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.

"Bridging Biology and Data with Clarity and Purpose."

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Research Website

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

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 change
Optimized and set standards for the organization as a whole

Training and Workshops

Bioinformatics Trainer

Organized and delivered hands-on training in Bioinformatics analyses and prgramming 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 delivered in 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

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.

R · Ollama · AI · Nature · Scientific Literature

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.

R · GENCODE · Annotations · Splicing · MaxEntScan