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Professional experience

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

Head of the Bioinformatics & IT Service. Development and coordination of bioinformatics support, scientific computing infrastructure, data analysis pipelines and IT services for cancer and aging research teams.

Main activities:

  • Management of the Bioinformatics & IT Service.
  • Bioinformatics support for genomics, transcriptomics, metagenomics and microbiome projects.
  • Development and maintenance of scientific computing, storage and web infrastructure.
  • Supervision of engineers, students and trainees.
  • Contribution to scientific publications, institutional projects and research collaborations.

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

Bioinformatics platform of the IHU (Institut hospitalo-universitaire) located at the Faculty of Medicine, La Timone, Marseille (previously known as the Rickettsia unit, URMITE - UMR 7278). The institute was headed by Pr. Didier Raoult. [permanent position at CNRS since 2012]

Activities : bioinformatics in microbiology, genomics and comparative genomics, including genome analysis, sequence annotation, database management, software development and support for collaborative research projects

Post-doctoral experiences

  • June 2009 to February 2012: Centre Antoine Lacassagne, University of Nice - Laboratoire PAORC “Planification Assistée par Ordinateurs en Radiothérapie des Cancers”.
    Postdoctoral researcher in biophysics: Modeling of the radiotherapy device « Papillon 50 » and simulations of the absorbed dose using Monte Carlo code PENELOPE (ANR project 08-TECS-015).
  • 2006 to June 2009: University of Nice - UMR 6543, Bioinformatics laboratory.
    Postdoctoral in bioinformatics : Developing new approaches to design PCR primers, development of a software to exchange biological data, achieving database of bacterial sequences (European project “Healthy-Water” FOOD-CT-2006-036306).

Earlier experiences

  • 2004 to 2005: PhD student, University of Nice, Bioinformatics laboratory.
    DNA chip design for micro organisms identification.
  • 2001 to 2003: PhD student + CNRS Engineer position, UMR 6078.
    Development of bioinformatics software and databases (project « Aquachip »:  identification of pathogenics bacteria in water).

See also: old trainings and other past experiences:

See also: old trainings and other past experiences:

  • 2001: Trainee in computer sciences (Master2), INRIA Sophia-Antipolis.
    Developing of prototype software to control an experimental marine simulator device (project «COMORE»).
  • from 2001 to 2003 : Miscellaneous Informatics

- Trainings: Linux administration, Perl programming, training centre PCS Avolys
- Individual project: creating a management software for legal information, Gubernatis lawyers institute
- Assistant network administrator : intrusion detection on the university network, University of Corte.

  • from 1999 to 2000 : Miscellaneous Biology - Ecology

- Technician in bacteriological analyses: Environmental Laboratory of Nice
- Training of Master 2: Environmental Impact of wild ungulate populations, Office National de la Chasse
- Training in ethology: ethology wolf in the wild, Mercantour National Park
- Training in ecology: analysis of the littoral fauna of Embiez island, Study Centre for Marine Animal Resources
- Training in entomology: study of the biodiversity of arthropods alpine meadows, Natural Park of Queyras


Education

PhD

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

See also: PhD summary:

See also: PhD summary:

The identification of organisms are still often based on phenotypical characters. However, such as an identification is approximate and difficult for micro-organisms. DNA micro-arrays appear to be a solution for a fast and reliable identification of a large number of species. This technique is relatively recent and it is still necessary to improve it, in particular at the conceptual level. Within this framework, the objective of my thesis was to implement new means for chip design. This work was completed through two projects: The project “Aquachip” aimed in designing 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. Such significant flow of information is often badly managed and slows down research. Consequently, we developed a dynamic numerical platform, the “E-dashboard” (MySQL, PHP), allowing all partners to manage data. This tool made it possible on the one hand to follow the progress of the various steps of the project and on the other hand to optimize exchanges between partners. In a second project, “Mycochip”, the objective was to develop a DNA array to identify ectomychorizian fungi. ITS sequences (Internal Transcribed Spacers) from a very divergent area located between ribosomal RNA genes are used for this study. The project initially required the development of a tool to retrieve sequences, « EmblEx » (Perl, MySQL), which is more specific and powerful than Entrez, SRS or ACNUC. Then, the ambiguous taxonomy of fungi led us to conceive a new method of classification through partitioning without alignment. Biological experiments showed that reliable probes could be determined by this approach.


University degrees

  • 2001 : DESS (=Master 2) - “Additional competences in computer sciences” - University of Corsica
    Mention « Databases and advanced programming ».
  • 2000 : Master 1 - “Biology of populations and ecosystems” - Aix-Marseille III University
    Mention « Biology of conservation et systems modeling ».
  • 1999 : Licence 3 - “Biology of organisms” - Aix-Marseille III University
    Mention « Research and specialization in animal biology ».
  • 1998 : DEUG (=Licence 1&2) - “Biology and geology” - Nice Sophia Antipolis University
    Mention « Sciences of life ».
contacts/croce/activities_education.txt · Last modified: by olivier

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