Imperial College London

Diego A. OyarzĂșn

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
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42 results found

Mannan AA, Liu D, Zhang F, OyarzĂșn DAet al., 2017, Fundamental Design Principles for Transcription-Factor-Based Metabolite Biosensors., ACS Synth Biol, Vol: 6, Pages: 1851-1859

Metabolite biosensors are central to current efforts toward precision engineering of metabolism. Although most research has focused on building new biosensors, their tunability remains poorly understood and is fundamental for their broad applicability. Here we asked how genetic modifications shape the dose-response curve of biosensors based on metabolite-responsive transcription factors. Using the lac system in Escherichia coli as a model system, we built promoter libraries with variable operator sites that reveal interdependencies between biosensor dynamic range and response threshold. We developed a phenomenological theory to quantify such design constraints in biosensors with various architectures and tunable parameters. Our theory reveals a maximal achievable dynamic range and exposes tunable parameters for orthogonal control of dynamic range and response threshold. Our work sheds light on fundamental limits of synthetic biology designs and provides quantitative guidelines for biosensor design in applications such as dynamic pathway control, strain optimization, and real-time monitoring of metabolism.

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

Peters AA, Oyarzun DA, Silva EI, Salgado MEet al., 2009, Analytic characterization of a stabilizing feedback for LTI plants, Proceedings of the European Control Conference, Budapest, Hungary, Pages: 231-235

CONFERENCE PAPER

Lezana P, Rodriguez J, Oyarzun DA, 2008, Cascaded multilevel inverter with regeneration capability and reduced number of switches, IEEE TRANSACTIONS ON INDUSTRIAL ELECTRONICS, Vol: 55, Pages: 1059-1066, ISSN: 0278-0046

JOURNAL ARTICLE

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