| Data | Título | Autor(es) | Tipo | Acesso |
| 24-Jun-2018 | Automated reconstruction and comparison of metabolic models for diverse fungal genomes | Edirisinghe, Janaka N.; Faria, José P.; Liu, Filipe Alexandre Wang, et al. | Resumo em ata de conferência | Acesso aberto |
| Fev-2015 | Enabling comparative modeling of closely related genomes: Example genus Brucella | Faria, José P.; Edirisinghe, Janaka N.; Davis, James J., et al. | Artigo | Acesso aberto |
| 24-Jun-2018 | Improving automated model reconstruction across phylogenetically diverse genome-scale metabolic models | Faria, José P.; Edirisinghe, Janaka N.; Seaver, Samuel M. D., et al. | Resumo em ata de conferência | Acesso aberto |
| Mar-2020 | MEMOTE for standardized genome-scale metabolic model testing | Lieven, Christian; Beber, Moritz E.; Olivier, Brett G., et al. | Carta ao editor | Acesso aberto |
| 31-Jul-2018 | Methods for automated genome-scale metabolic model reconstruction | Faria, José P.; Rocha, Miguel; Rocha, Isabel, et al. | Artigo | Acesso restrito UMinho |
| 19-Mar-2020 | Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing | Lieven, Christian; Beber, Moritz E.; Olivier, Brett G., et al. | Corrigenda | Acesso aberto |
| 8-Jun-2015 | Reconciling gene expression data with regulatory network models | Faria, José P.; Overbeek, Ross; Taylor, Ronald C., et al. | Resumo em ata de conferência | Acesso aberto |
| 8-Abr-2014 | Reconciling gene expression data with regulatory network models – a stimulon-based approach for integrated metabolic and regulatory modeling of Bacillus subtilis | Faria, José P.; Overbeek, Ross; Taylor, Ronald C., et al. | Resumo em ata de conferência | Acesso aberto |
| 2020 | Towards the reconstruction of integrated genome-scale models of metabolism and gene expression | Cruz, Fernando; Lima, Diogo; Faria, José P., et al. | Artigo em ata de conferência | Acesso aberto |
| 30-Abr-2021 | TranSyT, an innovative framework for identifying transport systems | Lagoa, Davide Rafael Santos; Faria, José P.; Liu, Filipe, et al. | Preprint | Acesso aberto |
| Ago-2023 | TranSyT, an innovative framework for identifying transport systems | Cunha, Emanuel Rodrigues; Lagoa, Davide Rafael Santos; Faria, José P., et al. | Artigo | Acesso restrito UMinho |
