Yannick DE OLIVEIRA

Programming & framework, Databases, Data management

 INRAE, Engineer

 yannick.de-oliveira@inrae.fr —   +33 (0)1 69 33 23 76


 Bioinformatics and Informatics
 Bioinformatics, Open Science & Systems

Implication de Yannick De Oliveira dans axe1 0% axe1 Understanding and shedding light on evolutionary mecanisms Axe1 Implication de Yannick De Oliveira dans axe2 30% axe2 Understanding and predicting the genetic bases of interactions Axe2 Implication de Yannick De Oliveira dans axe3 70% axe3 Understanding and mobilizing cultivated diversity to provide solutions for agriculture and its actors Axe3
 Publications    

  • Génétique Quantitative et Évolution - Le Moulon
  • Université Paris-Saclay, INRAE, CNRS, AgroParisTech
  • IDEEV
  • 12 route 128
  • 91190 Gif-sur-Yvette
Yannick DE OLIVEIRA

Education and positions

  • BioInformatics engineer (2009-…), INRAE
  • Head of development and customer support of a LIMS solution (2007-2009), Sibio
  • BioInformatics engineer (2004-2007), INRA, FLAGdb++ and UTILLdb
  • Master degree in BioInformatics (2004) « Etude de Génomes Outils Informatiques et Statistiques », Rouen.

Activities

Software engineering

Member of the ABI team (ABI-Soft), my activities are focused on the development of data management tools and software dedicated to genetics and their availability to our user communities. My role is to ensure the link between the research teams of the UMR and the developers of ABI-Soft and to define the development strategy of the team. The ABI-Soft team develops three data management tools: Thaliadb, SHiNeMaS and DiverCILand. All these tools are developed using technologies in which the team has a good expertise today: Python / Django & Django REST, PostgreSQL. On the software side, BioMercator and OptiMAS are maintained by the team with Java & R-Shiny technologies.

Lab data steward

As the lab data steward (RDO), I am required to assist the teams in the writing of their Data Management Plan (DMP) and/or in their approaches to the General Data Protection Regulation (GDPR). This is the case in the scope of the ANR project MoBiDiv . I also make sure to provide the best possible tools to the colleagues in the scope of FAIR (Findable, Accessible, Interoperable, Reusable) data production process.

CATI PlantBreed

As co-leader of the CATI PlantBreed (with Jacques Lagnel, UR GAFL) I contribute annually to the organization of the inter-CATIomics hackathon in collaboration with the leaders of 4 other CATI : BARIC , BIOS4Biol , BOOM , GREP .

Publications

  • De Oliveira Y. , Burlot L., Dawson JC., Goldringer I., Madi D., Rivière P., Steinbach D., van Frank G., Thomas M.. (2020) SHiNeMaS: a web tool dedicated to seed lots history, phenotyping and cultural practices. Plant Methods, 1 (16) 98
  • Lopez Arias DC., Chastellier A., Thouroude T., Bradeen J., Van Eck L., De Oliveira Y. , Paillard S., Foucher F., Hibrand-Saint Oyant L., Soufflet-Freslon V.. (2020) Characterization of black spot resistance in diploid roses with QTL detection, meta-analysis and candidate-gene identification. Theor Appl Genet,
  • Dalmais M., Schmidt J., Le Signor C., Moussy F., Burstin J., Savois V., Aubert G., Brunaud V., De Oliveira Y. , Guichard C., Thompson R., Bendahmane A.. (2008) UTILLdb, a Pisum sativum in silico forward and reverse genetics tool. Genome Biol, 2 (9) R43