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The main research areas: 1) Systems and Synthetic Biology. 2) Bioprocess Engineering 3) Bioentrepreneurship My research focuses on applied systems biology, with applications in bioprocess engineering, culture media engineering, metabolic engineering and more recently synthetic biology. I could define my activity as the conjugation of systems biology fundaments into useful technological platforms to solve relevant biotechnological problems. I have developed systems biology projects applied to biotherapeutics production in mammalian and microbial cultures, to biopolymers production using microbial cultures and also to the optimization of environmental processes. Much of my work combines different types of experimental activities, including bench or pilot scale bioreactor studies and high-throughput “omic” technologies (metabolomics, proteomics and transcriptomics) with comprehensive mathematical modeling and computational analysis. Although the core activity is computational, I also develop experimental activities mainly with the yeast Pichia pastoris, which I have selected as model system to demonstrate the value added by the systems biology technological platforms developed by the group. A very important aspect of my career is entrepreneurship directly supported by the scientific activities developed by the research group. Over the years I have increased considerably the time spent in entrepreneurial activities. I have organized the research group in a way to optimize value creation from knowledge and currently most of the PhDs are involved in entrepreneurial activities. I've contributed to the creation of 3 start-ups: MediaOmics - MediaOmics is a spin-off from FCT/UNL dedicated to the engineering, formulation and production of cell culture media. - MediaOmics uses a patented technology developed by the research group: PT no 105484 - "A cell functional enviromics method for the engineering of cell culture media”, May 2010, Inventors: Rui Oliveira, João Dias e Raquel Ferreira. International patent filling due soon. - MediaOmics has entered the Act2Enhance program by COTEC in 2011 with 75,000 € funds - MediaOmics has won the MIT-Portugal venture completion 2011 –life sciences track, and has been awarded with 100 000 € funds. Glyceropol - Glyceropol Is a star-up founded by Filipe Aguiar, a former student at FCT/UNL. - Glyceropol technology has been developed at FCT/UNL and IBET under several research contracts that originated three patents: WO 2008/127134 A1, WO 2010/013174 A2 , US 61/286,687 - Glyceropol has entered the Act2Prove program by COTEC in 2011 with 200,000 € funds GoGreen Engineering - The applicant is a co-founder and currently a manager of the company GoGreen engineering, Lda since 2007 - GoGreen is a company hosted at the Chemistry Department, FCT/UNL - GoGreen is a company dedicated to the engineering of green technologies based on bioprocesses and membrane separation processes. GoGreen has a track record of 5 contracts with the industry (4 national and 2 international)
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Identificação

Identificação pessoal

Nome completo
Rui Manuel Freitas Oliveira

Nomes de citação

  • Oliveira, Rui
  • Oliveira, R.

Identificadores de autor

Ciência ID
0018-8B87-53DC
ORCID iD
0000-0001-8077-4177

Telefones

Telefone
  • 2948356 (Profissional)

Idiomas

Idioma Conversação Leitura Escrita Compreensão Peer-review
Inglês Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1)
Alemão Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador independente (B1) Utilizador proficiente (C1)
Português Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1)
Formação
Grau Classificação
2015
Concluído
 n/a (Título de Agregado)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
"n/a" (TESE/DISSERTAÇÃO)
 n/a
1998
Concluído
 Bioverfahrenstechnik und Reaktionstechnik (Doctor of Philosophy)
Martin-Luther-Universität Halle-Wittenberg, Alemanha
"Bioprocess Modelling, Optimiation and Control Based on Hybrid Models" (TESE/DISSERTAÇÃO)
 summa cum laude
1992
Concluído
 Engenharia Química (Licenciatura)
Universidade do Porto Faculdade de Engenharia, Portugal
 15/20
Percurso profissional

Docência no Ensino Superior

Categoria Profissional
Instituição de acolhimento 		Empregador
2015/01/01 - Atual Professor Associado (Docente Universitário) Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2011/12/31 - Atual Professor Associado (Docente Universitário) Universidade Nova de Lisboa Departamento de Química, Portugal
2016 - 2018 Professor Associado (Docente Universitário) Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal
2007 - 2013 Professor Auxiliar (Docente Universitário) Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal
2001/07/01 - 2011/12/31 Assistente (Docente Universitário) Universidade Nova de Lisboa Departamento de Química, Portugal

Outros

Categoria Profissional
Instituição de acolhimento 		Empregador
2018/12/01 - Atual Co-founder and advisor NOVASIGN, Portugal
2014/01/01 - 2017/12/31 Chief-Executive-Officer Mediaomics SA, Portugal
2012/01/01 - 2017/12/31 Co-founder & manager GoGreen Solutions Lda, Portugal
2015 - 2015 I&D Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal
1999/01/01 - 2001/06/30 Post-doc researcher Universidade do Porto Departamento de Química e Bioquímica, Portugal
Projetos

Projeto

Designação Financiadores
2020/01/01 - Atual Bio Innovation of a Circular Economy for Plastics
info:eu-repo/grantAgreement/EC/H2020/870292/EU
Investigador
Instituto de Biologia Experimental e Tecnológica, Portugal
 Universidade do Algarve Faculdade de Ciências e Tecnologia
Em curso
2013/07/01 - 2016/12/31 Functional enviromics technologies
MEDIAOMICS
Investigador responsável
Universidade Nova de Lisboa, Portugal
Concluído
2013/05/01 - 2015/08/31 Cell functional enviromics: unravelling the function of environmental factors
info:eu-repo/grantAgreement/FCT/3599-PPCDT/128766/PT
Investigador responsável
Universidade do Algarve Faculdade de Ciências e Tecnologia
Concluído
2013/05/01 - 2015/08/31 Ambientómica funcional celular: identificação da função dos factores ambientais
PTDC/BBB-BSS/2800/2012
Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal

Instituto de Biologia Experimental e Tecnológica, Portugal

Associação para a Inovação e Desenvolvimento da FCT, Portugal
Fundação para a Ciência e a Tecnologia
Concluído
2012/02/01 - 2015/07/31 Smart particles for drug delivery to the colon and to the liver
info:eu-repo/grantAgreement/FCT/3599-PPCDT/119631/PT
Investigador
Universidade do Algarve Faculdade de Ciências e Tecnologia
Concluído
2012/02/01 - 2015/07/31 Partículas inteligentes para libertação de fármacos no cólon e no fígado
PTDC/EQU-EPR/119631/2010
Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal

Associação para a Inovação e Desenvolvimento da FCT, Portugal

Universidade de Lisboa Instituto Superior de Agronomia, Portugal

Instituto de Biologia Experimental e Tecnológica, Portugal
Fundação para a Ciência e a Tecnologia
Concluído
2014/02/01 - 2014/07/31 INOVATION IN SISTEMS AND SYNTHETIC BIOLOGY
SFRH/BSAB/1400/2014
 Fundação para a Ciência e a Tecnologia
Concluído
2013/07/01 - 2014/07/31 Produção de novos produtos de elevado valor acrescentado a partir de resíduos agro-industriais: Investigação através de ambientómica funcional
EXPL/AAG-REC/1207/2012
Instituto de Biologia Experimental e Tecnológica, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2010/02/01 - 2013/07/31 Melhoramento do transporte de oxigénio por nanopartículas magnéticas funcionalizadas FMP em fermentações microbianas altamente viscosas e não-Newtonianas para produção de biopolímeros: fundamentação teórica e viabilidade tecnológica
PTDC/EBB-EBI/103761/2008
Instituto de Biologia Experimental e Tecnológica, Portugal

