• 2017
  • A. A. Mannan , D. Liu, F. Zhang, D. A. Oyarzún. "Fundamental design principles for transcription-factor-based metabolite biosensors". ACS Synthetic Biology, in press, 2017. (Link) (PDF)

  • 2016
  • A. Y. Weiße, A. A. Mannan, D. A. Oyarzún. "Signaling Tug-of-War Delivers the Whole Message". Cell Systems, 3, pp 414-416, 2016. (Link) (PDF)
  • M. Beguerisse-Díaz, G. Bosque, D. A. Oyarzún, J. Picó, M. Barahona. "Context-dependent metabolic networks". Available online, 2016. arXiv:1605.01639
  • A. Sootla, D. A. Oyarzún, D. Angeli, and G.-B. Stan. "Shaping Pulses to Control Bistable Systems: Analysis, Computation and Counterexamples". Automatica, 63, pp 254-264, 2016. (Link) (Arxiv)

  • 2015
  • D. A. Oyarzún and M. Chaves. "Design of a bistable switch to control cellular uptake". Journal of the Royal Society Interface, (12) 2015. (Link) (PDF)
  • A. Y. Weiße, D. A. Oyarzún, V. Danos, and P. Swain. "A mechanistic link between cellular trade-offs, gene expression and cellular growth". PNAS, 112(9), 2015. (Link) (Biorxiv)
  • D. A. Oyarzún, J.-B. Lugagne and G.-B. Stan. "Noise propagation in synthetic gene circuits for metabolic control". ACS Synthetic Biology, 4(2), pp 116-126, 2015. (Link) (PDF)
  • S. Waldherr, D. A. Oyarzún and A. Bockmayr. "Dynamic optimization of metabolic networks coupled with gene expression". Journal of Theoretical Biology, 365, pp 469-485, 2015. (Link) (Arxiv)
  • A. Sootla, D. A. Oyarzún, D. Angeli and G.-B. Stan. "Shaping pulses to control bi-stable biological systems". In Proceedings of the American Control Conference, Chicago, 2015. (PDF)

  • 2014
  • D. A. Oyarzún, J. L. Bramhall, F. López-Caamal, F. M. Richards, D. Jodrell and B.-F. Krippendorff. "The EGFR demonstrates linear signal transmission". Integrative Biology, 8(6), 2014. (available online) (PDF) HOT Article of 2014
  • J. Kuntz, D. A. Oyarzún and G.-B. Stan. "Model reduction of genetic-metabolic systems using timescale separation". In System Theoretic Approaches to Systems and Synthetic Biology, Springer-Verlag, 2014. (PDF)
  • F. López-Caamal, D. A. Oyarzún, R. H. Middleton and M. R. García. "Spatial quantification of cytosolic Ca2+ accumulation in nonexcitable cells: an analytical study". IEEE/ACM Transactions on Computational Biology and Bioinformatics, 11(3), 2014. (Link) (PDF)

  • 2013
  • D. A. Oyarzún and G.-B. Stan. "Genetic control circuits for metabolism: design constraints and performance tradeoffs". Journal of the Royal Society Interface, 10(78): 20120671, 2013. (Link)
  • D. A. Oyarzún, F. López-Caamal, M. R. García, R. H. Middleton and A. Y. Weiße. "Cumulative signal transmission in nonlinear reaction-diffusion networks". PLOS One, 8(5):e62834, 2013. (Link)
  • A. Vignoni, D. A. Oyarzún, J. Picó and G.-B. Stan. "Population level control of gene expression via engineered cell-to-cell communication". In Proceedings of the European Control Conference, Zurich, pp. 3633-3639, 2013. (Link)
  • J.-B. Lugagne, D. A. Oyarzún and G.-B. Stan. "Stochastic simulation of enzymatic reactions under transcriptional feedback regulation". In Proceedings of the European Control Conference, Zurich, pp. 3646-3651, 2013. (Link)

  • 2012
  • D. A. Oyarzún, M. Chaves and M. Hoff-Hoffmeyer-Zlotnik. "Multistability and oscillations in genetic control of metabolism". Journal of Theoretical Biology, 295:139-153, 2012. (Link)
  • B.-F. Krippendorff, D. A. Oyarzún and W. Huisinga. "Predicting the F(ab)-mediated effect of monoclonal antibodies in vivo by combining cell-level kinetic and pharmacokinetic modelling". Journal of Pharmacokinetics and Pharmacodynamics, 39(2):125-139, 2012. (Link)
  • D. A. Oyarzún and G.-B. Stan. "Design constraints in an operon circuit for engineered control of metabolic networks". In Proceedings of the 51st IEEE Conference on Decision and Control, Maui, USA, pp. 3608–3613, 2012. (Link)
  • F. López-Caamal, M. R. García, D. A. Oyarzún and R. H. Middleton. "Analytic computation of the integrated response in nonlinear reaction-diffusion systems". In Proceedings of the 51st IEEE Conference on Decision and Control, Maui, USA, pp. 1047-1052, 2012. (Link)
  • D. A. Oyarzún and G.-B. Stan. "Design trade offs in a synthetic gene control circuit for metabolic networks". In Proceedings of the 31st American Control Conference, Montreal, Canada, pp. 2743-2748, 2012. (Link)

