Can spreadsheet solvers solve demanding optimization problems? - Eugénio C. Ferreira; Romualdo Salcedo (Comput. Appl. Eng. Educ., 2001)

Evolutionary Algorithms for Optimal Control in Fed-Batch Fermentation Processes. - Miguel Rocha 001; José Neves 001; Isabel Rocha; Eugénio C. Ferreira (EvoWorkshops, 2004)

A new representation in evolutionary algorithms for the optimization of bioprocesses. - Miguel Rocha 001; Isabel Rocha; Eugénio C. Ferreira (Congress on Evolutionary Computation, 2005)

NEOS Server Usage in Wastewater Treatment Cost Minimization. - Isabel A. Espírito-Santo; Edite M. G. P. Fernandes; M. Madalena Araújo; Eugénio C. Ferreira (ICCSA (4), 2005)

A Comparison of Algorithms for the Optimization of Fermentation Processes. - Rui Mendes 001; Isabel Rocha; Eugénio C. Ferreira; Miguel Rocha 001 (IEEE Congress on Evolutionary Computation, 2006)

Image analysis methodology to study the evolution of chromium penetration in chromium tannage. - António Luís Amaral; Manuel Mota; Eugénio C. Ferreira; A. Crispim (CompIMAGE, 2006)

Optimization of Bacterial Strains with Variable-Sized Evolutionary Algorithms. - Miguel Rocha 001; José P. Pinto; Isabel Rocha; Eugénio C. Ferreira (CIBCB, 2007)

Evaluating Simulated Annealing Algorithms in the Optimization of Bacterial Strains. - Miguel Rocha 001; Rui Mendes 001; Paulo Maia; José P. Pinto; Isabel Rocha; Eugénio C. Ferreira (EPIA Workshops, 2007)

Evaluating Evolutionary Algorithms and Differential Evolution for the Online Optimization of Fermentation Processes. - Miguel Rocha 001; José P. Pinto; Isabel Rocha; Eugénio C. Ferreira (EvoBIO, 2007)

Exact Fuzzy Observer for a Baker's Yeast Fed-Batch Fermentation Process. - Enrique J. Herrera-López; Bernardino Castillo; Jesús Ramírez; Eugénio C. Ferreira (FUZZ-IEEE, 2007)

Takagi-sugeno multiple-model controller for a continuous baking yeast fermentation process. - Enrique J. Herrera-López; Bernardino Castillo; Jesús Ramírez; Eugénio C. Ferreira (ICINCO-ICSO, 2007)

A framework for the development of Biomedical Text Mining software tools. - Anália Lourenço; Rafael Carreira; Sónia Carneiro; Paulo Maia; Daniel Glez-Peña; Florentino Fdez-Riverola; Eugénio C. Ferreira; Isabel Rocha; Miguel Rocha 001 (BIBE, 2008)

Evaluating evolutionary multiobjective algorithms for the in silico optimization of mutant strains. - Paulo Maia; Isabel Rocha; Eugénio C. Ferreira; Miguel Rocha 001 (BIBE, 2008)

A framework for the integrated analysis of metabolic and regulatory networks. - Rui Mendes 001; Anália Lourenço; Sónia Carneiro; Miguel Rocha 001; Isabel Rocha; Eugénio C. Ferreira (BIBE, 2008)

Data Integration Issues in the Reconstruction of the Genome-Scale Metabolic Model of Zymomonas Mobillis. - José P. Pinto; Oscar Dias; Anália Lourenço; Sónia Carneiro; Eugénio C. Ferreira; Isabel Rocha; Miguel Rocha 001 (IWPACBB, 2008)

Natural computation meta-heuristics for the in silico optimization of microbial strains. - Miguel Rocha 001; Paulo Maia; Rui Mendes 001; José P. Pinto; Eugénio C. Ferreira; Jens Nielsen; Kiran Raosaheb Patil; Isabel Rocha (BMC Bioinform., 2008)

Evolutionary Approaches for Strain Optimization Using Dynamic Models under a Metabolic Engineering Perspective. - Pedro Evangelista; Isabel Rocha; Eugénio C. Ferreira; Miguel Rocha 001 (EvoBIO, 2009)

Large Scale Dynamic Model Reconstruction for the Central Carbon Metabolism of Escherichia coli . - Rafael S. Costa; Daniel Machado; Isabel Rocha; Eugénio C. Ferreira (IWANN (2), 2009)

A Software Tool for the Simulation and Optimization of Dynamic Metabolic Models. - Pedro Evangelista; Isabel Rocha; Eugénio C. Ferreira; Miguel Rocha 001 (IWANN (2), 2009)

Biomedical Text Mining Applied to Document Retrieval and Semantic Indexing. - Anália Lourenço; Sónia Carneiro; Eugénio C. Ferreira; Rafael Carreira; Luis M. Rocha; Daniel Glez-Peña; José Ramón Méndez 001; Florentino Fdez-Riverola; Fernando Díaz 001; Isabel Rocha; Miguel Rocha 001 (IWANN (2), 2009)

A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems. - Daniel Machado; Rafael S. Costa; Miguel Rocha 001; Isabel Rocha; Bruce Tidor; Eugénio C. Ferreira (IWANN (2), 2009)

