Personal profile
External positions
Honorary Lecturer, Department of Mathematics, Imperial College London, United Kingdom.
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Collaborations and top research areas from the last five years
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Can protein expression be ‘solved’?
Baranowski, C., Martin, H. G., Oyarzún, D. A., Spinner, A., Desai, B., Petzold, C. J., Nikolados, E. M., Jaaks-Kraatz, S., Gaber, A., Chalkley, R. J., Scannell, D., Sevey, R., Jewett, M. C., Kelly, P. J. & DeBenedictis, E. A., 7 Nov 2025, In: Trends in biotechnology. 43, 11, p. 2724-2742 19 p.Research output: Contribution to journal › Review article › peer-review
Open AccessFile -
Accurate prediction of gene deletion phenotypes with Flux Cone Learning
Merzbacher, C., Mac Aodha, O. & Oyarzún, D. A., 26 Sept 2025, In: Nature Communications. 16, 1, p. 1-9 9 p., 8492.Research output: Contribution to journal › Article › peer-review
Open AccessFile -
Modeling host-pathway dynamics at the genome scale with machine learning
Merzbacher, C., Mac Aodha, O. & Oyarzún, D. A., 8 Jul 2025, In: Metabolic engineering. 91, p. 480-491 12 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Tuning ProteinMPNN to reduce protein visibility via MHC Class I through direct preference optimization
Gasser, H.-C., Oyarzún, D. A., Alfaro, J. A. & Rajan, A., 18 Mar 2025, In: Protein Engineering, Design & Selection (PEDS). 38, p. 1-13 13 p., gzaf003.Research output: Contribution to journal › Article › peer-review
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Improving the generalization of protein expression models with mechanistic sequence information
Shen, Y., Kudla, G. & Oyarzún, D. A., 28 Jan 2025, In: Nucleic Acids Research. 53, 3, p. 1-14 14 p., gkaf020.Research output: Contribution to journal › Article › peer-review
Open AccessFile
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The Carbon-Loop Sustainable Biomanufacturing Hub
Campopiano, D. (Principal Investigator), Horsfall, L. (Co-investigator), Masek, O. (Co-investigator), Oyarzun, D. (Co-investigator), Rosser, S. (Co-investigator), Sadler, J. (Co-investigator) & Wallace, S. (Co-investigator)
Engineering and Physical Sciences Research Council
31/10/25 → 30/10/32
Project: Research
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CYBER Engineering Biology Mission Award
Oyarzun, D. (Principal Investigator)
1/05/24 → 4/03/27
Project: Research
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Development of multiparametric high content screening and Artificial Intelligence tools to build an unbiased “Digital Phenomics” platform: Supporting next generation drug discovery to accelerate new treatments for glioblastoma pat
Carragher, N. (Principal Investigator), Brennan, P. (Co-investigator), Frame, M. (Co-investigator), Oyarzun, D. (Co-investigator) & Unciti-Broceta, A. (Co-investigator)
1/08/23 → 31/03/27
Project: Research
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Development of multiparametric high content screening and Artificial Intelligence tools to build an unbiased “Digital Phenomics” platform: Supporting next generation drug discovery to accelerate new treatments for glioblastoma pat
Oyarzun, D. (Principal Investigator), Brennan, P. (Co-investigator), Carragher, N. (Co-investigator), Frame, M. (Co-investigator) & Unciti-Broceta, A. (Co-investigator)
1/08/23 → 31/03/27
Project: Research
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Detecting synthetic proteins designed to avoid immune-surveillance
Oyarzun, D. (Principal Investigator)
1/10/22 → 30/09/24
Project: Research
Datasets
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Single-cell metabolic oscillations are pervasive and may alleviate a proteome constraint
Swain, P. (Creator), Wongprommoon, A. (Creator), Muñoz González, A. F. (Creator) & Oyarzun, D. (Creator), Edinburgh DataShare, 22 Nov 2024
DOI: 10.7488/ds/7845
Dataset
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SUPERSEDED - Single-cell metabolic oscillations are pervasive and may alleviate a proteome constraint
Muñoz González, A. F. (Creator), Wongprommoon, A. (Creator), Oyarzun, D. (Creator) & Swain, P. (Creator), Edinburgh DataShare, 15 Nov 2024
DOI: 10.7488/ds/7840
Dataset
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Risk-averse optimization of genetic circuits under uncertainty - Data
Kobiela, M. (Creator), Oyarzún, D. A. (Creator) & Gutmann, M. U. (Creator), Zenodo, 21 Aug 2024
DOI: 10.5281/zenodo.13355081, https://zenodo.org/records/13355081
Dataset
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Code and data for "Bayesian optimization for design of multiscale biological circuits"
Merzbacher, C. (Creator), Oyarzún, D. A. (Creator) & Aodha, O. M. (Creator), Zenodo, 11 May 2023
Dataset
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MFGpy: computation of mass flow graphs for genome-scale metabolic models
Freischem, L. (Creator) & Oyarzún, D. A. (Creator), Zenodo, 30 Apr 2023
Dataset