Our papers and preprints


  1. Large scale analysis of predicted protein structures links model features to in vivo behaviour
    Stam, Michael James, Laohakunakorn, Nadanai, Oyarzun, Diego A., and Wood, Christopher W.
    bioRxiv , 2024
  2. Guiding a language-model based protein design method towards MHC Class-I immune-visibility profiles for vaccines and therapeutics
    Gasser, Hans-Christof, Oyarzun, Diego, Rajan, Ajitha, and Alfaro, Javier
    bioRxiv , 2024
  3. Modelling dynamic host-pathway interactions at the genome scale
    Merzbacher, Charlotte, Aodha, Oisin Mac, and Oyarzún, Diego A.
    bioRxiv , 2024
  4. DNA representations and generalization performance of sequence-to-expression models
    Shen, Yuxin, Kudla, Grzegorz, and Oyarzún, Diego A.
    bioRxiv , 2024
  5. Integration of graph neural networks and genome-scale metabolic models for predicting gene essentiality
    Hasibi, Ramin, Michoel, Tom, and Oyarzún, Diego A
    npj Systems Biology and Applications , 2024
  6. Optimisation of surfactin yield in Bacillus using active learning and high-throughput mass spectrometry
    Valencia Albornoz, Ricardo, Oyarzún, Diego A., and Burgess, Karl
    Computational and Structural Biotechnology Journal , 2024
  7. A machine learning approach for predicting essentiality of metabolic genes
    Freischem, Lilli J., and Oyarzún, Diego A
    Synthetic Biology - Methods and Protocols: Methods in Molecular Biology , 2024


  1. Discovery of senolytics using machine learning
    Smer-Barreto, Vanessa, Quintanilla, Andrea, Elliott, Richard J. R., Dawson, John C., Sun, Jiugeng, Campa, Vı́ctor M., Lorente-Macı́as, Álvaro, Unciti-Broceta, Asier, Carragher, Neil O., Acosta, Juan Carlos, and Oyarzún, Diego A.
    Nature Communications , 14 , 2023
  2. Applications of artificial intelligence and machine learning in dynamic pathway engineering
    Merzbacher, Charlotte, and Oyarzún, Diego A
    Biochemical Society Transactions , 2023
  3. Deep learning for optimization of protein expression
    Nikolados, Evangelos-Marios, and Oyarzún, Diego A
    Current Opinion in Biotechnology , 81 , 2023
  4. Bayesian optimization for design of multiscale biological circuits
    Merzbacher, Charlotte, Mac Aodha, Oisin, and Oyarzún, Diego A
    ACS Synthetic Biology , 2023
  5. P1 bacteriophage-enabled delivery of CRISPR-Cas9 antimicrobial activity against Shigella flexneri
    Huan, Yang W, Torraca, Vincenzo, Brown, Russell, Fa-Arun, Jidapha, Miles, Sydney L, Oyarzún, Diego A, Mostowy, Serge, and Wang, Baojun
    ACS Synthetic Biology , 12 , 2023
  6. Vaxformer: Antigenicity-controlled Transformer for Vaccine Design Against SARS-CoV-2
    Gema, Aryo Pradipta, Kobiela, Michał, Fraisse, Achille, Rajan, Ajitha, Oyarzún, Diego A., and Alfaro, Javier Antonio
    ArXiv , 2023


