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@article{1854097,
author = {Beneš, Nikola and Brim, Luboš and Kadlecaj, Jakub and Pastva, Samuel and Šafránek, David},
article_number = {173},
doi = {http://dx.doi.org/10.1186/s12859-022-04708-9},
keywords = {Boolean networks; Attractor bifurcation; Symbolic computation; Software tool; type-1 interferons},
language = {eng},
issn = {1471-2105},
journal = {BMC Bioinformatics},
title = {Exploring attractor bifurcations in Boolean networks},
url = {https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-022-04708-9},
volume = {23},
year = {2022}
}
TY - JOUR
ID - 1854097
AU - Beneš, Nikola - Brim, Luboš - Kadlecaj, Jakub - Pastva, Samuel - Šafránek, David
PY - 2022
TI - Exploring attractor bifurcations in Boolean networks
JF - BMC Bioinformatics
VL - 23
IS - 173
SP - 1-18
EP - 1-18
SN - 14712105
KW - Boolean networks
KW - Attractor bifurcation
KW - Symbolic computation
KW - Software tool
KW - type-1 interferons
UR - https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-022-04708-9
N2 - Background Boolean networks (BNs) provide an effective modelling formalism for various complex biochemical phenomena. Their long term behaviour is represented by attractors–subsets of the state space towards which the BN eventually converges. These are then typically linked to different biological phenotypes. Depending on various logical parameters, the structure and quality of attractors can undergo a significant change, known as a bifurcation. We present a methodology for analysing bifurcations in asynchronous parametrised Boolean networks. Results In this paper, we propose a computational framework employing advanced symbolic graph algorithms that enable the analysis of large networks with hundreds of Boolean variables. To visualise the results of this analysis, we developed a novel interactive presentation technique based on decision trees, allowing us to quickly uncover parameters crucial to the changes in the attractor landscape. As a whole, the methodology is implemented in our tool AEON. We evaluate the method’s applicability on a complex human cell signalling network describing the activity of type-1 interferons and related molecules interacting with SARS-COV-2 virion. In particular, the analysis focuses on explaining the potential suppressive role of the recently proposed drug molecule GRL0617 on replication of the virus. Conclusions The proposed method creates a working analogy to the concept of bifurcation analysis widely used in kinetic modelling to reveal the impact of parameters on the system’s stability. The important feature of our tool is its unique capability to work fast with large-scale networks with a relatively large extent of unknown information. The results obtained in the case study are in agreement with the recent biological findings.
ER -
BENEŠ, Nikola, Luboš BRIM, Jakub KADLECAJ, Samuel PASTVA a David ŠAFRÁNEK. Exploring attractor bifurcations in Boolean networks. \textit{BMC Bioinformatics}. roč.~23, č.~173, s.~1-18. ISSN~1471-2105. doi:10.1186/s12859-022-04708-9. 2022.
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