Publications

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Submitted
Carinhas, Nuno, Rui Oliveira, Paula Marques Alves, Manuel J. T. Carrondo, and Ana P. Teixeira. "{Systems biotechnology of animal cells: the road to prediction}." {TRENDS IN BIOTECHNOLOGY}. {30} (Submitted): {377-385}. Abstract
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Alves, Vitor D., Filomena Freitas, Cristiana A. V. Torres, Madalena Cruz, Rodolfo Marques, Christian Grandfils, M. P. Goncalves, Rui Oliveira, and Maria A. M. Reis. "{Rheological and morphological characterization of the culture broth during exopolysaccharide production by Enterobacter sp.}." {CARBOHYDRATE POLYMERS}. {81} (Submitted): {758-764}. Abstract
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Simon, Levente L., Hajnalka Pataki, Gyoergy Marosi, Fabian Meemken, Konrad Hungerbuehler, Alfons Baiker, Srinivas Tummala, Brian Glennon, Martin Kuentz, Gerry Steele, Herman J. M. Kramer, James W. Rydzak, Zengping Chen, Julian Morris, Francois Kjell, Ravendra Singh, Rafiqul Gani, Krist V. Gernaey, Marjatta Louhi-Kultanen, John O'Reilly, Niklas Sandler, Osmo Antikainen, Jouko Yliruusi, Patrick Frohberg, Joachim Ulrich, Richard D. Braatz, Tom Leyssens, Moritz von Stosch, Rui Oliveira, Reginald B. H. Tan, Huiquan Wu, Mansoor Khan, Des O'Grady, Anjan Pandey, Remko Westra, Emmanuel Delle-Case, Detlef Pape, Daniele Angelosante, Yannick Maret, Olivier Steiger, Miklos Lenner, Kaoutar Abbou-Oucherif, Zoltan K. Nagy, James D. Litster, Vamsi Krishna Kamaraju, and Min-Sen Chiu. "{Assessment of Recent Process Analytical Technology (PAT) Trends: A Multiauthor Review}." {ORGANIC PROCESS RESEARCH & DEVELOPMENT}. {19} (Submitted): {3-62}. Abstract
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Carinhas, Nuno, Vicente Bernal, Adriana Y. Yokomizo, Manuel J. T. Carrondo, Rui Oliveira, and Paula M. Alves. "{Baculovirus production for gene therapy: the role of cell density, multiplicity of infection and medium exchange}." {APPLIED MICROBIOLOGY AND BIOTECHNOLOGY}. {81} (Submitted): {1041-1049}. Abstract
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Freitas, Filomena, Vitor D. Alves, Joana Pais, Nuno Costa, Cristina Oliveira, Luis Mafra, Loic Hilliou, Rui Oliveira, and Maria A. M. Reis. "{Characterization of an extracellular polysaccharide produced by a Pseudomonas strain grown on glycerol}." {BIORESOURCE TECHNOLOGY}. {100} (Submitted): {859-865}. Abstract
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Carinhas, Nuno, Vicente Bernal, Francisca Monteiro, Manuel J. T. Carrondo, Rui Oliveira, and Paula M. Alves. "{Improving baculovirus production at high cell density through manipulation of energy metabolism}." {METABOLIC ENGINEERING}. {12} (Submitted): {39-52}. Abstract
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Roldao, Antonio, Manuel J. T. Carrondo, Paula M. Alves, and R. Oliveira. "{Stochastic simulation of protein expression in the baculovirus/insect cells system}." {COMPUTERS & CHEMICAL ENGINEERING}. {32} (Submitted): {68-77}. Abstract
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Teixeira, Ana P., Carlos Alves, Paula M. Alves, Manuel J. T. Carrondo, and Rui Oliveira. "{Hybrid elementary flux analysis/nonparametric modeling: application for bioprocess control}." {BMC BIOINFORMATICS}. {8} (Submitted). Abstract
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von Stosch, Moritz, Rui Oliveira, Joana Peres, and Sebastiao Feyo de Azevedo. "{Hybrid semi-parametric modeling in process systems engineering: Past, present and future}." {COMPUTERS & CHEMICAL ENGINEERING}. {60} (Submitted): {86-101}. Abstract
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Teixeira, Ana P., Sonia Sa Santos, Nuno Carinhas, Rui Oliveira, and Paula M. Alves. "{Combining metabolic flux analysis tools and C-13 NMR to estimate intracellular fluxes of cultured astrocytes}." {NEUROCHEMISTRY INTERNATIONAL}. {52} (Submitted): {478-486}. Abstract
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Roldao, Antonio, Maria Candida M. Mellado, J. C. Lima, Manuel J. T. Carrondo, Paula M. Alves, and R. Oliveira. "{On the Effect of Thermodynamic Equilibrium on the Assembly Efficiency of Complex Multi-Layered Virus-Like Particles (VLP): the Case of Rotavirus VLP}." {PLOS COMPUTATIONAL BIOLOGY}. {8} (Submitted). Abstract
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Carinhas, Nuno, Vicente Bernal, Ana P. Teixeira, Manuel J. T. Carrondo, Paula M. Alves, and Rui Oliveira. "{Hybrid metabolic flux analysis: combining stoichiometric and statistical constraints to model the formation of complex recombinant products}." {BMC SYSTEMS BIOLOGY}. {5} (Submitted). Abstract
