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ORCIDEugénio C. Ferreira
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Journal Articles
- 2024
[j16]Fernando Cruz
, João Capela, Eugénio C. Ferreira, Miguel Rocha, Oscar Días:
BioISO: An Objective-Oriented Application for Assisting the Curation of Genome-Scale Metabolic Models. IEEE ACM Trans. Comput. Biol. Bioinform. 21(2): 215-226 (2024)- 2021
- [j15]Alexandre Oliveira, Joana Rodrigues, Eugénio Campos Ferreira, Lígia R. Rodrigues, Oscar Días:
A kinetic model of the central carbon metabolism for acrylic acid production in Escherichia coli. PLoS Comput. Biol. 17(3) (2021) - 2019
- [j14]Fernando Cruz, Davide Lagoa, João Mendes, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha, Oscar Días:
SamPler - a novel method for selecting parameters for gene functional annotation routines. BMC Bioinform. 20(1): 454:1-454:11 (2019) - [j13]Clara Sousa, Cristina Quintelas, Catarina Augusto, Eugénio C. Ferreira, Ricardo N. M. J. Páscoa:
Discrimination of Camellia japonica cultivars and chemometric models: An interlaboratory study. Comput. Electron. Agric. 159: 28-33 (2019) - 2017
- [j12]Oscar Días, Daniel Gomes, Paulo Vilaça, João G. R. Cardoso, Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha:
Genome-Wide Semi-Automated Annotation of Transporter Systems. IEEE ACM Trans. Comput. Biol. Bioinform. 14(2): 443-456 (2017) - 2014
- [j11]Miguel Rocha, Rui Mendes, Orlando Rocha, Isabel Rocha, Eugénio C. Ferreira:
Optimization of fed-batch fermentation processes with bio-inspired algorithms. Expert Syst. Appl. 41(5): 2186-2195 (2014) - 2012
- [j10]Daniel Machado, Zita Soons, Kiran Raosaheb Patil, Eugénio C. Ferreira, Isabel Rocha:
Random sampling of elementary flux modes in large-scale metabolic networks. Bioinform. 28(18): 515-521 (2012) - 2011
- [j9]Anália Lourenço, Sónia Carneiro, Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha:
Challenges in integrating Escherichia coli molecular biology data. Briefings Bioinform. 12(2): 91-103 (2011) - [j8]Rafael Carreira, Sónia Carneiro, Rui Pereira, Miguel Rocha, Isabel Rocha, Eugénio C. Ferreira, Anália Lourenço:
Semantic annotation of biological concepts interplaying microbial cellular responses. BMC Bioinform. 12: 460 (2011) - [j7]Anália Lourenço, Sónia Carneiro, José P. Pinto, Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha:
A Study of the Short and Long-term Regulation of E. coli Metabolic Pathways. J. Integr. Bioinform. 8(3) (2011) - 2010
- [j6]Rafael S. Costa, Daniel Machado, Isabel Rocha, Eugénio C. Ferreira:
Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis-Menten and approximate kinetic equations. Biosyst. 100(2): 150-157 (2010) - [j5]Isabel Rocha, Paulo Maia, Pedro Evangelista, Paulo Vilaça, Simão Soares, José P. Pinto, Jens Nielsen, Kiran Raosaheb Patil, Eugénio C. Ferreira, Miguel Rocha:
OptFlux: an open-source software platform for in silico metabolic engineering. BMC Syst. Biol. 4: 45 (2010) - [j4]Anália Lourenço, Rafael Carreira, Daniel Glez-Peña, José Ramón Méndez, Sónia Carneiro, Luis Mateus Rocha, Fernando Díaz, Eugénio C. Ferreira, Isabel Rocha, Florentino Fdez-Riverola, Miguel Rocha:
BioDR: Semantic indexing networks for biomedical document retrieval. Expert Syst. Appl. 37(4): 3444-3453 (2010) - 2009
- [j3]Anália Lourenço, Rafael Carreira, Sónia Carneiro, Paulo Maia, Daniel Glez-Peña, Florentino Fdez-Riverola, Eugénio C. Ferreira, Isabel Rocha, Miguel Rocha:
@Note: A workbench for Biomedical Text Mining. J. Biomed. Informatics 42(4): 710-720 (2009) - 2008
- [j2]Miguel Rocha, Paulo Maia, Rui Mendes, José P. Pinto, Eugénio C. Ferreira, Jens Nielsen, Kiran Raosaheb Patil, Isabel Rocha:
Natural computation meta-heuristics for the in silico optimization of microbial strains. BMC Bioinform. 9 (2008) - 2001
- [j1]Eugénio C. Ferreira, Romualdo Salcedo:
Can spreadsheet solvers solve demanding optimization problems? Comput. Appl. Eng. Educ. 9(1): 49-56 (2001)
Conference and Workshop Papers
- 2013
- [c24]Daniela P. Mesquita, Gianluca Selvaggio, Jorge R. Cunha, Cristiano S. Leal, António Luís Amaral, Eugénio C. Ferreira:
Image Analysis for Automatic Characterization of Polyhydroxyalcanoates Granules. ICIAR 2013: 790-797 - 2011
- [c23]Anália Lourenço, Sónia Carneiro, José P. Pinto, Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha:
Interpreting the Regulatory Interplay in E. coli Metabolic Pathways. PACBB 2011: 303-312 - [c22]Sónia Carneiro, Eugénio C. Ferreira, Isabel Rocha:
