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)

Metabolic Network Topology Reveals Transcriptional Regulatory Signatures of Type 2 Diabetes. - Aleksej Zelezniak; Tune H. Pers; Simão Soares; Mary Elizabeth Patti; Kiran Raosaheb Patil (PLoS Comput. Biol., 2010)

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)

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)