2019

  1. Analysis of a genetic-metabolic oscillator with piecewise linear models Chaves, Madalena, Oyarzún, Diego A., and Gouzé, Jean-Luc Journal of Theoretical Biology 2019
  2. Riboswitch identification using Ligase-Assisted Selection for the Enrichment of Responsive Ribozymes (LigASERR) Haines, Matthew C, Storch, Marko, Oyarzún, Diego A, Stan, Guy-Bart, and Baldwin, Geoff S Synthetic Biology 2019
  3. Multiobjective optimization of gene circuits for metabolic engineering Otero-Muras, Irene, Mannan, Ahmad A., Banga, Julio R., and Oyarzún, Diego A. In 8th IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE) 2019
  4. Growth Defects and Loss-of-Function in Synthetic Gene Circuits Nikolados, Evangelos Marios, Weiße, Andrea Y., Ceroni, Francesca, and Oyarzún, Diego A. ACS Synthetic Biology 2019
  5. Metabolite sequestration enables rapid recovery from nutrient depletion Hartline, Christopher, Mannan, Ahmad A., Zhang, Fuzhong, and Oyarzún, Diego A. bioRxiv 2019
  6. Stochastic modelling reveals mechanisms of metabolic heterogeneity Tonn, Mona K., Thomas, Philipp, Barahona, Mauricio, and Oyarzún, Diego A. Communications Biology 2019
  7. Dynamics of complex feedback architectures in metabolic pathways Chaves, Madalena, and Oyarzún, Diego A. Automatica 2019
  8. Multi-scale bursting in stochastic gene expression Cao, Zhixing, Filatova, Tatiana, Oyarzún, Diego A, and Grima, Ramon bioRxiv 2019

2018

  1. Host-circuit interactions explain unexpected behavior of a gene circuit . Boada, Yadira, Vignoni, Alejandro, Oyarzún, Diego A., and Picó, Jesus In 7th IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE) 2018
  2. The power of synthetic biology for bioproduction, remediation and pollution control Lorenzo, Víctor, Prather, Kristala LJ, Chen, Guo‐Qiang, O’Day, Elizabeth, Kameke, Conrad, Oyarzún, Diego A, Hosta‐Rigau, Leticia, Alsafar, Habiba, Cao, Cong, Ji, Weizhi, Okano, Hideyuki, Roberts, Richard J, Ronaghi, Mostafa, Yeung, Karen, Zhang, Feng, and Lee, Sang Yup EMBO reports 2018
  3. Flux-dependent graphs for metabolic networks Beguerisse-Díaz, Mariano, Bosque, Gabriel, Oyarzún, Diego, Picó, Jesús, and Barahona, Mauricio npj Systems Biology and Applications 2018
  4. Dynamic metabolic control: towards precision engineering of metabolism Liu, Di, Mannan, Ahmad A., Han, Yichao, Oyarzún, Diego A., and Zhang, Fuzhong Journal of Industrial Microbiology & Biotechnology 2018
  5. Are We There Yet? How and When Specific Biotechnologies Will Improve Human Health O’Day, Elizabeth, Hosta-Rigau, Leticia, Oyarzún, Diego A., Okano, Hideyuki, Lorenzo, Víctor, Kameke, Conrad, Alsafar, Habiba, Cao, Cong, Chen, Guo-Qiang, Ji, Weizhi, Roberts, Richard J., Ronaghi, Mostafa, Yeung, Karen, Zhang, Feng, and Lee, Sang Yup Biotechnology Journal 2018

2017

  1. Fundamental Design Principles for Transcription-Factor-Based Metabolite Biosensors Mannan, Ahmad A., Liu, Di, Zhang, Fuzhong, and Oyarzún, Diego A. ACS Synthetic Biology 2017

2016

  1. Shaping pulses to control bistable systems: Analysis, computation and counterexamples Sootla, Aivar, Oyarzún, Diego, Angeli, David, and Stan, Guy-Bart Automatica 2016

2015

  1. Shaping pulses to control bistable biological systems Sootla, A., Oyarzún, D. A., Angeli, D., and Stan, G.-B. In Proceedings of the American Control Conference 2015
  2. Dynamic optimization of metabolic networks coupled with gene expression Waldherr, Steffen, Oyarzún, Diego A., and Bockmayr, Alexander Journal of Theoretical Biology 2015
  3. Noise propagation in synthetic gene circuits for metabolic control. Oyarzún, Diego A, Lugagne, Jean-Baptiste, and Stan, Guy-Bart ACS Synthetic Biology 2015
  4. Design of a bistable switch to control cellular uptake Oyarzún, Diego A, and Chaves, Madalena Journal of The Royal Society Interface 2015

2014

  1. Spatial Quantification of Cytosolic Ca2+ Accumulation in Nonexcitable Cells:An Analytical Study López-Caamal, F., Oyarzún, D.A., Middleton, R.H., and García, M.R. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2014
  2. Model Reduction of Genetic-Metabolic Networks via Time Scale Separation Kuntz, Juan, Oyarzún, Diego, and Stan, Guy-Bart 2014
  3. The EGFR demonstrates linear signal transmission. Oyarzún, Diego A, Bramhall, Jo L, López-Caamal, Fernando, Richards, Frances M, Jodrell, Duncan I, and Krippendorff, Ben-Fillippo Integrative biology 2014

