5 documents found, page 1 of 1
In silico constraint-based strain optimization methods: the quest for optimal c...
Silva, P.; Rocha, Miguel; Rocha, I.Shifting from chemical to biotechnological processes is one of the cornerstones of 21st century industry. The production of a great range of chemicals via biotechnological means is a key challenge on the way toward a bio-based economy. However, this shift is occurring at a pace slower than initially expected. The development of efficient cell factories that allow for competitive production yields is of paramoun...
A computation tool for the estimation of biomass composition from genomic and t...
Santos, Sophia Torres; Rocha, IsabelGiven the huge potential impact of the growing number of complete genome-scale metabolic network reconstructions of organisms, it is necessary to use bioinformatics tools to simplify and accelerate the course of knowledge in this field. One essential component of genome-scale metabolic model is biomass equation, whose maximization is one of the most common objective functions used in Flux Balance Analysis formu...
Development of an integrated framework for minimal cut set enumeration in const...
Vieira, Vítor; Maia, Paulo; Rocha, Isabel; Rocha, MiguelUnder the realm of in silico Metabolic Engineering, pathway analysis approaches to strain optimization have shown a large potential as tools capable of providing an unbiased view over metabolic models. Most of these methods were difficult or impossible to use due to their heavy computational needs, since they are based in the calculation of elementary modes/minimal cut sets in large networks. However, a recent ...
Development of a framework for metabolic pathway analysis-driven strain optimiz...
Vieira, Vítor; Maia, Paulo; Rocha, Isabel; Rocha, MiguelGenome-scale metabolic models (GSMMs) have become important assets for rational design of compound overproduction using microbial cell factories. Most computational strain optimization methods (CSOM) using GSMMs, while useful in metabolic engineering, rely on the definition of questionable cell objectives, leading to some bias. Metabolic pathway analysis approaches do not require an objective function. Though t...
Genome-scale modeling of yeast: chronology, applications and critical perspectives
Lopes, Hélder; Rocha, IsabelOver the last 15 years, several genome-scale metabolic models (GSMMs) were developed for different yeast species, aiding both the elucidation of new biological processes and the shift toward a bio-based economy, through the design of in silico inspired cell factories. Here, an historical perspective of the GSMMs built over time for several yeast species is presented and the main inheritance patterns among the m...