Universidade do Porto Faculdade de Engenharia, Portugal
Fundação para a Ciência e a Tecnologia
Concluído
2010/02/01 - 2013/07/30 Enhancement of oxygen transport by functionalized magnetic nanoparticles (FMP) in non-Newtonian highly viscous microbial fermentations for biopolymer production: theoretical foundations and technological feasibility
info:eu-repo/grantAgreement/FCT/3599-PPCDT/103761/PT
Investigador responsável
Universidade do Algarve Faculdade de Ciências e Tecnologia
2010/04/01 - 2013/06/30 Biologia sintética no desenvolvimento de linhas celulares para produção biofármacos multiproteicos com estequiometria optimizada
PTDC/EBB-EBI/102266/2008
Instituto de Biologia Experimental e Tecnológica, Portugal

Universidade NOVA de Lisboa Faculdade de Ciências e Tecnologia, Portugal

Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Massachusetts Institute of Technology, Estados Unidos
Fundação para a Ciência e a Tecnologia
Concluído
2009/04/01 - 2012/09/30 Bridging Systems and Synthetic Biology for the development of Improved Microbial Cell Factories
info:eu-repo/grantAgreement/FCT/5876-PPCDTI/84035/PT
Investigador
Universidade do Algarve Faculdade de Ciências e Tecnologia
Concluído
2009/04/01 - 2012/09/30 Biologia de Sistemas e Biologia Sintética no desenvolvimento de Fábricas Celulares Microbianas melhoradas
MIT-Pt/BS-BB/0082/2008
Universidade do Minho, Portugal

Universidade do Minho Centro de Engenharia Biológica, Portugal

Instituto de Biologia Experimental e Tecnológica, Portugal

Universidade do Porto Faculdade de Engenharia, Portugal
Fundação para a Ciência e a Tecnologia
Concluído
2007/11/01 - 2011/10/31 Biological removal of xenobiotics from wastewater treatment systems
info:eu-repo/grantAgreement/FCT/3599-PPCDT/65702/PT
Investigador
Universidade do Algarve Faculdade de Ciências e Tecnologia
Concluído
2007/11/01 - 2011/10/31 Remoção biológica de compostos xenobióticos de sistemas de tratamento de águas residuais
PTDC/AMB/65702/2006
Instituto de Biologia Experimental e Tecnológica, Portugal

Universidade NOVA de Lisboa Faculdade de Ciências e Tecnologia, Portugal

Instituto Politécnico de Setúbal, Portugal
Fundação para a Ciência e a Tecnologia
Concluído
2007/06/01 - 2010/07/31 Novel stroke model for neuroprotective research: bioreaction of primary brain cell aggregates
info:eu-repo/grantAgreement/FCT/3599-PPCDT/69407/PT
Investigador
Universidade do Algarve Faculdade de Ciências e Tecnologia
Concluído
2007/06/01 - 2010/07/31 Desenvolvimento de um sistema de cultura celular para mimetização de acidentes vasculares cerebrais in vitro: agregados de células de cérebro como modelo.
PTDC/BIO/69407/2006
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Universidade NOVA de Lisboa Faculdade de Ciências e Tecnologia, Portugal
Fundação para a Ciência e a Tecnologia
Concluído
2007/01/01 - 2009/05/31 Advanced Control of BHK cultivation processes based on intracellular metabolic fluxes
info:eu-repo/grantAgreement/FCT/3599-PPCDT/82573/PT
Investigador responsável
Instituto de Biologia Experimental e Tecnológica, Portugal
 Universidade do Algarve Faculdade de Ciências e Tecnologia
2004/01/09 - 2008/08/31 Expanding membrane macroscale applications by exploring nanoscale material properties
NMP3-CT-2004-500623
Investigador
European Commission Sixth Framework Programme
Concluído
2007/01/01 - 2008/07/31 Tailored synthesis of biopolymers by mixed microbial cultures from molasses
info:eu-repo/grantAgreement/FCT/3599-PPCDT/82951/PT
Investigador
Universidade do Algarve Faculdade de Ciências e Tecnologia
Concluído
2005/06/01 - 2007/12/31 Automação Avançada de Processos Biológicos Baseada em Sistemas Híbridos do Tipo Caixa Cinzenta
POCI/BIO/56571/2004
Instituto de Biologia Experimental e Tecnológica, Portugal

Universidade do Porto Faculdade de Engenharia, Portugal
Fundação para a Ciência e a Tecnologia
Concluído
2005/06/01 - 2007/12/31 Controlo avançado de culturas de BHK baseado em fluxos metabólicos intracelulares
POCI/BIO/57927/2004
Instituto de Biologia Experimental e Tecnológica, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2005/02/01 - 2007/12/31 Sintese de biopolímeros "à medida" por culturas microbianas mistas a partir de melaços
POCI/BIO/55789/2004
Instituto de Biologia Experimental e Tecnológica, Portugal

Universidade do Porto Instituto de Ciências e Tecnologias Agrárias e Agro-Alimentares, Portugal
Fundação para a Ciência e a Tecnologia
Concluído
2005/06/01 - 2007/12/30 Advanced Bioprocess Automation Based on Hybrid Grey-Box Systems
info:eu-repo/grantAgreement/FCT/POCI/56571/PT
Investigador responsável
Instituto de Biologia Experimental e Tecnológica, Portugal
 Universidade do Algarve Faculdade de Ciências e Tecnologia
Concluído
2000/08/01 - 2004/07/31 BATCHPRO – Knowledge Driven Batch Production
HPRN-CT-2000-00039
Bolseiro de Pós-Doutoramento
European Commission
Concluído
Produções

