The Bioinformatics and Systems Biology group from the Centre of Biological Engineering at University of Minho has extensive experience in the development of algorithms and computational tools for metabolic engineering.
The University of Minho aims to be a University without borders, focusing on the regional, national and international socioeconomic & environmental development. UMinho is a research university, engaged in the valorization of chain knowledge-research, development and innovation.
The Centre of Biological Engineering (CEB), designated as “Excellent” by FCT, the Foundation for Science and Technology in Portugal, is a research unit located at UMinho that develops its activities on 4 interdisciplinary areas covering molecular, cellular and process scales, corresponding to the following thematic strands:
The outcomes of CEB in the last 5 years include 1250 peer-reviewed papers (23% in ISI D1 journals), 35 edited books, 177 book chapters and 89 PhD thesis concluded. The income budget derived from research projects (including industry research income) and from external funding bodies turns on average 5M €/year. CEB has also supported the formation of more than 15 spin-off and startup companies, with 15 patents to its name. CEB is widely recognized in the field of biotechnology and bioengineering and has all the laboratory facilities available that are relevant to this project.
The team participating in this project is part of the Bioinformatics and Systems Biology research lab within CEB, which has been developing computational tools for metabolic model reconstruction, simulation and optimization, including opensource projects such as OptFlux and Merlin. An important topic deals with the development of evolutionary algorithms for strain optimisation. Other topics relate to database integration, omics data analysis and mining through machine learning algorithms. The main applications include the identification of targets for metabolic engineering, aiming at constructing improved cellular factories for the production of succinic, fumaric or amino acids.
UMinho's key contributions to the ShikiFactory100 project include: metabolic engineering target predictions, and ML/DL-based molecular design. They are key contributors to Work Package 3: Design & Chemical Synthesis of New Products, and Work Package 5: In silico Metabolic Engineering.
The Principal Investigator for UMinho in the ShikiFactory100 project is Prof. Miguel Rocha.
Find out more about the University of Minho here.
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