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yousra291987/README.md

Dr. Yousra Ben Zouari

Computational Biologist · Multi-Omics · Regulatory Genomics · Epigenomics

📍 Strasbourg, France  |  📧 yousra.benzouari@gmail.com  |  🔗 LinkedIn

About

I'm a computational biologist with 10+ years of experience in multi-omics data integration, chromatin architecture, and regulatory genomics. I build end-to-end analytical frameworks — from experimental design and QC through to integrated, publication-ready insights — and I develop open-source tools that make complex genomic data accessible to the wider community.

My work sits at the intersection of 3D genome organization, epigenetic regulation, and disease-relevant gene control. I'm currently expanding into oncology computational biology.

Published Tools

Tool Description Publication
ChiCMaxima Non-parametric chromatin loop detection from Promoter Capture Hi-C, with GUI Genome Biology (2019)
VING High-quality visualization of NGS signals across genomic regions BMC Research Notes (2015)
4See Interactive browser for 4C-seq data exploration Front. Genetics (2020)

Selected Publications

  • Ben Zouari Y*, Joshi O*, et al. Polycomb Chromatin Topology Enables Long-Range Enhancer Recruitment during Craniofacial Development. Nature Communications (in press)
  • Kessler S*, Minoux M*, Joshi O*, Ben Zouari Y*, et al. A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest. Nature Communications (2023)
  • Chahar S*, Ben Zouari Y*, et al. Transcription induces context-dependent remodeling of chromatin architecture during differentiation. PLoS Biology (2023)
  • Ben Zouari Y, et al. ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C. Genome Biology (2019)

* Authors contributed equally

Technical Stack

Languages

Python R Bash

Frameworks & Tools

Snakemake Docker Singularity TensorFlow scikit-learn

Genomics

scRNA-seq RNA-seq ATAC-seq ChIP-seq Hi-C Capture Hi-C 4C-seq

What I'm Working On

  • 🧬 Applying multi-omics and regulatory genomics to oncology
  • 🤖 Building ML workflows for biological data analysis

Open to collaborations in computational oncology, regulatory genomics, and multi-omics tool development.

Pinned Loading

  1. ChiCMaxima ChiCMaxima Public

    ChiCMaxima: a pipeline for analyzing and identificantion of chromation loops in CHi-C promoters data.

    R 6 1

  2. PCHiC_workflow PCHiC_workflow Public

    End-to-end Snakemake pipeline for PCHi-C and Hi-C: QC, significant interaction detection, .hic generation, insulation scores, and TAD calling.

    R 1

  3. cncc-epigenetic-state-classifier cncc-epigenetic-state-classifier Public

    Tests seven ML classifiers on epigenetic state labels derived from multi-tissue CNC ChIP-seq data, focusing on resolving cell population heterogeneity in bulk ChIP-seq signal.

    Jupyter Notebook 1

  4. GNN_Chromatin_Activation GNN_Chromatin_Activation Public

    Python 1