A Systematic Modeling Approach to Elucidate the Triggering of the Stringent Response in Recombinant E. coli Systems. PACBB 2011: 313-320 - 2010
- [c21]Daniel Machado, Rafael S. Costa, Miguel Rocha, Isabel Rocha, Bruce Tidor, Eugénio C. Ferreira:
Model Transformation of Metabolic Networks using a Petri Net Based Framework. ACSD/Petri Nets Workshops 2010: 103-117 - [c20]Sónia Carneiro, Silas Granato Villas-Bôas, Isabel Rocha, Eugénio C. Ferreira:
Applying a Metabolic Footprinting Approach to Characterize the Impact of the Recombinant Protein Production in Escherichia coli. IWPACBB 2010: 193-200 - 2009
- [c19]Pedro Evangelista, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha:
Evolutionary Approaches for Strain Optimization Using Dynamic Models under a Metabolic Engineering Perspective. EvoBIO 2009: 140-151 - [c18]Anália Lourenço, Sónia Carneiro, Eugénio C. Ferreira, Rafael Carreira, Luis M. Rocha, Daniel Glez-Peña, José Ramón Méndez, Florentino Fdez-Riverola, Fernando Díaz, Isabel Rocha, Miguel Rocha:
Biomedical Text Mining Applied to Document Retrieval and Semantic Indexing. IWANN (2) 2009: 954-963 - [c17]Daniel Machado, Rafael S. Costa, Miguel Rocha, Isabel Rocha, Bruce Tidor, Eugénio C. Ferreira:
A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems. IWANN (2) 2009: 1063-1070 - [c16]Pedro Evangelista, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha:
A Software Tool for the Simulation and Optimization of Dynamic Metabolic Models. IWANN (2) 2009: 1071-1078 - [c15]Rafael S. Costa, Daniel Machado, Isabel Rocha, Eugénio C. Ferreira:
Large Scale Dynamic Model Reconstruction for the Central Carbon Metabolism of Escherichia coli . IWANN (2) 2009: 1079-1083 - 2008
- [c14]Anália Lourenço, Rafael Carreira, Sónia Carneiro, Paulo Maia, Daniel Glez-Peña, Florentino Fdez-Riverola, Eugénio C. Ferreira, Isabel Rocha, Miguel Rocha:
A framework for the development of Biomedical Text Mining software tools. BIBE 2008: 1-6 - [c13]Paulo Maia, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha:
Evaluating evolutionary multiobjective algorithms for the in silico optimization of mutant strains. BIBE 2008: 1-6 - [c12]Rui Mendes, Anália Lourenço, Sónia Carneiro, Miguel Rocha, Isabel Rocha, Eugénio C. Ferreira:
A framework for the integrated analysis of metabolic and regulatory networks. BIBE 2008: 1-6 - [c11]José P. Pinto, Oscar Días, Anália Lourenço, Sónia Carneiro, Eugénio C. Ferreira, Isabel Rocha, Miguel Rocha:
Data Integration Issues in the Reconstruction of the Genome-Scale Metabolic Model of Zymomonas Mobillis. IWPACBB 2008: 92-101 - 2007
- [c10]Miguel Rocha, José P. Pinto, Isabel Rocha, Eugénio C. Ferreira:
Optimization of Bacterial Strains with Variable-Sized Evolutionary Algorithms. CIBCB 2007: 331-337 - [c9]Miguel Rocha, Rui Mendes, Paulo Maia, José P. Pinto, Isabel Rocha, Eugénio C. Ferreira:
Evaluating Simulated Annealing Algorithms in the Optimization of Bacterial Strains. EPIA Workshops 2007: 473-484 - [c8]Miguel Rocha, José P. Pinto, Isabel Rocha, Eugénio C. Ferreira:
Evaluating Evolutionary Algorithms and Differential Evolution for the Online Optimization of Fermentation Processes. EvoBIO 2007: 236-246 - [c7]Enrique J. Herrera-López, Bernardino Castillo, Jesús Ramírez, Eugénio C. Ferreira:
Exact Fuzzy Observer for a Baker's Yeast Fed-Batch Fermentation Process. FUZZ-IEEE 2007: 1-6 - [c6]Enrique J. Herrera-López, Bernardino Castillo, Jesús Ramírez, Eugénio C. Ferreira:
Takagi-sugeno multiple-model controller for a continuous baking yeast fermentation process. ICINCO-ICSO 2007: 436-439 - 2006
- [c5]Rui Mendes, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha:
A Comparison of Algorithms for the Optimization of Fermentation Processes. IEEE Congress on Evolutionary Computation 2006: 2018-2025 - [c4]António Luís Amaral, Manuel Mota, Eugénio C. Ferreira, A. Crispim:
Image analysis methodology to study the evolution of chromium penetration in chromium tannage. CompIMAGE 2006: 53-56 - 2005
- [c3]Miguel Rocha, Isabel Rocha, Eugénio C. Ferreira:
A new representation in evolutionary algorithms for the optimization of bioprocesses. Congress on Evolutionary Computation 2005: 484-490 - [c2]Isabel A. Espírito-Santo, Edite M. G. P. Fernandes, M. Madalena Araújo, Eugénio C. Ferreira:
NEOS Server Usage in Wastewater Treatment Cost Minimization. ICCSA (4) 2005: 632-641 - 2004
- [c1]Miguel Rocha, José Neves, Isabel Rocha, Eugénio C. Ferreira:
Evolutionary Algorithms for Optimal Control in Fed-Batch Fermentation Processes. EvoWorkshops 2004: 84-93
Coauthor Index
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