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)

Optimization of fed-batch fermentation processes with bio-inspired algorithms. - Miguel Rocha 001; Rui Mendes 001; Orlando Rocha; Isabel Rocha; Eugénio C. Ferreira (Expert Syst. Appl., 2014)

JBiclustGE: Java API with unified biclustering algorithms for gene expression data analysis. - Orlando Rocha; Rui Mendes 001 (Knowl. Based Syst., 2018)

A computational framework for studying genome-scale regulatory models that combines gene expression data and optimization approaches - Orlando Rocha (2018)