IBET - Instituto de Biologia Experimental e Tecnologia

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• Antibiotic stress and virulence of enterococci
• Applied and environmental mycology
• Biochemical engineering laboratory
• Biomolecular diagnostics laboratory
• Bioseparation laboratory
• Control of Gene Expression
• Laboratory of Membrane Processes
• Microbial and enzyme technology laboratory
• Pharmacokinetics and Biopharmaceutical Analysis
• Plant cell biotechnology laboratory
• Systems biology and engineering

Research areas

The Systems Biology and Engineering (SBE) group core area is Applied Systems Biology. SBE is primiarily working at the interface between Cellular Biology, Systems Engineering, Process Engineering, Metabolic Engineering and Synthetic Biology. More specific topics of interest are the following:

• Hybrid semi-parametric computational Systems Biology – new computational methods that integrate the parametric and nonparamnetric modelling paradigms;
• In silico cell models synthesized from omic data sets. Development of data reconciliation methods of genomic, proteomic and metabolomic data sets based on Hybrid Systems theory.
• Fast bioprocess development. How to use models to accelerate process development in the sense of minimizing the experimental workload required to attain a given process performance.
• Bridging Systems Biology and Process Engineering; advanced methods for Process Analytical Technology (PAT) based on omic datasets and comprehensive in silico cell models.
• Advanced Cell Culture Media development supported by Systems Biology tools; a new paradigm for media development, from gene to media composition.
• Using Hybrid Semiparametric in silico cellular models for Metabolic Engineering and Synthetic Biology.
• Heterologous proteins production by recombinant yeast Pichia pastoris. Application of Systems Biology tools to maximize productivity and to control glycosylation.

Representative publications

• von Stosch, M., de Azevedo, SF, Oliveira, R. (2010Modelling biochemical networks with intrinsic time delays: a hybrid semi-parametric approach, BMC Systems Biology, 4:131
• Teixeira, A.P., Portugal, C.A.M., Carinhas, N., Dias, J.M.L., Crespo, J.P., Alves, P.M., Carrondo, M.J.T., Oliveira, R. In situ 2D fluorometry and chemometric monitoring of mammalian cell cultures (2009) Biotechnol Bioeng, 102 (4), pp. 1098-1106
• Dias, J.M.L., Oehmen, A., Serafim, L.S., Lemos, P.C., Reis, M.A.M., Oliveira, R. (2008) Metabolic modelling of polyhydroxyalkanoate copolymers production by mixed microbial cultures BMC Systems Biology , 2, art. no. 59
• Teixeira, A.P., Carinhas, N., Dias, J.M.L., Cruz, P., Alves, P.M., Carrondo, M.J.T., Oliveira, R. (2007) Hybrid semi-parametric mathematical systems: Bridging the gap between systems biology and process engineering J Biotechnology, 132 (4), pp. 418-425
• Teixeira, A.P., Alves, C., Alves, P.M., Carrondo, M.J.T., Oliveira, R. (2007) Hybrid elementary flux analysis/nonparametric modeling: Application for bioprocess control BMC Bioinformatics , 8, art. no. 30

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