Publicações

Artigo em conferência
  1. Seyong Jung; Jie Zhang; Rui Oliveira. "Iterative learning control of polyhydroxybutyrate production in a sequencing batch reactor". 2015.
    10.1109/mmar.2015.7283919
  2. Leblebici, M.E.; Fonte, C.M.; Costa, M.F.; Ataíde, F.; Garcia, M.P.; Silva, V.T.; Devic, T.; et al. "Continuous production of magnetic and metal-organic nanoparticles with netmix reactor". 2014.
  3. Dias, J.; Eusébio, M.; Serafim, L.; Oehmen, A.; Reis, M.A.M.; Oliveira, R.. "On-line metabolic flux analysis in a PHB production process". 2007.
  4. A. Teixeira; C. Alves; P.M. Alves; M.J.T. Carrondo; R. Oliveira. "Hybrid metabolic flux analysis/artificial neural network modeling of bioprocesses". 2005.
    10.1109/ichis.2005.59
  5. Oliveira, R.; Peres, J.; Feyo de Azevedo, S.. "Hybrid modelling of fermentation processes using artificial neural networks: A study on identification and stability". 2004.
  6. Peres, J.; Oliveira, R.; Feyo de Azevedo, S.. "Hybrid modelling of fermentation processes: A study on the use of modular neural networks for modelling cells reaction kinetics". 2004.
Artigo em revista
  1. José Pinto; João Rodrigues Correia Ramos; Costa, R; Rui Oliveira. "A General Hybrid Modeling Framework for Systems Biology Applications: Combining Mechanistic Knowledge with Deep Neural Networks under the SBML Standard". AI (2023): https://www.mdpi.com/2673-2688/4/1/14.
    10.3390/ai4010014
  2. João R. C. Ramos; Gil P. Oliveira; Patrick Dumas; Rui Oliveira. "Genome-scale modeling of Chinese hamster ovary cells by hybrid semi-parametric flux balance analysis". Bioprocess and Biosystems Engineering 45 11 (2022): 1889-1904. http://dx.doi.org/10.1007/s00449-022-02795-9.
    10.1007/s00449-022-02795-9
  3. R. Agharafeie; J.¿R.¿C. Ramos; R. Oliveira; J.¿M. Mendes. "Application of Hybrid Models in Biopharmaceutical Manufacturing". Chemie Ingenieur Technik 94 9 (2022): 1281-1282. http://dx.doi.org/10.1002/cite.202255039.
    10.1002/cite.202255039
  4. Pinto, J.; Mestre, M.; Ramos, J.; Costa, R.S.; Striedner, G.; Oliveira, R.. "A general deep hybrid model for bioreactor systems: Combining first principles with deep neural networks". Computers and Chemical Engineering 165 (2022): http://www.scopus.com/inward/record.url?eid=2-s2.0-85135937262&partnerID=MN8TOARS.
    10.1016/j.compchemeng.2022.107952
  5. José Pinto; Cristiana Rodrigues de Azevedo; Rui Oliveira; Moritz von Stosch. "A bootstrap-aggregated hybrid semi-parametric modeling framework for bioprocess development". Bioprocess and Biosystems Engineering 42 11 (2019): 1853-1865. http://dx.doi.org/10.1007/s00449-019-02181-y.
    10.1007/s00449-019-02181-y
  6. Portela, Rui M C; von Stosch, Moritz; Oliveira, Rui. "Hybrid semiparametric systems for quantitative sequence-activity modeling of synthetic biological parts". Synthetic Biology 3 1 (2018): http://dx.doi.org/10.1093/synbio/ysy010.
    10.1093/synbio/ysy010
  7. Portela, Rui M. C.; Vogl, Thomas; Ebner, Katharina; Oliveira, Rui; Glieder, Anton. "Pichia pastoris Alcohol Oxidase 1 (AOX1 ) Core Promoter Engineering by High Resolution Systematic Mutagenesis". Biotechnology Journal 13 3 (2017): 1700340. http://dx.doi.org/10.1002/biot.201700340.
    10.1002/biot.201700340
  8. Rodrigues de Azevedo, Cristiana; von Stosch, Moritz; Costa, Mariana S.; Ramos, A.M.; Cardoso, M. Margarida; Danhier, Fabienne; Préat, Véronique; Oliveira, Rui. "Modeling of the burst release from PLGA micro- and nanoparticles as function of physicochemical parameters and formulation characteristics". International Journal of Pharmaceutics 532 1 (2017): 229-240. http://dx.doi.org/10.1016/j.ijpharm.2017.08.118.
    10.1016/j.ijpharm.2017.08.118
  9. Marques, Rodolfo; von Stosch, Moritz; Portela, Rui M.C.; Torres, Cristiana A.V.; Antunes, Sílvia; Freitas, Filomena; Reis, Maria A.M.; Oliveira, Rui. "Hybrid modeling of microbial exopolysaccharide (EPS) production: The case of Enterobacter A47". Journal of Biotechnology 246 (2017): 61-70. http://dx.doi.org/10.1016/j.jbiotec.2017.01.017.
    10.1016/j.jbiotec.2017.01.017
  10. Portela, Rui M. C.; Vogl, Thomas; Kniely, Claudia; Fischer, Jasmin E.; Oliveira, Rui; Glieder, Anton. "Synthetic Core Promoters as Universal Parts for Fine-Tuning Expression in Different Yeast Species". ACS Synthetic Biology 6 3 (2016): 471-484. http://dx.doi.org/10.1021/acssynbio.6b00178.
    10.1021/acssynbio.6b00178
  11. Rui M.C. Portela; Thomas Vogl; Rui Oliveira; Anton Glieder. "Synthetic core promoters and 5' untranslated regions (UTRs) as universal parts for fine-tuning expression in different yeast species". New Biotechnology 33 (2016): S183-S183. http://dx.doi.org/10.1016/j.nbt.2016.06.1356.
    10.1016/j.nbt.2016.06.1356
  12. Rui Oliveira; Inês A. Isidro; Rui M.C. Portela. "Culture media engineering by projection to latent pathways: The case of Pichia pastoris X-33". New Biotechnology 33 (2016): S36-S37. http://dx.doi.org/10.1016/j.nbt.2016.06.852.
    10.1016/j.nbt.2016.06.852
  13. von Stosch, Moritz; Hamelink, Jan-Martijn; Oliveira, Rui. "Toward intensifying design of experiments in upstream bioprocess development: An industrialEscherichia colifeasibility study". Biotechnology Progress 32 5 (2016): 1343-1352. http://dx.doi.org/10.1002/btpr.2295.
    10.1002/btpr.2295
  14. von Stosch, Moritz; Rodrigues de Azevedo, Cristiana; Luis, Mauro; Feyo de Azevedo, Sebastiao; Oliveira, Rui. "A principal components method constrained by elementary flux modes: analysis of flux data sets". BMC Bioinformatics 17 1 (2016): http://dx.doi.org/10.1186/s12859-016-1063-0.
    10.1186/s12859-016-1063-0
  15. Isidro, Inês A.; Portela, Rui M.; Clemente, João J.; Cunha, António E.; Oliveira, Rui. "Hybrid metabolic flux analysis and recombinant protein prediction in Pichia pastoris X-33 cultures expressing a single-chain antibody fragment". Bioprocess and Biosystems Engineering 39 9 (2016): 1351-1363. http://dx.doi.org/10.1007/s00449-016-1611-z.
    10.1007/s00449-016-1611-z
  16. von Stosch, Moritz; Hamelink, Jan-Martijn; Oliveira, Rui. "Hybrid modeling as a QbD/PAT tool in process development: an industrial E. coli case study". Bioprocess and Biosystems Engineering 39 5 (2016): 773-784. http://dx.doi.org/10.1007/s00449-016-1557-1.
    10.1007/s00449-016-1557-1
  17. Isidro, Inês A.; Ferreira, Ana R.; Clemente, João J.; Cunha, António E.; Oliveira, Rui. "Analysis of culture media screening data by projection to latent pathways: The case of Pichia pastoris X-33". Journal of Biotechnology 217 (2016): 82-89. http://dx.doi.org/10.1016/j.jbiotec.2015.10.014.
    10.1016/j.jbiotec.2015.10.014
  18. Kawasaki, Regiane; Baraúna, Rafael A.; Silva, Artur; Carepo, Marta S. P.; Oliveira, Rui; Marques, Rodolfo; Ramos, Rommel T. J.; Schneider, Maria P. C.. "Reconstruction of the Fatty Acid Biosynthetic Pathway ofExiguobacterium antarcticumB7 Based on Genomic and Bibliomic Data". BioMed Research International 2016 (2016): 1-9. http://dx.doi.org/10.1155/2016/7863706.
    10.1155/2016/7863706
  19. Folch-Fortuny, Abel; Marques, Rodolfo; Isidro, Inês A.; Oliveira, Rui; Ferrer, Alberto. "Principal elementary mode analysis (PEMA)". Molecular BioSystems 12 3 (2016): 737-746. http://dx.doi.org/10.1039/c5mb00828j.
    10.1039/c5mb00828j
  20. Oliveira, Rui. "Hybrid modular mechanistic/ANN modelling of a wastewater phosphorus removal process". Computer Aided Chemical Engineering 21 (2016): 1717-1722.
  21. Simon, Levente L.; Pataki, Hajnalka; Marosi, György; Meemken, Fabian; Hungerbühler, Konrad; Baiker, Alfons; Tummala, Srinivas; et al. "Assessment of Recent Process Analytical Technology (PAT) Trends: A Multiauthor Review". Organic Process Research & Development 19 1 (2015): 3-62. http://dx.doi.org/10.1021/op500261y.
    10.1021/op500261y
  22. Pardelha, Filipa; Albuquerque, Maria G.E.; Reis, Maria A.M.; Oliveira, Rui; Dias, João M.L.. "Dynamic metabolic modelling of volatile fatty acids conversion to polyhydroxyalkanoates by a mixed microbial culture". New Biotechnology 31 4 (2014): 335-344. http://dx.doi.org/10.1016/j.nbt.2013.06.008.
    10.1016/j.nbt.2013.06.008
  23. Oliveira, Rui. "Optimisation of a Sequencing Batch Reactor for Production of Polyhydroxybutyrate Using Process Characterization Method and Neural Network Modeling". Computer Aided Chemical Engineering 33 (2014): 733-738. https://doi.org/10.1016/B978-0-444-63456-6.50123-X.
  24. von Stosch, Moritz; Davy, Steven; Francois, Kjell; Galvanauskas, Vytautas; Hamelink, Jan-Martijn; Luebbert, Andreas; Mayer, Martin; et al. "Hybrid modeling for quality by design and PAT-benefits and challenges of applications in biopharmaceutical industry". Biotechnology Journal 9 6 (2014): 719-726. http://dx.doi.org/10.1002/biot.201300385.
    10.1002/biot.201300385
  25. von Stosch, Moritz; Oliveira, Rui; Peres, Joana; Feyo de Azevedo, Sebastião. "Hybrid semi-parametric modeling in process systems engineering: Past, present and future". Computers & Chemical Engineering 60 (2014): 86-101. http://dx.doi.org/10.1016/j.compchemeng.2013.08.008.
    10.1016/j.compchemeng.2013.08.008
  26. Ferreira, A. R.; Dias, J. M. L.; von Stosch, M.; Clemente, J.; Cunha, A. E.; Oliveira, Rui. "Fast development of Pichia pastoris GS115 Mut+ cultures employing batch-to-batch control and hybrid semi-parametric modeling". Bioprocess and Biosystems Engineering 37 4 (2013): 629-639. http://dx.doi.org/10.1007/s00449-013-1029-9.
    10.1007/s00449-013-1029-9
  27. Pardelha, F.; Albuquerque, M.G.E.; Carvalho, G.; Reis, M.A.M.; Dias, J.M.L.; Oliveira, R.. "Segregated flux balance analysis constrained by population structure/function data: The case of PHA production by mixed microbial cultures". Biotechnology and Bioengineering 110 8 (2013): 2267-2276. http://dx.doi.org/10.1002/bit.24894.
    10.1002/bit.24894
  28. Dias, João M. L.; Oliveira, Rui; Semmens, Michael. "Modeling NOM removal by softening in a surface water treatment plant". Water Science and Technology 67 5 (2013): 1008-1016. http://dx.doi.org/10.2166/wst.2013.621.
