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refmyoussef-source/README.md

Hi there, I'm Youssef! πŸ‘‹

🧬 Microbiologist & Pathogen Bioinformatician

I bridge the gap between Wet-Lab Microbiology and Computational Data Science. My work focuses on leveraging genomic, transcriptomic, and metagenomic data to decode bacterial behavior, antibiotic resistance mechanisms (AMR), and microbial ecosystems.

With a strong foundation in microbiology, I build reproducible, automated pipelines to transform raw sequencing reads into actionable biological insights.

πŸ› οΈ Technical Toolbox

  • Languages: Python (Pandas, NumPy, Scikit-learn), R (Bioconductor), Bash/Linux Shell, Markdown
  • Transcriptomics (RNA-Seq): Single-cell RNA-Seq (Scanpy, Seurat), Bulk RNA-Seq, Pseudo-bulk, Differential Gene Expression (DESeq2)
  • Genomics & AMR: Variant Calling (GATK, BWA), Genome Assembly (SPAdes), Pangenomics (Roary), Functional Annotation (Prokka)
  • Metagenomics & Microbiome: 16S rRNA Profiling (QIIME 2), Shotgun Metagenomics, Microbial Dysbiosis Analysis
  • Workflow Automation & DevOps: Snakemake (High-Throughput Pipelines), Docker (Containerization), Git/GitHub

πŸ”¬ Core Portfolio Highlights

  • 🦠 Bacterial scRNA-Seq: Unveiled rare cell states and prophage induction in B. subtilis using unsupervised clustering (microSPLiT dataset).
  • πŸ’Š AMR Genomic Epidemiology: Built an automated Snakemake pipeline to track SNPs and resistance profiles across 96 MDR P. aeruginosa clinical strains.
  • πŸ§ͺ Host-Pathogen Transcriptomics: Profiled M. tuberculosis and K. pneumoniae core gene networks under heavy antibiotic stress.
  • πŸ“Š Microbiome Data Science: Implemented high-throughput metagenomics workflows to detect gut microbiome shifts in Crohn's Disease and Type 2 Diabetes.

πŸ“Š "Turning complex bacterial sequencing noise into meaningful biological signals."

Popular repositories Loading

  1. rnaseq_klebsiella_pipeline rnaseq_klebsiella_pipeline Public

    A complete bioinformatics pipeline (FastQC, fastp, HISAT2, featureCounts, DESeq2) for RNA-Seq DGE analysis of Klebsiella pneumoniae (WT vs. Ξ”cpxR).

    Jupyter Notebook 5

  2. project_variant_calling project_variant_calling Public

    Bioinformatics pipeline (GATK/BWA/SnpEff) to identify antibiotic resistance mutations (DAP/VAN) in Staphylococcus aureus.

    Jupyter Notebook 4

  3. Mtb_Genomic_Analysis- Mtb_Genomic_Analysis- Public

    A bioinformatics pipeline (SPAdes, Prokka, Roary) to identify novel PAS resistance SNPs in M. tuberculosis.

    Jupyter Notebook 3

  4. 16S_microbiome_analysis_crohns_disease 16S_microbiome_analysis_crohns_disease Public

    End-to-end 16S microbiome analysis (FASTQ to PCoA) of Crohn's Disease. Implements a QIIME 2 & Docker pipeline to identify significant phylogenetic dysbiosis (p=0.0007).

    Jupyter Notebook 3

  5. mdr-pa-genomic-epidemiology mdr-pa-genomic-epidemiology Public

    A reproducible Snakemake pipeline for the high-throughput genomic epidemiology of 96 MDR P. aeruginosa strains (BioProject PRJNA771342).

    Jupyter Notebook 2

  6. Shotgun_Metagenomics_Analysis Shotgun_Metagenomics_Analysis Public

    Shotgun metagenomics analysis pipeline for Type 2 Diabetes gut microbiome using Snakemake.

    Jupyter Notebook 1