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 T. Akutsu , M. Hayasida , W Ching and M. Ng , Control of Boolean Networks: Hardness Results and Algorithms for Tree Structured Networks, Journal of Theoretical Biology, 2007, 244: 670–679.
 E. J. Candes and T. Tao , Near-optimal Signal Recovery from Random Projections: Universal Encoding Strategies, IEEE Transactions on Information Theory, 2006, 52: 5406–5425.
 J. E. Celis , M. Kruhøfferm , I. Gromova , C. Frederiksen , M. Østergaard and T. F. Ørntoft , Gene Expression Profiling: Monitoring Transcription and Translation Products Using DNA Microarrays and Proteomics, FEBS Letters, 2000, 480(1): 2–16.
 W. Ching , S. Scholtes and S. Zhang , Numerical Algorithms for Estimating Traffic Between Zones in a Network, Engineering Optimisation, 36 (2004), 379–400.
 W. Ching , E. Fung , M. Ng and T. Akutsu , On Construction of Stochastic Genetic Networks Based on Gene Expression Sequences, International Journal of Neural Systems, 15 (2005), 297–310.
 W. Ching , S. Zhang , M. Ng and T. Akutsu , An Approximation Method for Solving the Steady-state Probability Distribution of Probabilistic Boolean Networks, Bioinformatics, 2007, 23: 1511–1518.
 W. Ching , S. Zhang , Y. Jiao , T. Akutsu and A. Wong , Optimal Control Policy for Probabilistic Boolean Networks with Hard Constraints, IET on Systems Biology, 2009, 3: 90–99.
 A. Conn , B. Gould and P. Toint , Trust-region Methods, SIAM Publications, Philadelphia, 2000.
 E. Dougherty , S. Kim and Y. Chen , Coefficient of Determination in Nonlinear Signal Processing, Signal Processing, 2000, 80: 2219–2235.
 H. De Jong , Modeling and Simulation of Genetic Regulatory Systems: A Literature Review, Journal of Computational Biology, 2002, 9: 69–103.
 S. Huang , Gene Expression Profiling, Genetic Networks, and Cellular States: An Integrating Concept for Tumorigenesis and Drug Discovery, Journal of Molecular Medicine, 1999, 77: 469–480.
 S. Huang and D. E. Ingber , Shape-dependent Control of Cell Growth, Differentiation, and Apop-tosis: Switching Between Attractors in Cell Regulatory Networks, Experimental Cell Research, 2000, 261: 91–103.
 S. Kauffman , Metabolic Stability and Epigenesis in Randomly Constructed Gene Nets, Journal of Theoretical Biology, 1969, 22: 437–467.
 R. Pal , I. Ivanov , A. Datta , M. Bittner and E. Dougherty , Generating Boolean Networks with a Prescribed Attractor Structure, Bioinformatics, 2005, 21: 4021–4025.
 C.E. Shannon , A Mathematical Theory of Communication, Bell System Technical Journal, 1948, 27: 379–423.
 I. Shmulevich , E. Dougherty , S. Kim and W. Zhang , Probabilistic Boolean Networks: A Rule-based Uncertainty Model for Gene Regulatory Networks, Bioinformatics, 2002, 18: 261–274.
 P. Smolen , D. Baxter and J. Byrne , Mathematical Modeling of Gene Network, Neuron, 2000, 26: 567–580.
 R. Somogyi and C. Sniegoski , Modeling the Complexity of Gene Networks: Understanding Multigenic and Pleiotropic Regulation, Complexity, 1996, 1: 45–63.
 Y. Xiao and E. R. Dougherty , The Impact of Function Perturbations in Boolean Networks, Bioinformatics, 2007, 23(10): 1265–1273.
 S. Zhang , W. Ching , M. Ng and T. Akutsu , Simulation Study in Probabilistic Boolean Network Models for Genetic Regulatory Networks, Journal of Data Mining and Bioinformatics, 2007, 1: 217–240.
 S. Zhang , W. Ching , N. Tsing , H. Leung and D. Guo , A New Multiple Regression Approach for the Construction of Genetic Regulatory Networks, Journal of Artificial Intelligence in Medicine, 2009, 48: 153–160.
 S. Zhang , W. Ching , X. Chen and N. Tsing , On Construction of PBNs from a Prescribed Stationary Distribution, Information Sciences, 2010, 180: 2560–2570.