TY - JOUR AU - Elowitz, M. B. AU - Levine, A. J. AU - Siggia, E. D. AU - Swain, P. S. PY - 2002 DA - 2002// TI - Stochastic gene expression in a single cell JO - Sci VL - 297 UR - https://doi.org/10.1126/science.1070919 DO - 10.1126/science.1070919 ID - Elowitz2002 ER - TY - JOUR AU - Pedraza, J. M. AU - van Oudenaarden, A. PY - 2005 DA - 2005// TI - Noise propagation in genetic networks JO - Sci VL - 307 UR - https://doi.org/10.1126/science.1109090 DO - 10.1126/science.1109090 ID - Pedraza2005 ER - TY - JOUR AU - Dunlop, M. AU - Cox, R. I. I. I. AU - Levine, J. AU - Murray, R. AU - Elowitz, M. PY - 2008 DA - 2008// TI - Regulatory activity revealed by dynamic correlations in gene expression noise JO - Nat Genet VL - 40 UR - https://doi.org/10.1038/ng.281 DO - 10.1038/ng.281 ID - Dunlop2008 ER - TY - JOUR AU - Kauffman, S. A. PY - 1969 DA - 1969// TI - Metabolic stability and epigenesis in randomly constructed genetic nets JO - Theor Biol VL - 22 UR - https://doi.org/10.1016/0022-5193(69)90015-0 DO - 10.1016/0022-5193(69)90015-0 ID - Kauffman1969 ER - TY - CHAP AU - Klipp, E. PY - 2005 DA - 2005// BT - Systems Biology in Practice: Concepts, Implementation and Application PB - Wiley-VCH CY - Weinheim, Germany UR - https://doi.org/10.1002/3527603603 DO - 10.1002/3527603603 ID - Klipp2005 ER - TY - JOUR AU - Qian, L. AU - Wang, H. AU - Dougherty, E. PY - 2008 DA - 2008// TI - Inference of noisy nonlinear differential equation models for gene regulatory networks using genetic programming and Kalman filtering JO - IEEE Trans Signal Process VL - 56 UR - https://doi.org/10.1109/TSP.2008.919638 DO - 10.1109/TSP.2008.919638 ID - Qian2008 ER - TY - JOUR AU - Gillespie, D. T. PY - 1976 DA - 1976// TI - A general method for numerically simulating the stochastic time evolution of coupled chemical reactions JO - J Comput Phys VL - 22 UR - https://doi.org/10.1016/0021-9991(76)90041-3 DO - 10.1016/0021-9991(76)90041-3 ID - Gillespie1976 ER - TY - JOUR AU - Gillespie, D. T. PY - 1977 DA - 1977// TI - Exact stochastic simulation of coupled chemical reactions JO - J Phys Chem VL - 81 UR - https://doi.org/10.1021/j100540a008 DO - 10.1021/j100540a008 ID - Gillespie1977 ER - TY - JOUR AU - Davidich, M. AU - Bornholt, S. PY - 2008 DA - 2008// TI - Boolean network model predicts cell cycle sequence of Fission yeast JO - PLoS One VL - 3 UR - https://doi.org/10.1371/journal.pone.0001672 DO - 10.1371/journal.pone.0001672 ID - Davidich2008 ER - TY - JOUR AU - Giacomantonio, C. E. AU - Goodhill, G. J. PY - 2010 DA - 2010// TI - A Boolean model of the gene regulatory network underlying Mammalian cortical area development JO - PLoS Comput Biol VL - 6 UR - https://doi.org/10.1371/journal.pcbi.1000936 DO - 10.1371/journal.pcbi.1000936 ID - Giacomantonio2010 ER - TY - JOUR AU - Huang, S. PY - 1999 DA - 1999// TI - Gene expression profiling, genetic networks, and cellular states: an integrating concept for tumorigenesis and drug discovery JO - J Mol Med VL - 77 UR - https://doi.org/10.1007/s001099900023 DO - 10.1007/s001099900023 ID - Huang1999 ER - TY - JOUR AU - Shmulevich, I. AU - Dougherty, E. R. AU - Zhang, W. PY - 2002 DA - 2002// TI - From Boolean to probabilistic Boolean networks as models of genetic regulatory networks JO - Proc IEEE VL - 90 UR - https://doi.org/10.1109/JPROC.2002.804686 DO - 10.1109/JPROC.2002.804686 ID - Shmulevich2002 ER - TY - JOUR AU - Dougherty, E. R. S. I. AU - Zhang, W. PY - 2002 DA - 2002// TI - Gene perturbation and intervention in probabilistic Boolean networks JO - Bioinform VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.10.1319 DO - 10.1093/bioinformatics/18.10.1319 ID - Dougherty2002 ER - TY - BOOK AU - Shmulevich, I. AU - Dougherty, E. PY - 2009 DA - 2009// TI - Probabilistic Boolean Networks: The Modeling and Control of Gene Regulatory Networks PB - SIAM CY - Philadelphia ID - Shmulevich2009 ER - TY - JOUR AU - Pal, R. AU - Datta, A. AU - Bittner, M. L. AU - Dougherty, E. R. PY - 2005 DA - 2005// TI - Intervention in context-sensitive probabilistic Boolean networks JO - Bioinform VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti131 DO - 10.1093/bioinformatics/bti131 ID - Pal2005 ER - TY - JOUR AU - Shmulevich, I. AU - Gluhovsky, I. AU - Hashimoto, R. F. AU - Dougherty, E. R. AU - Zhang, W. PY - 2003 DA - 2003// TI - Steady-state analysis of genetic regulatory networks modeled by probabilistic Boolean networks JO - Comp Funct Genomics VL - 4 UR - https://doi.org/10.1002/cfg.342 DO - 10.1002/cfg.342 ID - Shmulevich2003 ER - TY - JOUR AU - Rosenthal, J. S. PY - 1995 DA - 1995// TI - Minorization conditions and convergence rates for Markov chain Monte Carlo JO - J Am Stat Assoc VL - 90 UR - https://doi.org/10.1080/01621459.1995.10476548 DO - 10.1080/01621459.1995.10476548 ID - Rosenthal1995 ER - TY - JOUR AU - Zhang, S. AU - Ching, W. AU - Ng, M. AU - Akutsu, T. PY - 2007 DA - 2007// TI - Simulation study in probabilistic Boolean network models for genetic regulatory networks JO - Int J Data Min Bioinform VL - 1 UR - https://doi.org/10.1504/IJDMB.2007.011610 DO - 10.1504/IJDMB.2007.011610 ID - Zhang2007 ER - TY - JOUR AU - Brun, M. AU - Dougherty, E. R. AU - Shmulevich, I. PY - 2005 DA - 2005// TI - Steady-state probabilities for attractors in probabilistic Boolean networks JO - Signal Process VL - 85 UR - https://doi.org/10.1016/j.sigpro.2005.02.016 DO - 10.1016/j.sigpro.2005.02.016 ID - Brun2005 ER - TY - JOUR AU - Ching, W. AU - Zhang, S. AU - Ng, M. AU - Akutsu, T. PY - 2007 DA - 2007// TI - An approximation method for solving the steady-state probability distribution of probabilistic Boolean networks JO - Bioinform VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm142 DO - 10.1093/bioinformatics/btm142 ID - Ching2007 ER - TY - JOUR AU - Datta, A. AU - Choudhary, A. AU - Bittner, M. L. AU - Dougherty, E. R. PY - 2003 DA - 2003// TI - External control in markovian genetic regulatory networks JO - Mach Learn VL - 52 UR - https://doi.org/10.1023/A:1023909812213 DO - 10.1023/A:1023909812213 ID - Datta2003 ER - TY - JOUR AU - Datta, A. AU - Choudhary, A. AU - Bittner, M. L. AU - Dougherty, E. R. PY - 2004 DA - 2004// TI - External control in markovian genetic reegulatory networks: the imperfect information case JO - Bioinform VL - 20 UR - https://doi.org/10.1093/bioinformatics/bth008 DO - 10.1093/bioinformatics/bth008 ID - Datta2004 ER - TY - JOUR AU - Pal, R. PY - 2010 DA - 2010// TI - Context-sensitive probabilistic Boolean networks: steady-state properties, reduction, and steady-state approximation JO - IEEE Trans Signal Process VL - 58 UR - https://doi.org/10.1109/TSP.2009.2030832 DO - 10.1109/TSP.2009.2030832 ID - Pal2010 ER - TY - JOUR AU - Liang, J. AU - Han, J. PY - 2012 DA - 2012// TI - Stochastic Boolean networks: an efficient approach to modeling gene