B.M. Adams, H.T. Banks, H.-D. Kwon, and H.T. Tran Dynamic multidrug therapies for HIV: Optimal and STI control approaches Mathematical Biosciences and Engineering 1 2 2004 223 241
D. Angeli, and E.D. Sontag Monotone control systems IEEE Transactions on Automatic Control 48 10 2003 1684 1698
J.A.N. Brophy, and C.A. Voigt Principles of genetic circuit design Nature Methods 11 5 2014 508 520
L. Buşoniu, R. Babuška, B. De Schutter, and D. Ernst Reinforcement learning and dynamic programming using function approximators 2010 CRC Pr I Llc
I. Cataudella, K. Sneppen, K. Gerdes, and N. Mitarai Conditional cooperativity of toxin-antitoxin regulation can mediate bistability between growth and dormancy PLoS Computational Biology 9 8 2013 e1003174
L. Chisci, and P. Falugi Asymptotic tracking for constrained monotone systems IEEE Transactions on Automatic Control 51 5 2006 873 879
M.B. Elowitz, A.J. Levine, E.D. Siggia, and P.S. Swain Stochastic gene expression in a single cell Science Signalling 297 5584 2002 1183
T. Gardner, C.R. Cantor, and J.J. Collins Construction of a genetic toggle switch in escherichia coli Nature 403 2000 339 342
Gennat, M., & Tibken, B. (2008). Computing guaranteed bounds for uncertain cooperative and monotone nonlinear systems. In Preprints. IFAC world congress (pp. 4846-4851).
J. Jiang, X. Liang, and X.-Q. Zhao Saddle-point behavior for monotone semiflows and reaction-diffusion models Journal of Differential Equations 203 2 2004 313 330
H.K. Khalil Nonlinear systems 2002 Prentice Hall
A.S. Khalil, and J.J. Collins Synthetic biology: applications come of age Nature Reviews Genetics 11 5 2010 367 379
A. Levskaya, O.D. Weiner, W.A. Lim, and C.A. Voigt Spatiotemporal control of cell signalling using a light-switchable protein interaction Nature 461 2009 997 1001
F. Menolascina, M. Di Bernardo, and D. Di Bernardo Analysis, design and implementation of a novel scheme for in-vivo control of synthetic gene regulatory networks Automatica 47 6 2011 1265 1270 Special Issue on Systems Biology
J.T. Mettetal, D. Muzzey, C. Gomez-Uribe, and A. van Oudenaarden The frequency dependence of osmo-adaptation in saccharomyces cerevisiae Science 319 5862 2008 482 484
Meyer, P.-J., Girard, A., & Witrant, E. (2013). Controllability and invariance of monotone systems for robust ventilation automation in buildings. In Proc. IEEE conf. decision control (pp. 1289-1294).
A. Milias-Argeitis, S. Summers, J. Stewart-Ornstein, I. Zuleta, D. Pincus, H. El-Samad, and J. Lygeros In silico feedback for in vivo regulation of a gene expression circuit Nature Biotechnology 29 12 2011 1114 1116...
Pan, W., Sootla, A., & Stan, G.-B. (2014). Distributed reconstruction of nonlinear networks: An ADMM approach. In Preprints IFAC world congress. August (pp. 3208-3213).
P.E.M. Purnick, and R. Weiss The second wave of synthetic biology: from modules to systems Nature Reviews Molecular Cell Biology 10 6 2009 410 422
N. Ramdani, N. Meslem, and Y. Candau A hybrid bounding method for computing an over-approximation for the reachable set of uncertain nonlinear systems IEEE Transactions on Automatic Control 54 10 2009 2352 2364
N. Ramdani, N. Meslem, and Y. Candau Computing reachable sets for uncertain nonlinear monotone systems Nonlinear Analysis. Hybrid Systems 4 2 2010 263 278
E.D. Sontag Monotone and near-monotone biochemical networks Systems and Synthetic Biology 1 2 2007 59 87
Sootla, A. (2015). On monotonicity and propagation of order properties. In Proc. Am. control conf. Chicago, Il, June (pp. 3144-3149).
Sootla, A., Oyarzún, D., Angeli, D., & Stan, G.-B. (2015). Shaping pulses to control bistable biological systems. In Proc Amer. control conf. (pp. 3138-3143).
Sootla, A., Strelkowa, N., Ernst, D., Barahona, M., & Stan, G.-B. (2013). On reference tracking using reinforcement learning with application to gene regulatory networks. In Proc conf. decision control. Florence, Italy, December 10-13 (pp. 4086-4091).
Sootla, A., Strelkowa, N., Ernst, D., Barahona, M., & Stan, G.-B. (2014). Toggling the genetic switch using reinforcement learning. In Proc 9th french meeting on planning, decision making and learning. Liège, Belgium, May.
N. Strelkowa, and M. Barahona Switchable genetic oscillator operating in quasi-stable mode Journal of the Royal Society Interface 7 48 2010 1071 1082
M.E. Tipping Sparse Bayesian learning and the relevance vector machine Journal of Machine Learning Research 1 2001 211 244
J. Uhlendorf, A. Miermont, T. Delaveau, G. Charvin, F. Fages, S. Bottani, and P. Hersen Long-term model predictive control of gene expression at the population and single-cell levels Proceedings of the National Academy of Sciences 109 35 2012 14271 14276...
T. Wilhelm The smallest chemical reaction system with bistability BMC Systems Biology 3 1 2009 90
D. Wipf, S. Nagarajan, J. Platt, D. Koller, Y. Singer, and S. Roweis A new view of automatic relevance determination Advances in Neural Information Processing Systems 20 2008 1625 1632
J.W. Zwolak, J.J. Tyson, and L.T. Watson Finding all steady state solutions of chemical kinetic models Nonlinear Analysis: Real World Applications 5 5 2004 801 814