Phenotype Control of Partially Specified Boolean Networks

D 2023

Phenotype Control of Partially Specified Boolean Networks

BENEŠ, Nikola, Luboš BRIM, Samuel PASTVA, David ŠAFRÁNEK, Eva ŠMIJÁKOVÁ et. al.

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

Language

English

Type of outcome

Stať ve sborníku

Field of Study

10200 1.2 Computer and information sciences

Country of publisher

Luxembourg

Confidentiality degree

není předmětem státního či obchodního tajemství

Publication form

printed version "print"

References:

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

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

Abstract

V originále

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

Citovat

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.

@inproceedings{2308500,
   author = {Beneš, Nikola and Brim, Luboš and Pastva, Samuel and Šafránek, David and Šmijáková, Eva},
   address = {Luxembourg City, Luxembourg},
   booktitle = {Computational Methods in Systems Biology},
   doi = {http://dx.doi.org/10.1007/978-3-031-42697-1_2},
   editor = {Jun Pang, Joachim Niehren},
   keywords = {Boolean networks;Partial specification;Permanent control;Phenotype;Perturbation;Symbolic algorithm},
   howpublished = {tištěná verze "print"},
   language = {eng},
   location = {Luxembourg City, Luxembourg},
   isbn = {978-3-031-42696-4},
   pages = {18-35},
   publisher = {Springer Cham},
   title = {Phenotype Control of Partially Specified Boolean Networks},
   url = {https://link.springer.com/chapter/10.1007/978-3-031-42697-1_2},
   year = {2023}
}

TY  - JOUR
ID  - 2308500
AU  - Beneš, Nikola - Brim, Luboš - Pastva, Samuel - Šafránek, David - Šmijáková, Eva
PY  - 2023
TI  - Phenotype Control of Partially Specified Boolean Networks
PB  - Springer Cham
CY  - Luxembourg City, Luxembourg
SN  - 9783031426964
KW  - Boolean networks;Partial specification;Permanent control;Phenotype;Perturbation;Symbolic algorithm
UR  - https://link.springer.com/chapter/10.1007/978-3-031-42697-1_2
N2  - 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.
ER  -

BENEŠ, Nikola, Luboš BRIM, Samuel PASTVA, David ŠAFRÁNEK and Eva ŠMIJÁKOVÁ. Phenotype Control of Partially Specified Boolean Networks. In Jun Pang, Joachim Niehren. \textit{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.

Detailed Information on Publication Record