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

Personal Information

  • Address: Via Adolfo Ferrata 17, Pavia 27100 (PV), Italy
  • Email: aboualezz.monah@hsr.it

Professional Experience

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

  • Designed and implemented genomics, transcriptomics and proteomics data analyses, pipelines, and algorithms for biomedical research
  • Devised experiments and supported the research in the following research groups: (i) Retrovirus‑host interactions and innate immunity to gene transfer of Prof. Anna Kajaste‑Rudnitski, and (ii) Human hematopoietic development and disease modeling of Prof. Andrea Ditadi
  • Collaborate with leading researchers to support groundbreaking studies

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

  • Maintained core lessons for the Data Carpentry program
  • Reviewed submissions, discussions of change and set standards for the organization as a whole

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

  • Led a bioinformatics research project titled ’Characterization of Genomic and Splicing Features of Long Non‑Coding RNAs’ within the Computational Biology Unit supervised by Prof. Silvia Bione

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

  • Executed an integrated wet‑lab/bioinformatics project to characterize miRNA features and functions.
  • Gained hands‑on experience with computational methods and tools for small‑RNA data analysis under the supervision of Prof. Jorge A. Pinto Paiva

November 2015 - July 2017 Masters Internship, University of Pavia - Department of Biology and Biotechnology L.Spallanzani, Pavia - Italy

  • Executed a wet-lab research project titled ‘Influence of divalent cations on DNA methylation and the modulation of chromatin structure in an in situ ultrastructural study’ supervised by Prof. Marco Biggiogera

Teaching Experience

May 2025 - Current Associated Partner, MiCCrobioTackle - Leibniz Institute for Natural Product Research and Infection Biology, Jena - Germany

  • Delivering hands-on bioinformatics training workshops to PhD students within the MICCROBIOTACKLE consortium.

September 24 2024 - September 25 2024 Summer School Trainer, EMERALD Internation PhD Program for Medical Doctors, Berlin - Germany

  • Delivered a 2‑day workshop in ‘Advanced Techniques for Data Visualisation using R Programming Language’.

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

  • Organized and delivered PhD courses in the usage of R programming language for Bioinformatics analyses.

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

  • Bioinformatics workshops instructor and organizer
  • Training graduate and post-graduate biologists in Bioinformatics analyses

September 2019 - Current Software and Data Carpentry Instructor, The Carpentries organization, California - USA

  • Teaching foundational coding and data science skills to researchers in worldwide workshops
  • 30+ workshops delivered in Europe, USA and Saudi Arabia
  • Selected workshops:
    • Harvard Stem Cell Institute: Genomics workshop instructor: Variant calling workflow using AWS
    • United States Centers for Disease Control (CDC): Genomics workshop instructor: Variant calling workflow using AWS
    • Jackson Laboratory: Genomics workshop instructor: Variant calling workflow using AWS
    • Genentech, A member of the Roche group: Data Carpentry instructor: Data analysis and visualization in R
    • Max Delbrück Center for Molecular Medicine (MDC): Genomics workshop instructor: Variant calling workflow using AWS
    • Rutgers University: Genomics workshop instructor: Project management/ Introduction to cloud computing
    • Saudi Food and Drug Authority (sFDA): Data analysis and visualization in R
    • Atlanta University Center: Genomics workshop instructor: Variant calling workflow using AWS
    • George Washington University: Genomics workshop instructor: Variant calling workflow using AWS
    • NIH Network of the National Library of Medicine: Library Carpentry instructor: Databases and SQL
    • Florida International University: Software Carpentry instructor: R for reproducible analysis

October 2018 - September 2020 Bioinformatics Tutor, University of Pavia, Pavia - Italy

  • Bioinformatics Course - Masters in Molecular Biology and Genetics
  • Training and practical sessions in bioinformatics tools

Education

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

2015 - 2017 University of Pavia, Masters Degree in Molecular Biology and Genetics

