Publications

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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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Teixeira, A. P., J. J. Clemente, A. E. Cunha, M. J. T. Carrondo, and R. Oliveira. "{Bioprocess iterative batch-to-batch optimization based on hybrid parametric/nonparametric models}." {BIOTECHNOLOGY PROGRESS}. {22} (Submitted): {247-258}. 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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Isidro, Ines A., Ana R. Ferreira, Joao J. Clemente, Antonio E. Cunha, and Rui Oliveira. "{Analysis of culture media screening data by projection to latent pathways: The case of Pichia pastoris X-33}." {JOURNAL OF BIOTECHNOLOGY}. {217} (Submitted): {82-89}. 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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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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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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Santos, J. L. C., A. M. Hidalgo, R. Oliveira, S. Velizarov, and J. G. Crespo. "{Analysis of solvent flux through nanofiltration membranes by mechanistic, chemometric and hybrid modelling}." {JOURNAL OF MEMBRANE SCIENCE}. {300} (Submitted): {191-204}. Abstract
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Ferreira, A. R., J. M. L. Dias, M. von Stosch, J. Clemente, A. E. Cunha, and Rui Oliveira. "{Fast development of Pichia pastoris GS115 Mut(+) cultures employing batch-to-batch control and hybrid semi-parametric modeling}." {BIOPROCESS AND BIOSYSTEMS ENGINEERING}. {37} (Submitted): {629-639}. Abstract
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Glassey, Jarka, Krist V. Gernaey, Christoph Clemens, Torsten W. Schulz, Rui Oliveira, Gerald Striedner, and Carl-Fredrik Mandenius. "{Process analytical technology (PAT) for biopharmaceuticals}." {BIOTECHNOLOGY JOURNAL}. {6} (Submitted): {369-377}. 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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Freitas, F., J. Pais, V. D. Alves, M. Carvalheira, N. Costa, R. Oliveira, and M. A. M. Reis. "{Conversion of Glycerol-rich Product (GRP) into Biopolymers}." {CLEAN TECHNOLOGY 2008: BIO ENERGY, RENEWABLES, GREEN BUILDING, SMART GRID, STORAGE, AND WATER}. Eds. M. {Laudon, B. Romanowicz, and DL} Laird. {Clean Technol & Sustainable Ind Org; Greenberg Traurig LLP; Jackson Walker LLP; IDA Ireland; Opportunity Houston; Alston & Bird LLP; K & L Gates; Buchanan Ingersoll & Rooney PC; Foley & Larder, LLP; Pacific Crest Securities; RockPort Capital Partners; Fi, Submitted. {552-553}. Abstract
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Isidro, Ines A., Ana R. Ferreira, Joao J. Clemente, Antonio E. Cunha, Joao M. L. Dias, and Rui Oliveira. "{Design of Pathway-Level Bioprocess Monitoring and Control Strategies Supported by Metabolic Networks}." {MEASUREMENT, MONITORING, MODELLING AND CONTROL OF BIOPROCESSES}. Eds. CF {Mandenius, and NJ} TitchenerHooker. Vol. {132}. {Advances in Biochemical Engineering-Biotechnology}, {132}. Submitted. {193-215}. Abstract
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Teixeira, A., A. Cunha, J. Clemente, P. M. Alves, M. J. T. Carrondo, and R. Oliveira. "{Dynamic modelling and optimisation of a mammalian cells process using hybrid grey-box systems}." {Adaptive and Natural Computing Algorithms}. Eds. B. {Ribeiro, RF Albrecht, A. Dobnikar, DW Pearson, and NC} Steele. {SPRINGER COMPUTER SCIENCE}. Submitted. {296-299}. Abstract
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