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A computational tool for the simulation and optimization of microbial strains a...
Vilaça, Paulo; Rocha, I.; Rocha, MiguelBackground and scope Recently, a number of methods and tools have been proposed to allow the use of genome-scale metabolic models for the phenotype simulation and optimization of microbial strains, within the field of Metabolic Engineering (ME). One of the limitations of most of these algorithms and tools is the fact that only metabolic information is taken into account, disregarding knowledge on regulatory eve...
A study on the robustness of strain optimization algorithms
Vilaça, Paulo; Maia, Paulo; Rocha, Miguel5th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2011), ISBN 978-3-642-19913-4 ; In recent years, there have been considerable advances in the use of genome-scale metabolic models to provide accurate phenotype simulation methods, which in turn enabled the development of efficient strain optimization algorithms for Metabolic Engineering. In this work, we ad...
OptFlux : an open-source software platform for in silico metabolic engineering
Rocha, I.; Maia, Paulo; Evangelista, Pedro; Vilaça, Paulo; Soares, Simão; Pinto, José P.; Nielsen, Jens; Patil, Kiran Raosaheb; Ferreira, E. C.Background: Over the last few years a number of methods have been proposed for the phenotype simulation of microorganisms under different environmental and genetic conditions. These have been used as the basis to support the discovery of successful genetic modifications of the microbial metabolism to address industrial goals. However, the use of these methods has been restricted to bioinformaticians or other ex...
Metaheuristics for strain optimization using transcriptional information enrich...
Vilaça, Paulo; Maia, Paulo; Rocha, I.; Rocha, MiguelPublicado em "Evolutionary computation, machine learning and data mining in bioinformatics : 8th European Conference, EvoBIO 2010...", ISBN 978-3-642-12210-1 ; The identification of a set of genetic manipulations that result in a microbial strain with improved production capabilities of a metabolite with industrial interest is a big challenge in Metabolic Engineering. Evolutionary Algorithms and Simulated Anne...
A study on the effects of using gene-reaction rules on in silico strain optimiz...
Vilaça, Paulo; Maia, Paulo; Evangelista, Pedro; Ferreira, E. C.; Rocha, Miguel; Rocha, I.To identify a set of genetic manipulations that will result in a microbial strain with improved production capabilities of a metabolite / product of industrial interest, is one of the greatest challenges in Metabolic Engineering. This problem represents a complex combination between the development of accurate metabolic and regulatory models / networks, plus the need for appropriate simulation and optimization ...
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