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Jou D.,Autonomous University of Barcelona | Jou D.,Institute dEstudis Catalans | Sciacca M.,Autonomous University of Barcelona | Sciacca M.,University of Palermo | And 2 more authors.

We present a review of two thermal duality symmetries between two different kinds of systems: photons and cosmic string loops, and macro black holes and micro black holes, respectively. It also follows a third joint duality symmetry amongst them through thermal equilibrium and stability between macro black holes and photon gas, and micro black holes and string loop gas, respectively. The possible cosmological consequences of these symmetries are discussed. © 2015 by the authors. Source

Menconi G.,Istituto Nazionale di Alta Matematica | Battaglia G.,University of Pisa | Grossi R.,University of Pisa | Pisanti N.,University of Pisa | And 2 more authors.
BIOINFORMATICS 2011 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms

We aim at finding all the mobile elements in a genome and understanding their dynamic behavior. Comparative genomics of closely related organisms can provide the data for this kind of investigation. The comparison task requires a huge amount of computational resources, which in our approach we alleviate by exploiting the high similarity between homologous chromosomes of different strains of the same species. Our case study is for Ref Seq and two other strains of S. cerevisiæ. Our fast algorithm, called REGENDER, is driven by data analysis. We found that almost all the chromosomes are composed by resident genome (more than 90% is conserved). Most importantly, the inspection of the non-conserved regions revealed that these are putative mobile elements, thus confirming that our method is useful to quickly find mobile elements. The software tool REGENDER is available online at http://www.di.unipi.it/~gbattag/ regender. Source

Calcagnile L.M.,Normal School of Pisa | Menconi G.,Istituto Nazionale di Alta Matematica
Journal of Nonlinear Science

We numerically test the method of non-sequential recursive pair substitutions to estimate the entropy of an ergodic source. We compare its performance with other classical methods to estimate the entropy (empirical frequencies, return times, and Lyapunov exponent). We have considered as a benchmark for the methods several systems with different statistical properties: renewal processes, dynamical systems provided and not provided with a Markov partition, and slow or fast decay of correlations. Most experiments are supported by rigorous mathematical results, which are explained in the paper. © 2010 Springer Science+Business Media, LLC. Source

Menconi G.,Istituto Nazionale di Alta Matematica | Puliti A.,Gaslini Institute | Puliti A.,University of Genoa | Sbrana I.,University of Pisa | And 3 more authors.
Journal of Theoretical Biology

This paper presents a top-down strategy to detect features in genomic sequences. The strategy's core is to exploit dictionary-based compression algorithms and analyse the content of the automatically generated dictionary. We classify the different over-represented segments and in the case study we correlate them to experimentally identified or theoretically forecasted biological features. A large spectrum analysis reveals that the only feature co-located with the a priori extracted segments is the torsional flexibility of DNA, while non-B DNA configurations are anti-localized and other features are mostly independent of the extracted sequences. This analysis unravels complex relationships between the linguistic structures investigated under our approach and some known biological features. © 2010 Elsevier Ltd. Source

Menconi G.,Istituto Nazionale di Alta Matematica | Battaglia G.,University of Pisa | Grossi R.,University of Pisa | Pisanti N.,University of Pisa | And 3 more authors.
BMC Bioinformatics

Background: Mobile Genetic Elements (MGEs) are selfish DNA integrated in the genomes. Their detection is mainly based on consensus-like searches by scanning the investigated genome against the sequence of an already identified MGE. Mobilomics aims at discovering all the MGEs in a genome and understanding their dynamic behavior: The data for this kind of investigation can be provided by comparative genomics of closely related organisms. The amount of data thus involved requires a strong computational effort, which should be alleviated.Results: Our approach proposes to exploit the high similarity among homologous chromosomes of different strains of the same species, following a progressive comparative genomics philosophy. We introduce a software tool based on our new fast algorithm, called regender, which is able to identify the conserved regions between chromosomes. Our case study is represented by a unique recently available dataset of 39 different strains of S.cerevisiae, which regender is able to compare in few minutes. By exploring the non-conserved regions, where MGEs are mainly retrotransposons called Tys, and marking the candidate Tys based on their length, we are able to locate a priori and automatically all the already known Tys and map all the putative Tys in all the strains. The remaining putative mobile elements (PMEs) emerging from this intra-specific comparison are sharp markers of inter-specific evolution: indeed, many events of non-conservation among different yeast strains correspond to PMEs. A clustering based on the presence/absence of the candidate Tys in the strains suggests an evolutionary interconnection that is very similar to classic phylogenetic trees based on SNPs analysis, even though it is computed without using phylogenetic information.Conclusions: The case study indicates that the proposed methodology brings two major advantages: (a) it does not require any template sequence for the wanted MGEs and (b) it can be applied to infer MGEs also for low coverage genomes with unresolved bases, where traditional approaches are largely ineffective. © 2013 Menconi et al.; licensee BioMed Central Ltd. Source

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