    10.2166/wst.2013.621
  29. Oliveira, Rui. "Modelling of a Sequencing Batch Reactor for Producing Polyhydroxybutyrate with Mixed Microbial Culture Cultivation Process Using Neural Networks and Operation Regime Classification". Chemical engineering transactions 32 (2013): 1261-1266. https://doi.org/10.3303/CET1332211.
  30. Ganjian, A.; Zhang, J.; Dias, J.M.L.; Oliveira, R.. "Modelling of a sequencing batch reactor for producing polyhydroxybutyrate with mixed microbial culture cultivation process using neural networks and operation regime classification". Chemical Engineering Transactions 32 (2013): 1261-1266. http://www.scopus.com/inward/record.url?eid=2-s2.0-84879205252&partnerID=MN8TOARS.
    10.3303/CET1332211
  31. Pardelha, Filipa; Albuquerque, Maria G.E.; Reis, Maria A.M.; Dias, João M.L.; Oliveira, Rui. "Flux balance analysis of mixed microbial cultures: Application to the production of polyhydroxyalkanoates from complex mixtures of volatile fatty acids". Journal of Biotechnology 162 2-3 (2012): 336-345. http://dx.doi.org/10.1016/j.jbiotec.2012.08.017.
    10.1016/j.jbiotec.2012.08.017
  32. Roca, Christophe; Chagas, Bárbara; Farinha, Inês; Freitas, Filomena; Mafra, Luís; Aguiar, Filipe; Oliveira, Rui; Reis, Maria A.M.. "Production of yeast chitin–glucan complex from biodiesel industry byproduct". Process Biochemistry 47 11 (2012): 1670-1675. http://dx.doi.org/10.1016/j.procbio.2012.04.004.
    10.1016/j.procbio.2012.04.004
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  106. Oliveira, R.; Ferreira, E.C.; Feyo de Azevedo, S.. "Stability, dynamics of convergence and tuning of observer-based kinetics estimators". Journal of Process Control 12 2 (2002): 311-323. http://dx.doi.org/10.1016/s0959-1524(01)00031-2.
    10.1016/s0959-1524(01)00031-2
  107. Peres, J.; Oliveira, R.; Feyo de Azevedo, S.. "Knowledge based modular networks for process modelling and control". Computers & Chemical Engineering 25 4-6 (2001): 783-791. http://dx.doi.org/10.1016/s0098-1354(01)00665-2.
    10.1016/s0098-1354(01)00665-2
  108. R. Oliveira; R. Simutis; S. Feyo De Azevedo; A. Lübbert. "HYBNET, An Advanced Tool for Process Optimization and Control". IFAC Proceedings Volumes 31 8 (1998): 289-294. http://dx.doi.org/10.1016/s1474-6670(17)40200-x.
    10.1016/s1474-6670(17)40200-x
  109. Simutis, R; Oliveira, R; Manikowski, M; de Azevedo, S.Feyo; Lübbert, A. "How to increase the performance of models for process optimization and control". Journal of Biotechnology 59 1-2 (1997): 73-89. http://dx.doi.org/10.1016/s0168-1656(97)00166-1.
    10.1016/s0168-1656(97)00166-1
  110. Oliveira, R.; Ferreira, E.C.; Oliveira, F.; Feyo de Azevedo, S.. "A study on the convergence of observer-based kinetics estimators in stirred tank bioreactors". Journal of Process Control 6 6 (1996): 367-371. http://dx.doi.org/10.1016/0959-1524(95)00037-2.
    10.1016/0959-1524(95)00037-2
  111. R. Oliveira; E.C. Ferreira; S.Feyo de Azevedo. "Model-Based Estimation of Reaction Rates in Stirred Tank Bioreactors". IFAC Proceedings Volumes 28 3 (1995): 259-264. http://dx.doi.org/10.1016/s1474-6670(17)45640-0.
    10.1016/s1474-6670(17)45640-0
Capítulo de livro
  1. José Pinto; João Antunes; João Ramos; Rafael S. Costa; Rui Oliveira. "Modeling and optimization of bioreactor processes". 89-115. Elsevier, 2022.
    10.1016/b978-0-323-91167-2.00016-2
  2. De Azevedo, C.R.; Díaz, V.G.; Prado-Rubio, O.A.; Willis, M.J.; Préat, V.; Oliveira, R.; Von Stosch, M.. "Hybrid semiparametric modeling: A modular process systems engineering approach for the integration of available knowledge sources". 345-373. 2020.
  3. Stosch, Moritz von; Portela, Rui M. C.; Oliveira, Rui. "Hybrid Model Structures for Knowledge Integration". In Hybrid Modeling in Process Industries, 13-35. CRC Press, 2018.
    10.1201/9781351184373-2
  4. Stosch, Moritz von; Portela, Rui M. C.; Oliveira, Rui. "Hybrid Model Structures for Knowledge Integration". In Hybrid Modeling in Process Industries, 13-35. CRC Press, 2018.
    10.1201/9781351184373-2
  5. Oliveira, Rui. "Hybrid ANN-mechanistic models for general chemical and biochemical processes". In Artificial Neural Networks in Chemical Engineering, 229-256. 2017.
  6. von Stosch, Moritz; Carinhas, Nuno; Oliveira, Rui. "Hybrid Modeling for Systems Biology: Theory and Practice". In Modeling and Simulation in Science, Engineering and Technology, 367-388. Springer International Publishing, 2014.
    10.1007/978-3-319-08437-4_7
  7. von Stosch, Moritz; Carinhas, Nuno; Oliveira, Rui. "Hybrid Modeling for Systems Biology: Theory and Practice". In Modeling and Simulation in Science, Engineering and Technology, 367-388. Springer International Publishing, 2014.
    10.1007/978-3-319-08437-4_7
  8. Amin Ganjian; Jie Zhang; Rui Oliveira. "Optimisation of a Sequencing Batch Reactor for Production of Polyhydroxybutyrate Using Process Characterisation Method and Neural Network Modelling". 733-738. Elsevier, 2014.
    10.1016/b978-0-444-63456-6.50123-x
  9. Oliveira, Rui. "Design of Pathway-Level Bioprocess Monitoring and Control Strategies Supported by Metabolic Networks". In Advances in biochemical engineering/biotechnology. 2012.
  10. Oliveira, Rui. "On-line control strategies". In Comprehensive Biotechnology. 2011.
  11. Oliveira, Rui. "Hybrid modelling in membrane processes". In Nanoporous materials in energy and environment. 2011.
  12. J. Peres; F. Freitas; MAM Reis; S. Feyo de Azevedo; R. Oliveira. "Hybrid modular mechanistic/ANN modelling of a wastewater phosphorus removal process". 1717-1722. Elsevier, 2006.
    10.1016/s1570-7946(06)80295-6
  13. António Roldão; Helena L.A. Vieira; Manuel J.T. Carrondo; Paula M. Alves; R. Oliveira. "Rotavirus-like particle production: Simulation of protein production and particle assembly". 1673-1678. Elsevier, 2006.
    10.1016/s1570-7946(06)80288-9
  14. J. Peres; R. Oliveira; L.S. Serafim; P. Lemos; M.A. Reis; S. Feyo de Azevedo. "Hybrid Modelling of a PHA Production Process Using Modular Neural Networks". 733-738. Elsevier, 2004.
    10.1016/s1570-7946(04)80188-3
  15. J. Peres; R. Oliveira; S. Feyo de Azevedo. "Modelling cells reaction kinetics with artificial neural networks: A comparison of three network architectures". 839-844. Elsevier, 2003.
    10.1016/s1570-7946(03)80221-3
  16. Oliveira, Rui. "Instrumentation in the Dairy industries". In Encyclopedia of the Dairy Sciences. 2002.
  17. Oliveira, Rui. "Process Control in the Dairy industries". In Encyclopedia of the Dairy Sciences. 2002.
  18. Oliveira, R.; Georgieva, P.; Feyo de Azevedo, S.. "Plant and Equipment: Instrumentation and Process Control: Instrumentation". 234-241. 2002.
  19. Oliveira, Rui. "New Metodologies for Multiphase Bioreactors: Data Acquisition, Modelling and Control". In Novel Multiphase Bioreactors. 2001.
  20. Oliveira, Rui. "Hybrid modeling with neural networks and its utilization in bioprocess control.". In Bioreactor Engineering, 380-406. 1996.
  21. R. Oliveira; E.C. Ferreira; S. Feyo de Azevedo. "MODEL-BASED ESTIMATION OF REACTION RATES IN STIRRED TANK BIOREACTORS". 259-264. Elsevier, 1995.
    10.1016/b978-0-08-042377-7.50052-0
Livro
  1. Azevedo, C.; Lee, R.; Portela, R.M.C.; Von Stosch, M.; Oliveira, R.. Hybrid ann-mechanistic models for general chemical and biochemical processes. 2017.
  2. Isidro, I.A.; Ferreira, A.R.; Clemente, J.J.; Cunha, A.E.; Dias, J.M.L.; Oliveira, R.. Design of pathway-level bioprocess monitoring and control strategies supported by metabolic networks. 2013.
    10.1007/10_2012_168
  3. Santos, J.L.C.; Oliveira, R.; Crespo, J.G.. Hybrid modeling of membrane processes. 2011.
    10.4032/9789814303125
  4. Teixeira, A.P.; Oliveira, R.; Alves, P.M.; Carrondo, M.J.T.. Online Control Strategies. 2011.
    10.1016/B978-0-08-088504-9.00143-4
  5. von Stosch, M.; Oliveira, R.; J, P.; de Azevedo, S.F.. Hybrid semi-parametric modeling of biological systems: Application to spectroscopic data for the estimation of concentrations. 2010.
    10.1016/S1570-7946(10)28171-3
  6. Miguel Lopes Dias, J.#x.;o.; Lemos, P.; Serafim, L.#x.;s.; Oehmen, A.; A. M. Reis, M.; Oliveira, R.. Development and implementation of a nonparametric/metabolic model in the process optimisation of PHA production by mixed microbial cultures. 2007.
    10.1016/S1570-7946(07)80190-8
  7. Teixeira, A.; Alves, C.M.L.; Alves, P.M.; Carrondo, M.J.T.; Oliveira, R.. Hybrid metabolic flux analysis/data-driven modelling of bioprocesses. 2006.
    10.1016/S1570-7946(06)80287-7
  8. Oliveira, R.; Cunha, A.; Clemente, J.; Carrondo, M.J.T.. Model-based bioreactor optimisation based on hybrid first principles/artificial neural network dynamical models. 2004.
    10.1016/S1570-7946(04)80187-1
  9. Oliveira, R.. Combining first principles modelling and artificial neural networks: a general framework. 2003.
    10.1016/S1570-7946(03)80218-3
Pré-impressão
  1. Pinto J; Mestre M; Costa RS; Striedner G; Oliveira R. "A general deep hybrid model for bioreactor systems: combining first Principles equations with deep neural networks". 2022. http://europepmc.org/abstract/PPR/PPR515401.
    10.1101/2022.06.07.495118
  2. Agharafeie R; Oliveira R; Mendes JM. "Trend of the Application of Hybrid Artificial Neural Network Models in Bioprocesses". 2022. http://europepmc.org/abstract/PPR/PPR538572.
    10.22541/au.166188605.56941100/v1
Resumo em conferência
  1. Oliveira, Rui. "Process control and Systems Biology: Application to mammalian cell cultures". Trabalho apresentado em M3C Workshop - Process Analytical Technology for Biopharmaceuticals, Bologne, 2010.
Tese / Dissertação
  1. Oliveira, Rui. "Bioprocess Supervision, Control and Optimization Based on Hybrid Models". Doutoramento, Martin-Luther-Universität Halle-Wittenberg Institut für Biochemie und Biotechnologie, 1998.

