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—contacts:croce:croce2 [2026/05/21 14:32] (current) – created olivier
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 +====== 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
 +
 +[[https://bioinfomed.fr|bioinfomed.fr]] · [[https://www.ircan.org|IRCAN]] \\
 +E-mail: olivier.croce@cnrs.fr
 +
 +----
 +
 +===== Profile =====
 +
 +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.
 +
 +----
 +
 +===== 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
 +
 +==== 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
 +
 +==== 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
 +
 +==== 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 current activities =====
 +
 +  * 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: [[contacts:croce:activities|activities and responsibilities]]
 +
 +----
 +
 +===== Selected projects =====
 +
 +  * **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: [[contacts:croce:projects|selected projects]]
 +
 +----
 +
 +===== Selected publications =====
 +
 +A selection of recent or representative publications is listed below. A complete list is available here: [[contacts:croce:publications|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//.
 +
 +----
 +
 +===== Teaching =====
 +
 +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: [[contacts:croce:teaching|teaching activities]]
 +
 +----
 +
 +===== Student supervision =====
 +
 +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: [[contacts:croce:supervision|student supervision]]
 +
 +----
 +
 +===== Full CV =====
 +
 +  * [[contacts:croce:full_cv|Detailed academic CV]]
 +  * [[contacts:croce:publications|Complete publication list]]
 +  * [[contacts:croce:projects|Selected projects]]
contacts/croce/croce2.txt · Last modified: by olivier

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