Monah Abou Alezz, PhD
As a Postdoctoral Researcher in Computational Biology, I develop scalable and automated workflows to streamline the analysis of complex NGS and multi-omics datasets. My work empowers research teams by removing data bottlenecks, enhancing reproducibility, and transforming raw data into meaningful insights. Alongside pipeline development, I deliver hands-on training in Bioinformatics analyses and programming languages (R, Python, Bash), equipping scientists with the skills to apply Computational Biology methods effectively and independently.
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Areas of Expertise
Next-Generation Sequencing (NGS) Data Processing
Develop end-to-end pipelines for bulk and single-cell RNA-Seq, DNA-Seq, and targeted sequencing, transforming raw reads into high-confidence interpretable biological insights for research and clinical applications
Bioinformatics Data Visualisation and Interpretation
Design high-quality and reproducible visualizations of complex genomic, transcriptomic, and multi-omics datasets, enabling clear interpretation of data patterns and research-relevant insights
Statistical Analysis
Apply advanced statistical frameworks and bioinformatics methodologies to ensure reproducible, accurate analysis of complex biological datasets
Machine Learning & AI in Life and Medical Sciences
Develop and deploy machine learning and AI models for predictive biology, classification, feature extraction, and integrative analysis, tailored to high-dimensional biological datasets
Workflow Automation & Scalable Pipelines
Build modular, version-controlled pipelines using Snakemake, Nextflow, and scripting languages to streamline, automate, and scale bioinformatics workflows efficiently
Scientific Training & Capacity Building
Deliver hands-on workshops and mentoring in Bioinformatics analyses, R, Python, Bash, and Git, enabling researchers to adopt computational methods, develop reproducible workflows, and independently analyze complex datasets
Work Experience
Freelance Bioinformatician
Sepal AI · California, USA · Aug 2025 – Present
- Design and implement custom AI tools and AI-driven analytical workflows to accelerate biomedical research
- Streamline bioinformatics pipelines and generate high-quality, publication-ready visualizations
Postdoc Researcher · Computational Biologist
San Raffaele Telethon Institute for Gene Therapy (TIGET) · Milan, Italy · Oct 2020 – Present
- Developed and maintained bioinformatic and statistical workflows
- Performed data analysis, integration, and visualization and implemented novel bioinformatics methods
- Assisted in administering on-premises high-performance computing infrastructure
- Provided training and support to team members
Data Carpentry Lessons Maintainer
The Carpentries Organization · California, USA · Sep 2021 – Sep 2023
- Maintained core lessons for the Data Carpentry program
- Reviewed submissions and discussions of materials changes
- Optimized and set standards for the organization as a whole
Training and Workshops
Freelance Bioinformatics Trainer
Delivered multiple in-person workshops in Bioinformatics and data analysis for corporate training providers:
- BlackBird Training
- Global Horizon Training Center
- Agile Leaders Training
Bioinformatics Trainer
Organized and delivered hands-on training in Bioinformatics analyses and programming languages at the following institutes:
- Leibniz Institute for Natural Product Research and Infection Biology (MiCCrobioTackle program)
- EMERALD International PhD Program for Medical Doctors
- German Cancer Research Center (DKFZ)
- Max Delbrück Center for Molecular Medicine (MDC)
- San Raffaele Hospital
- Università degli Studi di Pavia
Carpentries Instructor
Delivered training sessions in foundational coding and data science skills to researchers in workshops across Europe, USA, and Saudi Arabia. Selected workshops:
- Harvard Stem Cell Institute
- United States Centers for Disease Control (CDC)
- Jackson Laboratory
- Genentech
- Saudi Food and Drug Authority (sFDA)
- Università degli Studi di Milano-Bicocca
Publications
My research spans computational biology, genomics, and transcriptomics, with a focus on developing innovative methods for NGS data analysis and pipeline development. My work has been published in peer-reviewed journals and has contributed to advancing our understanding of gene regulation and disease mechanisms.
View All Publications on Google Scholar
View All Publications on Google Scholar
Projects
NatChat: Chatting with Nature Journals Current Issue using a local Language Model
An R package designed to summarize all papers in the current issues of journals published by the Nature Portfolio
GencoDymo2: Comprehensive Analysis of GENCODE Annotations and Splice Site Motifs
GencoDymo2 is an R package tailored for dynamic extraction, exploration, and comparison of gene annotations from the GENCODE database for human and mouse genomes
Skills & Proficiencies
Programming & Databases
- R, Python, Bash/Shell, SQL, HTML, Perl
- NCBI, Ensembl, UCSC, GEO, KEGG, dbSNP
Machine Learning
- Scikit-learn, PyTorch
- Deep Learning (CNNs, ResNet)
- Model Evaluation
Workflow & Cloud
- Snakemake, Nextflow, Docker, Git, Conda
- Slurm, HPC
- AWS (S3, EC2), Alibaba Cloud
Omics Analysis
- RNA-Seq, ChIP-Seq, scRNA-Seq (Seurat, Scanpy), spatial transcriptomics
- Variant Calling (GATK), Hi-C
- GWAS, TWAS, eQTL
- Proteomics, Metabolomics, Lipidomics
Documentation & Governance
- Version Control
- RMarkdown, LaTeX
- Good Documentation Practice (GDP)
- Reproducibility and Open Science
Certifications
Certified Carpentries Instructor
Certified to teach Software Carpentry, Data Carpentry, and Library Carpentry workshops worldwide
The Carpentries Organization
Data Carpentry Curriculum Advisor
Contributed to curriculum development and lesson maintenance for genomics and ecology tracks
The Carpentries Organization
Machine Learning & AI for Bioinformatics
Comprehensive training in machine learning algorithms, deep learning frameworks, and AI applications for biological data analysis and predictive modeling
Udemy
Education
PhD in Genetics, Cellular and Molecular Biology
Università degli Studi di Pavia · 2017–2020
- Advanced Molecular Biology
- Bioinformatics
- Statistical Methods in Molecular Biology
- Algorithms & Data Structures
- Computational Approaches in Genetics
Masters in Molecular Biology and Genetics
Università degli Studi di Pavia · 2015–2017
- Advanced Molecular Biology
- Molecular Genetics
- Microbial Genetics
- Biotechnology
- Advanced Microscopy Techniques
Bachelor in Life Sciences
Lebanese University · 2012–2015
- Molecular Biology
- Medical Microbiology
- Immunology
- Neurobiology
- Biotechnology
Awards & Honors
Best Poster Prize
Awarded for outstanding research presentation at the prestigious EMBL-EMBO symposium on non-coding RNA biology
EMBL-EMBO Symposium: The Non-Coding Genome
Excellence in Teaching Award
Recognized for outstanding contributions to bioinformatics education and training
The Carpentries Organization
Graduate with Distinction
Graduated with honors from the Masters program in Molecular Biology and Genetics
Università degli Studi di Pavia · 2017
Languages
What People Say
Monah's training sessions transformed how our team approaches bioinformatics. His ability to explain complex concepts in accessible terms is remarkable. Our researchers are now confidently running their own analyses.
The pipelines Monah developed for our lab have significantly accelerated our research. His attention to reproducibility and documentation made it easy for the entire team to adopt and maintain the workflows.
An exceptional instructor who brings both depth of knowledge and genuine enthusiasm to teaching. The hands-on approach and real-world examples made the Carpentries workshop invaluable for our research staff.
Contact Me
Have a question or want to work together? Feel free to reach out!