regulatory networks JO - BMC Syst Biol VL - 6 UR - https://doi.org/10.1186/1752-0509-6-113 DO - 10.1186/1752-0509-6-113 ID - Liang2012 ER - TY - JOUR AU - Lahav, G. AU - Rosenfeld, N. AU - Sigal, A. AU - Geva-Zatorsky, N. AU - Levine, A. J. AU - Elowitz, M. B. AU - Alon, U. PY - 2004 DA - 2004// TI - Dynamics of the p53-Mdm2 feedback loop in individual cells JO - Nat Genet VL - 36 UR - https://doi.org/10.1038/ng1293 DO - 10.1038/ng1293 ID - Lahav2004 ER - TY - JOUR AU - Martin, S. AU - Zhang, Z. AU - Martino, A. AU - Faulon, J. -. L. PY - 2007 DA - 2007// TI - Boolean dynamics of genetic regulatory networks infer red from microarray time series data JO - Bioinform VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm021 DO - 10.1093/bioinformatics/btm021 ID - Martin2007 ER - TY - JOUR AU - Zhu, P. AU - Han, J. PY - 2014 DA - 2014// TI - Stochastic multiple-valued gene networks JO - IEEE Transac Biomed Circ Syst VL - 8 UR - https://doi.org/10.1109/TBCAS.2013.2291398 DO - 10.1109/TBCAS.2013.2291398 ID - Zhu2014 ER - TY - CHAP AU - Zhu, P. AU - Han, J. PY - 2014 DA - 2014// TI - Asynchronous stochastic Boolean networks as gene network models BT - J Comput Biol ID - Zhu2014 ER - TY - JOUR AU - Faryabi, B. AU - Vahedi, G. AU - Chamberland, J. F. AU - Datta, A. AU - Dougherty, E. R. PY - 2009 DA - 2009// TI - Intervention in context-sensitive probabilistic Boolean networks revisited JO - EURASIP J Bioinform Syst Biol VL - 2009 UR - https://doi.org/10.1155/2009/360864 DO - 10.1155/2009/360864 ID - Faryabi2009 ER - TY - JOUR AU - McAdams, H. H. AU - Shapiro, L. PY - 1995 DA - 1995// TI - Circuit simulation of genetic networks JO - Sci VL - 269 UR - https://doi.org/10.1126/science.7624793 DO - 10.1126/science.7624793 ID - McAdams1995 ER - TY - JOUR AU - Abdi, A. AU - Tahoori, M. B. AU - Emamian, E. S. PY - 2008 DA - 2008// TI - Fault diagnosis engineering of digital circuits can identify vulnerable molecules in complex cellular pathways JO - Sci Signal VL - 1 UR - https://doi.org/10.1126/scisignal.2000008 DO - 10.1126/scisignal.2000008 ID - Abdi2008 ER - TY - JOUR AU - Adar, R. AU - Benenson, Y. AU - Linshiz, G. AU - Rosner, A. AU - Tishby, N. AU - Shapiro, E. PY - 2004 DA - 2004// TI - Stochastic computing with biomolecular automata JO - PNAS VL - 101 UR - https://doi.org/10.1073/pnas.0400731101 DO - 10.1073/pnas.0400731101 ID - Adar2004 ER - TY - JOUR AU - Benenson, Y. AU - Gil, B. AU - Ben-Dor, U. AU - Adar, R. AU - Shapiro, E. PY - 2004 DA - 2004// TI - An autonomous molecular computer for logical control of gene expression JO - Nat VL - 429 UR - https://doi.org/10.1038/nature02551 DO - 10.1038/nature02551 ID - Benenson2004 ER - TY - JOUR AU - Gaines, B. R. PY - 1969 DA - 1969// TI - Stochastic computing systems JO - Adv Inf Syst Sci VL - 2 UR - https://doi.org/10.1007/978-1-4899-5841-9_2 DO - 10.1007/978-1-4899-5841-9_2 ID - Gaines1969 ER - TY - CHAP AU - Han, J. AU - Chen, H. AU - Liang, J. AU - Zhu, P. AU - Yang, Z. AU - Lombardi, F. PY - 2013 DA - 2013// TI - A Stochastic Computational Approach for Accurate and Efficient Reliability Evaluation BT - IEEE Transactions on Computers ID - Han2013 ER - TY - JOUR AU - Pal, R. AU - Datta, A. AU - Bittner, M. L. AU - Dougherty, E. R. PY - 2006 DA - 2006// TI - Optimal infinite horizon control for probabilistic Boolean networks JO - IEEE Trans Signal Process VL - 54 UR - https://doi.org/10.1109/TSP.2006.873740 