Monah Abou Alezz, PhD bio photo

Monah Abou Alezz, PhD

Postdoctoral researcher | Senior bioinformatician | 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
  • Date of Birth: 03/04/1994
  • Email: aboualezz.monah@hsr.it

Professional Experience

October 2020 - Current Postodoctoral researcher, Bioinformatics Core - San Raffaele Telethon Institute for Gene Therapy (TIGET), Milan - Italy

  • Conduct bioinformatics analysis and experimental design, develop and deploy data anakysis workflows for research projects on retrovirus-host interactions and human hematopoietic development.
  • Collaborate with leading researchers, Prof. Anna Kajaste-Rudnitski and Prof. Andrea Ditadi, to support groundbreaking studies.

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

  • Maintainer of core lessons of Data Carpentry
  • Review 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

  • Laboratory of Computational Biology
  • Project: Characterization of long non-coding RNAs genomic and splicing features
  • PI: Prof. Silvia Bione

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

  • Laboratory of Plant Genetics
  • Project: Bioinformatics characterization and identification of miRNAs in woody species
  • PI: Dr. Jorge A. Pinto Paiva

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

  • Laboratory of Cell and Neurobiology
  • Influence of divalent cations on DNA methylation and the modulation of chromatin structure in an in situ ultrastructural study
  • PI: Prof. Marco Biggiogera

July 2009 - July 2015 Laboratory Assistant, Lebanese Agriculture Research Institution (LARI), Tal Amara - Lebanon

  • Department of Crop Production
    • Project: Quality analysis on commercial wheat for classification and marketing
    • PI: Eng. Chafic Stephane
  • Department of Plant Breeding and Improvement
    • Project: Identification of new promising varieties of Triticum aestivum, Hordeum vulgare, and Lens culinaris with high productivity, good grain quality and good adaptation to different climatic conditions.
    • PI: Eng. Rabih Kabalan

Teaching Experience

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

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

Oral Presentations and Abstracts

2022 Costa Verdera H, Abou Alezz M, Cavalca E, Meneghini V, Mangiameli E, Giordano AMS, Singh I, Kuranda K, Ditadi A, Merelli I, Gritti A, Mingozzi F, Kajaste-Rudnitski A. Investigating the Role of Innate Immune Signaling in AAV-Mediated Gene Transfer in hiPSC-Derived CNS Models - ASGCT 25th Annual Meeting - Washington D.C, USA

2021 Unali G, Castiglioni I, Davide G, Matafora V, Abou Alezz M, Merelli I, De Matteo M, Di Fabio R, Bachi A, Kajaste-Rudnitski A. Identification of Hematopoietic Stem Cell-Specific Cyclosporine H Interactors for Improved Gene Therapy Protocols – Molecular Therapy Conference – Online conference

2020 Abou Alezz M, Celli L, Belotti G, Salviati L, Nicastro A, Alfieri R, Lisa A, Bione S. GC-AG introns features in long non-coding and protein-coding genes suggest their role in gene expression regulation - 22nd EMBL PhD Symposium: The Roaring 20s - Online conference

2020 Abou Alezz M, Celli L, Belotti G, Salviati L, Nicastro A, Alfieri R, Lisa A, Bione S. GC-AG introns features in long non-coding and protein-coding genes suggest their role in gene expression regulation” - Cancer Science Institute of Singapore: 6th RNA Biology Symposium 2020 - Online conference

2020 Abou Alezz M, Celli L, Belotti G, Salviati L, Nicastro A, Alfieri R, Lisa A, Bione S. GC-AG introns features in long non-coding and protein-coding genes suggest their role in gene expression regulation” - 25th Annual meeting of the RNA Society - Online conference

2020 Abou Alezz M, Celli L, Belotti G, Lisa A, Bione S. Unexpected features of GC-AG introns in long non-coding and protein-coding genes suggest a new role as regulatory elements – Pavia 3rd Annual Joint Symposium – LIFE SCIENCE 2020 - Pavia, Italy

2019 Abou Alezz M, Celli L, Belotti G, Bione S. Characterization of the genomic and splicing features of long non-coding RNAs using bioinformatics approaches - EMBL Symposia 2019: The Non-Coding Genome - Heidelberg, Germany

2018 Borowska M, Abou Alezz M, Jarząb M, Gomes C, Balestrazzi A, Paiva J. Preliminary overview on conserved miRNAs in Salix purpurea L. - Integrative Plant Biology Conference, IPG PAS - Poznań, Poland

2018 Abou Alezz M, Celli L, Bione S. Computational approach towards genomic characterization of human long non-coding RNA - EMBO Workshop 2018: From epigenome towards epitranscriptome in cell fate choice - Capri, Italy

2018 Masiello I, Siciliani S, Abou Alezz M, Bina V, Casali C, Stortiero M, Tollemeto V, Biggiogera M. High resolution dissection of interphase chromatin. Is 5-methylcytosine the main character in chromatin condensation? – 22nd International Chromosome Conference - Prague, Czech Republic

2017 Biggiogera M, Abou Alezz M, Bina V, Stortiero M, Tollemeto V, Masiello I. Heterogeneity of perichromatin fibril-associated factors - 25th Wilhelm Bernhard Workshop on the Cell Nucleus – Nizhny Novgorod, Russia

2016 Biggiogera M, Tollemeto V, Bina V, Abou Alezz M, Masiello I. Transcription time window applied to RNA modifications in HeLa cells – Nuclear structure and dynamics through the microscopes symposium - Pavia, Italy

Last updated: 2024-07-30