PCI Math Comp Biol

183

Title *

Marker and source-marker reprogramming of Most Permissive Boolean networks and ensembles with BoNesisuse asterix (*) to get italics

Authors *

Loïc PaulevéPlease use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"

Year *

2022

Picture *

Abstract *

<p style="text-align: justify;">Boolean networks (BNs) are discrete dynamical systems with applications to the modeling of cellular behaviors. In this paper, we demonstrate how the software BoNesis can be employed to exhaustively identify combinations of perturbations which enforce properties on their fixed points and attractors. We consider marker properties, which specify that some components are fixed to a specific value. We study 4 variants of the marker reprogramming problem: the reprogramming of fixed points, of minimal trap spaces, and of fixed points and minimal trap spaces reachable from a given initial configuration with the most permissive update mode. The perturbations consist of fixing a set of components to a fixed value. They can destroy and create new attractors. In each case, we give an upper bound on their theoretical computational complexity, and give an implementation of the resolution using the BoNesis Python framework. Finally, we lift the reprogramming problems to ensembles of BNs, as supported by BoNesis, bringing insight on possible and universal reprogramming strategies. This paper can be executed and modified interactively.</p>

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Keywords (optional)

boolean networks, control, attractors, gene regulatory networks

Methods that require specific expertise (optional)

NonePlease indicate the methods that may require specialised expertise during the peer review process (use a comma to separate various required expertises).

Thematic fields *

Combinatorics, Computational complexity, Dynamical systems, Molecular Biology, Systems biology

Suggested reviewers - Suggest up to 10 reviewers (provide names and Email addresses). (Optional)

Jorge Gómez Tejeda Zañudo [jgtz@broadinstitute.org ], Sven Thiele [thieles@mpi-magdeburg.mpg.de], Pedro Tiago Monteiro [Pedro.Tiago.Monteiro@tecnico.ulisboa.pt], Kwang-Hyun Cho [chk@kaist.ac.kr], Tatsuya Akutsu [kuicr.kyoto-u.ac.jp], Franck Delaplace [franck.delaplace@univ-evry.fr], Heike Siebert [siebert@mi.fu-berlin.de ]

e.g. John Doe john@doe.com

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Submission date

2022-08-31 15:00:21

Recommender

Sergiu Ivanov

Reviewers

Ismail Belgacem, Anonymous

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