Isabel Rocha

Publication Activity (10 Years)

Years Active: 2004-2023
Publications (10 Years): 15

Top Topics

Medical Devices

Evolutionary Methods

Biological Knowledge

Top Venues

PLoS Comput. Biol.

J. Integr. Bioinform.

Publications

Emanuel Cunha, Miguel Silva, Inês Chaves, Hüseyin Demirci, Davide Lagoa, Diogo Lima, Miguel Rocha, Isabel Rocha, Oscar Días
The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber. PLoS Comput. Biol. 19 (9) (2023)
Diana Széliová, Jerneja Stor, Isabella Thiel, Marcus Weinguny, Michael Hanscho, Gabriele Lhota, Nicole Borth, Jürgen Zanghellini, David E. Ruckerbauer, Isabel Rocha
Inclusion of maintenance energy improves the intracellular flux predictions of CHO. PLoS Comput. Biol. 17 (6) (2021)
Lionel Pazart, Sylvia Pelayo, T. Chevallier, Gabriel Gruionu, Philippe Mabo, Yves Bayon, Frédéric Barbot, Thomas Lihoreau, Catherine Roussel, Nicos Maglaveras, Eirini Lekka, H. A. Ferreira, Isabel Rocha, Liesbet Geris, C. Lavet
Threats and Opportunities for the Clinical Investigation of High-risk Medical Devices in the Context of the New European Regulations. BIODEVICES (2021)
Sara Abu Ajamieh, Diana Mîndroc-Filimon, Irene Mozo, Isabel Rocha
Xtrace: Novel Bioresorbable Device for Patent Foramen Ovale Closure. BIODEVICES (2020)
Vítor Vieira, Paulo Maia, Miguel Rocha, Isabel Rocha
Comparison of pathway analysis and constraint-based methods for cell factory design. BMC Bioinform. 20 (1) (2019)
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) (2019)
Jordi Escuder Tisaire, Elena Martín Rodrigo, Sofia Ribeiro, Mariachiara Ricci, Juan Sebastian Cuellar, Dimitrios I. Zeugolis, Yves Bayon, Isabel Rocha
Concept Design of a New Portable Medical Device for Lymphedema Monitoring: A EIT Health ClinMed Summer School Project. HEALTHINF (2019)
Bruno Pereira, Joana Miguel, Paulo Vilaça, Simão Soares, Isabel Rocha, Sónia Carneiro
Reconstruction of a genome-scale metabolic model for Actinobacillus succinogenes 130Z. BMC Syst. Biol. 12 (1) (2018)
Joana C. Xavier, Kiran Raosaheb Patil, Isabel Rocha
Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes. PLoS Comput. Biol. 14 (11) (2018)
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) (2017)
Paulo Maia, Isabel Rocha, Miguel Rocha
Identification of robust strain designs via tandem pFBA/LMOMA phenotype prediction. GECCO (Companion) (2017)
Sophia Santos, Isabel Rocha
Estimation of biomass composition from genomic and transcriptomic information. J. Integr. Bioinform. 13 (2) (2016)
Sophia Santos, Isabel Rocha
A Computation Tool for the Estimation of Biomass Composition from Genomic and Transcriptomic Information. PACBB (2016)
Vítor Vieira, Paulo Maia, Isabel Rocha, Miguel Rocha
Development of an Integrated Framework for Minimal Cut Set Enumeration in Constraint-Based Models. PACBB (2016)
Daniel Machado, Markus J. Herrgård, Isabel Rocha
Stoichiometric Representation of Gene-Protein-Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction. PLoS Comput. Biol. 12 (10) (2016)
Filipe Liu, Paulo Vilaça, Isabel Rocha, Miguel Rocha
Development and application of efficient pathway enumeration algorithms for metabolic engineering applications. Comput. Methods Programs Biomed. 118 (2) (2015)
Ana Alão Freitas, Hugo Costa, Miguel Rocha, Isabel Rocha
Extracting kinetic information from literature with KineticRE. J. Integr. Bioinform. 12 (4) (2015)
Ana Alão Freitas, Hugo Costa, Miguel Rocha, Isabel Rocha
A Text Mining Approach for the Extraction of Kinetic Information from Literature. PACBB (2015)
Rafael Carreira, Pedro Evangelista, Paulo Maia, Paulo Vilaça, Marcellinus Pont, Jean-François Tomb, Isabel Rocha, Miguel Rocha
CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data. BMC Syst. Biol. 8 (2014)
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) (2014)
Filipe Liu, Paulo Vilaça, Isabel Rocha, Miguel Rocha
Evaluating Pathway Enumeration Algorithms in Metabolic Engineering Case Studies. PACBB (2014)
José P. Faria, Ross A. Overbeek, Fangfang Xia, Miguel Rocha, Isabel Rocha, Christopher S. Henry
Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models. Briefings Bioinform. 15 (4) (2014)
Daniel Machado, Lígia R. Rodrigues, Isabel Rocha
A kinetic model for curcumin production in Escherichia coli. Biosyst. 125 (2014)
Paulo Maia, Isabel Rocha, Miguel Rocha
An integrated framework for strain optimization. IEEE Congress on Evolutionary Computation (2013)
Tiago Resende, Daniela M. Correia, Miguel Rocha, Isabel Rocha
Re-annotation of the genome sequence of Helicobacter pylori 26695. J. Integr. Bioinform. 10 (3) (2013)
Pedro Evangelista, Miguel Rocha, Isabel Rocha
Evolutionary computation for predicting optimal reaction knockouts and enzyme modulation strategies. IEEE Congress on Evolutionary Computation (2013)
Tiago Resende, Daniela M. Correia, Isabel Rocha
