Olivier Croce, PhD

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.

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.

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.

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.

CNRS 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.

• 2004–2005: PhD student, Université de Nice, Bioinformatics Laboratory. DNA chip design for micro-organism identification.
• 2001–2003: CNRS engineer position and (part of) PhD student, UMR 6078. Development of bioinformatics software and databases for the Aquachip project, dedicated to the identification of pathogenic bacteria in water.
• 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: Assistant network administrator, intrusion detection on the university network, University of Corsica.
• 1999–2000: Technician in bacteriological analyses, Environmental Laboratory of Nice.
• 1999–2000: Ecology, ethology and environmental field training, including Mercantour National Park, Embiez Island and Queyras Natural Park.

• 2005: PhD in Bioinformatics, Université Nice Sophia Antipolis. Thesis title: DNA chip design for the identification of micro-organisms. Jury: M. Gouy, J.-M. François, G. Perrière, R. Christen.
• 2001: DESS in Computer Science, Université de Corse Pascal Paoli, equivalent to a current Master 2 level.
• 2000: Maîtrise in Biology, Université de la Méditerranée, Marseille, equivalent to a current Master 1 level.
• Earlier university training in biology, ecology and environmental sciences.

• 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 include membership of the CNRS INSB Scientific Council, 2019–2023, and qualification for Assistant Professor positions, CNU section 65, Cell Biology.

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.

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.

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.

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.

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.

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.

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.

A complete publication list is available online: https://www.bioinfomed.fr. ORCID: 0000-0002-7342-3157.

• 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.
• Cherfils-Vicini J. et al. 2019. Cancer cells induce immune escape via glycocalyx changes controlled by the telomeric protein TRF2. EMBO Journal.