03/06/2020

PhD position: Machine learning to predict new gene regulatory variants involved in immunological diseases

This job offer has expired


  • ORGANISATION/COMPANY
    Laboratoire TAGC/INSERM U1090
  • RESEARCH FIELD
    Biological sciencesBiology
    Medical sciences
  • RESEARCHER PROFILE
    First Stage Researcher (R1)
    Recognised Researcher (R2)
    Established Researcher (R3)
    Leading Researcher (R4)
  • APPLICATION DEADLINE
    06/08/2020 00:00 - Europe/Brussels
  • LOCATION
    France › Marseille
  • TYPE OF CONTRACT
    Temporary
  • JOB STATUS
    Full-time

A 3-year PhD position is available from September-December 2020 at the Inserm U1090/TAGC and the I2M, UMR 7373 unit in Marseilles, France funded by the ANR and AMU’s Institute for Cancer and Immunology. The topic of this project is the use of "Machine learning to predict new gene regulatory variants involved in immunological diseases". The successful candidate will work under the joint supervision of Dr Aitor Gonzalez (TAGC), Dr Badih Ghattas (I2M) and Prof Pascal Rihet (TAGC).

Description of the PhD thesis project

It is expected that cancer is associated with variants altering on the one hand the proliferation of malignant cells and their ability to invade the host, and on the other hand the immunosurveillance mechanisms [1; 2] . Genome-wide association study (GWAS) is a key approach to link genetic factors to human phenotypes. Many SNPs identified by GWAS fall in non-coding regions and are likely gene regulatory variants.

Recently w e have developed a new method to train a supervised model with common regulatory variants associated to complex diseases that we have run on intergenic and intronic regions. Interestingly, our method has a good prediction performance for diseases related to the immune system [3].

In the present project, we expect the PhD student to use frequent variants associated to diseases related to the immune system to train the model. This model will be then used to prioritize regulatory variants arising in different tumors and immune system diseases such as acute myeloid (AML) and T-cell acute lymphoblastic leukemia (ALL). It is hypothesized hypothesize that such models would predict causal variants involved in tumorigenesis or anticancer immunosurveillance.



Funding category: Contrat doctoral

ANR and AMU’s Institute for Cancer and Immunology

PHD title: PhD in Bioinformatics

PHD Country: France

Offer Requirements

Specific Requirements

The candidate should have a Master’s degree in an area related to Bioinformatics, Biophysics, Population Genetics or Computer Science with a good background in statistics, data analysis and machine learning. He should be interested in a project that includes machine learning and human genetics. He should feel confortable with software programming with a preference for Python and data analysis. He should also have some knowledge of molecular biology and/or genetics. The expected start of this PhD position is between September and December 2020 and the funding runs for three years. In addition, teaching in Bioinformatics to Bachelor and Master students might be also possible.

Work location(s)
1 position(s) available at
Laboratoire TAGC/INSERM U1090
France
Marseille

EURAXESS offer ID: 528594
Posting organisation offer ID: 92344

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