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Published in:
Sequential Reprogramming of Boolean Networks Made Practical Read chapter Read first chapter

2019 | OriginalPaper | Chapter

Scalable Control of Asynchronous Boolean Networks

Authors : Cui Su, Soumya Paul, Jun Pang

Published in: Computational Methods in Systems Biology

Publisher: Springer International Publishing

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Abstract

We summarise our recent research results on developing efficient and scalable control methods for gene regulatory networks modelled as asynchronous Boolean networks. Our methods compute a minimal subset of nodes of a given Boolean network, such that (different types of) perturbations of these nodes, in one step or a sequence of steps, can drive the network (from an initial state) to a target steady state.

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Footnotes
1
We refer details on their evaluation to our previous works [1, 4, 5, 8, 9, 11].
 
Literature
1.
Baudin, A., Paul, S., Su, C., Pang, J.: Controlling large Boolean networks with single-step perturbations. Bioinformatics 35, i558–i567 (2019)CrossRef
2.
Kauffman, S.A.: Homeostasis and differentiation in random genetic control networks. Nature 224, 177–178 (1969)CrossRef
3.
Kim, J., Park, S., Cho, K.: Discovery of a kernel for controlling biomolecular regulatory networks. Sci. Rep. 3, 2223 (2013)CrossRef
4.
Mandon, H., Su, C., Haar, S., Pang, J., Paulevé, L.: Sequential reprogramming of Boolean networks made practical. In: Bortolussi, L., Sanguinetti, G. (eds.) CMSB 2019. LNBI, pp. 3–19. Springer, Cham (2019)
5.
Mandon, H., Su, C., Pang, J., Paul, S., Haar, S., Paulevé, L.: Algorithms for the sequential reprogramming of Boolean networks. IEEE/ACM Trans. Comput. Biol. Bioinf. (2019, accepted)
6.
Mizera, A., Pang, J., Su, C., Yuan, Q.: ASSA-PBN: a toolbox for probabilistic Boolean networks. IEEE/ACM Trans. Comput. Biol. Bioinf. 15(4), 1203–1216 (2018)CrossRef
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Paul, S., Su, C., Pang, J., Mizera, A.: A decomposition-based approach towards the control of Boolean networks. In: Proceedings of the 9th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, pp. 11–20. ACM Press (2018)
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Paul, S., Su, C., Pang, J., Mizera, A.: An efficient approach towards the source-target control of Boolean networks. IEEE/ACM Trans. Comput. Biol. Bioinf. (2019, accepted)
10.
Shmulevich, I., Dougherty, E.R.: Probabilistic Boolean Networks: The Modeling and Control of Gene Regulatory Networks. SIAM Press, New York (2010)CrossRef
11.
Su, C., Paul, S., Pang, J.: Controlling large Boolean networks with temporary and permanent perturbations. In: Proceedings of the 23rd International Symposium on Formal Methods. LNCS. Springer (2019, accepted)
12.
Trairatphisan, P., Mizera, A., Pang, J., Tantar, A.A., Sauter, T.: optPBN: an optimisation toolbox for probabilistic Boolean networks. PLoS ONE 9(7), e98001 (2014)CrossRef
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Wang, L.Z., et al.: A geometrical approach to control and controllability of nonlinear dynamical networks. Nat. Commun. 7, 11323 (2016)CrossRef
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Zañudo, J.G.T., Albert, R.: Cell fate reprogramming by control of intracellular network dynamics. PLoS Comput. Biol. 11(4), e1004193 (2015)CrossRef
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Zhao, Y., Kim, J., Filippone, M.: Aggregation algorithm towards large-scale Boolean network analysis. IEEE Trans. Autom. Control 58(8), 1976–1985 (2013)MathSciNetCrossRef
Metadata
Title
Scalable Control of Asynchronous Boolean Networks
Authors
Cui Su
Soumya Paul
Jun Pang
Copyright Year
2019
Book
Computational Methods in Systems Biology

Print ISBN: 978-3-030-31303-6

Electronic ISBN: 978-3-030-31304-3

Copyright Year: 2019

DOI
https://doi.org/10.1007/978-3-030-31304-3_28

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