Mots-Clés

bio/chemoinformatics data science database of omics data dynamic mapping machine learning

Description

Context

To promote a reasoned and sustainable agriculture, we are currently developing omics approaches and in this context, we study and interpret biological and chemical mechanisms involved between a host plant and its environment like its pathogenic and beneficial microorganisms.

Over the past few years, we were able to acquire valuable data related to the over- or under-expression of genes, the differences in protein production as well as the content evolution of a large number of metabolites coming from plants and microorganisms.

At this stage, it is essential to develop a data mining tool to manage and analyze this vast amount of experimental data. It would be also helpful to visualize these data through a dynamic molecular mapping. The purpose of this tool would be dedicated to help scientists for the interpretation of biological data to understand functions, roles and implications of biomolecules.

Tasks and Challenges

The main task of the candidate will be the creation of a user-friendly tool capable of dynamic molecular mapping. This will involve (i) proposing an architecture for the database, (ii) the compilation of experimental data (which may be supplemented with data from the literature) related to organisms and their organs as well as the constraints to which they are subjected (such as biotic and abiotic stresses), (iii) linking the database to a graphical interface for visualization (e.g. Cytoscape) by integrating biomolecules and metabolic pathways like iPath or Metexplore online solutions.

Essential requirements

• PhD in Bioinformatics or Chemoinformatics.
• High skills in database architecture and language.
• Good knowledge in biological pathways and software for data integration and visualization.
• General familiarity with omics approaches (transcriptomics, proteomics or metabolomics).
• Adaptation to a multi-disciplinary environment (analytical chemistry, biology, fungi and plant field).
• Demonstrated ability to work independently.
• Proven ability for team working, internal reporting through weekly meetings and conference presentations.

• Strong written, verbal, and interpersonal communication skills in French and English language (French is an asset).