Société Française de Bioinformatique

Mots-Clés

Multi-modal data integration, Deep learning, Machine Learning

Description

The “Learning Meaningful Representation of Life” group (PI Paul Villoutreix) of the Turing Center for Living Systems and the “Networks and Systems Biology” group (PI Anaïs Baudot) of the Marseille Medical Genetics Institute in Marseille have an open position for a Postdoctoral researcher in Machine Learning and bioinformatics for the study of Rare Diseases.  

Project: Biological processes are now being assessed at different levels, from genomics, to epigenomics, transcriptomics, metabolomics or proteomics. This data yields unprecedented opportunities to better understand biological systems in healthy and pathological states. Designing theoretical and computational approaches for the joint analysis of multi-omics datasets is currently one of the most relevant and challenging questions in computational biology. With rare diseases however, the task is staggering. It is estimated that about 300 million patients suffer from 5 000 to 8 000 rare genetic diseases worldwide, however, the access to patient samples is by definition limited. Our main objective in the CAMUDI project is to develop innovative approaches for multimodal data integration that can deal with a small number of samples.With this project we will explore artificial neural networks and multimodal autoencoders with transfer learning to integrate omics with images data. We will focus in particular on Facio Scapulo Humeral Dystrophy (FSHD), which is a peculiar form of muscular dystrophy with predominant weaknesses of specific muscles of the face and upper body.

Environment: The successful candidate will work in an interdisciplinary environment composed of mathematicians and computer scientists (https://bioml.lis-lab.fr - Villoutreix team) and bioinformaticians (https://www.marseille-medical-genetics.org/a-baudot/ - Baudot team). Moreover, the candidate will benefit from the vibrant environment of the Turing Center for Living Systems (https://centuri-livingsystems.org), and will be involved in the machine learning department of the Computer Science Lab (https://qarma.lis-lab.fr).

Qualifications:

• PhD in Bioinformatics, Computational Biology, Mathematical Biology, Computer Science, Applied Mathematics or related fields
• Experience in the development and application of Machine Learning methods
• Experience with -omics data
• A previous experience in the use and development of R/python packages for biological omics data analysis would be an asset
• Good communications skills in an interdisciplinary environment

Offer

Fully-funded position for 2 years in the scenic Mediterranean city of Marseille. The expected starting date is January 2023, or as soon as the position is filled. The salary will be based on experience. Applications can be sent directly to paul.villoutreix@univ-amu.fr. Please make sure that your application includes a motivation letter, a detailed CV and the contact information of 2 references.