Isabel Rocha

According to our database, Isabel Rocha authored at least 67 papers between 2004 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2023

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, Isabel Rocha, Oscar Días

PLoS Comput. Biol., 2023

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

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, Isabel Rocha, Liesbet Geris, C. Lavet

Proceedings of the 14th International Joint Conference on Biomedical Engineering Systems and Technologies, 2021

2020

Xtrace: Novel Bioresorbable Device for Patent Foramen Ovale Closure.

Sara Abu Ajamieh, Diana Mîndroc-Filimon, Irene Mozo, Isabel Rocha

Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2020), 2020

2019

Comparison of pathway analysis and constraint-based methods for cell factory design.

Vítor Vieira, Paulo Maia, Miguel Rocha, Isabel Rocha

BMC Bioinform., 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, Oscar Días

BMC Bioinform., 2019

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

Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019), 2019

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

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

2017

Genome-Wide Semi-Automated Annotation of Transporter Systems.

Oscar Días, Daniel Gomes, Paulo Vilaça, João G. R. Cardoso, Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha

IEEE ACM Trans. Comput. Biol. Bioinform., 2017

Identification of robust strain designs via tandem pFBA/LMOMA phenotype prediction.

Paulo Maia, Isabel Rocha, Miguel Rocha

Proceedings of the Genetic and Evolutionary Computation Conference, 2017

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

Estimation of biomass composition from genomic and transcriptomic information.

Sophia Santos, Isabel Rocha

J. Integr. Bioinform., 2016

Development of an Integrated Framework for Minimal Cut Set Enumeration in Constraint-Based Models.

Vítor Vieira, Paulo Maia, Isabel Rocha, Miguel Rocha

Proceedings of the 10th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2016

A Computation Tool for the Estimation of Biomass Composition from Genomic and Transcriptomic Information.

Sophia Santos, Isabel Rocha

Proceedings of the 10th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2016

2015

Extracting kinetic information from literature with KineticRE.

Ana Alão Freitas, Hugo Costa, Miguel Rocha, Isabel Rocha

J. Integr. Bioinform., 2015

Development and application of efficient pathway enumeration algorithms for metabolic engineering applications.

Filipe Liu, Paulo Vilaça, Isabel Rocha, Miguel Rocha

Comput. Methods Programs Biomed., 2015

A Text Mining Approach for the Extraction of Kinetic Information from Literature.

Ana Alão Freitas, Hugo Costa, Miguel Rocha, Isabel Rocha

Proceedings of the 9th International Conference on Practical Applications of Computational Biology and Bioinformatics, 2015

2014

Optimization of fed-batch fermentation processes with bio-inspired algorithms.

Miguel Rocha, Rui Mendes, Orlando Rocha, Isabel Rocha, Eugénio C. Ferreira

Expert Syst. Appl., 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

BMC Syst. Biol., 2014

A kinetic model for curcumin production in Escherichia coli.

Daniel Machado, Lígia R. Rodrigues, Isabel Rocha

Biosyst., 2014

Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models.

José P. Faria, Ross A. Overbeek, Fangfang Xia, Miguel Rocha, Isabel Rocha, Christopher S. Henry

Briefings Bioinform., 2014

Evaluating Pathway Enumeration Algorithms in Metabolic Engineering Case Studies.

Filipe Liu, Paulo Vilaça, Isabel Rocha, Miguel Rocha

Proceedings of the 8th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2014

2013

Re-annotation of the genome sequence of Helicobacter pylori 26695.

Tiago Resende, Daniela M. Correia, Miguel Rocha, Isabel Rocha

J. Integr. Bioinform., 2013

Assignment of Novel Functions to Helicobacter pylori 26695's Genome.

Tiago Resende, Daniela M. Correia, Isabel Rocha

Proceedings of the 7th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2013

An integrated framework for strain optimization.

Paulo Maia, Isabel Rocha, Miguel Rocha

Proceedings of the IEEE Congress on Evolutionary Computation, 2013

Evolutionary computation for predicting optimal reaction knockouts and enzyme modulation strategies.

