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Ippolito M.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca | Meloni S.,University College Dublin
Physical Review B - Condensed Matter and Materials Physics | Year: 2011

By means of molecular dynamics simulations based on the Billeter environment-dependent classical force field we studied the structural features of SiN x samples at various stoichiometries. Our results are in good agreement with experimental data and are able to reproduce some features which so far were not reproduced by simulations. In particular, we identified units containing N-N bonds, which are thought to be responsible for an unassigned peak in the radial distribution function obtained from neutron diffraction data and signals observed in electron spin resonance, x-ray photoemission spectroscopy, electron-energy-loss spectroscopy, and optical absorption experiments. We have identified defects which are thought to be responsible for the high concentration of charge traps that makes this material suitable for building nonvolatile memory devices. We analyzed the dependency of the concentration of these defects with the stoichiometry of the sample. © 2011 American Physical Society. Source


Giombini E.,University of Rome La Sapienza | Orsini M.,Center for Advanced Studies | Carrabino D.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca | Tramontano A.,University of Rome La Sapienza
BMC Bioinformatics | Year: 2010

Background: Bacterial infections represent a global health challenge. The identification of novel antibacterial targets for both therapy and vaccination is needed on a constant basis because resistance continues to spread worldwide at an alarming rate. Even infections that were once easy to treat are becoming difficult or, in some cases, impossible to cure. Ideal targets for both therapy and vaccination are bacterial proteins exposed on the surface of the organism, which are often involved in host-pathogen interaction. Their identification can greatly benefit from technologies such as bioinformatics, proteomics and DNA microarrays.Results: Here we describe a pipeline named SLEP (Surface Localization Extracellular Proteins), based on an automated optimal combination and sequence of usage of reliable available tools for the computational identification of the surfome, i.e. of the subset of proteins exposed on the surface of a bacterial cell.Conclusions: The tool not only simplifies the usage of these methods, but it also improves the results by selecting the specifying order and combination of the instruments. The tool is freely available at http://www.caspur.it/slep. © 2010 Giombini et al; licensee BioMed Central Ltd. Source


D'Onorio De Meo P.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca | D'Antonio M.,University of Bari | Griggio F.,University of Milan | Lupi R.,University of Milan | And 6 more authors.
Nucleic Acids Research | Year: 2012

The MITOchondrial genome database of metaZOAns (MitoZoa) is a public resource for comparative analyses of metazoan mitochondrial genomes (mtDNA) at both the sequence and genomic organizational levels. The main characteristics of the MitoZoa database are the careful revision of mtDNA entry annotations and the possibility of retrieving gene order and non-coding region (NCR) data in appropriate formats. The MitoZoa retrieval system enables basic and complex queries at various taxonomic levels using different search menus. MitoZoa 2.0 has been enhanced in several aspects, including: a re-annotation pipeline to check the correctness of protein-coding gene predictions; a standardized annotation of introns and of precursor ORFs whose functionality is post-transcriptionally recovered by RNA editing or programmed translational frameshifting; updates of taxon-related fields and a BLAST sequence similarity search tool. Database novelties and the definition of standard mtDNA annotation rules, together with the user-friendly retrieval system and the BLAST service, make MitoZoa a valuable resource for comparative and evolutionary analyses as well as a reference database to assist in the annotation of novel mtDNA sequences. MitoZoa is freely accessible at http://www.caspur.it/mitozoa. © The Author(s) 2011. Published by Oxford University Press. Source


Picardi E.,University of Bari | D'Antonio M.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca | Carrabino D.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca | Castrignano T.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca | And 2 more authors.
Bioinformatics | Year: 2011

Summary: ExpEdit is a web application for assessing RNA editing in human at known or user-specified sites supported by transcript data obtained by RNA-Seq experiments. Mapping data (in SAM/BAM format) or directly sequence reads [in FASTQ/short read archive (SRA) format] can be provided as input to carry out a comparative analysis against a large collection of known editing sites collected in DARNED database as well as other user-provided potentially edited positions. Results are shown as dynamic tables containing University of California, Santa Cruz (UCSC) links for a quick examination of the genomic context. © The Author 2011. Published by Oxford University Press. All rights reserved. Source


D'Antonio M.,University of Bari | D'Antonio M.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca | D'Onorio De Meo P.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca | D'Onorio De Meo P.,Consorzio Interuniversitario Of Supercalcolo | And 11 more authors.
BMC Bioinformatics | Year: 2013

Background: The advent of massively parallel sequencing technologies (Next Generation Sequencing, NGS) profoundly modified the landscape of human genetics.In particular, Whole Exome Sequencing (WES) is the NGS branch that focuses on the exonic regions of the eukaryotic genomes; exomes are ideal to help us understanding high-penetrance allelic variation and its relationship to phenotype. A complete WES analysis involves several steps which need to be suitably designed and arranged into an efficient pipeline.Managing a NGS analysis pipeline and its huge amount of produced data requires non trivial IT skills and computational power.Results: Our web resource WEP (Whole-Exome sequencing Pipeline web tool) performs a complete WES pipeline and provides easy access through interface to intermediate and final results. The WEP pipeline is composed of several steps:. 1) verification of input integrity and quality checks, read trimming and filtering; 2) gapped alignment; 3) BAM conversion, sorting and indexing; 4) duplicates removal; 5) alignment optimization around insertion/deletion (indel) positions; 6) recalibration of quality scores; 7) single nucleotide and deletion/insertion polymorphism (SNP and DIP) variant calling; 8) variant annotation; 9) result storage into custom databases to allow cross-linking and intersections, statistics and much more. In order to overcome the challenge of managing large amount of data and maximize the biological information extracted from them, our tool restricts the number of final results filtering data by customizable thresholds, facilitating the identification of functionally significant variants. Default threshold values are also provided at the analysis computation completion, tuned with the most common literature work published in recent years.Conclusions: Through our tool a user can perform the whole analysis without knowing the underlying hardware and software architecture, dealing with both paired and single end data. The interface provides an easy and intuitive access for data submission and a user-friendly web interface for annotated variant visualization.Non-IT mastered users can access through WEP to the most updated and tested WES algorithms, tuned to maximize the quality of called variants while minimizing artifacts and false positives.The web tool is available at the following web address: http://www.caspur.it/wep. © 2013 D'Antonio et al.; licensee BioMed Central Ltd. Source

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