@Note: A workbench for Biomedical Text Mining. - Anália Lourenço; Rafael Carreira; Sónia Carneiro; Paulo Maia; Daniel Glez-Peña; Florentino Fdez-Riverola; Eugénio C. Ferreira; Isabel Rocha; Miguel Rocha 001 (J. Biomed. Informatics, 2009)

Model Transformation of Metabolic Networks using a Petri Net Based Framework. - Daniel Machado; Rafael S. Costa; Miguel Rocha 001; Isabel Rocha; Bruce Tidor; Eugénio C. Ferreira (ACSD/Petri Nets Workshops, 2010)

Applying a Metabolic Footprinting Approach to Characterize the Impact of the Recombinant Protein Production in Escherichia coli. - Sónia Carneiro; Silas Granato Villas-Bôas; Isabel Rocha; Eugénio C. Ferreira (IWPACBB, 2010)

Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis-Menten and approximate kinetic equations. - Rafael S. Costa; Daniel Machado; Isabel Rocha; Eugénio C. Ferreira (Biosyst., 2010)

OptFlux: an open-source software platform for in silico metabolic engineering. - Isabel Rocha; Paulo Maia; Pedro Evangelista; Paulo Vilaça; Simão Soares; José P. Pinto; Jens Nielsen; Kiran Raosaheb Patil; Eugénio C. Ferreira; Miguel Rocha 001 (BMC Syst. Biol., 2010)

BioDR: Semantic indexing networks for biomedical document retrieval. - Anália Lourenço; Rafael Carreira; Daniel Glez-Peña; José Ramón Méndez 001; Sónia Carneiro; Luis Mateus Rocha; Fernando Díaz 001; Eugénio C. Ferreira; Isabel Rocha; Florentino Fdez-Riverola; Miguel Rocha 001 (Expert Syst. Appl., 2010)

A Systematic Modeling Approach to Elucidate the Triggering of the Stringent Response in Recombinant E. coli Systems. - Sónia Carneiro; Eugénio C. Ferreira; Isabel Rocha (PACBB, 2011)

Interpreting the Regulatory Interplay in E. coli Metabolic Pathways. - Anália Lourenço; Sónia Carneiro; José P. Pinto; Miguel Rocha 001; Eugénio C. Ferreira; Isabel Rocha (PACBB, 2011)

Challenges in integrating Escherichia coli molecular biology data. - Anália Lourenço; Sónia Carneiro; Miguel Rocha 001; Eugénio C. Ferreira; Isabel Rocha (Briefings Bioinform., 2011)

Semantic annotation of biological concepts interplaying microbial cellular responses. - Rafael Carreira; Sónia Carneiro; Rui Pereira; Miguel Rocha 001; Isabel Rocha; Eugénio C. Ferreira; Anália Lourenço (BMC Bioinform., 2011)

A Study of the Short and Long-term Regulation of E. coli Metabolic Pathways. - Anália Lourenço; Sónia Carneiro; José P. Pinto; Miguel Rocha 001; Eugénio C. Ferreira; Isabel Rocha (J. Integr. Bioinform., 2011)

Random sampling of elementary flux modes in large-scale metabolic networks. - Daniel Machado; Zita Soons; Kiran Raosaheb Patil; Eugénio C. Ferreira; Isabel Rocha (Bioinform., 2012)

Image Analysis for Automatic Characterization of Polyhydroxyalcanoates Granules. - Daniela P. Mesquita; Gianluca Selvaggio; Jorge R. Cunha; Cristiano S. Leal; António Luís Amaral; Eugénio C. Ferreira (ICIAR, 2013)

Optimization of fed-batch fermentation processes with bio-inspired algorithms. - Miguel Rocha 001; Rui Mendes 001; Orlando Rocha; Isabel Rocha; Eugénio C. Ferreira (Expert Syst. Appl., 2014)

Genome-Wide Semi-Automated Annotation of Transporter Systems. - Oscar Dias; Daniel Gomes; Paulo Vilaça; João G. R. Cardoso; Miguel Rocha 001; Eugénio C. Ferreira; Isabel Rocha (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

SamPler - a novel method for selecting parameters for gene functional annotation routines. - Fernando Cruz; Davide Lagoa; João Mendes; Isabel Rocha; Eugénio C. Ferreira; Miguel Rocha 001; Oscar Dias (BMC Bioinform., 2019)

Discrimination of Camellia japonica cultivars and chemometric models: An interlaboratory study. - Clara Sousa; Cristina Quintelas; Catarina Augusto; Eugénio C. Ferreira; Ricardo N. M. J. Páscoa (Comput. Electron. Agric., 2019)

A kinetic model of the central carbon metabolism for acrylic acid production in Escherichia coli. - Alexandre Oliveira; Joana Rodrigues; Eugénio Campos Ferreira; Lígia R. Rodrigues; Oscar Dias (PLoS Comput. Biol., 2021)

BioISO: An Objective-Oriented Application for Assisting the Curation of Genome-Scale Metabolic Models. - Fernando Cruz; João Capela; Eugénio C. Ferreira; Miguel Rocha 001; Oscar Dias (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)