Pedro Evangelista, Miguel Rocha, Isabel Rocha

Proceedings of the IEEE Congress on Evolutionary Computation, 2013

Algorithms to infer metabolic flux ratios from fluxomics data.

Rafael Carreira, Miguel Rocha, Silas Granato Villas-Bôas, Isabel Rocha

Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013

2012

Optimization Approaches for the <i>In Silico</i> Discovery of Optimal Targets for Gene Over/Underexpression.

Emanuel J. V. Gonçalves, Rui Pereira, Isabel Rocha, Miguel Rocha

J. Comput. Biol., 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

Int. J. Data Min. Bioinform., 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

Computational Tools for Strain Optimization by Tuning the Optimal Level of Gene Expression.

Emanuel J. V. Gonçalves, Isabel Rocha, Miguel Rocha

Proceedings of the 6th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2012

2011

A Study of the Short and Long-term Regulation of E. coli Metabolic Pathways.

Anália Lourenço, Sónia Carneiro, José P. Pinto, Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha

J. Integr. Bioinform., 2011

Semantic annotation of biological concepts interplaying microbial cellular responses.

Rafael Carreira, Sónia Carneiro, Rui Pereira, Miguel Rocha, Isabel Rocha, Eugénio C. Ferreira, Anália Lourenço

BMC Bioinform., 2011

A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/regulatory information.

Paulo Vilaça, Isabel Rocha, Miguel Rocha

Biosyst., 2011

Challenges in integrating <i>Escherichia coli</i> molecular biology data.

Anália Lourenço, Sónia Carneiro, Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha

Briefings Bioinform., 2011

Highlighting Metabolic Strategies Using Network Analysis over Strain Optimization Results.

José Pedro Pinto, Isabel Rocha, Miguel Rocha

Proceedings of the Pattern Recognition in Bioinformatics, 2011

Interpreting the Regulatory Interplay in <i>E. coli</i> Metabolic Pathways.

Anália Lourenço, Sónia Carneiro, José P. Pinto, Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha

Proceedings of the 5th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2011

A Systematic Modeling Approach to Elucidate the Triggering of the Stringent Response in Recombinant <i>E. coli</i> Systems.

Sónia Carneiro, Eugénio C. Ferreira, Isabel Rocha

Proceedings of the 5th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2011

New insight into arrhythmia onset using HRV and BPV analysis.

Gabriela Postolache, Mario Oliveira, Isabel Rocha, Pedro Silva Girão, Octavian Postolache

Proceedings of the 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2011

2010

BioDR: Semantic indexing networks for biomedical document retrieval.

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

Expert Syst. Appl., 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

BMC Syst. Biol., 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

Enhancing Elementary Flux Modes Analysis Using Filtering Techniques in an Integrated Environment.

Paulo Maia, Marcellinus Pont, Jean-François Tomb, Isabel Rocha, Miguel Rocha

Proceedings of the Advances in Bioinformatics, 2010

Applying a Metabolic Footprinting Approach to Characterize the Impact of the Recombinant Protein Production in <i>Escherichia coli</i>.

Sónia Carneiro, Silas Granato Villas-Bôas, Isabel Rocha, Eugénio C. Ferreira

Proceedings of the Advances in Bioinformatics, 2010

Metaheuristics for Strain Optimization Using Transcriptional Information Enriched Metabolic Models.

Paulo Vilaça, Paulo Maia, Isabel Rocha, Miguel Rocha

Proceedings of the Evolutionary Computation, 2010

A software tool for network topology analysis under a metabolic engineering perspective.

José P. Pinto, Isabel Rocha, Miguel Rocha

Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, 2010

Model Transformation of Metabolic Networks using a Petri Net Based Framework.

Daniel Machado, Rafael S. Costa, Miguel Rocha, Isabel Rocha, Bruce Tidor, Eugénio C. Ferreira

Proceedings of the Workshops of the 31st International Conference on Application and Theory of Petri Nets and Other Models of Concurrency (PETRI NETS 2010) and of the 10th International Conference on Application of Concurrency to System Design (ACSD 2010), 2010

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

J. Biomed. Informatics, 2009

A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems.