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Teixeira, Ana P., Tiago M. Duarte, Rui Oliveira, Manuel J. T. Carrondo, and Paula M. Alves. "{High-throughput analysis of animal cell cultures using two-dimensional fluorometry}." {JOURNAL OF BIOTECHNOLOGY}. {151} (Submitted): {255-260}. Abstract
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Carrondo, Manuel J. T., Paula M. Alves, Nuno Carinhas, Jarka Glassey, Friedemann Hesse, Otto-Wilhelm Merten, Martina Micheletti, Thomas Noll, Rui Oliveira, Udo Reichl, Arne Staby, Ana P. Teixeira, Henry Weichert, and Carl-Fredrik Mandenius. "{How can measurement, monitoring, modeling and control advance cell culture in industrial biotechnology?}." {BIOTECHNOLOGY JOURNAL}. {7} (Submitted): {1522-1529}. Abstract
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Pardelha, Filipa, Maria G. E. Albuquerque, Maria A. M. Reis, Joao M. L. Dias, and Rui Oliveira. "{Flux balance analysis of mixed microbial cultures: Application to the production of polyhydroxyalkanoates from complex mixtures of volatile fatty acids}." {JOURNAL OF BIOTECHNOLOGY}. {162} (Submitted): {336-345}. Abstract
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Torres, Cristiana A. V., Rodolfo Marques, Silvia Antunes, Vitor D. Alves, Isabel Sousa, Ana Maria Ramos, Rui Oliveira, Filomena Freitas, and Maria A. M. Reis. "{Kinetics of production and characterization of the fucose-containing exopolysaccharide from Enterobacter A47}." {JOURNAL OF BIOTECHNOLOGY}. {156} (Submitted): {261-267}. Abstract
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Teixeira, Ana P., Nuno Carinhas, Jodo M. L. Dias, Pedro Cruz, Paula M. Alves, Manuel J. T. Carrondo, and Rui Oliveira. "{Hybrid semi-parametric mathematical systems: Bridging the gap between systems biology and process engineering}." {JOURNAL OF BIOTECHNOLOGY}. {132} (Submitted): {418-425}. Abstract
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von Stosch, Moritz, Rui Oliveira, Joana Peres, and Sebastiao Feyo de Azevedo. "{A general hybrid semi-parametric process control framework}." {JOURNAL OF PROCESS CONTROL}. {22} (Submitted): {1171-1181}. Abstract
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Oliveira, R., R. Simutis, and SF de Azevedo. "{Design of a stable adaptive controller for driving aerobic fermentation processes near maximum oxygen transfer `capacity}." {JOURNAL OF PROCESS CONTROL}. {14} (Submitted): {617-626}. Abstract
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Pardelha, F., M. G. E. Albuquerque, G. Carvalho, M. A. M. Reis, J. M. L. Dias, and R. Oliveira. "{Segregated flux balance analysis constrained by population structure/function data: The case of PHA production by mixed microbial cultures}." {BIOTECHNOLOGY AND BIOENGINEERING}. {110} (Submitted): {2267-2276}. Abstract
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Teixeira, A., A. E. Cunha, J. J. Clemente, JL Moreira, HJ Cruz, P. M. Alves, M. J. T. Carrondo, and R. Oliveira. "{Modelling and optimization of a recombinant BHK-21 cultivation process using hybrid grey-box systems}." {JOURNAL OF BIOTECHNOLOGY}. {118} (Submitted): {290-303}. Abstract
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Goerke, Aaron R., Johannes Scholten, Nedim Emil Altaras, Ana Teixeira, Joao Clemente, Antonio Cunha, Rui Oliveira, and John G. Aunins. "{BIOT 328-Fast development of Pichia pastoris cultures based on hybrid semiparametric process control}." {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY}. {236} (Submitted). Abstract
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Peres, J., R. Oliveira, and Feyo S. de Azevedo. "{Bioprocess hybrid parametric/nonparametric modelling based on the concept of mixture of experts}." {BIOCHEMICAL ENGINEERING JOURNAL}. {39} (Submitted): {190-206}. Abstract
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Alves, Vitor D., Filomena Freitas, Cristiana A. V. Torres, Madalena Cruz, Rodolfo Marques, Christian Grandfils, M. P. Goncalves, Rui Oliveira, and Maria A. M. Reis. "{Rheological and morphological characterization of the culture broth during exopolysaccharide production by Enterobacter sp. (vol 80, pg 325, 2010)}." {CARBOHYDRATE POLYMERS}. {80} (Submitted): {325}. Abstract
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Oliveira, R., A. Cunha, J. Clemente, and M. J. T. Carrondo. "{Adaptive DO-based control of substrate feeding in high cell density cultures operated under oxygen transfer limitation}." {Adaptive and Natural Computing Algorithms}. Eds. B. {Ribeiro, RF Albrecht, A. Dobnikar, DW Pearson, and NC} Steele. {SPRINGER COMPUTER SCIENCE}. Submitted. {300-303}. Abstract
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