Mauro A. A. Castro

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Analysis of genome-wide expression data poses a challenge to extract relevant information. The usual approaches compare cellular expression levels relative to a pre-established control and genes are clustered based on the correlation of their expression levels. This implies that cluster definitions are dependent on the cellular metabolic state, eventually(More)
Apoptosis is essential for complex multicellular organisms and its failure is associated with genome instability and cancer. Interactions between apoptosis and genome-maintenance mechanisms have been extensively documented and include transactivation-independent and -dependent functions, in which the tumor-suppressor protein p53 works as a 'molecular node'(More)
Regardless the high degree of variation observed in solid tumor karyotypes, the use of diversity as a measurable phenomenon remains unexplored. Here we present a systematic cytogenetic analysis using Shannon's entropy as a measure for karyotypic diversity. Karyotypes from 14 epithelial tumor types (n = 1232) have the aneuploidy status scored, resulting in(More)
Genetic plasticity may be understood as the ability of a functional gene network to tolerate alterations in its components or structure. Usually, the studies involving gene modifications in the course of the evolution are concerned to nucleotide sequence alterations in closely related species. However, the analysis of large scale data about the distribution(More)
An important question nowadays is whether chromosome aberrations are random events or arise from an internal deterministic mechanism, which leads to the delicate task of quantifying the degree of randomness. For this purpose, we have defined several Shannon information functions to evaluate disorder inside a tumor and between tumors of the same kind. We(More)
UNLABELLED ViaComplex is an open-source application that builds landscape maps of gene expression networks. The motivation for this software comes from two previous publications (Nucleic Acids Res., 35, 1859-1867, 2007; Nucleic Acids Res., 36, 6269-6283, 2008). The first article presents a network-based model of genome stability pathways where we defined a(More)
Whole genome protein-protein association networks are not random and their topological properties stem from genome evolution mechanisms. In fact, more connected, but less clustered proteins are related to genes that, in general, present more paralogs as compared to other genes, indicating frequent previous gene duplication episodes. On the other hand, genes(More)
Growing evidence defines macrophages (Mφ) as plastic cells with wide-ranging states of activation and expression of different markers that are time and location dependent. Distinct from the simple M1/M2 dichotomy initially proposed, extensive diversity of macrophage phenotypes have been extensively demonstrated as characteristic features of(More)
A novel biological principle of cell-to-cell interaction based on membrane continuity of nanotubular channels has recently been described. These contacts are extremely dynamic and sensitive to mechanical stress, which causes their rapid breakage and retraction. Here we demonstrate that functional mechanical stress generated during cell division can disrupt(More)
SUMMARY Network-level visualization of functional data is a key aspect of both analysis and understanding of biological systems. In a continuing effort to create clear and integrated visualizations that facilitate the gathering of novel biological insights despite the overwhelming complexity of data, we present here the GrAph LANdscape VisualizaTion(More)