  • 2011
  • D. A. Oyarzún. "Optimal control of metabolic networks with saturable enzyme kinetics", IET Systems Biology, 2:110, 2011. (Link)
  • D. A. Oyarzún and M. Chaves. "Global gene regulation in metabolic networks". In Proceedings of the 18th IFAC World Congress, Milan, Italy, pp. 14838-14843, 2011. (Link)
  • D. A. Oyarzún and R. H. Middleton. "Optimal adaptation of metabolic networks in dynamic equilibrium". In Proceedings of the 30th American Control Conference, San Francisco, USA, pp. 2897-2902, 2011. (Link)

  • 2010
  • F. López-Caamal, D. A. Oyarzún, D. Kalamatianos and J. Moreno. "Control structure and limitations of biochemical networks". In Proceedings of the 29th American Control Conference, Baltimore, USA, pp. 6668-6673, 2010. (Link)

  • 2009
  • D. A. Oyarzún, B. P. Ingalls, R. H. Middleton, and D. Kalamatianos. "Sequential activation of metabolic pathways: a dynamic optimization approach". Bulletin of Mathematical Biology, 71(8):1851-1872, 2009. (Link)
  • B.-F. Krippendorff, D. A. Oyarzún and W. Huisinga. "Ligand accumulation counteracts therapeutic inhibition of receptor systems". In Proceedings of Foundations of Systems Biology & Engineering (FOSBE), Denver, USA, pp. 173-176, 2009. (Link)
  • A. Peters, D. A. Oyarzún, E. Silva, and M. Salgado. "Analytic characterization of a stabilizing feedback for LTI plants". In Proceedings of 10th European Control Conference, Budapest, Hungary, pp. 231-235, 2009. (Link)

  • 2008
  • P. Lezana, J. Rodríguez, and D. A. Oyarzún. "Cascaded multilevel inverter with regeneration capability and reduced number of switches". IEEE Transactions on Industrial Electronics, 55:1059-1066, 2008. (Link)
  • D. A. Oyarzún, B. Ingalls, R. Middleton, and D. Kalamatianos. "Optimal metabolic pathway activation". In Proceedings of the 17th IFAC World Congress, Seoul, Korea, pp. 12587-12592, 2008. (Link)

  • 2007
  • M. Salgado and D. A. Oyarzún. "Double objective optimal multivariable ripple-free deadbeat control". International Journal of Control, 80(5):763-773, 2007. (Link)
  • M. Salgado, D. A. Oyarzún, and E. Silva. "H2 optimal ripple-free deadbeat controller design". Automatica, 43(11):1961-1967, 2007. (Link)
  • E. Silva, D. A. Oyarzún, and M. Salgado. "On structurally constrained H2 performance bounds for stable MIMO plant models". IET Control Theory & Applications, 1(4):1033-1045, 2007. (Link)
  • D. A. Oyarzún and M. Salgado. "Optimal triangular approximation for linear stable multivariable systems". In Proceedings of the 26th American Control Conference, New York, USA, pp. 5158-5153, 2007. (Link)
  • D. A. Oyarzún and E. Silva. "Effect of downstream feedback on the achievable performance of feedback control loops for serial processes". In Proceedings of the 9th European Control Conference, Kos, Greece, pp. 1727-1733, 2007. (Link)
  • D. A. Oyarzún, B. Ingalls, and D. Kalamatianos. "Optimal metabolic regulation by time variation of enzyme activities: a control theoretic approach". In Proceedings of the 2nd Foundations of Systems Biology and Engineering, Stuttgart, Germany, pp. 491-496, 2007. (Link)

  • 2006
  • M. Salgado and D. A. Oyarzún. "Basic integrated modelling: a case study". International Journal on Electrical Engineering Education, 43(3):217-231, 2006.
  • D. A. Oyarzún and M. Salgado. "Suboptimal triangular controller design methodology for full MIMO stable systems". In Proceedings of the 6th biennial UKACC Control Conference, Glasgow, 2006. (Link)

  • 2005
  • P. Lezana, J. Rodríguez, D. A. Oyarzún, and J. Pontt. "Novel cell based on reduced single-phase active front end for multicell converters". In Proceedings of the 31st Annual Conference of the IEEE Industrial Electronics Society, Raleigh, USA, pp. 733-738, 2005. (Link)
  • M. Salgado and D. A. Oyarzún. "MIMO interactions in sampled-data systems". In Proceedings of the 16th IFAC World Congress, Prague, Czech Republic, 2005. (Link)

Theses
  • D. A. Oyarzún. "A control-theoretic approach to dynamic optimization of metabolic networks". PhD Thesis, NUI Maynooth, Ireland, 2010. (Link)
  • D. A. Oyarzún. "Límites en desempeƱo para lazos multivariables con controladores de estructura triangular". MSc Thesis, USM, Chile, 2006. (Link)