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A general strategy to determine the congruence between a hierarchical and a non-hierarchical classification

Background Classification procedures are widely used in phylogenetic inference, the analysis of expression profiles, the study of biological networks, etc. Many algorithms have been proposed to establish the similarity between two different classifications of the same elements. However, methods to determine significant coincidences between hierarchical and non-hierarchical...

CGIN1: A Retroviral Contribution to Mammalian Genomes

Antonio Marco 0 Ignacio Marn 0 Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University; and Instituto de Biomedicina de Valencia , Consejo Superior de

Clusters of microRNAs emerge by new hairpins in existing transcripts

Genetic linkage may result in the expression of multiple products from a polycistronic transcript, under the control of a single promoter. In animals, protein-coding polycistronic transcripts are rare. However, microRNAs are frequently clustered in the genomes of animals, and these clusters are often transcribed as a single unit. The evolution of microRNA clusters has been the...

Detection of microRNAs in color space

Antonio Marco 0 Sam Griffiths-Jones 0 Associate Editor: Martin Bishop 0 Faculty of Life Sciences, University of Manchester , Michael Smith Building, Oxford Road, M13 9PT Manchester, UK Motivation

Evolutionary and Structural Analyses of GDAP1, Involved in Charcot-Marie-Tooth Disease, Characterize a Novel Class of Glutathione Transferase-Related Genes

Antonio Marco 0 Ana Cuesta Laia Pedrola Francesc Palau Ignacio Marn 0 0 Departamento de Gene tica, Universidad de Valencia , Valencia , Spain; and Laboratory of Genetics and Molecular Medicine

Functional Shifts in Insect microRNA Evolution

MicroRNAs (miRNAs) are short endogenous RNA molecules that regulate gene expression at the posttranscriptional level and have been shown to play critical roles during animal development. The identification and comparison of miRNAs in metazoan species are therefore paramount for our understanding of the evolution of body plans. We have characterized 203 miRNAs from the red flour...

How Athila retrotransposons survive in the Arabidopsis genome

Background Transposable elements are selfish genetic sequences which only occasionally provide useful functions to their host species. In addition, models of mobile element evolution assume a second type of selfishness: elements of different familes do not cooperate, but they independently fight for their survival in the host genome. Results We show that recombination events...

Interactome and Gene Ontology provide congruent yet subtly different views of a eukaryotic cell

Background The characterization of the global functional structure of a cell is a major goal in bioinformatics and systems biology. Gene Ontology (GO) and the protein-protein interaction network offer alternative views of that structure. Results This study presents a comparison of the global structures of the Gene Ontology and the interactome of Saccharomyces cerevisiae...

Regulatory RNAs in the light of Drosophila genomics

Antonio Marco Many aspects of gene regulation are mediated by RNA molecules. However, regulatory RNAs have remained elusive until very recently. At least three types of small regulatory RNAs have

Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster

Motivation: In functional genomics, it is frequently useful to correlate expression levels of genes to identify transcription factor binding sites (TFBS) via the presence of common sequence motifs. The underlying assumption is that co-expressed genes are more likely to contain shared TFBS and, thus, TFBS can be identified computationally. Indeed, gene pairs with a very high...

SeedVicious: Analysis of microRNA target and near-target sites

specialised computing skills. Here I describe a new microRNA target prediction software that does Funding: This work was supported by a grant from the Wellcome Trust to Antonio Marco [grant number 200585/Z/16/Z ... . This work was supported by the Wellcome Trust [grant number 200585/Z/16/Z]. Author Contributions Conceptualization: Antonio Marco. Data curation: Antonio Marco. Formal analysis: Antonio Marco

Sex-Biased Expression of MicroRNAs in Schistosoma mansoni

Schistosomiasis is an important neglected tropical disease caused by digenean helminth parasites of the genus Schistosoma. Schistosomes are unusual in that they are dioecious and the adult worms live in the blood system. MicroRNAs play crucial roles during gene regulation and are likely to be important in sex differentiation in dioecious species. Here we characterize 112...

Structure, evolution and function of the bi-directionally transcribed iab-4/iab-8 microRNA locus in arthropods

In Drosophila melanogaster, the iab-4/iab-8 locus encodes bi-directionally transcribed microRNAs that regulate the function of flanking Hox transcription factors. We show that bi-directional transcription, temporal and spatial expression patterns and Hox regulatory function of the iab-4/iab-8 locus are conserved between fly and the beetle Tribolium castaneum. Computational...

The CEO as an Investor: The Capital Allocation Officer

2254-6235 The CEO as an Investor: A Framework for the Capital Allocation Officer José Antonio Marco Izquierdo Partner with Magnum Industrial Partners. Director of Iberwind Iberchem Grupo Nace