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

Skills

Bioinformatics Skills

  • Extensive experience in -omics data analysis: Expertise in genomics, transcriptomics, proteomics, and metabolomics data interpretation and integration
  • Advanced Proficiency in High-Throughput Sequencing Data Analysis: In-depth analysis of RNA-seq, single-cell RNA-seq, ChIP-seq, and ATAC-seq datasets, including quality control, alignment, differential expression analysis, and peak calling
  • Extensive experience in programming languages: R, Python, Bash, Perl, Julia
  • Skilled in leveraging cloud platforms, particularly AWS, for large-scale data processing and storage solutions
  • Proficient in applying machine learning algorithms and techniques to biological data for predictive modeling and pattern recognition
  • Comprehensive knowledge of Windows 7/8/10, macOS, and Linux environments
  • Expertise in Git, Bitbucket, Gitlab and GitHub for collaborative development, version tracking, and source code management
  • Basic knowledge in SQL for querying and managing biological databases.
  • Proficient in Microsoft Office Suite for professional documentation, data presentation, and communication.
  • Image Analysis and Visualization Software: Skilled in using Adobe Photoshop, ImageJ, Cell F, and GraphPad for image analysis, scientific visualization, and figure preparation.

Wet Laboratory Skills

  • Proficient in Microscopy utilization and samples preparation: electron microscopy (ZEISS EM 900), electron spectroscopic imaging, fluorescence microscopy, light microscopy (bright field, dark field, phase contrast, DIC)
  • Proficient in molecular biology lab techniques: DNA/RNA extraction, PCR, gene cloning, protein extraction, western blot, ELISA
  • Proficient in microbiology laboratory techniques: gram staining, bacterial cell culture, antibiotic specificity, bacterial identification biochemical testing.

Language Skills

  • Mother-tongue Language: Arabic
  • Proficient in English (C1) and Italian (B2) Languages
  • Novice in French (A2) and Polish (A2) Languages

Awards

2021 James Taylor Fellowship, 2021 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

Student research supervision

2020 Roasria S (BSc)

2019 Salviati L (MSc); Nicastro A (MSc); Belotti G (MSc);

2018 Celli L (MSc); Postiglione U (MSc); Baldrighi GN (BSc)

2017 Monaco L (MSc)

Publications

Articles

2025 Paillet J, Gaudeaux P, Abou Alezz M, Moirangthem RD, Cascione S, Corredera MM, Dolens AC, De Mulder K, Velghe I, Lavaert M, Vandekerckhove B, Noémie R, Corneau A, Sadek H, Rault P, Joshi A, De La Grange P, Staal F, Taghon T, Olivier N, Ditadi A, André I, Soheili TS. Ex vivo-generated lymphoid progenitors encompass both T cell and innate lymphoid cell fates. Front Immunol. 2025. doi: 10.3389/fimmu.2025.1617707

2025 Costa-Verdera H, Meneghini V, Fitzpatrick Z, Abou Alezz M, Fabyanic E, Hunag X, Dzhashiashvili Y, Ahiya A, Mangiameli E, Valeri E, Crivicich G, Piccolo S, Cuccovillo I, Caccia R, Kai Chan Y, Bertin B, Ronzitti G, Engel EA, Merelli I, Mingozzi F, Gritti A, Kuranda K, Kajaste-Rudnitski A. AAV vectors trigger DNA damage response-dependent pro-in ammatory signalling in human iPSC-derived CNS models and mouse brain. Nat Commun. 2025. doi: 10.1038/s41467-025-58778-3

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

2024 Valeri E, Breggion S, Barzaghi F, Abou Alezz M, Crivicich G, Pagani I, Forneris F, Sartirana C, Costantini M, Costi S, Marino A, Chiarotto E, Colavito D, Cimaz R, Merelli I, Vicenzi E, Aiuti A, Kajaste‐Rudnitski A. A novel STING variant triggers endothelial toxicity and SAVI disease. J Exp Med. 2024. doi: 10.1084/jem.20232167