2013

  1. Control of protein concentrations in heterogeneous cell populations Vignoni, Alejandro, Oyarzún, Diego A., Picó, Jesús, and Stan, Guy-Bart V In Proceeding of the European Control Conference 2013
  2. Stochastic simulation of enzymatic reactions under transcriptional feedback regulation Lugagne, Jean-Baptiste, Oyarzún, Diego A, and Stan, Guy-Bart V In Proceeding of the European Control Conference 2013
  3. Cumulative Signal Transmission in Nonlinear Reaction-Diffusion Networks Oyarzún, Diego A., López-Caamal, Fernando, García, Míriam R., Middleton, Richard H., and Weiße, Andrea Y. PLoS ONE 2013
  4. Synthetic gene circuits for metabolic control: design trade-offs and constraints. Oyarzún, Diego A., and Stan, Guy-Bart V Journal of the Royal Society, Interface / the Royal Society 2013

2012

  1. Analytic computation of the integrated response in nonlinear reaction-diffusion systems López-Caamal, F., Garcia, M.R., Oyarzún, D. A., and Middleton, R. In 51st IEEE Conference on Decision and Control 2012
  2. Design constraints in an operon circuit for engineered control of metabolic networks Oyarzún, D. A., and Stan, G.-B. In 51st Conference on Decision and Control 2012
  3. Design tradeoffs in a synthetic gene control circuit for metabolic networks Oyarzún, Diego A., and Stan, Guy-Bart In Proceedings of the American Control Conference 2012
  4. Predicting the F(ab)-mediated effect of monoclonal antibodies in vivo by combining cell-level kinetic and pharmacokinetic modelling. Krippendorff, B.-F., Oyarzún, D. A., and Huisinga, Wilhelm Journal of pharmacokinetics and pharmacodynamics 2012
  5. Multistability and oscillations in genetic control of metabolism Oyarzún, D. A., Chaves, M., and Hoff-Hoffmeyer-Zlotnik, M. Journal of theoretical biology 2012

2011

  1. Optimal control of metabolic networks with saturable enzyme kinetics. Oyarzún, D A IET systems biology 2011
  2. Optimal adaptation of metabolic networks in dynamic equilibrium Oyarzún, Diego A, and Middleton, Richard H In Proceedings of the American Control Conference 2011
  3. Global gene regulation in metabolic networks Oyarzún, Diego A., and Chaves, Madalena In Proceedings of the 18th IFAC World Congress 2011

2010

  1. Control structure and limitations of biochemical networks López-Caamal, F, Oyarzún, DA, Moreno, J, and Kalamatianos, D In Proceedings of the American Control Conference 2010

2009

  1. Sequential activation of metabolic pathways: a dynamic optimization approach. Oyarzún, Diego A, Ingalls, Brian P, Middleton, Richard H, and Kalamatianos, Dimitrios Bulletin of mathematical biology 2009
  2. Ligand accumulation counteracts therapeutic inhibition of receptor systems Krippendorff, BF, Oyarzun, DA, and Huisinga, W In Foundations of Systems Biology and Engineering 2009
  3. An analytic characterization of all stabilizing feedbacks for LTI plants Peters, A, Oyarzun, DA, Silva, Eduardo I., and Salgado, Mario E. In Proceeding of the European Control Conference 2009

2008

  1. Optimal metabolic pathway activation Oyarzun, D., Ingalls, B., Middleton, R., and Kalamatianos, D. In Proceedings of the IFAC World Congress 2008
  2. Cascaded Multilevel Inverter With Regeneration Capability and Reduced Number of Switches Lezana, P., Rodriguez, J., and Oyarzun, D. A IEEE Transactions on Industrial Electronics 2008

2007

  1. H\textlessinf\textgreater2\textless/inf\textgreater optimal ripple-free deadbeat controller design Salgado, M.E., Oyarzún, D.A., and Silva, E.I. Automatica 2007
  2. Optimal metabolic regulation by temporal variation of enzyme activities: a control theoretic approach Oyarzun, DA, Ingalls, Brian, and Kalamatianos, Dimitrios In Foundations of Systems Biology and Engineering 2007
  3. Effect of downstream feedback on the achievable performance of feedback control loops for serial processes Oyarzún, D., and Silva, Eduardo In Proceeding of the European Control Conference 2007
  4. Optimal triangular approximation for linear stable multivariable systems Oyarzun, Diego a., and Salgado, Mario E. In Proceedings of the American Control Conference 2007
  5. On structurally constrained H2 performance bounds for stable MIMO plant models Silva, E. I, Oyarzun, D. A, and Salgado, M. E IET Control Theory & Applications 2007
  6. H2 Optimal ripple-free deadbeat controller design Salgado, Mario E., Oyarzún, Diego A., and Silva, Eduardo I. Automatica 2007
  7. Double objective optimal multivariable ripple-free deadbeat control Salgado, M. E., and Oyarzún, D. A. International Journal of Control 2007

2006

  1. Suboptimal triangular controller design methodology for full MIMO stable systems Oyarzun, DA, and Salgado, Mario E. In Proceedings of the UKACC Conference 2006
  2. Basic integrated modelling: a case study Salgado, Mario E., and Oyarzún, Diego R. International Journal of Electrical Engineering Education 2006

2005

  1. MIMO interactions in sampled data systems Salgado, M, and Oyarzún, Diego R. In Proceedings of the 16th IFAC World Congress 2005
  2. Novel cell based on reduced single-phase active front end for multicell converters Lezana, P., Rodriguez, J., Rojas, D., and Pontt, J. In 31st Annual Conference of IEEE Industrial Electronics Society, 2005. IECON 2005. 2005