Biology subjects

Preste, R.

Publications and source records attributed to Preste, R..

3 recordsLinked to original sources

bioRxiv2019

Integration of genomic variation and phenotypic data using HmtPhenome

A full understanding of relationships between variants, genes, phenotypes and diseases is often overlooked when investigating mitochondrial functionality in both healthy and pathological situations. Gaining a comprehensive overview of this network can indeed offer interesting insights, and guide researchers and clinicians towards a full-spectrum knowledge of the mitochondrial system.\n\nGiven the current lack of tools addressing this need, we have developed HmtPhenome (https://www.hmtphenome.uniba.it), a new web resource that aims at providing a visual network of connections among variants, genes, phenotypes and diseases having any level of involvement in the mitochondrial functionality. Data are collected from several third party resources and aggregated on the fly, allowing users to clearly identify interesting relations between the involved entities. Tabular data with additional hyperlinks are also included in the output returned by HmtPhenome, so that users can extend their analysis with further information from external resources.

bioinformatics↗

bioRxiv2019

Human mitochondrial variant annotation with HmtNote

HmtNote is a Python package to annotate human mitochondrial variants from VCF files.\n\nVariants are annotated using a wide range of information, which are grouped into basic, cross-reference, variability and prediction subsets so that users can either select specific annotations of interest or use them altogether.\n\nAnnotations are performed using data from HmtVar, a recently published database of human mitochondrial variations, which collects information from several online resources as well as offering in-house pathogenicity predictions.\n\nHmtNote also allows users to download a local annotation database, that can be used to annotate variants offline, without having to rely on an internet connection.\n\nHmtNote is a free and open source package, and can be downloaded and installed from PyPI (https://pypi.org/project/hmtnote) or GitHub (https://github.com/robertopreste/HmtNote).

bioinformatics↗

bioRxiv2018

HmtVar: a brand-new resource for human mitochondrial variations and pathogenicity data

Human mitochondrial data are currently of great interest for both clinicians and researchers, due to the involvement of mitochondria in a number of physiological and pathological processes. Thanks to new sequencing technologies and modern databases, the huge amount of information about mitochondrial genome variability can be exploited to gain interesting insights into the relationship between DNA variants, phenotypes and diseases. For this reason, we have developed the new HmtVar resource, a variant-focused database which allows to explore a dataset of over 30000 human mitochondrial variants together with their pathogenicity prediction. Mitochondrial variation data, initially gathered from the HmtDB platform, are further integrated with in-house pathogenicity assessments based on well-established variants pathogenicity evaluation criteria, as well as with a set of additional annotations from third-party resources. This approach led to a comprehensive collection of information of crucial importance for human mitochondrial variation studies and investigation of common and rare diseases in which the mitochondrion is involved to some extent.\n\nHmtVar is accessible at https://www.hmtvar.uniba.it and its data can be retrieved using either a web interface through the Query page or a state-of-the-art API for programmatic access.

bioinformatics↗