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showing 10 items of 2689 documents
Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.
2017
Abstract: The Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO) has now been developing and promoting open community standards and software tools in the field of proteomics for 15 years. Under the guidance of the chair, co-chairs, and other leadership positions, the PSI working groups are tasked with the development and maintenance of community standards via special workshops and ongoing work. Among the existing, ratified standards, the PSI working groups continue to update PSI-MI XML, MITAB, mzML, mzIdentML, mzQuantML, mzTab, and the MIAPE (Minimum Information About a Proteomics Experiment) guidelines with the advance of new technologies and techniques. Furthe…
panISa: ab initio detection of insertion sequences in bacterial genomes from short read sequence data.
2018
Abstract Motivation The advent of next-generation sequencing has boosted the analysis of bacterial genome evolution. Insertion sequence (IS) elements play a key role in prokaryotic genome organization and evolution, but their repetitions in genomes complicate their detection from short-read data. Results PanISa is a software pipeline that identifies IS insertions ab initio in bacterial genomes from short-read data. It is a highly sensitive and precise tool based on the detection of read-mapping patterns at the insertion site. PanISa performs better than existing IS detection systems as it is based on a database-free approach. We applied it to a high-risk clone lineage of the pathogenic spec…
Simulation-based estimation of branching models for LTR retrotransposons
2017
Abstract Motivation LTR retrotransposons are mobile elements that are able, like retroviruses, to copy and move inside eukaryotic genomes. In the present work, we propose a branching model for studying the propagation of LTR retrotransposons in these genomes. This model allows us to take into account both the positions and the degradation level of LTR retrotransposons copies. In our model, the duplication rate is also allowed to vary with the degradation level. Results Various functions have been implemented in order to simulate their spread and visualization tools are proposed. Based on these simulation tools, we have developed a first method to evaluate the parameters of this propagation …
An Integrative Framework for the Construction of Big Functional Networks
2018
We present a methodology for biological data integration, aiming at building and analysing large functional networks which model complex genotype-phenotype associations. A functional network is a graph where nodes represent cellular components (e.g., genes, proteins, mRNA, etc.) and edges represent associations among such molecules. Different types of components may cohesist in the same network, and associations may be related to physical[biochemical interactions or functional/phenotipic relationships. Due to both the large amount of involved information and the computational complexity typical of the problems in this domain, the proposed framework is based on big data technologies (Spark a…
Methods for RNA Modification Mapping Using Deep Sequencing: Established and New Emerging Technologies
2019
New analytics of post-transcriptional RNA modifications have paved the way for a tremendous upswing of the biological and biomedical research in this field. This especially applies to methods that included RNA-Seq techniques, and which typically result in what is termed global scale modification mapping. In this process, positions inside a cell`s transcriptome are receiving a status of potential modification sites (so called modification calling), typically based on a score of some kind that issues from the particular method applied. The resulting data are thought to represent information that goes beyond what is contained in typical transcriptome data, and hence the field has taken to use …
The Role of Next-Generation Sequencing in the Diagnosis of Lysosomal Storage Disorders
2016
Next-generation sequencing (NGS) panels are used widely in clinical diagnostics to identify genetic causes of various monogenic disease groups including neurometabolic disorders and, more recently, lysosomal storage disorders (LSDs). Many new challenges have been introduced through these new technologies, both at the laboratory level and at the bioinformatics level, with consequences including new requirements for interpretation of results, and for genetic counseling. We review some recent examples of the application of NGS technologies, with purely diagnostic and with both diagnostic and research aims, for establishing a rapid genetic diagnosis in LSDs. Given that NGS can be applied in a w…
Inner Archipelagos in Sicily. From Culture-Based Development to Creativity-Oriented Evolution
2020
When Covid-19 arrived in Europe from the far East, the media and experts in economics and social sciences noticed that it was the expected discontinuity in the socio-economic development process. Really, the current phase has spread since the 1960s, when the application of econometric worldwide-spread development model was going to produce social inequalities, and consumption of physical, social, and cultural resources. Some places in Italy, far from the erosive and urban context and erosive metropolitan areas, are currently isolated seeds of a new cycle of life, because of the local community identity and the strong link between human, cultural, and natural components are currently working…
Innovative Green Technologies of Intensification for Valorization of Seafood and Their By-Products
2019
The activities linked to the fishing sector generate substantial quantities of by-products, which are often discarded or used as low-value ingredients in animal feed. However, these marine by-products are a prominent potential good source of bioactive compounds, with important functional properties that can be isolated or up-concentrated, giving them an added value in higher end markets, as for instance nutraceuticals and cosmetics. This valorization of fish by-products has been boosted by the increasing awareness of consumers regarding the relationship between diet and health, demanding new fish products with enhanced nutritional and functional properties. To obtain fish by-product-derived…
People with Disabilities and Disasters
2017
Investigations have collectively established that disasters affect people with disabilities both disproportionately and negatively. In addition, perceived disability status is often associated with stigma, creating a separate and unique barrier across societies and cultures, which can augment vulnerability to disasters. Relevant research is reviewed by academic genesis areas in this chapter, namely; 1) disaster-focused research, 2) mental health, 3) epidemiology and public health, and 4) disability studies. Research emanating from these disciplines reflects different epistemological assumptions about disability as well as varying knowledge about disability as a social and cultural const…
Comparing creative industries in Europe
2016
Creative industries are increasingly understood to contribute to localised innovation and dynamism. This paper provides a methodologically consistent comparison of creative industries across France, Great Britain, Italy and Spain. We map spatial agglomerations of creative activities showing evidence of urban concentration, which for Britain and France coincides with the dominance of capital cities, whilst for Spain and Italy, significant concentrations can also be found in secondary cities. The four countries also differ in the specialisation profiles and in the role played by policy makers. A lack of dove-tailing with the European Union smart agenda is argued to be a cause of concern.