4 documents found, page 1 of 1
Towards a multivariate analysis of genome-scale metabolic models derived from t...
Oliveira, Alexandre Rafael Machado; Cunha, Emanuel Rodrigues; Cruz, Fernando João Pereira da; Ribeiro, João Manuel Capela AraújoGenome-Scale metabolic models (GEMs) are a relevant tool in systems biology for in silico strain optimisation and drug discovery. An easier way to reconstruct a model is to use available GEMs as templates to create the initial draft, which can be curated up until a simulation-ready model is obtained. This approach is implemented in merlin's BiGG Integration Tool, which reconstructs models from existing GEMs pre...
merlin v4: an updated platform for reconstructing genome-scale metabolic models
Lima, Diogo Batista; Lagoa, Davide Rafael Santos; Cruz, Fernando João Pereira da; Bastos, José; Capela, João; Ferreira, Eugénio C.; Rocha, MiguelThe Metabolic Models Reconstruction Using Genome-Scale Information (merlin) software is an open source user-friendly Java application developed for Windows and Unix, aimed towards the reconstruction of genome-scale metabolic models. The development of merlin follows a design philosophy of automating time-consuming steps in the reconstruction of genome-scale metabolic models, while allowing users to control the ...
SamPler - a novel method for selecting parameters for gene functional annotatio...
Cruz, Fernando João Pereira da; Lagoa, Davide Rafael Santos; Mendes, João; Rocha, I.; Ferreira, Eugénio C.; Rocha, Miguel; Dias, OscarBackground: As genome sequencing projects grow rapidly, the diversity of organisms with recently assembled genome sequences peaks at an unprecedented scale, thereby highlighting the need to make gene functional annotations fast and efficient. However, the (high) quality of such annotations must be guaranteed, as this is the first indicator of the genomic potential of every organism. Automatic procedures help ac...
Genome-Scale Metabolic Network Reconstruction of the dairy bacterium Streptococ...
Cruz, Fernando João Pereira daThe dairy food industry is constantly changing as novel biotechnological techniques improve the manufacturing process of dairy products. Widely used over the years in the yogurt and cheese manufacturing, Streptococcus thermophilus is now considered as an extremely valuable lactic acid bacterium for the annual market of the dairy industry. A specific, but of easy-access knowledge regarding the thermophilic bacte...