| 2017 | GECCO | Identification of robust strain designs via tandem pFBA/LMOMA phenotype prediction. | Paulo Maia, Isabel Rocha, Miguel Rocha |
| 2016 | PACBB | A Computation Tool for the Estimation of Biomass Composition from Genomic and Transcriptomic Information. | Sophia Santos, Isabel Rocha |
| 2016 | PACBB | Development of an Integrated Framework for Minimal Cut Set Enumeration in Constraint-Based Models. | Vtor Vieira, Paulo Maia, Isabel Rocha, Miguel Rocha |
| 2015 | PACBB | A Text Mining Approach for the Extraction of Kinetic Information from Literature. | Ana Alo Freitas, Hugo Costa, Miguel Rocha, Isabel Rocha |
| 2014 | PACBB | Evaluating Pathway Enumeration Algorithms in Metabolic Engineering Case Studies. | Filipe Liu, Paulo Vilaa, Isabel Rocha, Miguel Rocha |
| 2013 | CEC | Evolutionary computation for predicting optimal reaction knockouts and enzyme modulation strategies. | Pedro Evangelista, Miguel Rocha, Isabel Rocha |
| 2013 | CEC | An integrated framework for strain optimization. | Paulo Maia, Isabel Rocha, Miguel Rocha |
| 2013 | PACBB | Assignment of Novel Functions to Helicobacter pylori 26695's Genome. | Tiago Resende, Daniela M. Correia, Isabel Rocha |
| 2012 | PACBB | Computational Tools for Strain Optimization by Tuning the Optimal Level of Gene Expression. | Emanuel J. V. Gonalves, Isabel Rocha, Miguel Rocha |
| 2011 | PACBB | A Systematic Modeling Approach to Elucidate the Triggering of the Stringent Response in Recombinant | Snia Carneiro, Eugnio C. Ferreira, Isabel Rocha |
| 2011 | PACBB | Interpreting the Regulatory Interplay in | Anlia Loureno, Snia Carneiro, Jos P. Pinto, Miguel Rocha, Eugnio C. Ferreira, Isabel Rocha |
| 2009 | IWANN | Large Scale Dynamic Model Reconstruction for the Central Carbon Metabolism of Escherichia coli . | Rafael S. Costa, Daniel Machado, Isabel Rocha, Eugnio C. Ferreira |
| 2009 | IWANN | A Software Tool for the Simulation and Optimization of Dynamic Metabolic Models. | Pedro Evangelista, Isabel Rocha, Eugnio C. Ferreira, Miguel Rocha |
| 2009 | IWANN | Biomedical Text Mining Applied to Document Retrieval and Semantic Indexing. | Anlia Loureno, Snia Carneiro, Eugnio C. Ferreira, Rafael Carreira, Luis M. Rocha, Daniel Glez-Pea, Jos Ramn Mndez, Florentino Fdez-Riverola, Fernando Daz, Isabel Rocha, Miguel Rocha |
| 2009 | IWANN | A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems. | Daniel Machado, Rafael S. Costa, Miguel Rocha, Isabel Rocha, Bruce Tidor, Eugnio C. Ferreira |
| 2008 | BIBE | A framework for the development of Biomedical Text Mining software tools. | Anlia Loureno, Rafael Carreira, Snia Carneiro, Paulo Maia, Daniel Glez-Pea, Florentino Fdez-Riverola, Eugnio C. Ferreira, Isabel Rocha, Miguel Rocha |
| 2008 | BIBE | Evaluating evolutionary multiobjective algorithms for the in silico optimization of mutant strains. | Paulo Maia, Isabel Rocha, Eugnio C. Ferreira, Miguel Rocha |
| 2008 | BIBE | A framework for the integrated analysis of metabolic and regulatory networks. | Rui Mendes, Anlia Loureno, Snia Carneiro, Miguel Rocha, Isabel Rocha, Eugnio C. Ferreira |
| 2007 | CIBCB | Optimization of Bacterial Strains with Variable-Sized Evolutionary Algorithms. | Miguel Rocha, Jos P. Pinto, Isabel Rocha, Eugnio C. Ferreira |
| 2007 | EPIA | Evaluating Simulated Annealing Algorithms in the Optimization of Bacterial Strains. | Miguel Rocha, Rui Mendes, Paulo Maia, Jos P. Pinto, Isabel Rocha, Eugnio C. Ferreira |
| 2006 | CEC | A Comparison of Algorithms for the Optimization of Fermentation Processes. | Rui Mendes, Isabel Rocha, Eugnio C. Ferreira, Miguel Rocha |
| 2005 | CEC | A new representation in evolutionary algorithms for the optimization of bioprocesses. | Miguel Rocha, Isabel Rocha, Eugnio C. Ferreira |