2024 Scarfò R, Randolph LN, Abou Alezz M, El Khoury M, Gersch A, Li Z, Luff S, Tavosanis A, Ramondo GF, Valsoni S, Cascione S, Didelon E, Passerini L, Amodio G, Brandas C, Villa A, Gregori S, Merelli I, Freund JN, Sturgeon C, Tavian M, Ditadi A. CD32 captures committed haemogenic endothelial cells during human embryonic development. Nat Cell Biol. 2024. doi: 10.1038/s41556‐024‐01403‐0

2023 Valeri E, Unali G, Piras F, Abou Alezz M, Pais G, Benedicenti F, Lidonnici MR, Cuccovillo I, Castiglioni I, Arévalo S, Spinozzi G, Merelli I, Behrendt R, Oo A, Kim B, Landau NR, Ferrari G, Montini E, Kajaste-Rudnitski A. Removal of innate immune barriers allows efficient transduction of quiescent human hematopoietic stem cells. Mol Ther. 2023. doi: 10.1016/j.ymthe.2023.11.020

2023 Unali G, Crivicich G, Pagani I, Abou Alezz M, Folchini F, Valeri E, Matafora V, Reisz JA, Giordano AMS, Cuccovillo I, Butta GM, Donnici L, D’Alessandro A, De Francesco R, Manganaro L, Cittaro D, Merelli I, Petrillo C, Bachi A, Vicenzi E, Kajaste-Rudnitski A. Interferon-inducible phospholipids govern IFITM3-dependent endosomal antiviral immunity. EMBO J. 2023. doi.org/10.15252/embj.2022112234

2023 Giordano AMS, Abou Alezz M, Merelli I, Kajaste-Rudnitski A. Protocol to differentiate monolayer human induced pluripotent stem cells into inflammatory responsive astrocytes. STAR Protoc. 2023. doi.org/10.1016/j.xpro.2023.102142

2022 Giordano AMS, Luciani M, Gatto F, Abou Alezz M, Begh C, Della Volpe L, Migliara A, Valsoni S, Genua M, Dzieciatkowska M, Frati G, Tahraoui-Bories J, Giliani SC, Orcesi S, Fazzi E, Ostuni R, D’Alessandro A, Di Micco R, Merelli I, Lombardo A, Reijns MAM, Gromak N, Gritti A, Kajaste-Rudnitski A. DNA damage contributes to neurotoxic inflammation in Aicardi-Gouti res syndrome astrocytes. J Exp Med. 2022. doi.org/10.1084/jem.20211121

2020 Abou Alezz M, Celli L, Belotti G, Lisa A and Bione S. GC-AG Introns Features in Long Non-coding and Protein-Coding Genes Suggest Their Role in Gene Expression Regulation. Front. Genet. 2020 11:488. doi:10.3389/fgene.2020.00488

Book Chapters

2024 Abou Alezz M, Artificial Intelligence Bioinformatics Systems for the Diagnosis and Treatment of Rare Diseases: Integration and Implementation. In: Vulpiani G (ed.) Diritto, Intelligenza Artificiale e Medicina. Un dialogo interdisciplinare. Napoli: Edizioni Scientifiche Italiane. 2024. ISBN: 978-88-495-5722-0

Software

2025 Abou Alezz M. NatChat: Chatting with Nature Journals Current Issue using a local Language Model. R-package version 1.1.0. https://monahton.github.io/NatChat. 2025. doi:10.5281/zenodo.15482472

2025 Abou Alezz M. GencoDymo2: Comprehensive Analysis of GENCODE Annotations and Splice Site Motifs. R-package version 1.0.1. https://github.com/monahton/GencoDymo2. 2025. doi:10.5281/zenodo.15302316

2020 Abou Alezz M, Salviati L, Alfieri R, Bione S. GencoDymo: Data Extraction and Manipulation from the GENCODE Database. R-package version 0.2.1. https://github.com/monahton/GencoDymo. 2020. doi:10.5281/zenodo.3605995

Last updated: 2025-05-31