Experience

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  Università degli studi di bari

  Mar 2019 - Mar 2020

  Internship trainee

  - Bioinformatic analysis and investigations at a single cell level regarding mitochondrial genomes. - mt-DNA comparison and variant annotation through a well-built pipeline using tools such as SRA Toolkit, FastQC, TrimGalore!, BWA, SAMtools, MToolBox and HmtVar - My effort resulted in a published paper on 'Genes' as a co-author

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  Consiglio nazionale delle ricerche

  May 2021 - Sept 2023

  Designing and building a relational database in order to collect, query, and further analyze both data and metadata of human gut and salivary microbiota in diverse pathological conditions. The activities are part of the OR 3.4 of the BIOMIS project (see here for more: http://www.ibiom.cnr.it/attivita/progetto-biomis-costituzione-della-biobanca-del-microbiota-intestinale-e-salivare-umano-dalla-disbiosi-alla-simbiosi/) and they have been carried out using R Shiny platform in order to produce a web app that is able to query a previously created relational database, allowing users to download filtered datasets and perform data visualization trials on them. By doing so, box plots, scatter plots, and other kinds of plots are produced and can be downloaded in ready-to-publish pdf format files.You can reach the end product via the link below.Please note that due to the source of our data, which is mostly personal and private, authentication is required in order to view the content. Feel free to contact me if you want to access it or if you simply would like to know more about it. I will leave a couple of screens below to showcase what I managed to produce. Show less Working on the HmtDB project, improving and updating one of the most relevant human mitochondrial databases and resources out there. HmtDB is an open resource created to support population genetics and mitochondrial disease studies, part of the Elixir Data Resources (https://elixir-europe.org/services/tag/genes-and-genomes). The database hosts human mitochondrial genome sequences annotated with population and variability data. Classifier tools implemented in HmtDB allow the prediction of the haplogroup for any human mitochondrial genome currently stored in HmtDB or externally submitted de novo by an end-user.HmtDB hosts human mitochondrial genomes derived from the public primary INSDC databases, personal submissions, and the application of the MToolBox pipeline to NGS data, such as genomes coming from the 1000Genomes project.My role consisted of general updates of the database, upgrades of resources and data, and major bug fixes. Furthermore, I moved the whole platform to an upgraded version of Ubuntu for safety reasons, I fixed the APIs (the RD-connect one and the in-house-developed basic API) which had both functional issues, and I restored the download of multi-alignments and site-variability data.Lastly, I performed a full updating stage of DB data with new entries from the GenBank source.*CURRENTLY UNMANTAINED* Show less

  • Assegnista di ricerca

    Jun 2023 - Sept 2023

  • Assegnista di ricerca

    Jun 2022 - May 2023

  • Assegnista di ricerca

    May 2021 - May 2022
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  European school of molecular medicine (semm)

  Oct 2023 - now

  Phd student in computation biology

  Recent advances in sequencing technologies have paved the way for personalized medicine and clinical genomics, providing unprecedented insights into the genetic basis of human health and disease. The recent introduction of long-read technologies can resolve genomic regions inaccessible to short-read sequencing, but a reliable benchmark assessment is missing yet. The early part of my project presents a comparative evaluation of long-read and short-read sequencing data, aiming at elucidating their strengths and limitations through the investigation of family pedigrees, which represents a powerful approach for the identification of transmitted alleles and/or de novo mutations. We investigated a family trio with a pediatric proband affected by a rare disease for which WGS analysis based on short reads resulted in ineffective diagnosis. Our results confirmed the powerful impact of long-read technologies on genotyping accuracy and the identification of complex genomic rearrangements, showing unmatched effectiveness on repetitive regions and structural variations, promising results that can open unprecedented doors to possibly determine a diagnosis for this tough case.I already presented my early results at the notorious HUGO international congress in Rome in April 2024, as well as showcasing them at the SIBBM congress in Trento (where I was awarded a travel grant) and FEBS-CIB congress in Milan, between June and July 2024.The intense benchmarking activity led to a complete workflow published in September 2024 on protocols.io Show less