Oscar Dias

TL;DR: The merlin tool is a user-friendly Java application that aids the reconstruction of genome-scale metabolic models for any organism that has its genome sequenced, and expedites the transition from genomic data to draft metabolic models reconstructions exported in the SBML standard format.

Abstract: The Metabolic Models Reconstruction Using Genome-Scale Information (merlin) tool is a user-friendly Java application that aids the reconstruction of genome-scale metabolic models for any organism that has its genome sequenced. It performs the major steps of the reconstruction process, including the functional genomic annotation of the whole genome and subsequent construction of the portfolio of reactions. Moreover, merlin includes tools for the identification and annotation of genes encoding transport proteins, generating the transport reactions for those carriers. It also performs the compartmentalisation of the model, predicting the organelle localisation of the proteins encoded in the genome and thus the localisation of the metabolites involved in the reactions promoted by such enzymes. The gene-proteins-reactions (GPR) associations are automatically generated and included in the model. Finally, merlin expedites the transition from genomic data to draft metabolic models reconstructions exported in the SBML standard format, allowing the user to have a preliminary view of the biochemical network, which can be manually curated within the environment provided by merlin.

TL;DR: In the current work the implementation of image analysis and PLS techniques has shown to provide important information for better understanding the behavior of activated sludge processes, and to predict, at some extent, the sludge volume index.

TL;DR: This study provides a high-resolution view of staphylococcal viral genetic diversity, and insights into their gene flux patterns within and across different phage groups (cluster and subclusters) providing insight into their evolution.

TL;DR: The first genome-scale metabolic model of Kluyveromyces lactis, iOD907, is described, partially compartmentalized (four compartments), composed of 1867 reactions and 1476 metabolites, which is able to predict the behavior of K. lactis under different environmental conditions and genetic perturbations.