Assignment of Novel Functions to Helicobacter pylori 26695's Genome. PACBB (2013)
Rafael Carreira, Miguel Rocha, Silas Granato Villas-Bôas, Isabel Rocha
Algorithms to infer metabolic flux ratios from fluxomics data. BIBM (2013)
Emanuel J. V. Gonçalves, Isabel Rocha, Miguel Rocha
Computational Tools for Strain Optimization by Tuning the Optimal Level of Gene Expression. PACBB (2012)
Emanuel J. V. Gonçalves, Rui Pereira, Isabel Rocha, Miguel Rocha
Discovery of Optimal Targets for Gene Over/Underexpression. J. Comput. Biol. 19 (2) (2012)
Paulo Maia, Paulo Vilaça, Isabel Rocha, Marcellinus Pont, Jean-François Tomb, Miguel Rocha
An integrated computational environment for elementary modes analysis of biochemical networks. Int. J. Data Min. Bioinform. 6 (4) (2012)
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) (2012)
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)
Gabriela Postolache, Mario Oliveira, Isabel Rocha, Pedro Silva Girão, Octavian Postolache
New insight into arrhythmia onset using HRV and BPV analysis. EMBC (2011)
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 (2011)
Anália Lourenço, Sónia Carneiro, José P. Pinto, Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha
Metabolic Pathways. PACBB (2011)
Anália Lourenço, Sónia Carneiro, Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha
molecular biology data. Briefings Bioinform. 12 (2) (2011)
Paulo Vilaça, Isabel Rocha, Miguel Rocha
A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/regulatory information. Biosyst. 103 (3) (2011)
Sónia Carneiro, Eugénio C. Ferreira, Isabel Rocha
Systems. PACBB (2011)
José Pedro Pinto, Isabel Rocha, Miguel Rocha
Highlighting Metabolic Strategies Using Network Analysis over Strain Optimization Results. PRIB (2011)
José P. Pinto, Isabel Rocha, Miguel Rocha
A software tool for network topology analysis under a metabolic engineering perspective. BCB (2010)
Paulo Maia, Marcellinus Pont, Jean-François Tomb, Isabel Rocha, Miguel Rocha
Enhancing Elementary Flux Modes Analysis Using Filtering Techniques in an Integrated Environment. IWPACBB (2010)
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) (2010)
Sónia Carneiro, Silas Granato Villas-Bôas, Isabel Rocha, Eugénio C. Ferreira
. IWPACBB (2010)
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 (2010)
Paulo Vilaça, Paulo Maia, Isabel Rocha, Miguel Rocha
Metaheuristics for Strain Optimization Using Transcriptional Information Enriched Metabolic Models. EvoBIO (2010)
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)
Anália Lourenço, Rafael Carreira, Daniel Glez-Peña, José Ramon 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) (2010)
Pedro Evangelista, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha
A Software Tool for the Simulation and Optimization of Dynamic Metabolic Models. IWANN (2) (2009)
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) (2009)
Anália Lourenço, Sónia Carneiro, Eugénio C. Ferreira, Rafael Carreira, Luis Mateus Rocha, Daniel Glez-Peña, José Ramon Méndez, Florentino Fdez-Riverola, Fernando Díaz, Isabel Rocha, Miguel Rocha
Biomedical Text Mining Applied to Document Retrieval and Semantic Indexing. IWANN (2) (2009)
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)
Pedro Evangelista, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha
Evolutionary Approaches for Strain Optimization Using Dynamic Models under a Metabolic Engineering Perspective. EvoBIO (2009)
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)
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)
Eduardo Valente, Isabel Rocha, Miguel Rocha
Modelling Fed-Batch Fermentation Processes: An Approach Based on Artificial Neural Networks. IWPACBB (2008)
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)
Paulo Maia, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha
Evaluating evolutionary multiobjective algorithms for the in silico optimization of mutant strains. BIBE (2008)
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)
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)
Miguel Rocha, José P. Pinto, Isabel Rocha, Eugénio C. Ferreira
Optimization of Bacterial Strains with Variable-Sized Evolutionary Algorithms. CIBCB (2007)
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)
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)
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)
Miguel Rocha, Isabel Rocha, Eugénio C. Ferreira
A new representation in evolutionary algorithms for the optimization of bioprocesses. Congress on Evolutionary Computation (2005)
Kiran Raosaheb Patil, Isabel Rocha, Jochen Förster, Jens Nielsen
metabolic engineering. BMC Bioinform. 6 (2005)
Miguel Rocha, José Neves, Isabel Rocha, Eugénio C. Ferreira
Evolutionary Algorithms for Optimal Control in Fed-Batch Fermentation Processes. EvoWorkshops (2004)