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International Conference on Bioinformatics and Biomedical Engineering

IWBBIO 2016: Bioinformatics and Biomedical Engineering pp 315–321Cite as

Using Nets-Within-Nets for Modeling Differentiating Cells in the Epigenetic Landscape

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Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9656))

Abstract

In this work the authors propose the use of a high-level Petri net formalism for modeling developmental processes at the cell level, taking explicitly into account the role of epigenetic regulation.

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References

  1. Goldberg, A.D., Allis, C.D., Bernstein, E.: Epigenetics: A Landscape Takes Shape. Cell 128(4), 635–638 (2007)

    Article  Google Scholar 

  2. Waddington, C.A.: Organisers & Genes. Cambridge University Press, Cambridge (1940)

    Google Scholar 

  3. Wikipedia contributors, “C. H. Waddington– Epigenetic landscape” Wikipedia, The Free Encyclopedia, https://en.wikipedia.org/wiki/C._H._Waddington#Epigenetic_landscape. Accessed 5 December 2015

  4. Fisher, J., Henzinger, T.A.: Executable Cell Biology. Nat. Biotechnol. 25, 1239–1249 (2007)

    Article  Google Scholar 

  5. Benso, A., Di Carlo, S., Politano, G., Savino, A., Vasciaveo, A.: An extended gene protein/products Boolean network model including post-transcriptional regulation. Theor. Biol. Med. Model. 11 (2014)

    Google Scholar 

  6. Huang, S.: The molecular and mathematical basis of Waddington’s epigenetic landscape: a framework for post-Darwinian biology? Bio Essays 34, 149–157 (2012)

    Google Scholar 

  7. Jensen, K.: Colored Petri Nets: Basic Concepts, Analysis Methods and Practical Use, vol. 1. Springer, Heidelberg (2013)

    Google Scholar 

  8. Heiner, M., Gilbert, D., Donaldson, R.: Petri nets for systems and synthetic biology. In: Bernardo, M., Degano, P., Zavattaro, G. (eds.) SFM 2008. LNCS, vol. 5016, pp. 215–264. Springer, Heidelberg (2008)

    Chapter  Google Scholar 

  9. Yang, J., Lian, J., Pu, H., Gao, R.: Modeling the genetic information transmission based on colored petri nets. In: Proceeding of the IEEE International Conference on Information and Automation Hailar, China (2014)

    Google Scholar 

  10. Chaouiya, C.: Petri net modelling of biological networks. Oxford J. Brief Bioinform 8, 210–219 (2007)

    Article  Google Scholar 

  11. Koch, I.: Petri nets in systems biology. Softw. Syst. Model. 14, 703–710 (2015)

    Article  Google Scholar 

  12. Wikipedia contributors, “Petri Net” Wikipedia, The Free Encyclopedia. https://en.wikipedia.org/wiki/Petri_net. Accessed 05 December 2015

  13. Valk, R.: Petri nets as token objects: an introduction to elementary object nets. In: Silva, M., Desel, J. (eds.) ICATPN 1998. LNCS, vol. 1420, pp. 1–24. Springer, Heidelberg (2000)

    Chapter  Google Scholar 

  14. Wikipedia contributors, “Nets within nets” Wikipedia, The Free Encyclopedia. https://en.wikipedia.org/wiki/Nets_within_Nets. Accessed 05 December 2015

  15. Cabac, L., Duvigneau, M., Moldt, D., Rölke, H.: Modeling dynamic architectures using nets-within-nets. In: Ciardo, G., Darondeau, P. (eds.) ICATPN 2005. LNCS, vol. 3536, pp. 148–167. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  16. Köhler, M.: Mobile Object Net Systems: Petri Nets as Active Tokens, Technical report 320. Universitat Hamburg (2002)

    Google Scholar 

  17. Valk, R.: Concurrency in Communicating Object Petri Nets, Concurrent OOP and PN, pp. 164–195. Springer-Verlag, Heidelberg (2001)

    MATH  Google Scholar 

  18. Takahashi, K., Yamanaka, S., Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors, Cell, 2006

    Google Scholar 

  19. Lin, T., Ambasudhan, R., Yuan, X., et al.: A chemical platform for improved induction of human iPSCs. Nat. Methods 6, 805–808 (2009)

    Article  Google Scholar 

  20. Chen, K., Novak, B.: Network dynamics and cell physiology. Nat. Rev. Mol. Cell Biol. 2(12), 908–916 (2001). doi:10.1038/35103078

    Article  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Control and Computer Engineering, Politecnico Di Torino, Corso Duca Degli Abruzzi 24, Torino, Italy

    Roberta Bardini, Alfredo Benso, Stefano Di Carlo, Gianfranco Politano & Alessandro Savino

Authors
  1. Roberta Bardini
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  2. Alfredo Benso
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  3. Stefano Di Carlo
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  4. Gianfranco Politano
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  5. Alessandro Savino
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Corresponding author

Correspondence to Stefano Di Carlo .

Editor information

Editors and Affiliations

  1. Universidad de Granada, Granada, Spain

    Francisco Ortuño

  2. Universidad de Granada, Granada, Spain

    Ignacio Rojas

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© 2016 Springer International Publishing Switzerland

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Bardini, R., Benso, A., Di Carlo, S., Politano, G., Savino, A. (2016). Using Nets-Within-Nets for Modeling Differentiating Cells in the Epigenetic Landscape. In: Ortuño, F., Rojas, I. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2016. Lecture Notes in Computer Science(), vol 9656. Springer, Cham. https://doi.org/10.1007/978-3-319-31744-1_28

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  • DOI: https://doi.org/10.1007/978-3-319-31744-1_28

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-31743-4

  • Online ISBN: 978-3-319-31744-1

  • eBook Packages: Computer ScienceComputer Science (R0)

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