Olivier Croce, PhD

CNRS Research Engineer (IRHC)
Head of the Bioinformatics & IT Service
Institute for Research on Cancer and Aging of Nice (IRCAN)
INSERM U1081 - CNRS UMR 7284 - Université Côte d’Azur

bioinfomed.fr · IRCAN
E-mail: olivier.croce@cnrs.fr

I am a CNRS research engineer specializing in bioinformatics, scientific computing and the analysis of high-throughput biological data. I currently lead the Bioinformatics & IT service at IRCAN, where I support research teams in the design, processing, interpretation and reproducible analysis of complex biological datasets.

My work combines computational biology, next-generation and third-generation sequencing, microbiome analysis, genomics, transcriptomics, software development, Linux-based scientific infrastructure, and user-oriented support for research projects.

I have a dual background in biology and computer science, with long-standing experience in developing bioinformatics tools, managing research data, supervising students and engineers, and teaching programming and bioinformatics at university level.

• NGS and long-read sequencing data analysis
• Genomics, metagenomics and microbiome profiling
• Transcriptomics and RNA-seq analysis
• Genome assembly, annotation and comparative genomics
• Sequence analysis, k-mer approaches and motif detection
• Reproducible pipelines and scientific data processing

• Linux servers and scientific computing environments
• Storage, backup and data organization for research teams
• Web services, databases and internal scientific platforms
• Docker-based services and collaborative tools
• User support, training and service management

• Python scripting and bioinformatics tool development
• Data parsing, automation and workflow design
• Web tools and lightweight scientific applications
• Git/GitHub-based code sharing and documentation

• Support for experimental design and data analysis strategies
• Collaboration with biology, microbiology, cancer and aging research teams
• Student and engineer supervision
• Contribution to institutional reporting and scientific publications

• Head of the Bioinformatics & IT service at IRCAN.
• CSSI for UMR7284.
• Member of the IRCAN laboratory council.
• Member of the CNRS DR20 CRDPS.
• Regular expert for ITA/ITRF juries and engineer ranking committees.
• University teaching in bioinformatics, microbiome analysis and Python programming.

See also: activities and responsibilities

• Nanopore microbiome analysis: comparison of full-length 16S rRNA sequencing and shotgun metagenomics for gut microbiome profiling.
• EpitopeMapper / sequence comparison tools: development of k-mer-based approaches for identifying shared, unique or conserved peptide/protein sequence patterns.
• IRCAN scientific computing infrastructure: administration and development of bioinformatics resources, storage organization, internal documentation and user support.
• Multi-omics support: RNA-seq, genomics, metagenomics and custom analysis pipelines for IRCAN research teams.

See also: selected projects

A selection of recent or representative publications is listed below. A complete list is available here: full publication list.

• Iltis C. et al. 2025. A ganglioside-based immune checkpoint enables senescent cells to evade immunosurveillance during aging. Nature Aging.
• Colson D. et al. 2024. Dosimetry and Monte Carlo modelling of the Papillon+ contact X-ray brachytherapy device. Brachytherapy.
• Mendez-Bermudez A. et al. 2022. Selective pericentromeric heterochromatin dismantling caused by TP53 activation during senescence. Nucleic Acids Research.
• Ben Khedher M. et al. 2022. Application and challenge of third-generation sequencing for clinical bacterial studies. International Journal of Molecular Sciences.
• Robin J.D. et al. 2020. Mitochondrial function in skeletal myofibers is controlled by a TRF2-SIRT3 axis over lifetime. Aging Cell.

I have been involved in university teaching since 2006, mainly in bioinformatics, programming, genomics, metagenomics, microbiome analysis and scientific data processing.

Current teaching includes:

• High-throughput sequencing and microbiome studies, Medicine, Université Côte d’Azur.
• Introduction to metagenomics, genome assembly and 16S rRNA barcoding, Master Life and Health Sciences.
• Introduction to Python for Master students in economic expertise, social interactions and cognitive sciences.

See also: teaching activities

I regularly supervise or co-supervise Master students, engineers, PhD students and postdoctoral researchers on topics related to bioinformatics, genomics, microbiome analysis, transcriptomics, scientific software and data infrastructure.

See also: student supervision

• Detailed academic CV
• Complete publication list
• Selected projects