publications

2024

1. Integrating MHC Class I visibility targets into the ProteinMPNN protein design process

   Gasser, Hans-Christof, Oyarzún, Diego A., Alfaro, Javier, and Rajan, Ajitha

   bioRxiv , 2024
2. A Call for Caution When Using Network Methods to Study Multimorbidity: An Illustration Using Data from the Canadian Longitudinal Study on Aging (CLSA)

   Griffith, Lauren E., Brini, Alberto, Muniz-Terrera, Graciela, John, Philip D. St, Stirland, Lucy E., Mayhew, Alexandra, Oyarzún, Diego A., and Heuvel, Edwin van den

   Journal of Clinical Epidemiology , 2024
3. Low-dimensional representations of genome-scale metabolism

   Cain, Samuel, Merzbacher, Charlotte, and Oyarzún, Diego A.

   bioRxiv , 2024
4. Large scale analysis of predicted protein structures links model features to in vivo behaviour

   Stam, Michael James, Laohakunakorn, Nadanai, Oyarzún, Diego A., and Wood, Christopher W.

   bioRxiv , 2024
5. Guiding a language-model based protein design method towards MHC Class-I immune-visibility targets in vaccines and therapeutics

   Gasser, Hans-Christof, Oyarzún, Diego A., Rajan, Ajitha, and Alfaro, Javier Antonio

   ImmunoInformatics , 14 , 2024
6. Modelling dynamic host-pathway interactions at the genome scale

   Merzbacher, Charlotte, Mac Aodha, Oisin, and Oyarzún, Diego A.

   bioRxiv , 2024
7. DNA representations and generalization performance of sequence-to-expression models

   Shen, Yuxin, Kudla, Grzegorz, and Oyarzún, Diego A.

   bioRxiv , 2024
8. 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
9. 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
10. 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

2023

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

2022

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

2021

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

2020

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

2019

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

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 , 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

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 , 6 , 2017

2016

1. Shaping pulses to control bistable systems: Analysis, computation and counterexamples

   Sootla, Aivar, Oyarzún, Diego, Angeli, David, and Stan, Guy-Bart

   Automatica , 63 , 2016

2015

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

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 , 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

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 , 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

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 , 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

2011

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

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 , 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

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 , 55 , 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 , 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

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 , 43 , 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