Computing maximal and minimal trap spaces of Boolean networks

Springer Science and Business Media LLC - Tập 14 Số 4 - Trang 535-544 - 2015
Hannes Klarner1, Alexander Bockmayr1, Heike Siebert1
1Freie Universität Berlin, FB Mathematik und Informatik, Arnimallee 6, 14195, Berlin, Germany

Tóm tắt

Từ khóa


Tài liệu tham khảo

Crama Y, Hammer PL (2011) Boolean functions: theory, algorithms, and applications, vol 142. Cambridge University Press, Cambridge

Dubrova E, Teslenko M (2011) A SAT-based algorithm for finding attractors in synchronous boolean networks. IEEE/ACM Trans Comput Biol Bioinform (TCBB) 8(5):1393–1399

Fogelman-Soulie F (1985) Parallel and sequential computation on boolean networks. Theor comput sci 40:275–300

Garg A, Di Cara A, Xenarios I, Mendoza L, De Micheli G (2008) Synchronous versus asynchronous modeling of gene regulatory networks. Bioinform 24(17):1917–1925

Gebser M, Kaminski R, Kaufmann B, Ostrowski M, Schaub T, Schneider M (2011) Potassco: the potsdam answer set solving collection. Ai Commun 24(2):107–124

Gershenson C (2004) Updating schemes in random boolean networks: do they really matter. In: Artificial life IX Proceedings of the 9th international conference on the simulation and synthesis of living systems, MIT Press, pp 238–243

Grieco L, Calzone L, Bernard-Pierrot I, Radvanyi F, Kahn-Perlès B, Thieffry D (2013) Integrative modelling of the influence of mapk network on cancer cell fate decision. PLoS comput Biol 9(10):e1003,286

Gurobi Optimization I (2015) Gurobi optimizer reference manual. www.gurobi.com

Jabbour S, Marques-Silva J, Sais L, Salhi Y (2014) Enumerating prime implicants of propositional formulae in conjunctive normal form. In: Fermé E, Leite J (eds) Logics in artificial intelligence. Springer, pp 152–165

Kauffman SA (1993) The origins of order: self organization and selection in evolution. Oxford University Press, USA

Klarner H (2015) www.sourceforge.net/Projects/BoolNetFixpoints

Klarner H, Bockmayr A, Siebert H (2014) Computing symbolic steady states of boolean networks. In: Was J, Sirakoulis G, Bandini S (eds) Cellular Automata, Lecture Notes in Computer Science, vol 8751, Springer International Publishing, pp 561–570

Müssel C, Hopfensitz M, Kestler HA (2010) Boolnet—an R package for generation, reconstruction, and analysis of boolean networks. Bioinformatics 10:1378–1380

Paulevé L, Chancellor C, Folschette M, Magnin M, Roux O (2014) Analyzing large network dynamics with process hitting. Log Model Biol Syst pp 125–166. doi: 10.1002/9781119005223.ch4

Siebert H (2011) Analysis of discrete bioregulatory networks using symbolic steady states. Bull Math Biol 73:873–898. doi: 10.1007/s11538-010-9609-1

Wang RS, Saadatpour A, Albert R (2012) Boolean modeling in systems biology: an overview of methodology and applications. Phys Biol 9(5):055,001

Zañudo JG, Albert R (2013) An effective network reduction approach to find the dynamical repertoire of discrete dynamic networks. Chaos: an interdisciplinary. J Nonlinear Sci 23(2):025–111