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PhD student in bioinformatics (M/W)

This offer is available in the following languages:
Français - Anglais

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General information

Reference : UMR7288-CATCOR-033
Workplace : MARSEILLE 09
Date of publication : Monday, December 03, 2018
Scientific Responsible name : Bianca HABERMANN
Type of Contract : PhD Student contract / Thesis offer
Contract Period : 36 months
Start date of the thesis : 1 February 2019
Proportion of work : Full time
Remuneration : 1 768,55 € gross monthly

Description of the thesis topic

Visual data mining (VMD) is a powerful method for the deep exploration of -omics data. The mitoXplorer platform developed in our lab is a user-friendly, highly interactive VMD platform that allows users to explore the expression dynamics of mitochondria-associated genes (mito-genes) in a variety of different tissues, organisms and conditions.
In the course of the MITO-DYNAMICS project, this thesis projects centers around the extension of the mitoXplorer platform and its application to study the dynamics of mitochondria during muscle ageing in two different model systems.
Central to the study is the enhancement of mitoXplorer to be able to integrate mito-genes into the cellular context, by incoporating tools for data integration. These include the integration of epigenetic data, as well as of data for the exploration of the regulatory network of mito-genes. Moreover, numerical values stemming from physiological parameters, in the form of mitochondrial metabolic measurements, as well as morphological measurements should be incoporated in the mitoXplorer platform to correlate expression dynamics to changes in mitochondrial metabolism and structure.

Work Context

- The PhD student will have two responsibilites :
1) the data analysis of -omics data coming from NGS and proteomics studies ;
2) the programmatic extension of the mitoXplorer platform.
He/she will have to have prior knowledge in programming in Python, Javascript and Java, as well as regularily use statistical analysis software, such as R, and perform NGS-based and proteomics-based data analysis using state-of-the-art software.

In order to perform the necessary tasks in this project, the student will apply data analysis pipelines from the NGS-sequence analysis, as well as proteomics field, as well as perform statistical analysis using R. He/she will work with software tools designed in the lab or outside, including mitoXplorer, viPEr/PEANuT, AnnoMiner.
He/she will routinely have to programm, using the programming languages Python, Java and Javascript.
He/she will have to regularily present results, report on programming progress, as well as present his/her work in group meetings in English.

The PhD student will be supervised by Dr Bianca Habermann, group leader of the « Computational Biology » team (http://www.ibdm.univ-mrs.fr/equipe/computational-biology/) at the Institute of Developmental Biology of Marseille (IBDM). The IBDM is located on the Luminy Campus. It has 240 employees, including Reserachers, Engineers and technical staff, as well as non-permanent CDDs, PostDocs, Phd-student and master students in 21 research teams and 11 service platforms. The IBDM is a mixed-entity research institute of the CNRS and the Aix-Marseille University (AMU), studying developmental biologies and associated pathologies.

Required competences:
- Ability to work in a team
- Good interpersonal skills
- Strong knowledge of programming
- Good command of English: written and spoken
- Good ability to adapt to new techniques

Constraints and risks

Schedules can be variable

Additional Information

Please post your CV, cover letter and recommendation letter.

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