Description

I am a bioinformatician with 8 years of experience, including 4.5 years in the biotech industry as a Lead Bioinformatician. I hold a PhD in Genomics and Bioinformatics and a Master’s degree in Bioinformatics and Biostatistics.

My expertise focuses on developing automated bioinformatics pipelines and analyzing multi-omics datasets.

Skills:

Programming: Python, R, RMarkdown, Bash, Snakemake, Nextflow
Version Control: Git, GitLab
HPC Computing: Sun Grid Engine (SGE), SLURM, access to Scaleway computing infrastructure
NGS Data Analysis: DNA-Seq, RNA-Seq, Tn-Seq, 16S, metagenomics, sequence alignment, SNP analysis, phylogeny
Proteomics: Mass spectrometry, Olink
Functional Analysis: Pathway enrichment, HMM models, Gene Ontology, GSEA
Statistical Analysis: Alpha & beta diversity, rarefaction curves, DESeq2, Limma, DPGP, Random Forest.

Contact: I am available for Bioinformatics Services, Development of pipelines, Data analysis - Metagenomics, RNASeq, genome assembly and more. Custom-made solutions.

Industry field of expertise

Languages

French
Native or bilingual
English
Native or bilingual
Arabic
Native or bilingual

Workplace preferences

Can work on-site

Marseille (up to 50km)

BIOASTER
Bioinformatician
BIOTECH
April 2021 - November 2025 (4 years and 7 months)
Lyon, France
Development and maintenance of bioinformatics workflows using Nextflow, Snakemake, Python, R, and Bash.

Transcriptomics, metagenomics, and proteomics data analysis, from raw data quality control to statistical and biological interpretation, performed on HPC clusters using SLURM and Sun Grid Engine.

Development of an automated workflow generating a final HTML report for each project, providing clear and actionable results, including publication-ready figures and tables.

Expertise in projects related to the human microbiome, biomarker discovery for drug development, and vaccine research.

Involved throughout the entire project lifecycle, from requirement definition and methodological design to analysis execution and presentation of results to clients.
HTML HPC Snakemake Python Nextflow
DOE Joint Genome Institute
Mission
September 2019 - December 2019 (3 months)
Berkley, United States
Development and application of HMM models for gene identification and classification across 656 fungal genomes

Phylogenetic analysis to group identified genes into four functional clades and predict the type of catalyzed cyclization

Identification of specific amino acid motifs to improve the accuracy of functional predictions

Mining and annotation of large genomic databases, integrating sequence and phylogenetic information
Python RStudio Genomics Machine learning Analyse prédictive
Institut national de recherche pour l'agriculture
PhD
BIOTECH
January 2018 - April 2021 (3 years and 3 months)
Marseille, France
Comparative analysis of fungal genomes (~1,000 genomes):

Identification of gene families, analysis of gene family expansions, phylogenetic reconstruction, and investigation of evolutionary trajectories.

Large-scale functional analyses to characterize enzymatic repertoires involved in lignocellulose degradation, combining genome annotation, sequence comparison, and exploration of genetic diversity.

Development of a dedicated tool for automated enzyme identification, applied to the analysis of 1,420 fungal genomes and the detection of more than 11,000 candidate genes.
R Python Biostatistiques Enzyme Génomique