Benjamin Demaille

Background

About Benjamin Demaille

As a Bioinformatics Engineer at the Institute of Psychiatry and Neuroscience of Paris (IPNP, INSERM U1266), I specialize in the development and maintenance of bioinformatics workflows for high-throughput data analysis in neuroscience and psychiatry. My work covers bulk RNA-seq, single-cell RNA-seq (10x Genomics), spatial transcriptomics (10x Visium, Vizgen MERFISH), whole-genome bisulfite sequencing (WGBS), GWAS, and polygenic risk score (PRS) analysis. I manage data processing pipelines from raw data to biological interpretation. This includes quality control, normalization, clustering, dimensionality reduction, differential expression, annotation, and gene set enrichment. I use tools such as Seurat, DESeq2, SoupX, dmrseq, bsseq, DSS, Bismark, CellRanger, MultiNicheNet, and visualization packages in R and Python. I ensure reproducibility with Snakemake, Git, and R Markdown, and provide technical support and training to research teams. At Institut Curie (U932 – Stroma and Immunity team), I previously led analysis of bulk and single-cell RNA-seq data using Kallisto, DESeq2, and Seurat to support cancer immunology research. I also worked with Vizgen MERFISH and 10x Visium datasets, contributing to the spatial transcriptomic characterization of tumor microenvironments. Earlier at IFB-Core and ARTBio (Sorbonne University), I helped design SARS-CoV-2 genomic surveillance workflows for national-scale monitoring projects, gaining experience in workflow orchestration and collaborative tool deployment. My profile combines strong programming skills (R, Python, Bash), solid foundations in genomics and transcriptomics, and a commitment to clear scientific communication. I regularly develop internal documentation and training materials to promote autonomy and reproducibility among collaborators.