@article(ay2009, author = {Ferhat Ay and Fei Xu and Tamer Kahveci}, year = {2009}, title = {Scalable steady state analysis of Boolean biological regulatory networks}, journal = {PloS one}, volume = {4}, number = {12}, pages = {e7992}, doi = {10.1371/journal.pone.0007992}, ) @article(newsem, author = {Belaïd Benhamou and Pierre Siegel}, year = {2012}, title = {A New Semantics for Logic Programs Capturing and Extending the Stable Model Semantics}, journal = {Tools with Artificial Intelligence (ICTAI)}, pages = {25--32}, doi = {10.1109/ICTAI.2012.167}, ) @article(davidich2008, author = {Maria I Davidich and Stefan Bornholdt}, year = {2008}, title = {Boolean network model predicts cell cycle sequence of fission yeast}, journal = {PloS one}, volume = {3}, number = {2}, pages = {e1672}, doi = {10.1371/journal.pone.0001672}, ) @article(dejong2002, author = {De Jong, Hidde}, year = {2002}, title = {Modeling and simulation of genetic regulatory systems: a literature review}, journal = {Journal of computational biology}, volume = {9}, number = {1}, pages = {67--103}, doi = {10.1089/10665270252833208}, ) @article(garg2008, author = {Abhishek Garg and Di Cara, Alessandro and Ioannis Xenarios and Luis Mendoza and De Micheli, Giovanni}, year = {2008}, title = {Synchronous versus asynchronous modeling of gene regulatory networks}, journal = {Bioinformatics}, volume = {24}, number = {17}, pages = {1917--1925}, doi = {10.1093/bioinformatics/btn336}, ) @article(garg2007, author = {Abhishek Garg and Ioannis Xenarios and Luis Mendoza and Giovanni DeMicheli}, year = {2007}, title = {An efficient method for dynamic analysis of gene regulatory networks and in silico gene perturbation experiments}, pages = {62--76}, doi = {10.1007/978-3-540-71681-5\_5}, ) @article(jacob1961, author = {Fran{\c{c}}ois Jacob and Jacques Monod}, year = {1961}, title = {Genetic regulatory mechanisms in the synthesis of proteins}, journal = {Journal of molecular biology}, volume = {3}, number = {3}, pages = {318--356}, doi = {10.1016/S0022-2836(61)80072-7}, ) @article(method2018, author = {Tarek Khaled and Belaïd Benhamou and Pierre Siegel}, year = {2018}, title = {A new method for computing stable models in logic programming}, journal = {Tools with Artificial Intelligence (ICTAI)}, pages = {800--807}, doi = {10.1109/ICTAI.2018.00125}, ) @article(mushthofa2014, author = {Mushthofa Mushthofa and Gustavo Torres and Van de Peer, Yves and Kathleen Marchal and De Cock, Martine}, year = {2014}, title = {ASP-G: an ASP-based method for finding attractors in genetic regulatory networks}, journal = {Bioinformatics}, volume = {30}, number = {21}, pages = {3086--3092}, doi = {10.1093/bioinformatics/btu481}, )