On the Complexity of Inference and Completion of Boolean Networks from Given Singleton Attractors

[1]  A. Mochizuki,et al.  Analyzing steady states of dynamics of bio-molecules from the structure of regulatory networks. , 2010, Journal of theoretical biology.

[2]  Abdul Salam Jarrah,et al.  The Dynamics of Conjunctive and Disjunctive Boolean Networks , 2008, 0805.0275.

[3]  A. Garg,et al.  Synchronous versus asynchronous modeling of gene regulatory networks , 2008, Bioinform..

[4]  Aniruddha Datta,et al.  Generating Boolean networks with a prescribed attractor structure , 2005, Bioinform..

[5]  Eric Goles Ch.,et al.  Fixed points and maximal independent sets in AND-OR networks , 2004, Discret. Appl. Math..

[6]  B. Drossel,et al.  Number and length of attractors in a critical Kauffman model with connectivity one. , 2004, Physical review letters.

[7]  Eric Goles Ch.,et al.  Positive and negative circuits in discrete neural networks , 2004, IEEE Transactions on Neural Networks.

[8]  Tatsuya Akutsu,et al.  Determining a Singleton Attractor of a Boolean Network with Nested Canalyzing Functions , 2011, J. Comput. Biol..

[9]  Martine Labbé,et al.  Identification of all steady states in large networks by logical analysis , 2003, Bulletin of mathematical biology.

[10]  Julio M. Ottino,et al.  Cascading failure and robustness in metabolic networks , 2008, Proceedings of the National Academy of Sciences.

[11]  Abdul Salam Jarrah,et al.  The Dynamics of Conjunctive and Disjunctive Boolean Network Models , 2010, Bulletin of mathematical biology.

[12]  Oliver Ebenhöh,et al.  Expanding Metabolic Networks: Scopes of Compounds, Robustness, and Evolution , 2005, Journal of Molecular Evolution.

[13]  B. Samuelsson,et al.  Superpolynomial growth in the number of attractors in Kauffman networks. , 2003, Physical review letters.

[14]  Stuart A. Kauffman,et al.  The origins of order , 1993 .

[15]  Michael K. Ng,et al.  Algorithms for Finding Small Attractors in Boolean Networks , 2007, EURASIP J. Bioinform. Syst. Biol..

[16]  Tatsuya Akutsu,et al.  Determining a singleton attractor of an AND/OR Boolean network in O(1.587n) time , 2010, Inf. Process. Lett..

[17]  Eric Goles Ch.,et al.  Sequential operator for filtering cycles in Boolean networks , 2010, Adv. Appl. Math..

[18]  D. Irons Improving the efficiency of attractor cycle identification in Boolean networks , 2006 .

[19]  Hisao Tamaki,et al.  A directed path-decomposition approach to exactly identifying attractors of boolean networks , 2010, 2010 10th International Symposium on Communications and Information Technologies.

[20]  Kiyoko F. Aoki-Kinoshita,et al.  Modeling genetic regulatory networks: a delay discrete dynamical model approach , 2012, J. Syst. Sci. Complex..

[21]  Andrew Wuensche,et al.  A model of transcriptional regulatory networks based on biases in the observed regulation rules , 2002, Complex..

[22]  Simone Linz,et al.  The Complexity of Finding Multiple Solutions to Betweenness and Quartet Compatibility , 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[23]  Abdul Salam Jarrah,et al.  Nested Canalyzing, Unate Cascade, and Polynomial Functions. , 2006, Physica D. Nonlinear phenomena.

[24]  Giorgio Parisi,et al.  Finite size corrections to random Boolean networks , 2006 .

[25]  Katsumi Inoue,et al.  Proceedings of the Twenty-Second International Joint Conference on Artificial Intelligence Logic Programming for Boolean Networks , 2022 .

[26]  T. Yato,et al.  Complexity and Completeness of Finding Another Solution and Its Application to Puzzles , 2003, IEICE Trans. Fundam. Electron. Commun. Comput. Sci..

[27]  Yi Ming Zou,et al.  Modeling and analyzing complex biological networks incooperating experimental information on both network topology and stable states , 2010, Bioinform..

[28]  Hidde de Jong,et al.  Modeling and Simulation of Genetic Regulatory Systems: A Literature Review , 2002, J. Comput. Biol..

[29]  D. Cheng,et al.  Identification of Boolean control networks , 2011, Autom..

[30]  Satoru Miyano,et al.  Identification of Genetic Networks from a Small Number of Gene Expression Patterns Under the Boolean Network Model , 1998, Pacific Symposium on Biocomputing.

[31]  Tatsuya Akutsu,et al.  Finding a Periodic Attractor of a Boolean Network , 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[32]  T. Perkins,et al.  A Trade-Off between Sample Complexity and Computational Complexity in Learning Boolean Networks from Time-Series Data , 2010, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[33]  S Fuhrman,et al.  Reveal, a general reverse engineering algorithm for inference of genetic network architectures. , 1998, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[34]  Akutsu,et al.  A System for Identifying Genetic Networks from Gene Expression Patterns Produced by Gene Disruptions and Overexpressions. , 1998, Genome informatics. Workshop on Genome Informatics.

[35]  Maxim Teslenko,et al.  A SAT-Based Algorithm for Finding Attractors in Synchronous Boolean Networks , 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[36]  Jean-Philippe Vert,et al.  Analysis of the impact degree distribution in metabolic networks using branching process approximation , 2011, 1108.2588.