Propriedade Intelectual

Patente
  1. Oliveira, Rui. 2013. "Natural biocomposite powder prepared from Pichia pastoris biomass, method of preparation and its use as excipient".
  2. Oliveira, Rui. 2012. "A functional enviromics method for cell culture media engineering".
  3. Oliveira, Rui. 2011. "A Functional Enviromics method for cell culture media engineering". Portugal.
  4. Oliveira, Rui. 2010. "Biopolímero bacteriano contendo fucose". Portugal.
  5. Oliveira, Rui. 2010. "Fucose-containing bacterial biopolymer.". Estados Unidos.
  6. Oliveira, Rui. 2009. "Process for the co-production of chitin, its derivatives and polymers containing glucose, mannose and/or galactose, by the fermentation of the yeast Pichia pastoris.".
  7. Oliveira, Rui. 2008. "Co-Produção de quitina e polímeros contendo glucose, manose e/ou galactose, por cultivo da levedura Pichia pastoris". Portugal.
  8. Oliveira, Rui. 2008. "Galactose-rich polymer, process for the production of the polymer and its applications".
  9. Oliveira, Rui. 2007. "Polímero à base de galactose, processo para a sua obtenção e respectivas utilizações". Portugal.

Outros

Outra produção
  1. Hybrid Semiparametric Modeling: A Modular Process Systems Engineering Approach for the Integration of Available Knowledge Sources. 2019. Cristiana Rodrigues Azevedo; Victor Grisales Díaz; Oscar Andrés Prado-Rubio; Mark J. Willis; Véronique Préat; Rui Oliveira; Moritz Stosch. http://dx.doi.org/10.1002/9781119513957.ch14.
    10.1002/9781119513957.ch14
Atividades

