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General Information

Full Name Alessandro Barberis
Languages Italian, English

Skills

Programming Languages R • Python • Java • bash • C • C++ • Matlab
Bioinformatics limma • DESeq2 • edgeR • clusterProfiler • biomaRt • Seurat • scanpy
Machine Learning Frameworks Scikit-learn • TensorFlow • Keras • PyTorch
Data Manipulation data.table • dplyr • stringr • Pandas • NumPy • Polars
Data Visualisation ggplot2 • plotly • DT • ComplexHeatmap • EnhancedVolcano
Reporting R markdown • Quarto • Jupyter Notebook
Pipeline Development Nextflow • Terra
Version Control & Code Collaboration Git • Bitbucket
High Performance Computing Google Cloud Platform • Cluster • GPU • FPGA
Database Development & Management SQL • MySQL • PostgreSQL • MariaDB • MongoDB • Hibernate
Front-end Development HTML • CSS • JavaScript • jQuery

Experience

  • 2024 - now
    Senior Computational Biologist
    Computational Biology Team
    WhiteLab Genomics, Paris, France
  • 2024 - now
    Consultant
    Insulin-like Growth Factor (IGF) group
    Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
  • 2024 - now
    Academic Visitor
    Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
  • 2023 - 2023
    Consultant
    Senya Therapeutics
  • 2022 - 2023
    Senior Postdoctoral Researcher
    Insulin-like Growth Factor (IGF) group
    Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
  • 2020 - now
    Lecturer in Bioinformatics for MSc in Precision Cancer Medicine
    Department of Oncology, University of Oxford, Oxford, United Kingdom
  • 2020 - 2021
    Lecturer in Statistics for MSc in Radiation Biology
    Department of Oncology, University of Oxford, Oxford, United Kingdom
  • 2014-2022
    Postdoctoral Researcher
    Computational Biology and Integrative Genomics (CBIG) group
    Department of Oncology, University of Oxford, Oxford, United Kingdom

Education

  • 2014
    PhD in Electronics, Computer Science, and Electrical Engineering
    Department of Engineering, University of Pavia, Pavia, Italy
  • 2010
    MSc in Computer Science Engineering
    Department of Engineering, University of Pavia, Pavia, Italy
  • 2007
    BSc in Computer Science Engineering
    Department of Engineering, University of Pavia, Pavia, Italy

Open Source Projects

  • 2023
    featscreen
    • R package providing ready-to-use functions for feature screening
  • 2023
    nf-rnaseq
    • Nextflow RNA-seq bioinformatics pipeline
  • 2022-now
    sigscores
    • R package providing ready-to-use functions to compute summary scores

Honors and Awards

  • 2013
    • 4th position at the Altera Design Contest Innovate Italy
  • 2010
    • PhD Scholarship funded by the Italian Ministry of Research and Education

Research Interests

  • Computational Cancer Biology
    • Identification of robust biomarkers to improve radiotherapy effectiveness
    • Derivation of robust multi-omic classifiers for clinical translation
  • Prostate Cancer Biology
    • Identification of insulin-like growth factors' (IGFs) contribution to prostate cancer biology
  • Data Analysis & Machine Learning
    • Development of novel robust and reproducible computational methodologies
    • Multimodal data integration

Other Interests

  • Hobbies: Reading novels, playing the guitar, cooking, visiting museums and art galleries