19 Result(s)
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Tiziana Castrignanò
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Article
Open AccessIntegrated de novo transcriptome of Culex pipiens mosquito larvae as a resource for genetic control strategies
We present a de novo transcriptome of the mosquito vector Culex pipiens, assembled by sequences of susceptible and insecticide resistant larvae. The high quality of the assembly was confirmed by TransRate and BUS...
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Chapter and Conference Paper
IGUANER - DIfferential Gene Expression and fUnctionAl aNalyzER
In the past fifteen years, the advent of Next-Generation Sequencing technologies, characterized by high efficiency and reduced costs, has marked a pivotal turn for research across various fields including mole...
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Article
Open AccessDe novo transcriptome assembly of an Antarctic nematode for the study of thermal adaptation in marine parasites
Understanding the genomic underpinnings of thermal adaptation is a hot topic in eco-evolutionary studies of parasites. Marine heteroxenous parasites have complex life cycles encompassing a free-living larval s...
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Article
Open AccessDe novo transcriptome assembly and annotation for gene discovery in Salamandra salamandra at the larval stage
Dispersal is a key process in ecology and evolutionary biology, as it shapes biodiversity patterns over space and time. Attitude to disperse is unevenly distributed among individuals within populations, and th...
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Article
Open AccessBrain de novo transcriptome assembly of a toad species showing polymorphic anti-predatory behavior
Understanding the genomic underpinnings of antipredatory behaviors is a hot topic in eco-evolutionary research. Yellow-bellied toad of the genus Bombina are textbook examples of the deimatic display, a time-struc...
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Article
Open AccessDe novo transcriptome assembly and annotation of the third stage larvae of the zoonotic parasite Anisakis pegreffii
Anisakis pegreffii is a zoonotic parasite requiring marine organisms to complete its life-history. Human infection (anisakiasis) occurs when the third stage larvae (L3) are accidentally ingested with raw or under...
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Chapter and Conference Paper
ParSMURF-NG: A Machine Learning High Performance Computing System for the Analysis of Imbalanced Big Omics Data
In the context of Genomic and Precision Medicine, prediction problems are often characterized by a high imbalance between classes and Big Data. This requires specialized tools, as traditional Machine Learning ...
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Protocol
RNA Editing Detection in HPC Infrastructures
RNA editing by A-to-I deamination is a relevant co/posttranscriptional modification carried out by ADAR enzymes. In humans, it has pivotal cellular effects and its deregulation has been linked to a variety of ...
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Protocol
RAP: A Web Tool for RNA-Seq Data Analysis
Since 1950 main studies of RNA regarded its role in the protein synthesis. Later insights showed that only a small portion of RNA codes for proteins where the rest could have different functional roles. With t...
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Article
Open AccessA gene expression atlas for different kinds of stress in the mouse brain
Stressful experiences are part of everyday life and animals have evolved physiological and behavioral responses aimed at co** with stress and maintaining homeostasis. However, repeated or intense stress can ...
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Article
Open AccessHPC-REDItools: a novel HPC-aware tool for improved large scale RNA-editing analysis
RNA editing is a widespread co-/post-transcriptional mechanism that alters primary RNA sequences through the modification of specific nucleotides and it can increase both the transcriptome and proteome diversi...
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Article
Open AccessELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community
The advent of Next Generation Sequencing (NGS) technologies and the concomitant reduction in sequencing costs allows unprecedented high throughput profiling of biological systems in a cost-efficient manner. Mo...
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Article
Open AccessCoVaCS: a consensus variant calling system
The advent and ongoing development of next generation sequencing technologies (NGS) has led to a rapid increase in the rate of human genome re-sequencing data, paving the way for personalized genomics and prec...
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Article
Open AccessGenetic dissection of Sharka disease tolerance in peach (P. persica L. Batsch)
Plum pox virus (PPV), agent of Sharka disease, is the most important quarantine pathogen of peach (P. persica L. Batsch). Extensive evaluation of peach germplasm has highlighted the la...
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Article
Open AccessRAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application
The study of RNA has been dramatically improved by the introduction of Next Generation Sequencing platforms allowing massive and cheap sequencing of selected RNA fractions, also providing information on strand...
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Protocol
Exploring the RNA Editing Potential of RNA-Seq Data by ExpEdit
Revealing the impact of A-to-I RNA editing in RNA-Seq experiments is relevant in humans because RNA editing can influence gene expression. In addition, its deregulation has been linked to a variety of human di...
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Article
General features of the transcriptional response of mammalian cells to low- and high-LET irradiation
To understand the general features of the transcriptional response of mammalian cells to ionizing radiation we performed a meta-analysis of a transcriptomic dataset referring to 202 different irradiation condi...
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Article
Open AccessWEP: a high-performance analysis pipeline for whole-exome data
The advent of massively parallel sequencing technologies (Next Generation Sequencing, NGS) profoundly modified the landscape of human genetics.
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Article
Open AccessThe MEPS server for identifying protein conformational epitopes
One of the most interesting problems in molecular immunology is epitope map**, i.e. the identification of the regions of interaction between an antigen and an antibody. The solution to this problem, even if ...
