Rui Manuel Freitas Oliveira

Associate Professor with Aggregation
Secção de Engenharia Química e Bioquímica
(+351) 212948385
(+351) 212948550

Research Interests

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 

Main Publications

“Bioprocess Iterative Batch-to-Batch Optimization Based on Hybrid Parametric/Nonparametric Models”. Ana P. Teixeira, João J. Clemente, António E. Cunha, Manuel J. T. Carrondo, R. Oliveira. Biotechnol. Prog., 22(1), 247 -258, 2006.

“Intracellular Dynamics in Rotavirus-like Particles Production: Evaluation of Multigene and Monocistronic Infection Strategies”. A. Roldao, H. L. A. Vieira, P.M. Alves, R. Oliveira, M.J.T. Carrondo. Proc. Biochem., 41(10), 2188-2199, 2006.

“Adaptive Dissolved Oxygen Control Through the Glycerol Feeding in a Recombinant Pichia pastoris Cultivation in Conditions of Oxygen Transfer Limitation”. R. Oliveira, J. J. Clemente, A. E. Cunha, M. J. T. Carrondo. J. Biotechnol., 116, 35-50, 2005.

“Modelling and Optimisation of a Recombinant BHK-21 Cultivation Process Using Hybrid Grey-Box Systems”. A. Teixeira, Helder Cruz, A. Cunha, J. Clemente, P. Alves, M. J. T Carrondo, R. Oliveira. J. Biotechnol., 118, 290-303, 2005.

“Mathematical Modelling of a Mixed Culture Cultivation Process For the Production of Polyhydroxybutyrate”. J. M. L. Dias, L. S. Serafim, P. C. Lemos, M.A.M. Reis, R. Oliveira Biotechnol. Bioeng., 92(2), 209-222, 2005.