Imperial College London

Diego A. Oyarzún

Faculty of Natural SciencesDepartment of Mathematics

Research Fellow
 
 
 
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Contact

 

d.oyarzun Website

 
 
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Location

 

6M48Huxley BuildingSouth Kensington Campus

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Summary

 

Publications

Publication Type
Year
to

44 results found

Liu D, Mannan AA, Han Y, Oyarzún DA, Zhang Fet al., 2018, Dynamic metabolic control: towards precision engineering of metabolism., J Ind Microbiol Biotechnol

Advances in metabolic engineering have led to the synthesis of a wide variety of valuable chemicals in microorganisms. The key to commercializing these processes is the improvement of titer, productivity, yield, and robustness. Traditional approaches to enhancing production use the "push-pull-block" strategy that modulates enzyme expression under static control. However, strains are often optimized for specific laboratory set-up and are sensitive to environmental fluctuations. Exposure to sub-optimal growth conditions during large-scale fermentation often reduces their production capacity. Moreover, static control of engineered pathways may imbalance cofactors or cause the accumulation of toxic intermediates, which imposes burden on the host and results in decreased production. To overcome these problems, the last decade has witnessed the emergence of a new technology that uses synthetic regulation to control heterologous pathways dynamically, in ways akin to regulatory networks found in nature. Here, we review natural metabolic control strategies and recent developments in how they inspire the engineering of dynamically regulated pathways. We further discuss the challenges of designing and engineering dynamic control and highlight how model-based design can provide a powerful formalism to engineer dynamic control circuits, which together with the tools of synthetic biology, can work to enhance microbial production.

JOURNAL ARTICLE

de Lorenzo V, Prather KL, Chen G-Q, O'Day E, von Kameke C, Oyarzún DA, Hosta-Rigau L, Alsafar H, Cao C, Ji W, Okano H, Roberts RJ, Ronaghi M, Yeung K, Zhang F, Lee SYet al., 2018, The power of synthetic biology for bioproduction, remediation and pollution control, EMBO Reports, Vol: 19, ISSN: 1469-221X

JOURNAL ARTICLE

Mannan AA, Liu D, Zhang F, Oyarzun DAet al., 2017, Fundamental Design Principles for Transcription-Factor-Based Metabolite Biosensors, ACS SYNTHETIC BIOLOGY, Vol: 6, Pages: 1851-1859, ISSN: 2161-5063

JOURNAL ARTICLE

Sootla A, Oyarzun D, Angeli D, Stan G-Bet al., 2016, Shaping pulses to control bistable systems: Analysis, computation and counterexamples, AUTOMATICA, Vol: 63, Pages: 254-264, ISSN: 0005-1098

JOURNAL ARTICLE

Weisse AY, Mannan AA, Oyarzun DA, 2016, Signaling Tug-of-War Delivers the Whole Message, CELL SYSTEMS, Vol: 3, Pages: 414-416, ISSN: 2405-4712

JOURNAL ARTICLE

Oyarzun DA, Chaves M, 2015, Design of a bistable switch to control cellular uptake, JOURNAL OF THE ROYAL SOCIETY INTERFACE, Vol: 12, ISSN: 1742-5689

JOURNAL ARTICLE

Oyarzun DA, Lugagne J-B, Stan G-BV, 2015, Noise Propagation in Synthetic Gene Circuits for Metabolic Control, ACS SYNTHETIC BIOLOGY, Vol: 4, Pages: 116-125, ISSN: 2161-5063

JOURNAL ARTICLE

Sootla A, Oyarzun D, Angeli D, Stan G-Bet al., 2015, Shaping Pulses to Control Bistable Biological Systems., American Control Conference, Publisher: IEEE, Pages: 3138-3143, ISSN: 0743-1619

CONFERENCE PAPER

Waldherr S, Oyarzun DA, Bockmayr A, 2015, Dynamic optimization of metabolic networks coupled with gene expression, JOURNAL OF THEORETICAL BIOLOGY, Vol: 365, Pages: 469-485, ISSN: 0022-5193

JOURNAL ARTICLE

Weisse AY, Oyarzun DA, Danos V, Swain PSet al., 2015, Mechanistic links between cellular trade-offs, gene expression, and growth, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 112, Pages: E1038-E1047, ISSN: 0027-8424

JOURNAL ARTICLE

Lopez-Caamal F, Oyarzun DA, Middleton RH, Garcia MRet al., 2014, Spatial Quantification of Cytosolic Ca2+ Accumulation in Nonexcitable Cells: An Analytical Study, IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, Vol: 11, Pages: 592-603, ISSN: 1545-5963

JOURNAL ARTICLE

Oyarzun DA, Bramhall JL, Lopez-Caamal F, Richards FM, Jodrell DI, Krippendorff B-Fet al., 2014, The EGFR demonstrates linear signal transmission, INTEGRATIVE BIOLOGY, Vol: 6, Pages: 736-742, ISSN: 1757-9694

