Koray MALCI

Research

My research aims to develop novel solutions for health and sustainability by leveraging synthetic biology and microbial engineering. Within this scope, I apply cutting-edge approaches to design and engineer microbial systems with new-to-nature functions, with the broader goal of addressing real-world challenges.

My work spans several interconnected research areas, including synthetic biology, microbial engineering, protein engineering, and living materials. I also integrate systems biology and computational approaches, bioinformatics, process optimisation, and laboratory automation to accelerate the design–build–test–learn cycle across these research domains.
 

Synthetic biology enables rational programming of biological systems to perform functions that they do not naturally possess. In my research, this includes engineering microbial cells to produce high-value chemicals, drug precursors, biofuels, and biomaterials through bioproduction processes. Synthetic biology also encompasses the development of genetic toolkits and the application of emerging technologies to improve in vitro processes, such as more specific and sensitive molecular diagnostic methods.

Microbial engineering focuses on the systematic design and optimisation of microorganisms as chassis for biotechnological applications. This includes the expression of heterologous or engineered proteins, as well as the construction and optimisation of metabolic pathways for the synthesis of target molecules. Within this scope, both prokaryotic hosts, such as bacterial species, and eukaryotic hosts, such as yeast, can be used as chassis organisms. Developing new genetic manipulation strategies, expanding toolkits for non-model organisms, and improving or scaling bioprocesses are also key aspects of this research area.

Protein engineering involves the design and optimisation of proteins to improve properties such as activity, stability, substrate specificity, and expression. Through this approach, novel enzymes and functional proteins can be developed for applications including waste degradation, industrial bioprocess optimisation, molecular detection, and biosensing. Protein engineering can also support metabolic engineering by improving pathway performance and enhancing the production of valuable chemicals or biomass.

Living materials represent an emerging field at the interface of synthetic biology and materials science. In this area, materials are developed that incorporate living organisms or biologically active components, enabling them to sense, respond to, and adapt to environmental stimuli. Such smart and adaptive materials have potential applications ranging from structural and functional biomaterials to diagnostics, therapeutics, and environmental sensing.

Currently, I am focused on the Val-PLAS project, an EU-funded MSCA-PF project. In this study, we aim to valorise plastic waste using intelligent microbial systems, where co-cultures of two engineered microorganisms degrade and upcycle plastic waste simultaneously. The Val-PLAS project is carried out with the Institute of Environmental Sciences, with collaboration from the Technical University of Denmark, particularly for the discovery and engineering of novel plastic-degrading enzymes using artificial intelligence and data mining. This interdisciplinary project aims to develop innovative strategies for plastic degradation and waste valorisation. By combining microbial engineering, enzyme discovery, synthetic biology, and bioprocess development, Val- PLAS aims to directly convert plastic waste into high-value chemicals, including drug precursors.

Selected Publications

• Malcı, K., Meng, F., Galez, H., Franja Da Silva, A., Caro-Astorga, J., Batt, G., & Ellis, T. (2026). Slowpoke: An automated Golden Gate cloning workflow for Opentrons OT- 2 and Flex. ACS Synthetic Biology.
   
• Oh, J.-J., van der Linden, F. H., Malcı, K., van der Valk, R. A., Ellis, T., & Aubin-Tam, M.-E. (2025). Bacterially grown living materials with resistant and on-demand functionality. Science Advances, 11(41), eadw8278.
   
• Caro-Astorga, J., Rogan, M., Malcı, K., Ming, H., Debenedictis, E., James, P., & Ellis, T. (2025). SubtiToolKit: A bioengineering kit for Bacillus subtilis and Gram-positive bacteria. Trends in Biotechnology, 43(6), 1446–1469.
   
• Malcı, K., Santibanez, R., Jonguitud-Borrego, N., Santoyo-Garcia, J. H., Kerkhoven, E. J., & Rios-Solis, L. (2023). Improved production of Taxol precursors in S. cerevisiae using combinatorial in silico design and metabolic engineering. Microbial Cell Factories, 22(1), 243.
   
• Malcı, K., Jonguitud-Borrego, N., van der Straten Waillet, H., Puodziunaite, U., Johnston, E. J., Rosser, S. J., & Rios-Solis, L. (2022). ACtivE: Assembly and CRISPR- targeted in vivo editing for yeast genome engineering using minimum reagents and time. ACS Synthetic Biology, 11(11), 3629–3643.
   
• Malcı, K., Walls, L. E., & Rios-Solis, L. (2022). Rational design of CRISPR/Cas12a- RPA-based one-pot COVID-19 detection with design of experiments. ACS Synthetic Biology, 11(4), 1555–1567.