Apresentação oral de trabalho

Título da apresentação Nome do evento
Anfitrião (Local do evento)
2019/03/19 In silico culture media design based on prior metabolic knowledge 2nd Annual Bioprocessing Summit Europe
(Lisbon, Portugal)
2019/02/20 In silico culture media design based on prior metabolic knowledge
Glaxo-Smith-Klein (Brussels, Bélgica)
2018/10/08 Understanding Culture Media Variability Bioproduction
(Dublin, Irlanda)
2017/12/11 From projection to latent structures to projection tolatent pathways
BOKU University
2017/07/05 An intuitive introduction to hybrid modeling 3rd Hybrid modeling summer school
(Viena, Áustria)
2017/03/07 Innovation in systems biology and engineering Jornadas de Inovação
Instituto Superior Técnico
2016/09/05 Towards systematic culture media engineering Summer school in Computational Biology
Universidade de Coimbra (Portugal)
2016/05/23 Cell functional enviromics for culture medium engineering
BOKU University (Viena, Áustria)
2015/11/30 Hybrid semiparametric modeling for process systems engineering: examples from biological systems
BASF (Ludwigshafen)
2015/09/23 Cell functional enviromics: unravelling the function of environmental factors ISPROF - International Symposium Profiling
(Caparica, Portugal)
2015/06/08 Pathway level culture media engineering Metabolic Pathway Analysis (MPA)
(Braga, Portugal)
2013/09/23 Hybrid modeling for systems biology: theory and practice EUPAT6
(Porto, Portugal)
2013/09/04 Hybrid model identification and descrimination 2nd Hybrid modeling summer school
(Lisbon, Portugal)
2012/11/12 Cell functional enviromics: unravelling the function of environmental factors
Instituto Superior Técnico (Lisboa, Portugal)
2012/02/29 A Systems and Synthetic Biology framework for pathway level culture media engineering: application to Pichia pastoris
(Alpbach, Áustria)
2012/02/29 Systems and Synthetic Biology framework for pathway level culture media engineering: application to Pichia pastoris
(Alpbach, Áustria)
2010/10/03 Fucose-containing bacterial polysaccharide produced from glycerol byproduct International Symposium on BioPolymers 2010 (ISBP 2010)
(Stuttgart, Alemanha)
2010/09/14 Production of chitin-glucan complex (CGC) from biodiesel industry by-product 14th International Biotechnology Symposium and Exhibition (IBS 2010)
(Rimini, Itália)
2010/09/14 New Microbial Fucose-Containing Polysaccharide: Rheological Studies. 14th International Biotechnology Symposium and Exhibition (IBS 2010)
(Rimini, Itália)
2010/09/14 Conversion of glycerol into a new high-value fucose-containing bacterial exopolysaccharide 14th International Biotechnology Symposium and Exhibition (IBS 2010)
(Rimini, Itália)
2010/09/11 Yeast Chitin-Glucan Complex 23rd European Conference on Biomaterials (ESB2010)
(Tampere, Finlândia)
2010/09/11 Novel Fucose-Containing Bacterial Exopolysaccharide 23rd European Conference on Biomaterials (ESB2010)
(Tampere, Finlândia)
2010/09/05 Process control and Systems Biology: application to mammalian cell cultures M3C Workshop- Process Analytical Technology for Biopharmaceuticals
(Bologna, Itália)
2010/09/05 On-line adaptive metabolic flux analysis of misspecified metabolic networks 8th European Symposium on Biochemical Engineering Science (ESBES 8)
(Bologna, Itália)
2010/09/05 Process control and Systems Biology: application to mammalian cell cultures 8th European Symposium on Biochemical Engineering Science - M3C Workshop - Process Analytical Technology for Biopharmaceuticals
(Bologna, Itália)
2010/07/11 Novel Fucose-containing EPS: production and characterization. 43rd IUPAC World Polymer Congress (MACRO2010)
(Glasgow, Reino Unido)
2010/06/06 Chemometric modelling of a membrane ultra-filtration process European Symposium on Computer Aided Process Engineering (ESCAPE 20)
(Ischia, Itália)
2010/06/06 Production of chitin-glucan complex from a biodiesel industry by-product V Iberoamerican Chitin Symposium (SIAQ 2010)
(Santiago, Chile)
2010/04/11 Characterization of biodegradable films obtained from a new microbial polysaccharide VII Ibero-American Conference on Membrane Science and Technology (CITEM 2010)
(Sintra, Portugal)
2010/04/09 Metabolic modelling and optimization of polyhydroxyalkanoates production using mixed microbial cultures and renewable resources. Mixed Culture Polyhydroxyalkanoates Production (MMC PHA)
(Lisbon, Portugal)
2010/04/09 Advanced monitoring of PHA production Mixed Culture Polyhydroxyalkanoates Production (MMC PHA)
(Lisbon, Portugal)
2010 “Manipulating the energy metabolism for increased baculovirus production: a bridge between metabolic and bioprocess engineering Cell Culture Engineering XII, 2010
2010 Hybrid semi-parametric modelling of biological systems: application to the spectroscopic data Proc of Computer Aided Chemical Engineering (ESCAPE-20)
(Ichia, Itália)
2010 Hybrid metabolic flux analysis: a powerful tool to assist bioprocess optimization 5th European Biotechnology Workshop
2010 Baculovirus for gene therapy: use of metabolomics for production and membrane processes for purification Cell Line Development and Engineering 2010
(Prague, República Checa)
2009/11/18 Chitin-Glucan Complex Production by Pichia pastoris Using Crude Glycerol 5th European Symposium on Biopolymers (ESBP 2009)
(Funchal, Portugal)
2009/11/18 Conversion of Glycerol into Value-Added Bacterial Extracellular Polysaccharides. 5th European Symposium on Biopolymers (ESBP 2009)
(Funchal, Portugal)
2009/11/05 Improving titer and glycosylation homogeneity of an antibody fragment in a Mut+ Pichia pastoris process. Mass Spec Europe (MSE)
(Barcelona, Espanha)
2009/09/28 Hybrid semi-parametric systems: a Systems Biology perspective 1st summer school of the IMPRS
Max-Planck Institute for Dynamics of Complex Technical Systems (Magdeburg, Alemanha)
2009/09/23 Conversion of glycerol byproduct into value-added bacterial polysaccharide. INTB/INPB 2009 – The 6th International Conference on textile and Polymer Biotechnology / COST Actions 868 and MP0701
(Ghent, Bélgica)
2009/09/21 New value-added bacterial extracellular polysaccharide produced from glycerol byproduct Polysaccharides as a Source of Advanced Materials
(Turku/Abo, Finlândia)
2009/09/13 A hybrid semi-parametric approach to dynamical modelling of biological systems based on delayed differential equations, Abstracts of the 14th European Congress on Biotechnology,
(Barcelona, Espanha)
2009/09 Analysis of oxygen transport enhancement by functionalized magnetic nanoparticles (FMP) in biopolymer production processes 14th European Congress on Biotechnology
(Barcelona, Espanha)
2009/07/12 Production of Value-Added Bacterial Polysaccharides from Glycerol Byproduct from the Biodiesel Industry. M.A.M. European Polymer Congress (EPF'09)
(Graz, Áustria)
2009/07 Extraction and purification of cell wall polysaccharides from Pichia pastoris biomass. European Polymer Congress (EPF'09)
(Graz, Áustria)
2009/06/10 Metabolic modelling and optimisation of polyhydroxyalkanoates production from sugar cane molasses by mixed microbial cultures International Conference on Renewable Resources & Biorefineries
(Gent, Bélgica)
2009 A strategy to improve insect cells productivity through manipulation of metabolic pathways ESACT 2009
2009 A novel approach to constraints based modeling: combining mechanistic and statistical constraints to reduce the solution space Biochemical Engineering XVI
2009 Optimizing bioprocessing of baculovirus for gene therapy: use of metabolomic tools for production and membrane processes for purification 9th PEACe
(Wyoming, Estados Unidos)
2009 Baculovirus for gene therapy: use of metabolomics for production and membrane processes for purification. Combined Meeting of ESGCT, GSZ, DG-GT and ISCT
(Hannover, Alemanha)
2008/09/15 Predicting Recombinant Protein Expression in the Baculovirus/Insect Cells System: A Stochastic/Structured Modeling Approach ESF 2nd Functional Dynamics Conference
(Rotenburg ob der Tauber, Alemanha)
2008/09/04 Adaptive control of glycerol & methanol feeding in recombinant Pichia pastoris cultures: Impact on antibody titre CHEMPOR2008
