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barbavegeta/README.md

Hi, I’m Salvatore

Bioinformatics · Statistical Genetics · Health Data Science
London, United Kingdom

About Me

Biomedical scientist with 7+ years in clinical and genomic laboratories (UCLH, CooperGenomics), now working on computational analysis of genomic and clinical data: sequencing pipelines, Mendelian randomisation, single-cell transcriptomics and longitudinal models of disease progression.

Featured Projects

Parkinson's disease & GPNMB

Project What it does
Proteome-wide MR scan Nextflow pipeline testing ~2,900 plasma proteins as causal candidates for PD (cis-MR + colocalisation)
GPNMB MR & colocalisation MSc dissertation: MR, Bayesian colocalisation and SuSiE for GPNMB in PD
GPNMB single-nucleus RNA-seq Donor-aware pseudobulk analysis of 83k substantia nigra nuclei
PPMI progression models Mixed-effects and Cox models of motor and cognitive decline in 1,789 patients
GPNMB & glioma survival Pre-specified, confounding-aware Cox analysis of TCGA glioma

Genomics, health data & ML

Project What it does
Synthea → OMOP + RAG FHIR to OMOP CDM with dbt, then cited RAG over clinical notes, evaluated against SQL
RegulonML Predicting regulatory variant effects in unseen promoters from sequence and TF motifs
M. tuberculosis WGS workflow Galaxy workflow from QC to annotated resistance variants
RNA-seq Nextflow pipeline Containerised FASTQ → DESeq2 workflow
More projects

Tech Stack

Languages: Python · R · SQL · Bash
Bioinformatics: Nextflow · STAR · HISAT2 · SAMtools · bcftools · DESeq2
Statistics: Mendelian randomisation · coloc · SuSiE · mixed-effects · survival analysis
Data & Cloud: PostgreSQL · dbt · OMOP · Docker · AWS · Google Cloud
Visualisation: ggplot2 · matplotlib · seaborn · Tableau

Education

MSc Bioinformatics · Atlantic Technological University · 2025–2026
MSc Cell & Gene Therapy · University College London · 2021–2023
BSc Biomedical Science · University of Catania · 2014–2017

Certifications
  • Johns Hopkins: Genomic Data Science Specialization
  • Wellcome: Bioinformatics for Biologists (Linux, Bash, R) · Analysing and Interpreting Genomics Datasets
  • Ulster University: Coding Skills for Biologists
  • IBM: Machine Learning · AI Engineering
  • Google: Data Analytics · Advanced Data Analytics · IT Automation with Python · Project Management · Business Intelligence
  • Google Cloud: Architecting with Google Kubernetes Engine
  • AWS: Cloud Practitioner Essentials · Cloud Solutions Architect
  • freeCodeCamp: Data Analysis with Python · Relational Databases · Scientific Computing with Python
  • DE<code>LIFE: Genomes, Networks & Pathways · Data Science & Machine Learning with Python

Pinned Loading

  1. mtb-wgs-galaxy-workflow mtb-wgs-galaxy-workflow Public

    Galaxy-based WGS variant analysis workflow for Mycobacterium tuberculosis, covering QC, alignment, coverage assessment, variant calling, annotation, and IGV-supported interpretation of resistance-a…

  2. RNA-seq_Nextflow_Pipeline_with_Docker RNA-seq_Nextflow_Pipeline_with_Docker Public

    Minimal end-to-end RNA-seq pipeline: FASTQ -> FastQC -> cutadapt -> STAR -> sorted BAM -> featureCounts -> MultiQC → DESeq2

    HTML 5

  3. Genomic_Data_Science_Specialization Genomic_Data_Science_Specialization Public

    Personal solutions, scripts, and command logs from the Johns Hopkins Genomic Data Science Specialization (alignment, RNA-seq, variant calling, and database querying).

    Jupyter Notebook 1

  4. Google_Advanced_Data_Analytics-Salifort_Motors Google_Advanced_Data_Analytics-Salifort_Motors Public

    HR analytics capstone for the Google Advanced Data Analytics certificate, building classification models to understand and predict employee attrition at Salifort Motors.

    HTML

  5. Google_Advanced_Data_Analytics-TikTok_Project Google_Advanced_Data_Analytics-TikTok_Project Public

    Google Advanced Data Analytics project analysing TikTok engagement data to uncover content patterns and factors linked to higher user interaction.

    Jupyter Notebook

  6. GPNMB-Parkinson-MR-Colocalisation GPNMB-Parkinson-MR-Colocalisation Public

    MSc Bioinformatics project investigating GPNMB in Parkinson's disease using Mendelian randomisation, LD-aware sensitivity analysis, Bayesian colocalisation and SuSiE.

    R