Daniele Capocefalo
Research Engineer at Institut Pasteur
Paris, Ile-de-France, Italy
Summary
👤
Senior🎓
Top SchoolDaniele Capocefalo is a research engineer and bioinformatician with over a decade of international experience translating complex multi-omics data into actionable biological insights across developmental biology, cancer, immunology and neurogenomics. He bridges wet and dry labs, building reproducible, containerized pipelines (Nextflow/Snakemake, Docker/Singularity) and implementing FAIR practices to scale analyses on HPC while mentoring collaborators. His work spans single-cell, spatial and bulk omics using state-of-the-art tools and bespoke ML/AI methods for trajectory inference, GRN reconstruction and multilayer network models that link disease ontologies to cell-type mechanisms. He has led independent projects at Institut Pasteur and Human Technopole, contributed to international consortia, and developed open frameworks for molecular network analysis used in translational and clinical contexts. Comfortable both writing grant proposals and training users, he combines a PhD in bioinformatics with hands-on molecular biology experience to expedite wet-lab/computational collaborations. A subtle strength is his track record of adapting graph-theory concepts from ecology and social sciences to reveal hidden regulatory structures in complex omics datasets.
10 years of coding experience
11 years of employment as a software developer
Doctor of Philosophy - PhD, Bioinformatics, Doctor of Philosophy - PhD, Bioinformatics at Sapienza Università di RomaMaster of Science - MS, Bioinformatics, Master of Science - MS, Bioinformatics at University of Rome Tor Vergata
Italian, English, French
Github Skills (61)
seurat10
community-detection10
topological-data-analysis9
transcriptomics8
gene-expression8
network-analysis8
bioinformatics7
stacked7
infer7
matrix-factorization7
high-performance7
python7
network7
rna-seq7
heatmap6
Programming languages (6)
Github contributions (5)
mazzalab/pyntacle
Jan 2018 - Apr 2019
A high performance python package for network analysis based on non canonical metrics
Contributions:263 commits, 4 PRs, 205 pushes in 1 year 2 months
graph-analysispythonperformancetopological-data-analysisnetwork
cantinilab/.github
Jul 2024 - Mar 2025
home page
Contributions:2 reviews, 3 PRs, 56 pushes in 8 months
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