PhD student position in Bioinformatics / Computational biology

Institution/Company:
CHU de Quebec / Laval University
Location:
Quebec City , QC, Canada
Job Type:
  • PhD
Degree Level Required:
Bachelor's, Masters
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PhD student position in Bioinformatics / Computational biology

The so-called ‘omics’ technologies (genomics, transcriptomics, proteomics, metabolomics, etc.) are powerful assets to understand biological mechanisms. However, these technologies generate a huge amount of heterogeneous massive data. A new generation of bioinformatics tools is thus necessary to make optimal use of experimental data in multi-omic contexts.

The strategic goal of our bioinformatics laboratory is the development of tools and data analysis strategies for the treatment of multi-omics large datasets. Those tools will be developed in the context of multi-omics research and biomarker signatures interpretation linked to biological knowledge. This position is funded by the Natural Sciences and Engineering Research of Canada for the next four years.

The objectives of this position will be to develop an integrated methodology using massive data to validate gene signatures in silico and to uncover mechanisms and functions of gene signatures. The student will work with a platform, based on distributed full-text search engine technology, already in place in the laboratory. This platform aims to alleviate the challenges related to optimal use of public datasets through data-mining and semantic web strategy, but also offer visualization and interpretation of large biological datasets from heterogeneous sources.

The selected candidate will work in collaboration with another PhD student and will be under the supervision of Dr Arnaud Droit. Dr Droit team is composed of about 15 members, including several research assistants available to help the students to achieve their projects. He will evolve in this dynamic group of bioinformaticians at the CHU de Québec Research Center and will have access to Compute Canada high performance computing (HPC) facilities. The bioinformatics group work in close collaboration with Compute Canada to port software tools to HPC infrastructure. The group also work in close collaboration with the various core facilities

Responsibilities:

1.Develop methodologies using massive data to validate gene signatures in silico

  1. Assess the quality of relations between databases
  2. Build networks to explore relationships of the gene signature with bioinformatics knowledge
  3. Integrate visualization adapted to the interpretation of biological big data

Qualifications:

  1. Master degree in computer science, bioinformatics, statistics or biostatistics or equivalent experience
  2. Proficiency with at least one language such as python, R or Java
  3. Experience programming in JavaScript and visualisation libraries (e.g. D3.js)
  4. Experience web technologies is a plus.
  5. Experience with data mining strategies is a plus
  6. Knowledge of genomics is a plus
  7. Good communication skills, self-organisation skills and adaptability are required
  • How to Apply

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