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

olivier.croce@cnrs.fr
olivier.croce@univ-cotedazur.fr
bioinfomed.fr
bioinfo.ircan.org
ORCID

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.

Professional experience

Since 2015 — CNRS Research Engineer, Senior Class (IRHC), IRCAN, Nice

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

Main responsibilities:

Management and development of the Bioinformatics & IT Service.
Bioinformatics support for genomics, transcriptomics, metagenomics, microbiome and multi-omics projects.
Design, deployment and maintenance of scientific computing, storage, backup and web infrastructure.
Development of reproducible analysis workflows and custom bioinformatics tools.
Supervision of engineers, students and trainees.
Contribution to scientific publications, institutional projects and collaborative research programs.

2012 to mid-2015 — CNRS Research Engineer, URMITE / IHU, Marseille

Bioinformatics platform of the IHU Méditerranée Infection, located at the Faculty of Medicine, La Timone, Marseille, previously known as the Rickettsia Unit, URMITE - UMR 7278. The institute was headed by Prof. Didier Raoult.

Main activities:

Bioinformatics in microbiology, genomics and comparative genomics.
Genome analysis, bacterial genome annotation and comparative analysis.
Database management, software development and support for collaborative research projects.
Bioinformatics support for high-throughput bacterial sequencing projects.

2009–2012 — Postdoctoral researcher in biophysics, Centre Antoine Lacassagne / Université de Nice

Laboratoire PAORC, “Planification Assistée par Ordinateur en Radiothérapie des Cancers”.

Modelling of the Papillon 50 radiotherapy device.
Simulation of absorbed doses using the Monte Carlo PENELOPE code.
Work performed in the context of the ANR project 08-TECS-015.

2006–2009 — Postdoctoral researcher in bioinformatics, Université de Nice

UMR 6543, Bioinformatics Laboratory.

Development of new approaches to design PCR primers.
Development of software for biological data exchange.
Construction and management of bacterial sequence databases.
Contribution to the European Healthy-Water project, FOOD-CT-2006-036306.

Earlier experience

2004–2005: PhD student, Université de Nice, Bioinformatics Laboratory. DNA chip design for micro-organism identification.
2001–2003: PhD student and CNRS engineer position, UMR 6078. Development of bioinformatics software and databases for the Aquachip project, dedicated to the identification of pathogenic bacteria in water.

Earlier technical and scientific experiences

2001: Trainee in computer science, Master 2, INRIA Sophia Antipolis. Development of prototype software to control an experimental marine simulator device, COMORE project.
2001–2003: Linux administration, Perl programming and training at PCS Avolys.
2001–2003: Individual project: creation of management software for legal information, Gubernatis lawyers institute.
2001–2003: Assistant network administrator, intrusion detection on the university network, University of Corsica.
1999–2000: Technician in bacteriological analyses, Environmental Laboratory of Nice.
1999–2000: Environmental impact of wild ungulate populations, Office National de la Chasse.
1999–2000: Ethology training on wolves in the wild, Mercantour National Park.
1999–2000: Ecology training on the littoral fauna of Embiez Island.
1999–2000: Entomology training on arthropod biodiversity in alpine meadows, Natural Park of Queyras.

Education

PhD

PhD in Bioinformatics, Université Nice Sophia Antipolis, obtained in 2005.
Thesis title: DNA chip design for the identification of micro-organisms.
Jury: M. Gouy, J.-M. François, G. Perrière, R. Christen.

PhD summary

The identification of organisms is still often based on phenotypical characters. However, such identification is approximate and difficult for micro-organisms. DNA microarrays appeared as a solution for fast and reliable identification of a large number of species. This technique was relatively recent at the time and still required conceptual improvements. Within this framework, the objective of my thesis was to implement new approaches for DNA chip design.

This work was completed through two projects. The Aquachip project aimed to design a DNA array for the identification of pathogenic bacteria present in bathing and drinking water. The project grouped several European laboratories that had to exchange a large amount of data. To facilitate this data flow, we developed a dynamic digital platform, the E-dashboard, based on MySQL and PHP, allowing partners to manage biological data.

University degrees

2005: PhD in Bioinformatics, Université Nice Sophia Antipolis.
Master-level training in biology, bioinformatics and computer science.
Earlier university training at the interface of biology, ecology, computer science and biomedical applications.

Current responsibilities and institutional activities

Head of the Bioinformatics & IT Service at IRCAN.
Information Systems Security Correspondent (CSSI) for UMR7284.
Member of the IRCAN laboratory council.
Elected member of the CNRS DR20 “Commission régionale du développement professionnel et social”.
Regular expert for ITA/ITRF juries and engineer ranking committees.
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.
University teaching in bioinformatics, microbiome analysis and Python programming.

Past commitments

Member of the CNRS INSB Scientific Council (Conseil Scientifique d’Institut), 2019–2023.
Qualification for Assistant Professor positions, CNU section 65, Cell Biology.

Selected 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.

Teaching

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

Current teaching activities include:

High-throughput sequencing and its applications to microbiome studies, Medicine, Université Côte d’Azur.
Introduction to metagenomics, genome assembly and 16S rRNA barcoding, Master of Life and Health Sciences, Université Côte d’Azur.
Introduction to Python, Master 1 Economic Expertise, Social Interactions and Economic Dynamics, Cognitive Sciences, Université Côte d’Azur.

Past teaching activities include biomedical engineering, medical dosimetry and radioprotection, C++ object-oriented programming, Python programming, medical files and DICOM format, bacterial genome assembly and primer design.

Supervision of students and trainees

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.

Main supervision topics include:

Microbiome and metagenomic analysis, including breast cancer and gut microbiota projects.
Long-read sequencing, bacterial genome assembly and annotation.
RNA-seq and multi-omics data analysis.
Detection of sequence signatures and k-mer-based approaches.
Bioinformatics web tools, databases and scientific data infrastructure.

Recent publications

A complete publication list is available here: full publication list. ORCID: 0000-0002-7342-3157.

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.
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.

Online resources

This detailed CV is maintained as an online academic profile. A printable version is available here: printable CV.

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