Aminael Sánchez-Rodríguez

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BACKGROUND Microarrays are the main technology for large-scale transcriptional gene expression profiling, but the large bodies of data available in public databases are not useful due to the large heterogeneity. There are several initiatives that attempt to bundle these data into expression compendia, but such resources for bacterial organisms are scarce(More)
Increasingly large-scale expression compendia for different species are becoming available. By exploiting the modularity of the coexpression network, these compendia can be used to identify biological processes for which the expression behavior is conserved over different species. However, comparing module networks across species is not trivial. The(More)
Escherichia coli K12 is a commensal bacteria and one of the best-studied model organisms. Salmonella enterica serovar Typhimurium, on the other hand, is a facultative intracellular pathogen. These two prokaryotic species can be considered related phylogenetically, and they share a large amount of their genetic material, which is commonly termed the "core(More)
Bulk segregant analysis (BSA) coupled to high throughput sequencing is a powerful method to map genomic regions related with phenotypes of interest. It relies on crossing two parents, one inferior and one superior for a trait of interest. Segregants displaying the trait of the superior parent are pooled, the DNA extracted and sequenced. Genomic regions(More)
BACKGROUND Previous studies in Ascomycetes have shown that the function of gene families of which the size is considerably larger in extant pathogens than in non-pathogens could be related to pathogenicity traits. However, by only comparing gene inventories in extant species, no insights can be gained into the evolutionary process that gave rise to these(More)
Alignment-free classifiers are especially useful in the functional classification of protein classes with variable homology and different domain structures. Thus, the Topological Indices to BioPolymers (TI2BioP) methodology (Agüero-Chapin et al., 2010) inspired in both the TOPS-MODE and the MARCH-INSIDE methodologies allows the calculation of simple(More)
The study of type III RNases constitutes an important area in molecular biology. It is known that the pac1+ gene encodes a particular RNase III that shares low amino acid similarity with other genes despite having a double-stranded ribonuclease activity. Bioinformatics methods based on sequence alignment may fail when there is a low amino acidic identity(More)
Bacterial interactions with the environment- and/or host largely depend on the bacterial glycome. The specificities of a bacterial glycome are largely determined by glycosyltransferases (GTs), the enzymes involved in transferring sugar moieties from an activated donor to a specific substrate. Of these GTs their coding regions, but mainly also their(More)
The ITS2 gene class shows a high sequence divergence among its members that have complicated its annotation and its use for reconstructing phylogenies at a higher taxonomical level (beyond species and genus). Several alignment strategies have been implemented to improve the ITS2 annotation quality and its use for phylogenetic inferences. Although, alignment(More)
Clonal populations accumulate mutations over time, resulting in different haplotypes. Deep sequencing of such a population in principle provides information to reconstruct these haplotypes and the frequency at which the haplotypes occur. However, this reconstruction is technically not trivial, especially not in clonal systems with a relatively low mutation(More)