Determining a singleton attractor of a boolean network with nested canalyzing functions

التفاصيل البيبلوغرافية
العنوان: Determining a singleton attractor of a boolean network with nested canalyzing functions
المؤلفون: Masaki Yamamoto, Takeyuki Tamura, Avraham A. Melkman, Tatsuya Akutsu
المصدر: Journal of computational biology : a journal of computational molecular cell biology. 18(10)
سنة النشر: 2011
مصطلحات موضوعية: Boolean network, singleton attractor, Combinatorics, Chain (algebraic topology), Attractor, Genetics, Computer Simulation, Molecular Biology, Time complexity, Mathematics, Discrete mathematics, Degree (graph theory), Models, Genetic, Singleton, Systems Biology, Computational Biology, Computational Mathematics, Kinetics, Computational Theory and Mathematics, Gene Expression Regulation, Nonlinear Dynamics, Modeling and Simulation, Bounded function, SAT, nested canalyzing function, Boolean satisfiability problem, Algorithms
الوصف: In this article, we study the problem of finding a singleton attractor for several biologically important subclasses of Boolean networks (BNs). The problem of finding a singleton attractor in a BN is known to be NP-hard in general. For BNs consisting of n nested canalyzing functions, we present an O(1.799(n)) time algorithm. The core part of this development is an O(min(2(k/2) · 2(m/2), 2(k)) · poly(k, m)) time algorithm for the satisfiability problem for m nested canalyzing functions over k variables. For BNs consisting of chain functions, a subclass of nested canalyzing functions, we present an O(1.619(n)) time algorithm and show that the problem remains NP-hard, even though the satisfiability problem for m chain functions over k variables is solvable in polynomial time. Finally, we present an o(2(n)) time algorithm for bounded degree BNs consisting of canalyzing functions.
وصف الملف: application/pdf
تدمد: 1557-8666
URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a30511fba29a7036f1815aa69fa695fd
https://pubmed.ncbi.nlm.nih.gov/21554129
Rights: OPEN
رقم الانضمام: edsair.doi.dedup.....a30511fba29a7036f1815aa69fa695fd
قاعدة البيانات: OpenAIRE