Rui Manuel Freitas Oliveira

Full Professor
Chemical and Biochemical Engineering Section
(+351) 212948385

Associate Professor Chemical and Biological Engineering

Head of the Systems Biology and Engineering research group 

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

Rui M. C. Portela, Moritz von Stosch, Rui Oliveira (2018) Hybrid semiparametric systems for quantitative sequence-activity modeling of synthetic biological parts, Synthetic Biology, 3(1)

Rodolfo Marques, Moritz von Stosch, Rui M. C. Portela, Cristiana A.V. Torres, Sílvia Antunes, Filomena Freitas, Maria A. M. Reis, Rui Oliveira (2017) Hybrid modeling of microbial exopolysaccharide (EPS) production: the case of Enterobacter A47, Journal of Biotechnology, 246, pp 61-70

Moritz von Stosch , Jan-Martijn Hamelink, Rui Oliveira (2016) Towards intensifying Design of Experiments in upstream bioprocess development: An industrial E. coli feasibility study, Biotechnol Prog. 2016, doi: 10.1002/btpr.2295

Moritz von Stosch , Jan-Martijn Hamelink, Rui Oliveira (2016) Hybrid modeling as a QbD/PAT tool in process development: an industrial E. coli case study, Bioprocess and Biosystems Engineering, pp 1-12

Inês A. Isidro, Rui M. Portela, João J. Clemente, António E. Cunha, Rui Oliveira (2016) Hybrid metabolic flux analysis and recombinant protein prediction in Pichia pastoris X-33 cultures expressing a single-chain antibody fragment, Bioprocess Biosyst Eng. 2016 Sep;39(9):1351-63. doi: 10.1007/s00449-016-1611-z

Inês A. Isidro, Ana R. Ferreira, João J. Clemente, António E. Cunha, Rui Oliveira (2016) Analysis of culture media screening data by projection to latent pathways: The case of Pichia pastoris X-33, Journal of Biotechnology, 217,  pp  82–89

Teixeira, A.P., Dias, J.M.L., Carinhas, N., Sousa, M., Clemente, J.J., Cunha, A.E., von Stosch, M., Alves, P.M., Carrondo, M.J.T., Oliveira, R. (2011) Cell functional enviromics: unravelling the function of environmental factors, BMC Systems Biology, 5, art. no. 92

Carinhas, N., Bernal, V., Teixeira, A.P., Carrondo, M.J.T., Alves, P.M., Oliveira, R. (2011) Hybrid metabolic flux analysis: combining stoichiometric and statistical constraints to model the formation of complex recombinant products , BMC Systems Biology, 5, 34.

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.

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

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

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

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

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

Oliveira, R. (2004) Combining first principles modelling and artificial neural networks: A general framework (2004) Computers and Chemical Engineering, 28 (5), pp. 755-766.