Emanuel J. V. Gonçalves

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Cells process signals using complex and dynamic networks. Studying how this is performed in a context and cell type specific way is essential to understand signaling both in physiological and diseased situations. Context-specific medium/high throughput proteomic data measured upon perturbation is now relatively easy to obtain but formalisms that can take(More)
In most animal species females are the sex with the limiting reproductive rate, which promotes the predominance of male intra-sexual competition, active courtship and more developed epigamic characters in males (Trivers 1985). In some species, however, sex-role reversal occurs, and the females actively court and compete for mates (insects: Gwynne 1981;(More)
SUMMARY Drug versus Disease (DvD) provides a pipeline, available through R or Cytoscape, for the comparison of drug and disease gene expression profiles from public microarray repositories. Negatively correlated profiles can be used to generate hypotheses of drug-repurposing, whereas positively correlated profiles may be used to infer side effects of drugs.(More)
To test the effect of seed treatment with fungicides on the development of mycorrhizal fungi, bean seeds were treated with fungicide dry or vehicled in the organic solvents, ethanol or dichloromethane and then planted in soil inoculated with the mycorrhizal fungus Glomus macrocarpum and/or the plant pathogenic fungus Fusarium solani. Measurements were made(More)
Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise quantitative data, and that they are well-suited for studies of large networks. While numerous groups have developed specific(More)
Systems biology has to increasingly cope with large- and multi-scale biological systems. Many successful in silico representations and simulations of various cellular modules proved mathematical modelling to be an important tool in gaining a solid understanding of biological phenomena. However, models spanning different functional layers (e.g. metabolism,(More)
A standard graphical notation is essential to facilitate exchange of network representations of biological processes. Towards this end, the Systems Biology Graphical Notation (SBGN) has been proposed, and it is already supported by a number of tools. However, support for SBGN in Cytoscape, one of the most widely used platforms in biology to visualise and(More)
Marine Protected Areas (MPAs) have been widely proposed as a fisheries management tool in addition to their conservation purposes. Despite this, few studies have satisfactorily assessed the dynamics of fishers' adaptations to the loss of fishing grounds. Here we used data from before, during and after the implementation of the management plan of a temperate(More)
Blenniid fish exhibit a polygynandric mating system with parental care restricted to males. Nest-holder males defend a breeding territory centered on their nest, usually a crevice or hole in a rocky substrate, to which they attract females to spawn. Females, on the other hand, must search for nests in order to spawn and usually are the choosy sex, producing(More)
This paper presents a comparative analysis of territoriality in three intertidal (Lipophrys pholis, Coryphoblennius galerita, Salaria pavo) and two subtidal (Tripterygion delaisi, Parablennius pilicornis) blennioid fishes. Focal-animal observations of males guarding eggs showed that: (i) intertidal species had smaller territories that were less frequently(More)