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)

Evolutionary programming as a platform for in silico metabolic engineering. - Kiran Raosaheb Patil; Isabel Rocha; Jochen Förster; Jens Nielsen (BMC Bioinform., 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)

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)

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)

Modelling Fed-Batch Fermentation Processes: An Approach Based on Artificial Neural Networks. - Eduardo Valente; 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)

A software tool for network topology analysis under a metabolic engineering perspective. - José P. Pinto; Isabel Rocha; Miguel Rocha 001 (BCB, 2010)

Metaheuristics for Strain Optimization Using Transcriptional Information Enriched Metabolic Models. - Paulo Vilaça; Paulo Maia; Isabel Rocha; Miguel Rocha 001 (EvoBIO, 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)

Enhancing Elementary Flux Modes Analysis Using Filtering Techniques in an Integrated Environment. - Paulo Maia; Marcellinus Pont; Jean-François Tomb; Isabel Rocha; Miguel Rocha 001 (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)

New insight into arrhythmia onset using HRV and BPV analysis. - Gabriela Postolache; Mario Oliveira; Isabel Rocha; Pedro Silva Girão; Octavian Postolache (EMBC, 2011)

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)

Highlighting Metabolic Strategies Using Network Analysis over Strain Optimization Results. - José Pedro Pinto; Isabel Rocha; Miguel Rocha 001 (PRIB, 2011)

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

A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/regulatory information. - Paulo Vilaça; Isabel Rocha; Miguel Rocha 001 (Biosyst., 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)

Computational Tools for Strain Optimization by Tuning the Optimal Level of Gene Expression. - Emanuel J. V. Gonçalves; Isabel Rocha; Miguel Rocha 001 (PACBB, 2012)

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)

An integrated computational environment for elementary modes analysis of biochemical networks. - Paulo Maia; Paulo Vilaça; Isabel Rocha; Marcellinus Pont; Jean-François Tomb; Miguel Rocha 001 (Int. J. Data Min. Bioinform., 2012)

Optimization Approaches for the In Silico Discovery of Optimal Targets for Gene Over/Underexpression. - Emanuel J. V. Gonçalves; Rui Pereira; Isabel Rocha; Miguel Rocha 001 (J. Comput. Biol., 2012)

Algorithms to infer metabolic flux ratios from fluxomics data. - Rafael Carreira; Miguel Rocha 001; Silas Granato Villas-Bôas; Isabel Rocha (BIBM, 2013)

Evolutionary computation for predicting optimal reaction knockouts and enzyme modulation strategies. - Pedro Evangelista; Miguel Rocha 001; Isabel Rocha (IEEE Congress on Evolutionary Computation, 2013)

An integrated framework for strain optimization. - Paulo Maia; Isabel Rocha; Miguel Rocha 001 (IEEE Congress on Evolutionary Computation, 2013)

Assignment of Novel Functions to Helicobacter pylori 26695's Genome. - Tiago Resende; Daniela M. Correia; Isabel Rocha (PACBB, 2013)

Re-annotation of the genome sequence of Helicobacter pylori 26695. - Tiago Resende; Daniela M. Correia; Miguel Rocha 001; Isabel Rocha (J. Integr. Bioinform., 2013)

Evaluating Pathway Enumeration Algorithms in Metabolic Engineering Case Studies. - Filipe Liu; Paulo Vilaça; Isabel Rocha; Miguel Rocha 001 (PACBB, 2014)

Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models. - José P. Faria; Ross A. Overbeek; Fangfang Xia; Miguel Rocha 001; Isabel Rocha; Christopher S. Henry (Briefings Bioinform., 2014)

A kinetic model for curcumin production in Escherichia coli. - Daniel Machado; Lígia R. Rodrigues; Isabel Rocha (Biosyst., 2014)

CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data. - Rafael Carreira; Pedro Evangelista; Paulo Maia; Paulo Vilaça; Marcellinus Pont; Jean-François Tomb; Isabel Rocha; Miguel Rocha 001 (BMC Syst. Biol., 2014)

