| Issue Date | Title | Author(s) | Type | Access |
| 2022 | Exploring Xylella fastidiosas metabolic traits using a GSM model of the phytopathogenic bacterium | Oliveira, Alexandre Rafael Machado; Cunha, Emanuel Rodrigues; Silva, Miguel, et al. | Book part | Restricted access (UMinho) |
| 25-Feb-2021 | merlin v4. 0: an updated platform for the reconstruction of high-quality genome-scale metabolic models | Capela, João; Lagoa, D.; Rodrigues, Rúben, et al. | Preprint | Open access |
| 24-Jun-2022 | merlin, an improved framework for the reconstruction of high-quality genome-scale metabolic models | Capela, João; Lagoa, Davide Rafael Santos; Rodrigues, Rúben André Costa, et al. | Article | Open access |
| 2022 | Systematic assessment of template-based genome-scale metabolic models created with the BiGG Integration Tool | Oliveira, Alexandre Rafael Machado; Cunha, Emanuel; Cruz, Fernando João Pereira, et al. | Article | Open access |
| 2023 | Systems biology's role in leveraging microalgal biomass potential: Current status and future perspectives | Cunha, Emanuel; Sousa, Vítor; Geada, Pedro, et al. | Article | Open access |
| 10-Mar-2021 | The first multi-tissue diel cycle genome-scale metabolic model of a woody plant highlights the role of the secondary metabolism pathways in Quercus suber | Cunha, Emanuel; Silva, Miguel; Chaves, Inês, et al. | Preprint | Open access |
| 2022 | Towards a multivariate analysis of genome-scale metabolic models derived from the BiGG models database | Oliveira, Alexandre Rafael Machado; Cunha, Emanuel Rodrigues; Cruz, Fernando João Pereira da, et al. | Conference paper | Open access |
| 2021 | Towards the reconstruction of the genome-scale metabolic model of Lactobacillus acidophilus La-14 | Cunha, Emanuel; Zeidan, Ahmad; Dias, Oscar | Conference paper | Open access |
| 30-Apr-2021 | TranSyT, an innovative framework for identifying transport systems | Lagoa, Davide Rafael Santos; Faria, José P.; Liu, Filipe, et al. | Preprint | Open access |