Daniel Machado, Rafael S. Costa, Miguel Rocha, Isabel Rocha, Bruce Tidor, Eugénio C. Ferreira

Proceedings of the Distributed Computing, 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, Florentino Fdez-Riverola, Fernando Díaz, Isabel Rocha, Miguel Rocha

Proceedings of the Distributed Computing, 2009

A Software Tool for the Simulation and Optimization of Dynamic Metabolic Models.

Pedro Evangelista, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha

Proceedings of the Distributed Computing, 2009

Large Scale Dynamic Model Reconstruction for the Central Carbon Metabolism of Escherichia coli .

Rafael S. Costa, Daniel Machado, Isabel Rocha, Eugénio C. Ferreira

Proceedings of the Distributed Computing, 2009

Evolutionary Approaches for Strain Optimization Using Dynamic Models under a Metabolic Engineering Perspective.

Pedro Evangelista, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha

Proceedings of the Evolutionary Computation, 2009

2008

Natural computation meta-heuristics for the in silico optimization of microbial strains.

Miguel Rocha, Paulo Maia, Rui Mendes, José P. Pinto, Eugénio C. Ferreira, Jens Nielsen, Kiran Raosaheb Patil, Isabel Rocha

BMC Bioinform., 2008

Modelling Fed-Batch Fermentation Processes: An Approach Based on Artificial Neural Networks.

Eduardo Valente, Isabel Rocha, Miguel Rocha

Proceedings of the 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics, 2008

Data Integration Issues in the Reconstruction of the Genome-Scale Metabolic Model of Zymomonas Mobillis.

José P. Pinto, Oscar Días, Anália Lourenço, Sónia Carneiro, Eugénio C. Ferreira, Isabel Rocha, Miguel Rocha

Proceedings of the 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics, 2008

A framework for the integrated analysis of metabolic and regulatory networks.

Rui Mendes, Anália Lourenço, Sónia Carneiro, Miguel Rocha, Isabel Rocha, Eugénio C. Ferreira

Proceedings of the 8th IEEE International Conference on Bioinformatics and Bioengineering, 2008

Evaluating evolutionary multiobjective algorithms for the in silico optimization of mutant strains.

Paulo Maia, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha

Proceedings of the 8th IEEE International Conference on Bioinformatics and Bioengineering, 2008

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

Proceedings of the 8th IEEE International Conference on Bioinformatics and Bioengineering, 2008

2007

Evaluating Evolutionary Algorithms and Differential Evolution for the Online Optimization of Fermentation Processes.

Miguel Rocha, José P. Pinto, Isabel Rocha, Eugénio C. Ferreira

Proceedings of the Evolutionary Computation, 2007

Evaluating Simulated Annealing Algorithms in the Optimization of Bacterial Strains.

Miguel Rocha, Rui Mendes, Paulo Maia, José P. Pinto, Isabel Rocha, Eugénio C. Ferreira

Proceedings of the Progress in Artificial Intelligence, 2007

Optimization of Bacterial Strains with Variable-Sized Evolutionary Algorithms.

Miguel Rocha, José P. Pinto, Isabel Rocha, Eugénio C. Ferreira

Proceedings of the 2007 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2007

2006

A Comparison of Algorithms for the Optimization of Fermentation Processes.

Rui Mendes, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha

Proceedings of the IEEE International Conference on Evolutionary Computation, 2006

2005

Evolutionary programming as a platform for <i>in silico </i>metabolic engineering.

Kiran Raosaheb Patil, Isabel Rocha, Jochen Förster, Jens Nielsen

BMC Bioinform., 2005

A new representation in evolutionary algorithms for the optimization of bioprocesses.

Miguel Rocha, Isabel Rocha, Eugénio C. Ferreira

Proceedings of the IEEE Congress on Evolutionary Computation, 2005

2004

Evolutionary Algorithms for Optimal Control in Fed-Batch Fermentation Processes.

Miguel Rocha, José Neves, Isabel Rocha, Eugénio C. Ferreira

Proceedings of the Applications of Evolutionary Computing, 2004