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 Bioinformatician, San Raffaele Telethon Institute for Gene Therapy (TIGET), Milan - Italy

Designed and implemented genomics, tramscriptomics 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

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 - July 2024 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

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. 2020. GC-AG Introns Features in Long Non-coding and Protein-Coding Genes Suggest Their Role in Gene Expression Regulation. Front. Genet. 11:488. doi:10.3389/fgene.2020.00488

Software

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

Last updated: 2024-12-12

Monah Abou Alezz, PhD