Phenotype Control of Partially Specified Boolean Networks

BENEŠ, Nikola, Luboš BRIM, Samuel PASTVA, David ŠAFRÁNEK and Eva ŠMIJÁKOVÁ. Phenotype Control of Partially Specified Boolean Networks. In Jun Pang, Joachim Niehren. Computational Methods in Systems Biology. Luxembourg City, Luxembourg: Springer Cham, 2023, p. 18-35. ISBN 978-3-031-42696-4. Available from: https://dx.doi.org/10.1007/978-3-031-42697-1_2.

Basic information

• Original name: Phenotype Control of Partially Specified Boolean Networks
• Authors: BENEŠ, Nikola (203 Czech Republic, belonging to the institution), Luboš BRIM (203 Czech Republic, belonging to the institution), Samuel PASTVA (703 Slovakia), David ŠAFRÁNEK (203 Czech Republic, belonging to the institution) and Eva ŠMIJÁKOVÁ (703 Slovakia, belonging to the institution).
• Edition: Luxembourg City, Luxembourg, Computational Methods in Systems Biology, p. 18-35, 18 pp. 2023.
• Publisher: Springer Cham

Other information

• Original language: English
• Type of outcome: Proceedings paper
• Field of Study: 10200 1.2 Computer and information sciences
• Country of publisher: Luxembourg
• Confidentiality degree: is not subject to a state or trade secret
• Publication form: printed version "print"
• WWW: URL
• Impact factor: Impact factor: 0.402 in 2005
• RIV identification code: RIV/00216224:14330/23:00131639
• Organization unit: Faculty of Informatics
• ISBN: 978-3-031-42696-4
• ISSN: 0302-9743
• Doi: http://dx.doi.org/10.1007/978-3-031-42697-1_2
• UT WoS: 001156280600002
• Keywords in English: Boolean networks;Partial specification;Permanent control;Phenotype;Perturbation;Symbolic algorithm
• Tags: International impact, Reviewed

Abstract

Partially specified Boolean networks (PSBNs) represent a promising framework for the qualitative modelling of biological systems in which the logic of interactions is not completely known. Phenotype control aims to stabilise the network in states exhibiting specific traits. In this paper, we define the phenotype control problem in the context of asynchronous PSBNs and propose a novel semi-symbolic algorithm for solving this problem with permanent variable perturbations.

Links

• GA22-10845S, research and development project: Name: Studium role polyhydroxyalkanoátů u bakterie Schlegelella thermodepolymerans – slibného bakteriálního kandidáta pro biotechnologie nové generace (Acronym: PHAST)

Investor: Czech Science Foundation, Unraveling the role of polyhydroxyalkanoates in Schlegelella thermodepolymerans – promising environmental bacterium for next generation biotechnology

• MUNI/A/1081/2022, interní kód MU: Name: Modelování, analýza a verifikace (2023)

Investor: Masaryk University

• MUNI/G/1771/2020, interní kód MU: Name: Computational reconstruction of mechanistic framework underlying receptor tyrosine kinase function in signal transduction (Acronym: FGFSIGMOD)

Investor: Masaryk University, INTERDISCIPLINARY - Interdisciplinary research projects