5 documents found, page 1 of 1
Systems biology's role in leveraging microalgal biomass potential: Current stat...
Cunha, Emanuel; Sousa, Vítor; Geada, Pedro; Teixeira, J. A.; Vicente, A. A.; Dias, OscarMicroalgae are an eco-friendly and alternative source of several compounds that can be applied in numerous biotechnological branches such as cosmetics, food, or pharmaceutical industries. However, the commercialization of products from microalgae has still some drawbacks, among which it is possible to highlight the low biomass and compounds' productivities at industrial level. The common strategies to improve t...
Systematic assessment of template-based genome-scale metabolic models created w...
Oliveira, Alexandre Rafael Machado; Cunha, Emanuel; Cruz, Fernando João Pereira; Capela, João; Sequeira, J. C.; Sampaio, Marta; Ganâncio, CláudiaGenome-scale metabolic models (GEMs) are essential tools for in silico phenotype prediction and strain optimisation. The most straightforward GEMs reconstruction approach uses published models as templates to generate theinitial draft, requiring further curation. Such an approachis used by BiGG Integration Tool (BIT), available for merlin users. This tool uses models from BiGG Models database as templates for t...
The first multi-tissue diel cycle genome-scale metabolic model of a woody plant...
Cunha, Emanuel; Silva, Miguel; Chaves, Inês; Demirci, H.; Lagoa, Davide Rafael Santos; Lima, Diogo; Rocha, Miguel; Rocha, I.; Dias, OscarIn the last decade, genome-scale metabolic models have been increasingly used to study plant metabolic behavior at the tissue and multi-tissue level under different environmental conditions. Quercus suber, also known as the cork oak tree, is one of the most important forest communities of the Mediterranean/Iberian region. In this work, we present the genome-scale metabolic model of the Q. suber (iEC7871), the f...
Towards the reconstruction of the genome-scale metabolic model of Lactobacillus...
Cunha, Emanuel; Zeidan, Ahmad; Dias, OscarLactobacillus acidophilus is a probiotic lactic acid bacterium used in food and dietary supplements for many years. However, despite its importance for industrial development and recognized health-promoting effects, no genome-scale metabolic model has been reported. A GSM model for L. acidophilus La-14 was developed, accounting 494 genes and 783 reactions. A genome annotation was performed to identify the metab...
merlin v4. 0: an updated platform for the reconstruction of high-quality genome...
Capela, João; Lagoa, D.; Rodrigues, Rúben; Cunha, Emanuel; Cruz, Fernando; Barbosa, Ana; Bastos, J.; Lima, Diogo; Ferreira, Eugénio C.; Rocha, MiguelGenome-scale metabolic models have been recognised as useful tools for better understanding living organisms metabolism. merlin (https://www.merlin-sysbio.org/) is an open-source and user-friendly resource that hastens the models reconstruction process, conjugating manual and automatic procedures while leveraging the users expertise with a curation-oriented graphical interface. An updated and redesigned version...