Monah Abou Alezz, PhD bio photo

Monah Abou Alezz, PhD

Postdoctoral researcher | Senior computational biologist | Trainer.

Welcome to my research world. Highlighting my academic and research journey.

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Curriculum vitae

Professional Summary

Computational biologist with 10+ years of experience in multi-omics data analysis, pipeline development, and biomedical research. Proven expertise in genomics, transcriptomics, proteomics, and single-cell analyses, with strong programming skills in R, Python, and Bash. Published author with 10+ peer-reviewed articles in high-impact journals (Nature Communications, Nature Cell Biology, EMBO J, J Exp Med). Passionate educator with 30+ international workshops delivered across Europe and the USA. Seeking to leverage computational expertise and research leadership in advancing precision medicine and therapeutic innovation.

Professional Experience

August 2025 - Present Freelance Bioinformatician, Sepal AI, California, USA

  • Design and implement custom AI tools and AI-driven analytical workflows to accelerate biomedical research
  • Develop bioinformatics pipelines and generate publication-ready visualizations for clients

October 2020 - Present Postdoctoral Researcher | Senior Computational Biologist, San Raffaele Telethon Institute for Gene Therapy (TIGET), Milan, Italy

  • Lead computational analyses for genomics, transcriptomics, proteomics, and single-cell datasets supporting gene therapy research
  • Develop and maintain reproducible bioinformatics pipelines for high-throughput sequencing data (RNA-seq, scRNA-seq, ChIP-seq, ATAC-seq)
  • Collaborate with two research groups: Retrovirus-Host Interactions and Innate Immunity (Prof. Anna Kajaste-Rudnitski) and Human Hematopoietic Development and Disease Modeling (Prof. Andrea Ditadi)
  • Co-author 10+ publications in high-impact journals including Nature Communications, Nature Cell Biology, EMBO J, and J Exp Med

September 2021 - September 2023 Data Carpentry Lessons Maintainer, The Carpentries Organization, California, USA

  • Maintained and updated core lessons for the Data Carpentry curriculum
  • Reviewed community submissions, led discussions on pedagogical standards, and established best practices

October 2017 - September 2020 PhD Researcher, Institute of Molecular Genetics Luigi Luca Cavalli-Sforza, National Research Council, Pavia, Italy

  • Led bioinformatics research project on genomic and splicing characterization of long non-coding RNAs
  • Developed the GencoDymo R package for GENCODE database analysis (published and cited)
  • Supervised by Prof. Silvia Bione within the Computational Biology Unit

July 2017 - October 2017 ERASMUS+ Research Trainee, Polish Academy of Sciences, Poznan, Poland

  • Conducted integrated wet-lab/bioinformatics project characterizing miRNA features and functions
  • Gained expertise in computational methods for small-RNA data analysis under Prof. Jorge A. Pinto Paiva

November 2015 - July 2017 Master’s Research Intern, University of Pavia, Pavia, Italy

  • Executed wet-lab research on the influence of divalent cations on DNA methylation and chromatin structure
  • Utilized advanced microscopy techniques for ultrastructural analysis; supervised by Prof. Marco Biggiogera

Teaching & Training Experience

July 2025 - Present Freelance Trainer, Global Horizon Training Center, London, United Kingdom

  • Deliver in-person workshops on applied data science and AI for corporate professionals
  • Focus on data analysis workflows, reproducible research, and model interpretation

May 2025 - Present Associated Partner, MiCCrobioTackle Consortium - Leibniz Institute, Jena, Germany

  • Deliver hands-on bioinformatics training workshops to PhD students within the EU-funded consortium MiCCrobioTackle

March 2024 - Present Bioinformatics Trainer, German Cancer Research Center (DKFZ), Heidelberg, Germany

  • Organize and deliver PhD-level courses in bioinformatics analyses including programming, data visualisation, omics analyses, project organisation and scientific writing.

January 2023 - Present Bioinformatics Trainer, Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany

  • Design and deliver bioinformatics workshops for graduate and postgraduate researchers
  • Train researchers in computational approaches for biological data analysis

September 2024 Summer School Trainer, EMERALD International PhD Program, Berlin, Germany

  • Delivered 2-day intensive workshop on “Advanced Techniques for Data Visualization using R”

September 2019 - Present Certified Instructor, The Carpentries Organization, California, USA

  • Teach foundational coding and data science skills to researchers worldwide
  • Delivered 30+ workshops across Europe, USA, and Saudi Arabia
  • Selected Workshops:
    • Harvard Stem Cell Institute – Genomics: Variant Calling Workflow (AWS)
    • US Centers for Disease Control (CDC) – Genomics: Variant Calling Workflow (AWS)
    • Jackson Laboratory – Genomics: Variant Calling Workflow (AWS)
    • Genentech (Roche) – Data Analysis and Visualization in R
    • Max Delbrück Center (MDC) – Genomics: Variant Calling Workflow (AWS)
    • Saudi Food and Drug Authority (sFDA) – Data Analysis and Visualization in R
    • NIH National Library of Medicine – Library Carpentry: Databases and SQL

