Société Française de Bioinformatique

Mots-Clés

metabolism deep learning epigenetics cardiovascular Artificial Intelligence methylation mass spectrometry

Description

An interdiscpiplinary PhD scholarship funded by CNRS is available at the European Genomic Institute for Diabetes (Lille, France) in the groups “Microbiome and Metabolome and Metabolic Diseases” supervised by Prof. Marc-Emmanuel Dumas and “Artificial Intelligence for precision medicine of cardiometabolic disorders” supervised by Dr. Nicolas Gambardella, in collaboration with colleagues at Imperial College London.
The PhD student will develop AI models to evaluate cardiac age from raw electrocardiogram (ECG) waveforms, epigenetic age from DNA methylation (DNAm), and metabolomic age from ultra-high performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-HRMS) metabolomic data. The project entails:
• Management of project data (various datasets available in the lab for >12,000 patients)
• Development of machine learning pre-processing methodologies for raw ECG waveforms to develop and implement ECG clocks to derive cardiac age
• Development and implementation of DNA methylation epigenetic clocks and metabolomic clocks
• Implementation of AI-based multimodal analyses and visualisation
The student will play a key role in influencing the project: design of workflow, optimisation and benchmarking, prioritisation and interpretation of results and be responsible for data processing and scientific dissemination of results (drafting of scientific articles in English and participation in conferences).
Required skills:
• MSc or equivalent in computational biology/medicine, bioinformatics, machine learning, AI or similar subject
• Experience in functional genomics and/or metabolomics
• Experience in artificial intelligence, particularly machine learning (deep learning is a plus)
• Proficiency in Python, and if possible R, programming
• Mastery of spoken and written English (B2 or above)
• Autonomy, rigor, critical thinking, ability to work within an international team
The student will join the U1283/UMR8199 EGENODIA (head: Philippe Froguel). The Institute provides an excellent intellectual environment and the infrastructure required to carry out the project, with direct access to state-of-the-art platforms including metabolomics by high-resolution mass spectrometry, high-throughput sequencing, and a large computing infrastructure.
This PhD studentship is part of the International Research Project in Integrative Metabolism between CNRS, the University of Lille and Imperial College London. The PhD Student will collaborate with researchers at Imperial College London and travel regularly to Imperial for training and research.