsp90 promotes phenotypic diversity through network evolution," PLOS Biology, Public Library of Science, vol. 16(11), pages 1-29, November.
    2. Javier Santos-Moreno & Eve Tasiudi & Hadiastri Kusumawardhani & Joerg Stelling & Yolanda Schaerli, 2023. "Robustness and innovation in synthetic genotype networks," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    3. Stefano Ciliberti & Olivier C Martin & Andreas Wagner, 2007. "Robustness Can Evolve Gradually in Complex Regulatory Gene Networks with Varying Topology," PLOS Computational Biology, Public Library of Science, vol. 3(2), pages 1-10, February.
    4. Casper J Breuker & James S Patterson & Christian Peter Klingenberg, 2006. "A Single Basis for Developmental Buffering of Drosophila Wing Shape," PLOS ONE, Public Library of Science, vol. 1(1), pages 1-7, December.
    5. T. Ochiai & J. C. Nacher, 2007. "Stochastic analysis of autoregulatory gene expression dynamics," Mathematical and Computer Modelling of Dynamical Systems, Taylor & Francis Journals, vol. 14(4), pages 377-388, November.
    6. Blasi, Monica Francesca & Casorelli, Ida & Colosimo, Alfredo & Blasi, Francesco Simone & Bignami, Margherita & Giuliani, Alessandro, 2005. "A recursive network approach can identify constitutive regulatory circuits in gene expression data," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 348(C), pages 349-370.
    7. Payne, Joshua L., 2016. "No tradeoff between versatility and robustness in gene circuit motifs," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 449(C), pages 192-199.
    8. Valenti, D. & Tranchina, L. & Brai, M. & Caruso, A. & Cosentino, C. & Spagnolo, B., 2008. "Environmental metal pollution considered as noise: Effects on the spatial distribution of benthic foraminifera in two coastal marine areas of Sicily (Southern Italy)," Ecological Modelling, Elsevier, vol. 213(3), pages 449-462.
    9. Frederic Li Mow Chee & Bruno Beernaert & Billie G. C. Griffith & Alexander E. P. Loftus & Yatendra Kumar & Jimi C. Wills & Martin Lee & Jessica Valli & Ann P. Wheeler & J. Douglas Armstrong & Maddy Pa, 2023. "Mena regulates nesprin-2 to control actin–nuclear lamina associations, trans-nuclear membrane signalling and gene expression," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    10. Tobias May & Lee Eccleston & Sabrina Herrmann & Hansjörg Hauser & Jorge Goncalves & Dagmar Wirth, 2008. "Bimodal and Hysteretic Expression in Mammalian Cells from a Synthetic Gene Circuit," PLOS ONE, Public Library of Science, vol. 3(6), pages 1-7, June.
    11. Seyed Yahya Anvar & Allan Tucker & Veronica Vinciotti & Andrea Venema & Gert-Jan B van Ommen & Silvere M van der Maarel & Vered Raz & Peter A C ‘t Hoen, 2011. "Interspecies Translation of Disease Networks Increases Robustness and Predictive Accuracy," PLOS Computational Biology, Public Library of Science, vol. 7(11), pages 1-14, November.
    12. Michael W Klymkowsky & Kathy Garvin-Doxas, 2008. "Recognizing Student Misconceptions through Ed's Tools and the Biology Concept Inventory," PLOS Biology, Public Library of Science, vol. 6(1), pages 1-4, January.
    13. Diana Monteoliva & Christina B McCarthy & Luis Diambra, 2013. "Noise Minimisation in Gene Expression Switches," PLOS ONE, Public Library of Science, vol. 8(12), pages 1-9, December.
    14. Joshua S Weitz & Philip N Benfey & Ned S Wingreen, 2007. "Evolution, Interactions, and Biological Networks," PLOS Biology, Public Library of Science, vol. 5(1), pages 1-3, January.
    15. Marc S Sherman & Barak A Cohen, 2014. "A Computational Framework for Analyzing Stochasticity in Gene Expression," PLOS Computational Biology, Public Library of Science, vol. 10(5), pages 1-13, May.
    16. Bo Xu & Hongfei Lin & Yang Chen & Zhihao Yang & Hongfang Liu, 2013. "Protein Complex Identification by Integrating Protein-Protein Interaction Evidence from Multiple Sources," PLOS ONE, Public Library of Science, vol. 8(12), pages 1-12, December.
    17. Robrecht Cannoodt & Joeri Ruyssinck & Jan Ramon & Katleen De Preter & Yvan Saeys, 2018. "IncGraph: Incremental graphlet counting for topology optimisation," PLOS ONE, Public Library of Science, vol. 13(4), pages 1-11, April.
    18. Margaritis Voliotis & Philipp Thomas & Ramon Grima & Clive G Bowsher, 2016. "Stochastic Simulation of Biomolecular Networks in Dynamic Environments," PLOS Computational Biology, Public Library of Science, vol. 12(6), pages 1-18, June.
    19. Chen, Aimin & Tian, Tianhai & Chen, Yiren & Zhou, Tianshou, 2022. "Stochastic analysis of a complex gene-expression model," Chaos, Solitons & Fractals, Elsevier, vol. 160(C).
    20. Adam F Prasanphanich & Douglas E White & Margaret A Gran & Melissa L Kemp, 2016. "Kinetic Modeling of ABCG2 Transporter Heterogeneity: A Quantitative, Single-Cell Analysis of the Side Population Assay," PLOS Computational Biology, Public Library of Science, vol. 12(11), pages 1-35, November.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:eee:phsmap:v:387:y:2008:i:8:p:2170-2186. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Catherine Liu (email available below). General contact details of provider: http://www.journals.elsevier.com/physica-a-statistical-mechpplications/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.