DO - 10.1109/TSP.2006.873740 ID - Pal2006 ER - TY - JOUR AU - Faryabi, B. AU - Datta, A. AU - Dougherty, E. R. PY - 2007 DA - 2007// TI - On approximate stochastic control in genetic regulatory networks JO - IET Syst Biol VL - 1 UR - https://doi.org/10.1049/iet-syb:20070015 DO - 10.1049/iet-syb:20070015 ID - Faryabi2007 ER - TY - JOUR AU - Layek, R. AU - Datta, A. AU - Pal, R. AU - Dougherty, E. R. PY - 2009 DA - 2009// TI - Adaptive intervention in probabilistic Boolean networks JO - Bioinform VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp349 DO - 10.1093/bioinformatics/btp349 ID - Layek2009 ER - TY - JOUR AU - Qian, X. AU - Dougherty, E. R. PY - 2008 DA - 2008// TI - Effect of function perturbation on the steady-state distribution of genetic regulatory networks: optimal structural intervention JO - IEEE Trans Signal Process VL - 56 UR - https://doi.org/10.1109/TSP.2008.928089 DO - 10.1109/TSP.2008.928089 ID - Qian2008 ER - TY - JOUR AU - Qian, X. AU - Ivanov, I. AU - Ghaffari, N. AU - Dougherty, E. R. PY - 2009 DA - 2009// TI - Intervention in gene regulatory networks via greedy control policies based on long-run behavior JO - BMC Syst Biol VL - 3 UR - https://doi.org/10.1186/1752-0509-3-61 DO - 10.1186/1752-0509-3-61 ID - Qian2009 ER - TY - BOOK AU - Weinberg, R. A. PY - 2006 DA - 2006// TI - The Biology of Cancer PB - Garland Science CY - New York ID - Weinberg2006 ER - TY - JOUR AU - Vogelstein, B. AU - Lane, D. AU - Levine, A. J. PY - 2000 DA - 2000// TI - Surfing the p53 network JO - Nat VL - 408 UR - https://doi.org/10.1038/35042675 DO - 10.1038/35042675 ID - Vogelstein2000 ER - TY - JOUR AU - Batchelor, E. AU - Loewer, A. AU - Lahav, G. PY - 2009 DA - 2009// TI - The ups and downs of p53: understanding protein dynamics in single cells JO - Nat Rev Cancer VL - 9 UR - https://doi.org/10.1038/nrc2604 DO - 10.1038/nrc2604 ID - Batchelor2009 ER - TY - JOUR AU - Ciliberto, A. AU - Novak, B. AU - Tyson, J. J. PY - 2005 DA - 2005// TI - Steady states and oscillations in the p53-Mdm2 network JO - Cell Cycle VL - 4 ID - Ciliberto2005 ER - TY - JOUR AU - Abou-Jaoude, W. AU - Ouattara, D. AU - Kaufman, M. PY - 2009 DA - 2009// TI - From structure to dynamics: frequency tuning in the p53-mdm2 network: I: logical approach JO - J Theor Biol VL - 258 UR - https://doi.org/10.1016/j.jtbi.2009.02.005 DO - 10.1016/j.jtbi.2009.02.005 ID - Abou-Jaoude2009 ER - TY - JOUR AU - Murrugarra, D. AU - Veliz-Cuba, A. AU - Aguilar, B. AU - Arat, S. AU - Laubenbacher, R. PY - 2012 DA - 2012// TI - Modeling stochasticity and variability in gene regulatory networks JO - EURASIP J Bioinform Syst Biol VL - 1 UR - https://doi.org/10.1186/1687-4153-2012-5 DO - 10.1186/1687-4153-2012-5 ID - Murrugarra2012 ER - TY - JOUR AU - Fuller, G. N. AU - Rhee, C. H. AU - Hess, K. R. AU - Caskey, L. S. AU - Wang, R. AU - Bruner, J. M. AU - Yung, W. K. AU - Zhang, W. PY - 1999 DA - 1999// TI - Reactivation of insulin-like growth factor binding protein 2 expression in glioblastoma multiforme: a revelation by parallel gene expression profiling JO - Cancer Res VL - 59 ID - Fuller1999 ER - TY - JOUR AU - Ge, H. AU - Qian, M. PY - 2009 DA - 2009// TI - Boolean network approach to negative feedback loops of the p53 pathways: synchronized dynamics and stochastic limit cycles JO - J Comput Biol VL - 16 UR - https://doi.org/10.1089/cmb.2007.0181 DO - 10.1089/cmb.2007.0181 ID - Ge2009 ER -