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)

A Text Mining Approach for the Extraction of Kinetic Information from Literature. - Ana Alão Freitas; Hugo Costa; Miguel Rocha 001; Isabel Rocha (PACBB, 2015)

Development and application of efficient pathway enumeration algorithms for metabolic engineering applications. - Filipe Liu; Paulo Vilaça; Isabel Rocha; Miguel Rocha 001 (Comput. Methods Programs Biomed., 2015)

Extracting kinetic information from literature with KineticRE. - Ana Alão Freitas; Hugo Costa; Miguel Rocha 001; Isabel Rocha (J. Integr. Bioinform., 2015)

A Computation Tool for the Estimation of Biomass Composition from Genomic and Transcriptomic Information. - Sophia Santos; Isabel Rocha (PACBB, 2016)

Development of an Integrated Framework for Minimal Cut Set Enumeration in Constraint-Based Models. - Vítor Vieira; Paulo Maia; Isabel Rocha; Miguel Rocha 001 (PACBB, 2016)

Estimation of biomass composition from genomic and transcriptomic information. - Sophia Santos; Isabel Rocha (J. Integr. Bioinform., 2016)

Stoichiometric Representation of Gene-Protein-Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction. - Daniel Machado; Markus J. Herrgård; Isabel Rocha (PLoS Comput. Biol., 2016)

Identification of robust strain designs via tandem pFBA/LMOMA phenotype prediction. - Paulo Maia; Isabel Rocha; Miguel Rocha 001 (GECCO (Companion), 2017)

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)

Reconstruction of a genome-scale metabolic model for Actinobacillus succinogenes 130Z. - Bruno Pereira; Joana Miguel; Paulo Vilaça; Simão Soares; Isabel Rocha; Sónia Carneiro (BMC Syst. Biol., 2018)

Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes. - Joana C. Xavier; Kiran Raosaheb Patil; Isabel Rocha (PLoS Comput. Biol., 2018)

Concept Design of a New Portable Medical Device for Lymphedema Monitoring: A EIT Health ClinMed Summer School Project. - Jordi Escuder Tisaire; Elena Martín Rodrigo; Sofia Ribeiro; Mariachiara Ricci; Juan Sebastian Cuellar; Dimitrios I. Zeugolis; Yves Bayon; Isabel Rocha (HEALTHINF, 2019)

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)

Comparison of pathway analysis and constraint-based methods for cell factory design. - Vítor Vieira; Paulo Maia; Miguel Rocha 001; Isabel Rocha (BMC Bioinform., 2019)

Xtrace: Novel Bioresorbable Device for Patent Foramen Ovale Closure. - Sara Abu Ajamieh; Diana Mîndroc-Filimon; Irene Mozo; Isabel Rocha (BIODEVICES, 2020)

Threats and Opportunities for the Clinical Investigation of High-risk Medical Devices in the Context of the New European Regulations. - Lionel Pazart; Sylvia Pelayo; Thierry Chevallier; Gabriel Gruionu; Philippe Mabo; Yves Bayon; Frédéric Barbot; Thomas Lihoreau; Catherine Roussel; Nicos Maglaveras; Eirini Lekka; Hugo Alexandre Ferreira; et al. (BIODEVICES, 2021)

Inclusion of maintenance energy improves the intracellular flux predictions of CHO. - Diana Széliová; Jerneja Stor; Isabella Thiel; Marcus Weinguny; Michael Hanscho; Gabriele Lhota; Nicole Borth; Jürgen Zanghellini; David E. Ruckerbauer; Isabel Rocha (PLoS Comput. Biol., 2021)

The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber. - Emanuel Cunha; Miguel Silva; Inês Chaves; Hüseyin Demirci; Davide Lagoa; Diogo Lima; Miguel Rocha 001; Isabel Rocha; Oscar Dias (PLoS Comput. Biol., 2023)