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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...
Metabolic network topology reveals transcriptional regulatory signatures of typ...
Zelezniak, Aleksej; Pers, Tune H.; Soares, Simão; Patti, Mary Elizabeth; Patil, Kiran RaosahebType 2 diabetes mellitus (T2DM) is a disorder characterized by both insulin resistance and impaired insulin secretion. Recent transcriptomics studies related to T2DM have revealed changes in expression of a large number of metabolic genes in a variety of tissues. Identification of the molecular mechanisms underlying these transcriptional changes and their impact on the cellular metabolic phenotype is a challeng...
Heuristics for simulated annealing search of active sub-networks in bio-molecul...
Soares, Simão; Rocha, I.; Patil, Kiran RaosahebDifferent kinds of ‘omics’ data for several organisms and bio-molecular interaction networks (e.g. reconstructed networks of biochemical reactions and protein-protein physical interactions) are becoming very common nowadays. These bio-molecular networks are being used as a platform to integrate genome-scale ‘omics’ datasets. Identification of sub-networks in these large networks that show maximum collective res...
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