The Bioinformatics and Systems Biology research group (BiSBi) performs research at the intersection of Bioinformatics and Artificial Intelligence (AI), emphasizing its application in the life sciences and biological modelling efforts within the field of Systems Biology.

Our primary objective is to develop algorithms and computational tools that synergize data-driven and knowledge-driven approaches. This pursuit aims to develop predictive models of biological systems, fostering breakthroughs in areas such as metabolic engineering, food sciences and drug discovery.

Our key achievements encompass novel algorithms and computational tools for metabolic model reconstruction and strain optimization, utilizing generative AI for proposing novel sweetener compounds, and systematically evaluating methods for drug synergy prediction and context-specific human metabolic models (e.g. cancer, stem cells, etc). Additionally, the group has developed the first metabolic models for woody plants.

Technologically, the group specializes in several areas, such as core Bioinformatics tools, constraint-based and dynamic models, Machine and deep learning applied to Bioinformatics and Chemoinformatics, Generative AI models and optimization engines for compounds and proteins, as well as Natural Language Processing/ Biomedical text mining, among others.

Our work extends to actively developing and applying open-source software libraries and end-user tools, which include projects like OptFlux for metabolic engineering and @Note for biomedical text mining. Recent efforts include Python packages such as DeepMol and Propythia, for machine and deep learning, as well as Troppo, COBAMP and MewPy, in the systems biology domain.

Within an interdisciplinary profile, BiSBi group also actively seeks collaborations within CEB, other research centres at the University of Minho (e.g. ICVS) and nationally (e.g. ITQB/NOVA, FCUP, INESC-ID) and internationally (e.g. Leiden UMC, UCL, Argonne NL, UFSC-Brazil, U. Cambridge, EMBL).

Furthermore, the technology developed within the group, was crucial in the creation of spin-off companies, such as Silico Life (www.silicolife.com) focusing on strain optimization for the development of novel bioprocesses and recently securing a series A of around 10 million euros, and more recently OmniumAI (www.omniumai.com), specialized in AI-based solutions for the life sciences, with a particular focus on the food industry.