Publications

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Book Chapter
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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Conference Paper
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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Oliveira, R., and R. Salcedo. "{Benchmark testing of simulated annealing, adaptive random search and genetic algorithms for the global optimization of bioprocesses}." {Adaptive and Natural Computing Algorithms}. Eds. B. {Ribeiro, RF Albrecht, A. Dobnikar, DW Pearson, and NC} Steele. {SPRINGER COMPUTER SCIENCE}. Submitted. {292-295}. 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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Ganjian, Amin, Jie Zhang, Joao M. L. Dias, and Rui Oliveira. "{Modelling of a Sequencing Batch Reactor for Producing Polyhydroxybutyrate with Mixed Microbial Culture Cultivation Process Using Neural Networks and Operation Regime Classification}." {ICHEAP-11: 11TH INTERNATIONAL CONFERENCE ON CHEMICAL AND PROCESS ENGINEERING, PTS 1-4}. Eds. S. {Pierucci, and JJ} Klemes. Vol. {32}. {Chemical Engineering Transactions}, {32}. Submitted. {1261-1266}. Abstract
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Journal Article
Ferreira, A. R., F. Ataide, M. von Stosch, J. M. L. Dias, J. J. Clemente, A. E. Cunha, and R. Oliveira. "{Application of adaptive DO-stat feeding control to Pichia pastoris X33 cultures expressing a single chain antibody fragment (scFv)}." {BIOPROCESS AND BIOSYSTEMS ENGINEERING}. {35} (Submitted): {1603-1614}. 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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Teixeira, Ana P., Joao M. L. Dias, Nuno Carinhas, Marcos Sousa, Joao J. Clemente, Antonio E. Cunha, Moritz von Stosch, Paula M. Alves, Manuel J. T. Carrondo, and Rui Oliveira. "{Cell functional enviromics: Unravelling the function of environmental factors}." {BMC SYSTEMS BIOLOGY}. {5} (Submitted). Abstract
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Pardelha, Filipa, Maria G. E. Albuquerque, Maria A. M. Reis, Rui Oliveira, and Joao M. L. Dias. "{Dynamic metabolic modelling of volatile fatty acids conversion to polyhydroxyalkanoates by a mixed microbial culture}." {NEW BIOTECHNOLOGY}. {31} (Submitted): {335-344}. 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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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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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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von Stosch, Moritz, Steven Davy, Kjell Francois, Vytautas Galvanauskas, Jan-Martijn Hamelink, Andreas Luebbert, Martin Mayer, Rui Oliveira, Ronan O'Kennedy, Paul Rice, and Jarka Glassey. "{Hybrid modeling for quality by design and PAT - benefits and challenges of applications in biopharmaceutical industry}." {BIOTECHNOLOGY JOURNAL}. {9} (Submitted): {719-726}. 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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Teixeira, Ana P., Carla A. M. Portugal, Nuno Carinhas, Joao M. L. Dias, Joao P. Crespo, Paula M. Alves, M. J. T. Carrondo, and Rui Oliveira. "{In Situ 2D Fluorometry and Chemometric Monitoring of Mammalian Cell Cultures}." {BIOTECHNOLOGY AND BIOENGINEERING}. {102} (Submitted): {1098-1106}. Abstract
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Teixeira, A. P., J. M. L. Dias, P. M. Alves, M. J. T. Carrondo, and R. Oliveira. "{Macroscopic control of intracellular fluxes: application to mammalian cell cultures}." {NEW BIOTECHNOLOGY}. {25} (Submitted): {S332}. Abstract
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Dias, J. M. L., L. S. Serafim, P. C. Lemos, M. A. M. Reis, and R. Oliveira. "{Mathematical modelling of a mixed culture cultivation process for the production of polyhydroxybutyrate}." {BIOTECHNOLOGY AND BIOENGINEERING}. {92} (Submitted): {209-222}. Abstract
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Pardelha, F., M. G. E. Albuquerque, M. A. M. Reis, R. Oliveira, and J. M. L. Dias. "{Metabolic modeling of polyhydroxyalkanoates (PHA) production from complex mixtures of competing volatile fatty acids (VFA) by mixed microbial cultures (MMC)}." {JOURNAL OF BIOTECHNOLOGY}. {150} (Submitted): {S565}. Abstract
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Dias, Joao M. L., Adrian Oehmen, Luisa S. Serafim, Paulo C. Lemos, Maria A. M. Reis, and Rui Oliveira. "{Metabolic modelling of polyhydroxyalkanoate copolymers production by mixed microbial cultures}." {BMC SYSTEMS BIOLOGY}. {2} (Submitted). Abstract
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Dias, Joao M. L., Rui Oliveira, and Michael Semmens. "{Modeling NOM removal by softening in a surface water treatment plant}." {WATER SCIENCE AND TECHNOLOGY}. {67} (Submitted): {1008-1016}. Abstract
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Dias, Joao M. L., Filipa Pardelha, Mario Eusebio, Maria A. M. Reis, and Rui Oliveira. "{On-Line Adaptive Metabolic Flux Analysis: Application to PHB Production by Mixed Microbial Cultures}." {BIOTECHNOLOGY PROGRESS}. {25} (Submitted): {390-398}. Abstract
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Dias, Joao M. L., Filipa Pardelha, Mario Eusebio, Maria A. M. Reis, and Rui Oliveira. "{On-line monitoring of PHB production by mixed microbial cultures using respirometry, titrimetry and chemometric modelling}." {PROCESS BIOCHEMISTRY}. {44} (Submitted): {419-427}. Abstract
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Ferreira, Ana R., Joao M. L. Dias, Ana P. Teixeira, Nuno Carinhas, Rui M. C. Portela, Ines A. Isidro, Moritz von Stosch, and Rui Oliveira. "{Projection to latent pathways (PLP): a constrained projection to latent variables (PLS) method for elementary flux modes discrimination}." {BMC SYSTEMS BIOLOGY}. {5} (Submitted). Abstract
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Guerreiro, L., P. M. Pereira, I. M. Fonseca, R. M. Martin-Aranda, A. M. Ramos, J. M. L. Dias, R. Oliveira, and J. Vital. "{PVA embedded hydrotalcite membranes as basic catalysts for biodiesel synthesis by soybean oil methanolysis}." {CATALYSIS TODAY}. {156} (Submitted): {191-197}. Abstract
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Dias, Joao M. L., Paulo C. Lemos, Luisa S. Serafim, Cristina Oliveira, Marta Eiroa, Maria G. E. Albuquerque, Ana M. Ramos, Rui Oliveira, and Maria A. M. Reis. "{Recent advances in polyhydroxyalkanoate production by mixed aerobic cultures: From the substrate to the final product}." {MACROMOLECULAR BIOSCIENCE}. {6} (Submitted): {885-906}. Abstract
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