(Brage, Portugal)
2008/09/04 Stochastic Modelling of the Baculovirus/Insect Cells System: Prediction of Recombinant Protein Expression 10th International Chemical Engineering Conference
(Braga, Portugal)
2008/09 In situ 2D fluorometry for monitoring the physiological state of mammalian cell cultures 5th RPP meeting
(Itália)
2008/09 Biopolymers production by microbial fermentation on Glycerol-rich Product. 10th International Chemical and Biological Engineering Conference – Chempor 2008
(Braga, Portugal)
2008/06/01 Predictive Modeling in Rotavirus-Like Particles Production: Improving Upstream and Downstream Processing Design Vaccine Technology II
(Albufeira, Portugal)
2008/06 Conversion of Glycerol-rich Product (GRP) into Biopolymers Clean Technology 2008 – CTSI Clean Technology & Sustainable Industries Conference & Trade Show
(Boston, Estados Unidos)
2008/06 Production of biopolymers by Pseudomonas Strain grown on Glycerol-rich Product. International Workshop on Biomacromolecules 2008 – Renewable, Degradable and Biomedical polymers,
(Stockholm, Suécia)
2008 In situ 2D fluorometry for monitoring the physiological state of mammalian cell cultures.” RPP 2008
2008 Improvement of baculovirus vectors production based on the metabolic characterization and modelling of Sf-9 cultures CHEMPOR 2008
2008 Metabolic modelling and characterization of uninfected and infected Sf9 cultures: a basis for improving Baculovirus vectors production ESBES 2008
2008 Engineering challenges in the production of baculovirus vectors for gene therapy with Sf 9 insect cells. ESBES 2008
2008 An insight into the cell density effect in the baculovirus insect cell system by analysis of the dynamics of energetic metabolism RPP 2008
2008 New microbial galactose-rich polysaccharide produced from glycerol: properties and applications. Innovation for Sustainable Production 2008, i-SUP 2008
(Bruges, Bélgica)
2008 Macroscopic control of intracellular regulation: application to mammalian cell cultures Metabolic Engineering VII
(Puerto Vallarta, México)
2008 Macroscopic control of intracellular regulation: application to mammalian cell cultures CHEMPOR 10th
(Braga, Portugal)
2008 Macroscopic control of intracellular regulation: application to mammalian cell cultures Metabolic Engineering VII
(Puerto Vallarta, México)
2007/10 Production of a Galactose-Rich Polysaccharide and Polyhydroxyalkanoates by a Pseudomonas Strain Using Glycerol as Carbon Source. 4th European Symposium on Biopolymers
(Kusadasi, Turquia)
2007/10 Biodegradable films from a galactose-rich polysaccharide produced by a Pseudomonas strain from glycerol, 2007: 1st International conference on biodegradable polymers and sustainable composites
(Alicante, Espanha)
2007 Monitoring and optimal control of the fluxome in recombinant BHK cultures, 20th ESACT meeting
(Dresden, Alemanha)
2006/10/26 Optimization and control of recombinant Pichia pastoris cultures
Merck&Co (West Point, Estados Unidos)
2006/07/09 Rotavirus-Like Particle Production: Simulation of Protein Production and Particle Assembly 9th ISPSE + 16th ESCAPE
(Garmisch-Partenkirchen, Alemanha)
2006/04/23 Modeling rotavirus VLPs production: infection, gene expression and VLPs assembly Cell Culture Engineering X
(Whistler,BC, Canadá)
2006 HYBMFA: a bioinformatics’ tool for batch-to-batch bioprocess optimisation supported by elementary flux analysis. RPPM 2006
(Barcelona, Espanha)
2006 Dynamic optimisation of a recombinant BHK-21 culture based on elementary flux analysis and hybrid parametric/nonparametric modeling Recombinant Protein Production Meeting
(Barcelona, Espanha)
2006 Hybrid metabolic flux analysis/data-driven modelling of bioprocesses 16th ESCAPE and 9th PSE
(Parten-Kirchen, Alemanha)
2005/11/06 Hybrid metabolic flux analysis/artificial neural network modeling of bioprocesses. HIS05 proceedings
(Rio de Janeiro, Brasil)
2005/10/05 Modelling and optimisation of BHK-21 cultures expressing the human fusion glycoprotein IgG1-IL2 Cell culture and upstream processing
(Lisboa, Portugal)
2005/09/21 Modeling and Control of Rotavirus Virus-Like Particle Production: Baculovirus DNA Replication, mRNA Synthesis and Protein Production Chempor 2005, 9th International Chemical Engineering Conference
(Coimbra, Portugal)
2005/09/21 Modeling and Control of Rotavirus Virus-Like Particle Production: Baculovirus DNA Replication, mRNA Synthesis and Protein Production hempor 2005, 9th International Chemical Engineering Conference
(Coimbra, Portugal)
2005/09/21 Model-based developement of a novel process for polyhydroxybutyrate production by mixed culture Chempor 2005, 9th International Chemical Engineering Conference
(Coimbra, Portugal)
2005/09/18 Modelling Integrated Production for Rotavirus Like Particle Production in the Baculo Insect Cell System 7th Conference Protein Expression in Animal Cell
(Island of Crete, Grécia)
2005/04/24 Rotavirus-like Particles production: Baculovirus DNA replication, mRNA synthesis and protein production 1st European Rotavirus Biology Meeting
( Château d’Esclimont, Paris, França)
2005/03/21 Benchmark testing of simulated annealing, adaptive random search and genetic algorithms for the global optimization of bioprocesses ICANNGA-05, 5th International Conference on Adaptive and Natural Computing Algorithms
(Lisbon, Portugal)
2005/03/21 Dynamic modelling and optimisation of a mammallian cells process using hybrid grey-box systems ICANNGA-05, 5th International Conference on Adaptive and Natural Computing Algorithms
(Lisbon, Portugal)
2005/03/21 Adaptive DO-based control of substrate feeding in high cell density cultures operated under oxygen transfer limitation ICANNGA-05, 5th International Conference on Adaptive and Natural Computing Algorithms
(Lisbon, Portugal)
2005 Hybrid metabolic flux analysis/artificial neural network modeling of bioprocesses 5th International Conference on HIS
(Brasil)
2004/05/16 Model-based Bioreactor Optimisation based on hybrid first principles/artificial neural network dynamical models European Symposium on Computer-Aided Process Engineering, ESCAPE-14
(Lisbon, Portugal)
2004/03/28 Hybrid modelling of fermentation processes: a study on the use of modular neural networks for modelling cells reaction kinetics CAB9: 9th International Symposium on Computer Applications in Biotechnology
(Nancy, França)
2004/03/28 Hybrid modelling of fermentation processes using artificial neural networks: a study on identification and stability CAB9: 9th International Symposium on Computer Applications in Biotechnology
(Nancy, França)
2004 Dynamic modelling of a BHK culture expressing the fusion glycoprotein IgG1-IL2. ESBES04
(Stutgart, Alemanha)
2004 Modelling and optimisation of a BHK-21 culture expressing the fusion glycoprotein IgG1-IL2 CAC
(Lisbon, Portugal)
2003/11/16 Bioreactor optimisation based on hybrid first principles/artificial neural network models AIChE Annual Meeting
(San Francisco, Estados Unidos)
2003/06/01 Combining first principles modelling and artificial neural networks: a general framework ESCAPE-13: European Symposium on Computer Aided Process Engineering
(Lappeenranta, Finlândia)
2001/06/26 Methods of Knowledge Engineering for Batch Process Operation 3rd European Congress of Chemical Engineering (ECCE-3)
(Nuremberg, Alemanha)
1998/09/16 Hybrid Networks: A New Approach for Bioprocess Modeling ESBES-2 2nd European Symposium on Biochemical Engineering Science
(Porto, Portugal)
1997/04/04 Optimierung der Produktion rekombinanter Proteine mit Hilfe Hybrider Prozeßmodelle Referate der DECHEMA Fachausschußsitzung GVC-Reaktionstechnik,
(Wurzburg, Alemanha)
1996 HYBNET, a new tool for advanced process modeling ESBES-1 1st European Symposium on Biochemical Engineering Science,
(Dublin, Irlanda)
1995/05/14 Model-Based Estimation of Reaction Rates in Stirred Tank Bioreactors 6th Int. Conference on Computer Applications in Biotechnology - CAB6
(Garmisch-Partenkirchen, Alemanha)
1993/04/04 DIGICON - A Generalized Feedback-Feedforward DIGital CONtroller CHEMPOR-93, Int. Chem Engng Conf.
(Porto, Portugal)

