Boolean network analysis through the joint use of linear algebra and algebraic geometry.

Authors:
Laura Menini
Laura Menini
Università di Roma Tor Vergata
Corrado Possieri
Corrado Possieri
Dipartimento di Elettronica e Telecomunicazioni

J Theor Biol 2019 Jul 15;472:46-53. Epub 2019 Apr 15.

Dipartimento di Ingegneria Civile e Ingegneria Informatica, Università di Roma Tor Vergata, Roma 00133, Italy. Electronic address:

Among the various phenomena that can be modeled by Boolean networks, i.e., discrete-time dynamical systems with binary state variables, gene regulatory interactions are especially well known. Therefore, the analysis of Boolean networks is critical, e.g., to identify genetic pathways and to predict the effects of mutations on the cell functionality. Two methodologies (i.e., the semi-tensor product and the Gröbner bases over finite fields) have recently been proposed to tackle the problem of determining cycles and attractors (with the corresponding basin of attraction) for such systems. Here, it is shown that, by suitably coupling methodologies taken from these two fields (i.e., linear algebra and algebraic geometry), it is not only possible to determine cycles and attractors, but also to find closed-form solutions of the Boolean network. Such a goal is pursued by finding an immersion that recasts the Boolean dynamics in a linear form and by computing the closed-form solution of the latter system. The effectiveness of this technique is demonstrated by fully computing the solutions of the Boolean network modeling the differentiation of the Th-lymphocyte, a type of white blood cells involved in the human adaptive immune system.

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Source
https://linkinghub.elsevier.com/retrieve/pii/S00225193193015
Publisher Site
http://dx.doi.org/10.1016/j.jtbi.2019.04.012DOI Listing
July 2019
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