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Olivier Croce, PhD
CNRS Research Engineer, Senior Class (IRHC)
Head of the Bioinformatics & IT Service
IRCAN — Institute for Research on Cancer and Aging of Nice
INSERM U1081 · CNRS UMR 7284 · Université Côte d’Azur
Profile
I am a CNRS research engineer specializing in bioinformatics, scientific computing and the analysis of high-throughput biological data. I have a PhD and a dual background in biology and computer science. 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 am also interested in exploring genomes and biological sequences using in silico approaches, existing tools and custom developments to detect meaningful hidden patterns or cryptic information.
Main expertise
Bioinformatics and computational biology
- 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.
Software development
- 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.
Additional biomedical expertise
- Monte Carlo simulation for biomedical applications, including PENELOPE code.
- Dosimetric measurements, radiation–matter interactions and medical imaging data (DICOM format).
Scientific computing and IT infrastructure
- 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.
Research support and project coordination
- 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.
Selected activities
- Head of the Bioinformatics & IT service at IRCAN.
- University teaching in bioinformatics, microbiome analysis and Python programming.
- Regular expert for ITA/ITRF juries (ITRF - BAP A & BAP E) and engineer ranking committees.
- Information Systems Security Correspondent (CSSI) for UMR7284.
- Elected member of the CNRS DR20 “Commission régionale du développement professionnel et social”.
- Member of the IRCAN laboratory council.
- Expert for the Scientific User Committee of the Institut Sophia Agrobiotech bioinformatics platform.
- Member of professional networks: SFBI, DevLog, Bioinfo@UniCA, and local bioinformatics communities.
Selected current projects
Nanopore sequencing and microbiome analysis
I am involved in projects using Oxford Nanopore long-read sequencing for microbiome and metagenomic analysis, including the comparison of full-length 16S rRNA sequencing and shotgun metagenomics for gut microbiome profiling. Current collaborations include projects with IRCAN, Dubai Hospital and the Scientific Centre of Monaco.
Multi-omics and transcriptomics support
Support for RNA-seq, genomics, metagenomics and multi-omics data analysis for IRCAN research teams, including experimental design, workflow development, statistical analysis and biological interpretation.
EpitopeMapper and k-mer sequence comparison
Development of k-mer-based approaches for identifying shared, unique or conserved peptide and protein sequence patterns across large proteomes. These tools aim to support exploratory analyses of immunogenicity, sequence similarity and motif detection.
Scientific computing infrastructure
Design, deployment and maintenance of Linux-based scientific computing environments, shared storage systems, backup strategies, internal web services and collaborative platforms for research data.
Five last publications
- Kellermann G, et al. 2026. Comprehensive mapping of identical sequences across human proteins emphasizes the widespread issue of shared epitopes in self-antigens. NAR Genom Bioinform.
- Chevalier A. et al. 2026. Genomic determinants of Bacillus cereus and outcomes of infection in preterm neonates: a multicentre retrospective study. Clinical Microbiology and Infection.
- Andreoni-Pham R. et al. 2025. Whole body regeneration deploys a rewired embryonic gene regulatory network logic. Nature Communications.
- 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.
The complete publication list is available here: full publication list. Communications are listed here.
Teaching
I have been involved in university teaching since 2006 (50–60 hours/year, for various Masters), 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
Supervision of students and trainees
I regularly supervise or co-supervise (over 30 people) Master students, engineers, PhD students and postdoctoral researchers on topics related to bioinformatics, genomics, microbiome analysis, transcriptomics, scientific software and data infrastructure.
See also: students supervision
Professional background
- Since 2015: CNRS Research Engineer at IRCAN, Head of the Bioinformatics & IT Service.
- 2012–2015: CNRS Bioinformatician / research engineer in microbiology and genomics, Marseille.
- Earlier background: PhD and training at the interface of biology, bioinformatics and biomedical sciences.
See also Activities and Education details
Full CV
contacts/croce/croce2.txt · Last modified: by olivier