  1. Generating Immune-aware SARS-CoV-2 Spike Proteins for Universal Vaccine Design
    Phillips, Dominic, Gasser, Hans-Christof, Kamp, Sebestyén, Pałkowski, Aleksander, Rabalski, Lukasz, Oyarzún, Diego A., Rajan, Ajitha, and Alfaro, Javier Antonio
    In Proceedings of the 1st Workshop on Healthcare AI and COVID-19, ICML 2022 , 184 , 2022
  2. Modeling isogenic cancer cell response upon varying TRAIL stimulations to decipher the kinetic determinants of cell fate decision
    Péré, Marielle, Oyarzún, Diego A., Roux, Jérémie, and Chaves, Madalena
    In 9th IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE) , 2022
  3. Prediction of gene essentiality using machine learning and genome-scale metabolic models
    Freischem, Lilli J., Barahona, Mauricio, and Oyarzún, Diego A.
    In 9th IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE) , 2022
  4. Integrated methylome and phenome study of the circulating proteome reveals markers pertinent to brain health
    Gadd, Danni A, Hillary, Robert F, McCartney, Daniel L, Shi, Liu, Stolicyn, Aleks, Robertson, Neil A., Walker, Rosie M, McGeachan, Robert I, Campbell, Archie, Xueyi, Shen, Barbu, Miruna C, Green, Claire, Morris, Stewart W, Harris, Mathew A, Backhouse, Ellen V, Wardlaw, Joanna M, Steele, J Douglas, Oyarzún, Diego A, Muniz-Terrera, Graciela, Ritchie, Craig, Nevado-Holgado, Alejo, Chandra, Tamir, Hayward, Caroline, Evans, Kathryn L, Porteous, David J, Cox, Simon R, Whalley, Heather C, McIntosh, Andrew M, and Marioni, Riccardo E
    Nature Communications , 13 , 2022
  5. Trade-Offs in Biosensor Optimization for Dynamic Pathway Engineering
    Verma, Babita K., Mannan, Ahmad A., Zhang, Fuzhong, and Oyarzún, Diego A.
    ACS Synthetic Biology , 11 , 2022
  6. Accuracy and data efficiency in deep learning models of protein expression
    Nikolados, Evangelos-Marios, Wongprommoon, Arin, Mac Aodha, Oisin, Cambray, Guillaume, and Oyarzún, Diego A.
    Nature Communications , 13 , 2022
  7. Stabilisation of Antithetic Control via Molecular Buffering
    Hancock, Edward J, and Oyarzún, Diego A
    Journal of the Royal Society Interface , 2022


  1. Systems level profiling of chemotherapy-induced stress resolution in cancer cells reveals druggable trade-offs
    Saavedra-Garcia, Paula, Roman-Trufero, Monica, Alsadah, Hibah A, Blighe, Kevin, Lopez-Jimenez, Elena, Christoforou, Marilena, Penfold, Lucy, Capece, Daria, Xiong, Xiaobei, Miao, Yiru, Parzych, Katarzyna, Caputo, Valentina Sofia, Siskos, Alexandros P, Encheva, Vesela, Liu, Zijing, Thiel, Denise, Kaiser, Martin F, Piazza, Paolo, Chaidos, Aris, Karadimitris, Anastasios, Franzoso, Guido, Snijders, Ambrosius P., Keun, Hector C., Oyarzún, Diego A., Barahona, Mauricio, and Auner, Holger W
    PNAS , 118 , 2021
  2. Microbial polysaccharides: An emerging family of natural biomaterials for cancer therapy and diagnostics
    Prateeksha, , Sharma, Vivek K., Liu, Xiaowen, Oyarzún, Diego A., Abdel-Azeem, Ahmed M., Atanasov, Atanas G., Hesham, Abd El-Latif, Barik, Saroj K., Gupta, Vijai Kumar, and Singh, Brahma N.
    Seminars in Cancer Biology , 2021
  3. Prediction of cellular burden with host-circuit models
    Nikolados, Evangelos-marios, Weiße, Andrea Y, and Oyarzú́n, Diego A
    Synthetic Gene Circuits: Methods in Molecular Biology , 2021
  4. Opportunities at the interface of network science and metabolic modelling
    Dusad, Varshit, Thiel, Denise A, Barahona, Mauricio, Keun, Hector C, and Oyarzún, Diego A
    Frontiers in Bioengineering and Biotechnology , 9 , 2021


  1. Genotype-phenotype map of an RNA-ligand complex
    Puchta, Olga, Sobczyk, Grzegorz, Smer-barreto, Vanessa, Ireland, Hollie, Oyarzún, Diego A, Bujnicki, Janusz M, Whyte, Graeme, and Kudla, Grzegorz
    bioRxiv , 2020
  2. Computation of single-cell metabolite distributions using mixture models
    Tonn, Mona K, Thomas, Philipp, Barahona, Mauricio, and Oyarzún, Diego A
    Frontiers in Cell and Development Biology , 8 , 2020
  3. Metabolite sequestration enables rapid recovery from fatty acid depletion in Escherichia coli
    Hartline, Christopher J., Mannan, Ahmad A., Liu, Di, Zhang, Fuzhong, and Oyarzún, Diego A.
    mBio , 11 , 2020
  4. A stochastic model of gene expression with polymerase recruitment and pause release
    Cao, Zhixing, Filatova, Tatiana, Oyarzún, Diego A., and Grima, Ramon
    Biophysical Journal , 2020