JOURNAL ARTICLE

Kuntz J, Oyarzún DA, Stan GB, 2013, Model reduction of genetic-metabolic systems using timescale separation, System Theoretic Approaches to Systems and Synthetic Biology (to appear), Publisher: Springer-Verlag

BOOK CHAPTER

Lugagne J-B, Oyarzun DA, Stan G-BV, 2013, Stochastic simulation of enzymatic reactions under transcriptional feedback regulation, European Control Conference (ECC), Publisher: IEEE, Pages: 3646-3651

CONFERENCE PAPER

Oyarzun DA, Lopez-Caamal F, Garcia MR, Middleton RH, Weisse AYet al., 2013, Cumulative Signal Transmission in Nonlinear Reaction-Diffusion Networks, PLOS ONE, Vol: 8, ISSN: 1932-6203

JOURNAL ARTICLE

Oyarzun DA, Stan G-BV, 2013, Synthetic gene circuits for metabolic control: design trade-offs and constraints, JOURNAL OF THE ROYAL SOCIETY INTERFACE, Vol: 10, ISSN: 1742-5689

JOURNAL ARTICLE

Vignoni A, Oyarzun DA, Pico J, Stan G-Bet al., 2013, Control of protein concentrations in heterogeneous cell populations, European Control Conference (ECC), Publisher: IEEE, Pages: 3633-3639

CONFERENCE PAPER

Krippendorff B-F, Oyarzun DA, Huisinga W, 2012, Predicting the F(ab)-mediated effect of monoclonal antibodies in vivo by combining cell-level kinetic and pharmacokinetic modelling, JOURNAL OF PHARMACOKINETICS AND PHARMACODYNAMICS, Vol: 39, Pages: 125-139, ISSN: 1567-567X

JOURNAL ARTICLE

Lopez-Caamal F, Garcia MR, Oyarzun DA, Middleton RHet al., 2012, Analytic computation of the integrated response in nonlinear reaction-diffusion systems, 51st IEEE Annual Conference on Decision and Control (CDC), Publisher: IEEE, Pages: 1047-1052, ISSN: 0743-1546

CONFERENCE PAPER

Oyarzun DA, Chaves M, Hoff-Hoffmeyer-Zlotnik M, 2012, Multistability and oscillations in genetic control of metabolism, JOURNAL OF THEORETICAL BIOLOGY, Vol: 295, Pages: 139-153, ISSN: 0022-5193

JOURNAL ARTICLE

Oyarzun DA, Stan G-B, 2012, Design tradeoffs in a synthetic gene control circuit for metabolic networks, American Control Conference (ACC), Publisher: IEEE COMPUTER SOC, Pages: 2743-2748, ISSN: 0743-1619

CONFERENCE PAPER

Oyarzun DA, Stan G-B, 2012, Design constraints in an operon circuit for engineered control of metabolic networks, 51st IEEE Annual Conference on Decision and Control (CDC), Publisher: IEEE, Pages: 3608-3613, ISSN: 0191-2216

CONFERENCE PAPER

Oyarzun DA, 2011, Optimal control of metabolic networks with saturable enzyme kinetics, IET SYSTEMS BIOLOGY, Vol: 5, Pages: 110-119, ISSN: 1751-8849

JOURNAL ARTICLE

Oyarzun DA, Chaves M, 2011, Global gene regulation in metabolic networks, Proceedings of the 18th IFAC World Congress, Milan, Italy, Pages: 14838-14843

CONFERENCE PAPER

Oyarzun DA, Middleton RH, 2011, Optimal adaptation of metabolic networks in dynamic equilibrium, American Control Conference (ACC), Publisher: IEEE, Pages: 2897-2902, ISSN: 0743-1619

CONFERENCE PAPER

Lopez-Caamal F, Oyarzun DA, Moreno JA, Kalamatianos Det al., 2010, Control structure and limitations of biochemical networks, American Control Conference, Publisher: IEEE, Pages: 6668-6673, ISSN: 0743-1619

CONFERENCE PAPER

Oyarzun DA, 2010, A control-theoretic approach to dynamic optimization of metabolic networks

THESIS DISSERTATION

Oyarzun DA, 2010, A control-theoretic approach to dynamic optimization of metabolic networks, Phd Thesis, National University of Ireland, Maynooth

REPORT

Krippendorff B, Oyarzun DA, Huisinga W, 2009, Ligand accumulation counteracts therapeutic inhibition in receptor systems, Proceedings of Foundations of Systems Biology & Engineering, Denver, USA, Pages: 173-176

CONFERENCE PAPER

Oyarzun DA, Ingalls BP, Middleton RH, Kalamatianos Det al., 2009, Sequential Activation of Metabolic Pathways: a Dynamic Optimization Approach, BULLETIN OF MATHEMATICAL BIOLOGY, Vol: 71, Pages: 1851-1872, ISSN: 0092-8240

JOURNAL ARTICLE

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