Publications by authors named "Pietro Mandreoli"
Technological advances in high-throughput technologies improve our ability to explore the molecular mechanisms of life. Computational infrastructures for scientific applications fulfil a critical role in harnessing this potential. However, there is an ongoing need to improve accessibility and implement robust data security technologies to allow the processing of sensitive data, particularly human genetic data.
View Article and Find Full Text PDFrCASC is a modular workflow providing an integrated environment for single-cell RNA-seq (scRNA-Seq) data analysis exploiting Docker containers to achieve functional and computational reproducibility. It was initially developed as an R package usable also through a Java GUI. However, the Java frontend cannot be employed when running rCASC on a remote server, a typical setup due to the significant computational resources commonly needed to analyze scRNA-Seq data.
View Article and Find Full Text PDFBackground: Improving the availability and usability of data and analytical tools is a critical precondition for further advancing modern biological and biomedical research. For instance, one of the many ramifications of the COVID-19 global pandemic has been to make even more evident the importance of having bioinformatics tools and data readily actionable by researchers through convenient access points and supported by adequate IT infrastructures. One of the most successful efforts in improving the availability and usability of bioinformatics tools and data is represented by the Galaxy workflow manager and its thriving community.
View Article and Find Full Text PDFIn diploid organisms, two copies of each allele are normally inherited from parents. Paternal and maternal alleles can be regulated and expressed unequally, which is referred to as allele-specific expression (ASE). In this work, we present aScan, a novel method for the identification of ASE from the analysis of matched individual genomic and RNA sequencing data.
View Article and Find Full Text PDFMotivation: Clinical applications of genome re-sequencing technologies typically generate large amounts of data that need to be carefully annotated and interpreted to identify genetic variants potentially associated with pathological conditions. In this context, accurate and reproducible methods for the functional annotation and prioritization of genetic variants are of fundamental importance.
Results: In this article, we present VINYL, a flexible and fully automated system for the functional annotation and prioritization of genetic variants.
Summary: While over 200 000 genomic sequences are currently available through dedicated repositories, ad hoc methods for the functional annotation of SARS-CoV-2 genomes do not harness all currently available resources for the annotation of functionally relevant genomic sites. Here, we present CorGAT, a novel tool for the functional annotation of SARS-CoV-2 genomic variants. By comparisons with other state of the art methods we demonstrate that, by providing a more comprehensive and rich annotation, our method can facilitate the identification of evolutionary patterns in the genome of SARS-CoV-2.
View Article and Find Full Text PDFBackground: While the popular workflow manager Galaxy is currently made available through several publicly accessible servers, there are scenarios where users can be better served by full administrative control over a private Galaxy instance, including, but not limited to, concerns about data privacy, customisation needs, prioritisation of particular job types, tools development, and training activities. In such cases, a cloud-based Galaxy virtual instance represents an alternative that equips the user with complete control over the Galaxy instance itself without the burden of the hardware and software infrastructure involved in running and maintaining a Galaxy server.
Results: We present Laniakea, a complete software solution to set up a "Galaxy on-demand" platform as a service.