Orientação

Título / Tema
Papel desempenhado 		Curso (Tipo)
Instituição / Organização
2019 - Atual Digital Ultra-fast Biologics Development: Application to CHO expressing mAB (funded by FCT SFRH/BD/146104/2019, Supervisor Rui Oliveira FCTUNL; co-supervisor Gerald Striedner BOKU University)
Orientador
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2012 - 2017 A Hybrid Systems Framework to Design Standard Biological Parts for Synthetic Biology: Application to Pichia pastoris (Funded by FCT SFRH/BD/51577/2011)
Orientador
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2012/03/01 - 2016/12/20 Functional Enviromics: Application for bioprocess monitoring and control (Funded by FCT: SFRH/BD/70768/2010) (Supervisor Rui Oliveira; Co-supervisor Anton Glieder (TU-Graz) (MIT-Portugal program)
Orientador
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2011/01/01 - 2015/12/20 Engineering extracellular polysaccharide production by Enterobacter sp.: a Systems Biology approach ( Funded by FCT: SFRH/BD/67033/2009)
Orientador
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2011/01/01 - 2015/12/20 Enhanced oxygen transport using functionalized magnetic nanoparticles: modeling and scale-up, (Supervisor: Rui Oliveira; Co-supervisor Ascensão Miranda Reis), Funded by FCT: SFRH/BD/43956/2008; Concluded December 2015
Orientador
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2009 - 2013 Recombinant proteins production by Pichia pastoris: strategies for glycosylation control, (Supervisor: Rui Oliveira; Co-supervisor: António Cunha), Concluded January 2013, Funded by FCT: SFRH/BD/36285/2007
Orientador
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2008 - 2012 Polyhydroxyalkanoates production by mixed microbial cultures: new strategies for high cell density and high PHA storage capacity, (Supervisor: Ascensão Miranda Reis; Co-supervisor: Rui Oliveira), Funded by FCT: SFRH/BD/38763/2007
Orientador
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2008 - 2011 Moritz Von Stosch. New Strategies for Process Control Based on Hybrid Semi-parametric Mathematical Systems. (Supervisor: Sebastião Feyo de Azevedo (FEUP), co-supervisor Rui Oliveira (Nova)), Funded by FCT: SFRH/BD/36990/2007, Concluded in december 2011
Coorientador
Universidade do Porto Faculdade de Engenharia, Portugal
2008 - 2011 Nuno Carinhas, Development of a high cell density process for the production of Baculovirus vectors, PhD dissertation concluded in September 2011 (Supervisor: Paula Alves, Co-supervisor Rui Oliveira), Funded by FCT: SFRH/BD/36676/2007
Coorientador
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2006 - 2010 António Manuel Missionário Roldão, Production Optimization of Rotavirus-Like Particles: A Systems Biology Approach, Concluded PhD dissertation in June 2010 (Supervisor Manuel Carrondo; Co-supervisor: Rui Oliveira), Funded by FCT SFRH/BD/21910/2005
Coorientador
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2004 - 2008 Ana Margarida Palma Teixeira, Bridging Systems Biology and Bioprocess Engineering: Application to Mammalian Cell Cultures, PhD dissertation concluded in June 2007, Supervisor Rui Oliveira; Co-supervisor Manuel Carrondo, Funded by FCT: SFRH/BD/13712/2003
Orientador
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2004 - 2008 Metabolic modelling and optimization of polyhydroxyalkanoates production by mixed microbial cultures, PhD dissertation concluded in May 2007 (Supervisor: Rui Oliveira; Co-supervisor: Ascensão Miranda Reis), Funded by FCT: SFRH/BD/13714/2003
Orientador
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2001 - 2006 Mário Fernando José Eusébio, Development of an universal interface for chemical and biochemical process monitoring and control, PhD dissertation concluded in April 2006, supervisor J. P. B. Mota, co-supervisor Rui Oliveira
Coorientador
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2001 - 2005 Maria Joana Monteiro de Carvalho Peres, Bioprocess hybrid modelling based on knowledge engineering methods, PhD dissertation concluded in June 2005, supervisor: Sebastião Feyo de Azevedo, co-supervisor Rui Oliveira
Coorientador
Universidade do Porto Faculdade de Engenharia, Portugal
Distinções

Outra distinção

2011 First prize of the MIT-Portugal venture competion track life scienses awarded with 100k € to start a culture media venture
2008 Prize of SHIC’08 – Solvay & Hovione Ideas Challenge 2008, "production of extracellular polysaccharides (EPS) by the bacterium Pseudomonas oleovorans using glycerol byproduct generated by the biodiesel industry as the substrate"
2007 Prémio de mérito científico Santander Totta/Universidade Nova de Lisboa "Bridging Systems Biology and Process Engineering: Strategies to the Deleopment of New Genaration Biopharmateuticals"
1998 Marthin-Luther Universitaet Medal –PhD dissertation Bioprocess Supervision, Control and Optimization Based on Hybrid Models concluded with summa cum laude (Rui Oliveira)