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

A Study on the Robustness of Strain Optimization Algorithms. - Paulo Vilaça; Paulo Maia; Miguel Rocha 001 (PACBB, 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)

An Algorithm to Assemble Gene-Protein-Reaction Associations for Genome-Scale Metabolic Model Reconstruction. - João G. R. Cardoso; Paulo Vilaça; Simão Soares; Miguel Rocha 001 (PRIB, 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)

Network Visualization Tools to Enhance Metabolic Engineering Platforms. - Alberto Noronha; Paulo Vilaça; Miguel Rocha 001 (PACBB, 2013)

Reg4OptFlux: an OptFlux plug-in that comprises meta-heuristics approaches for Metabolic engineering using integrated models. - Orlando Rocha; Paulo Vilaça; Miguel Rocha 001; Rui Mendes 001 (NaBIC, 2014)

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

An integrated network visualization framework towards metabolic engineering applications. - Alberto Noronha; Paulo Vilaça; Miguel Rocha 001 (BMC Bioinform., 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)

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)

A Critical Evaluation of Automatic Atom Mapping Algorithms and Tools. - Nuno Osório; Paulo Vilaça; Miguel Rocha 001 (PACBB, 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)

In Silico Predictions for Fucoxanthin Production by the Diatom Phaeodactylum Tricornutum. - Cláudia M. Bauer; Paulo Vilaça; Fernanda Ramlov; Eva Regina de Oliveira; Débora Cabral Nazário; Caroline Schmitz; Rafaela Gordo Corrêa; Miguel Rocha 001; Marcelo Maraschin (PACBB, 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)