  1. Pathways to cellular supremacy in biocomputing
    Grozinger, Lewis, Amos, Martyn, Gorochowski, Thomas E, Carbonell, Pablo, Oyarzún, Diego A, Stoof, Ruud, Fellermann, Harold, Zuliani, Paolo, Tas, Huseyin, and Goñi-moreno, Angel
    Nature Communications , 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 , 4 , 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 , 8 , 2019
  5. Stochastic modelling reveals mechanisms of metabolic heterogeneity
    Tonn, Mona K., Thomas, Philipp, Barahona, Mauricio, and Oyarzún, Diego A.
    Communications Biology , 2 , 2019
  6. Dynamics of complex feedback architectures in metabolic pathways
    Chaves, Madalena, and Oyarzún, Diego A.
    Automatica , 99 , 2019
  7. Analysis of a genetic-metabolic oscillator with piecewise linear models
    Chaves, Madalena, Oyarzún, Diego A., and Gouzé, Jean-Luc
    Journal of Theoretical Biology , 462 , 2019


  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 , 19 , 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 , 4 , 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 , 45 , 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


  1. Fundamental Design Principles for Transcription-Factor-Based Metabolite Biosensors
    Mannan, Ahmad A., Liu, Di, Zhang, Fuzhong, and Oyarzún, Diego A.
    ACS Synthetic Biology , 6 , 2017


  1. Shaping pulses to control bistable systems: Analysis, computation and counterexamples
    Sootla, Aivar, Oyarzún, Diego, Angeli, David, and Stan, Guy-Bart
    Automatica , 63 , 2016


  1. Mechanistic links between cellular trade-offs, gene expression, and growth
    Weisse, Andrea Y., Oyarzún, Diego A., Danos, Vincent, and Swain, Peter S.
    Proceedings of the National Academy of Sciences , 112 , 2015
  2. 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-July , 2015
  3. Dynamic optimization of metabolic networks coupled with gene expression
    Waldherr, Steffen, Oyarzún, Diego A., and Bockmayr, Alexander
    Journal of Theoretical Biology , 365 , 2015
  4. Noise propagation in synthetic gene circuits for metabolic control.
    Oyarzún, Diego A, Lugagne, Jean-Baptiste, and Stan, Guy-Bart
    ACS Synthetic Biology , 4 , 2015
  5. Design of a bistable switch to control cellular uptake
    Oyarzún, Diego A, and Chaves, Madalena
    Journal of The Royal Society Interface , 12 , 2015


  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 , 11 , 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 , 8 , 2014


  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 , 8 , 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 , 10 , 2013


  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 , 39 , 2012
  5. Multistability and oscillations in genetic control of metabolism
    Oyarzún, D. A., Chaves, M., and Hoff-Hoffmeyer-Zlotnik, M.
    Journal of theoretical biology , 295 , 2012


  1. Optimal control of metabolic networks with saturable enzyme kinetics.
    Oyarzún, D A
    IET systems biology , 5 , 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


  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


  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 , 71 , 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


  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 , 55 , 2008


  1. H\textlessinf\textgreater2\textless/inf\textgreater optimal ripple-free deadbeat controller design
    Salgado, M.E., Oyarzún, D.A., and Silva, E.I.
    Automatica , 43 , 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 , 1 , 2007
  6. H2 Optimal ripple-free deadbeat controller design
    Salgado, Mario E., Oyarzún, Diego A., and Silva, Eduardo I.
    Automatica , 43 , 2007
  7. Double objective optimal multivariable ripple-free deadbeat control
    Salgado, M. E., and Oyarzún, D. A.
    International Journal of Control , 80 , 2007


  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 , 43 , 2006


  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