Project
AA1-17
Beyond Attractors: Understanding the Transient and Modular Behaviour of Boolean Networks
Project Heads
Elisa Tonello
Project Members
Elisa Tonello
Project Duration
01.01.2023 − 31.12.2024
Located at
FU Berlin
Description
Boolean networks are used extensively to model biological processes. The associated dynamics are usually defined as directed graphs with the assumption of asynchronicity of updates. Analyses of Boolean dynamics are often restricted to the asymptotic behaviour, and say very little about transient behaviour or modularity of attractors.
We propose to expand the analysis of Boolean dynamics by applying techniques of complex network theory to extend our understanding of transient behaviour and of the structure of cyclic attractors. The identification and interpretation of modules in Boolean models can provide a significant contribution in the understanding of biological processes involved for instance in differentiation or phenotype acquisition, with potential application in the control of cellular and spatial decision-making.
External Website
Related Publications
- Richard, A. and Tonello, E., 2023. Attractor separation and signed cycles in asynchronous Boolean networks. Theoretical Computer Science, p.113706.
- Naldi, A., Richard, A. and Tonello, E., 2023. Linear cuts in Boolean networks. Natural Computing, pp.1-21.
- Tonello, E. and Paulevé, L., 2023. Attractor identification in asynchronous Boolean dynamics with network reduction. In 21st International Conference on Computational Methods in Systems Biology (CMSB 2023).
- Schwieger, R. and Tonello, E., 2024. Reduction for asynchronous Boolean networks: elimination of negatively autoregulated components. Discrete Mathematics & Theoretical Computer Science, 25 (Automata, Logic and Semantics).
- Tonello, E. and Paulevé, L., 2024. Phenotype control and elimination of variables in Boolean networks. Peer Community Journal, Volume 4, article no. e79 (Mathematical & Computational Biology).
- Yousefian, M., Tonello, E., Frank, A.S., Siebert, H. and Röblitz, S., 2024, September. Uncovering Dynamic Structures Within Cyclic Attractors of Asynchronous Boolean Networks with Spectral Clustering. In International Conference on Computational Methods in Systems Biology (pp. 226-246).
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