Mots-Clés

transcriptomic analyses Galaxy machine learning programmation

Description

Host laboratory :

Our laboratory is located in Lille (Northern France), a very active and attractive city at the intersection of Brussels, Paris, and London. The unit is part of the University of Lille, Lille University Hospital, Institut Pasteur de Lille and the European Genomic Institute for Diabetes (EGID, http://www.egid.fr).

Our laboratory has a long-standing interest in mechanisms involved in the development of metabolic diseases (https://u1011.pasteur-lille.fr/5/home/). Our unit comprises over 100 people with a broad range of expertise and interests ranging from molecular biology to clinical research. Bioinformatics is used for data mining in projects involving omics data within the different teams of the laboratory. The successful candidate will be hosted in team “Molecular analysis of gene regulation in cardiometabolic diseases” (https://u1011.pasteur-lille.fr/5/the-unit/theme-4-integrated-molecular-analysis-of-gene-expression-in-liver-diseases/).

Job description :

The successful candidate will be under the supervision of a Bioinformatic IR and will contribute/support the bioinformatics team in its effort to develop bioinformatic tools and procedures allowing to provide manageable information to biologists. The candidate will use his/her skills to achieve the 3 inter-related following tasks:

1. Tools development for data analysis and data exploration:

Our laboratory has set up a local instance of Galaxy for omics data mining. In addition to public tools, this instance comprises in-house developed pipelines such as GIANT (Galaxy-based Interactive tools for ANalysis of Transcriptomic data) (Vandel et al. Sci Rep. 2020). The successful candidate will work to maintain this local instance of Galaxy and extend available tools and functions. In particular, he/she will provide a standardized, comprehensive and user friendly transcriptomic analysis pipeline for bulk and single-cell RNA-seq data.

In addition, the candidate will be in charge of the laboratory omics data repository. He/she will implement a standardized procedure for data collection, storage and subsequent re-analyses through our local instance of Galaxy.

2. Support for data mining:

In parallel, he/she will provide specific support to biologists with regards to transcriptomic data analyses. Furthermore he/she will collaborate with bioinformaticians and biologists to implement novel strategies to handle and combine heterogeneous omics data by applying Machine Learning methods

3. Scientific monitoring of bioinformatical tools:

The candidate will be involved in identifying, testing and setting up analyses with the most appropriate tools in order to mine omics data with biologically-oriented questions defined in collaboration with collaborators in the laboratory.

Candidate profile : Master in bioinformatics

Primary skills/experiences: 

• Experience in transcriptomic data analyses (microarrays and/or RNA-seq data)
• Knowledge in Galaxy use and in Galaxy tools development/installation
• Knowledge of Machine Learning principles and experience in its application on omics data would be strongly appreciated
• programmation in R and/or Python

Additional skills /experiences :

• A previous experience in integration of omics data and/or single-cell RNA-seq would be an asset
• Organizational skills, ability to provide synthetic and didactic presentation of scientific results are also required
• Ability to efficiently work and interact with biologist in a pluridisciplinary environment
• Autonomy and team spirit