October 2018 - September 2020 Bioinformatics Teaching Assistant, University of Pavia, Pavia, Italy

  • Delivered practical sessions for the Bioinformatics Course (Master’s in Molecular Biology and Genetics)

Education

2017 - 2020 PhD in Genetics, Molecular and Cellular Biology University of Pavia, Pavia, Italy

  • Thesis: Characterization of Genomic and Splicing Features of Long Non-Coding RNAs
  • Conducted at the Institute of Molecular Genetics Luigi Luca Cavalli-Sforza (CNR)

2015 - 2017 Master’s Degree in Molecular Biology and Genetics University of Pavia, Pavia, Italy

2012 - 2015 Bachelor’s Degree in Earth and Life Sciences Lebanese University, Lebanon

Technical Skills

Programming & Scripting

  • R, Python, Bash, Perl, Julia

Bioinformatics & Data Analysis

  • Multi-omics analysis: genomics, transcriptomics, proteomics, metabolomics, lipidomics
  • High-throughput sequencing: RNA-seq, scRNA-seq, ChIP-seq, ATAC-seq, Spatial transcriptomics
  • Bioinformatics analyses workflows using Snakemake and Nextflow
  • Machine learning for biological data and predictive modeling

Tools & Platforms

  • Cloud computing: AWS (EC2, S3, Glacier), Alibaba Professional
  • Version control: Git, GitHub, GitLab, Bitbucket
  • Databases: SQL, biological databases (GENCODE, Ensembl, UCSC)
  • Visualization: ggplot2, GraphPad, Adobe Photoshop, ImageJ
  • Interactive web applications using Shiny

Operating Systems

  • Linux, macOS, Windows

Wet Laboratory

  • Microscopy: electron microscopy, fluorescence microscopy, light microscopy
  • Molecular biology: DNA/RNA extraction, PCR, cloning, western blot, ELISA
  • Microbiology: bacterial culture, gram staining, biochemical testing

Languages

  • Arabic – Native
  • English – Proficient (C1)
  • Italian – Upper Intermediate (B2)
  • French – Elementary (A2)
  • Polish – Elementary (A2)

Projects

March 2024 - February 2025 EARLY – dEsigning an ARtificial inteLligence-based sYstem, University of Macerata, Italy

  • Multidisciplinary project involving medical doctors, engineers, lawyers, and researchers
  • Designed an AI tool for improving diagnosis, treatment, and monitoring of patients with rare diseases while preserving fundamental rights by law

Awards & Grants

2021 James Taylor Fellowship – Galaxy Community Conference (GCC2021) 2019 Best Poster Prize – EMBL-EMBO Symposium: The Non-Coding Genome 2018 Fellowship Grant – AIRC Foundation 2018 Travel Grant – INTEROMICS 2017 Fellowship Grant – Besta Neurological Institute 2017 ERASMUS+ Fellowship – University of Pavia 2015 EDiSU Full Scholarship – University of Pavia

Student Supervision

Master’s Students: Salviati L (2019), Nicastro A (2019), Belotti G (2019), Celli L (2018), Postiglione U (2018), Monaco L (2017)

Bachelor’s Students: Roasria S (2020), Baldrighi GN (2018)

Publications

For complete publication list, see Publications

First Author:

  • Abou Alezz M et al. (2020) GC-AG Introns Features in Long Non-Coding and Protein-Coding Genes Suggest Their Role in Gene Expression Regulation. Front. Genet. doi:10.3389/fgene.2020.00488

Last Author:

  • El Boustani M, Mouawad N, Abou Alezz M. (2024) AP3M2: A key regulator from the nervous system modulates autophagy in colorectal cancer. Tissue Cell. doi:10.1016/j.tice.2024.102593

Co-Author (Selected):

  • Costa-Verdera H, …, Abou Alezz M, et al. (2025) AAV vectors trigger DNA damage response-dependent pro-inflammatory signalling. Nat Commun. doi:10.1038/s41467-025-58778-3
  • Scarfò R, …, Abou Alezz M, et al. (2024) CD32 captures committed haemogenic endothelial cells. Nat Cell Biol. doi:10.1038/s41556-024-01403-0
  • Valeri E, …, Abou Alezz M, et al. (2024) A novel STING variant triggers endothelial toxicity and SAVI disease. J Exp Med. doi:10.1084/jem.20232167
  • Unali G, …, Abou Alezz M, et al. (2023) Interferon-inducible phospholipids govern IFITM3-dependent endosomal antiviral immunity. EMBO J. doi:10.15252/embj.2022112234

Book Chapter:

  • Abou Alezz M (2024) AI Bioinformatics Systems for Rare Diseases. In: Diritto, Intelligenza Artificiale e Medicina. Edizioni Scientifiche Italiane. ISBN: 978-88-495-5722-0

Software:

  • NatChat (2025) – R package for LLM-based interaction with Nature journals. doi:10.5281/zenodo.15482472
  • GencoDymo2 (2025) – GENCODE annotation analysis. doi:10.5281/zenodo.15302316
  • GencoDymo (2020) – GENCODE database extraction tools. doi:10.5281/zenodo.3605995

Contact

Last updated: 2026-02-08