Isabel Rocha

Daniel Machado, Zita Soons, Kiran Raosaheb Patil, Eugénio C. Ferreira, Isabel Rocha: Random sampling of elementary flux modes in large-scale metabolic networks. Bioinformatics 28(18): 515-521 (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. IJDMB 6(4): 382-395 (2012)

Emanuel Gonçalves, Rui Pereira, Isabel Rocha, Miguel Rocha: Optimization Approaches for the In Silico Discovery of Optimal Targets for Gene Over/Underexpression. Journal of Computational Biology 19(2): 102-114 (2012)

Emanuel Gonçalves, Isabel Rocha, Miguel Rocha: Computational Tools for Strain Optimization by Tuning the Optimal Level of Gene Expression. PACBB 2012: 251-258

Anália Lourenço, Sónia Carneiro, Miguel Rocha, Eugénio C. Ferreira, Isabel Rocha: Challenges in integrating Escherichia coli molecular biology data. Briefings in Bioinformatics 12(2): 91-103 (2011)

Paulo Vilaça, Isabel Rocha, Miguel Rocha: A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/regulatory information. Biosystems 103(3): 435-441 (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 Bioinformatics 12: 460 (2011)

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. Integrative Bioinformatics 8(3) (2011)

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

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

José Pedro Pinto, Isabel Rocha, Miguel Rocha: Highlighting Metabolic Strategies Using Network Analysis over Strain Optimization Results. PRIB 2011: 109-120

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. Biosystems 100(2): 150-157 (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): 3444-3453 (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: 103-117

José P. Pinto, Isabel Rocha, Miguel Rocha: A software tool for network topology analysis under a metabolic engineering perspective. BCB 2010: 569-578

Paulo Vilaça, Paulo Maia, Isabel Rocha, Miguel Rocha: Metaheuristics for Strain Optimization Using Transcriptional Information Enriched Metabolic Models. EvoBIO 2010: 205-216

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

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: 217-224

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. Journal of Biomedical Informatics 42(4): 710-720 (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: 140-151

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: 954-963

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

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

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

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 Bioinformatics 9 (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: 1-6

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

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

Eduardo Valente, Isabel Rocha, Miguel Rocha: Modelling Fed-Batch Fermentation Processes: An Approach Based on Artificial Neural Networks. IWPACBB 2008: 30-39

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

Miguel Rocha, José P. Pinto, Isabel Rocha, Eugénio C. Ferreira: Optimization of Bacterial Strains with Variable-Sized Evolutionary Algorithms. CIBCB 2007: 331-337

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

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

Kiran Raosaheb Patil, Isabel Rocha, Jochen Förster, Jens Nielsen: Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics 6: 308 (2005)

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

Miguel Rocha, José Neves, Isabel Rocha, Eugénio C. Ferreira: Evolutionary Algorithms for Optimal Control in Fed-Batch Fermentation Processes. EvoWorkshops 2004: 84-93