Biomolecular control group
Systems & Synthetic Biology at the University of Edinburgh




what we do
Our team develops methods to study molecular processes in living cells. We use mathematics and computation to understand natural networks and to design novel systems for biotechnology and biomedicine. We employ a wide range of methods, such as machine learning, control theory, stochastic analysis and network theory. Large parts of our work are in collaboration with Systems and Synthetic Biology labs in the UK and abroad.
who we are
The group lead is Diego Oyarzún and includes research students and postdocs. Together we gather expertise in many disciplines like machine learning, mathematics, biochemistry and bioinformatics.
where we work
We are very lucky to be located at the School of Informatics and the School of Biological Sciences of the University of Edinburgh, in one of the most vibrant European capitals. We are members of the Edinburgh Centre for Engineering Biology.
our recent science
- Integration of kinetic and genome-scale metabolic models
- Active learning for DNA sequence optimization
- Machine learning and genome-scale metabolic models for gene deletion phenotypes
- Can protein expression be solved?
- Discovery of drug candidates against brain cancer
- Using mechanistic knowledge in sequence-to-expression models
- Risk-averse design of synthetic gene circuits
- Graph neural networks for predicting gene essentiality
news
Jun 29, 2025 | Yuxin’s paper on sequence optimization with active learning is out in preprint. |
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Jun 28, 2025 | Congrats to our undergrad alumnus Andreas for his ezSTEP paper accepted at CIBB 2025! |
Jun 20, 2025 | Flux Cone Learning - our method to predict gene deletion phenotypes is out in preprint. |
Jun 17, 2025 | Charlotte’s algorithm for predicting host-pathway dynamics published in Metabolic Engineering. |
Jun 15, 2025 | Many team members have been speaking at various venues in Edinburgh and beyond, congrats to Lucas, Yuxin, Achille and Michal for great lectures across the board! |
Jun 1, 2025 | Our perspective on protein expression modelling appeared in Trends in Biotechnology - thanks to Align to Innovation for making this happen. |
May 15, 2025 | Many congratulations to Zuzanna for passing her PhD viva! |
Mar 25, 2025 | Vanessa’s paper on new drug candidates against brain cancer is out in preprint, great collaboration with Neil Carragher’s team! |
Feb 10, 2025 | Yuxin’s paper on generalization of sequence-to-expression models is out in Nucleic Acids Research, congrats! |
Dec 1, 2024 | Arin’s paper on single-cell metabolic oscillations is out in preprint - this is part of a great collaboration with the Swain lab. |