Mots-Clés
metabolomics
artificial intelligence
ageing
cardiovascular
Description
Missions
A Research Engineer position is available at the research group “Metabolome, Microbiome and Metabolic diseases” directed by Dr. Marc-Emmanuel Dumas and hosted by European Genomic Institute for Diabetes (EGID, UMR 1283/8199 Inserm/CNRS, Institut Pasteur de Lille, CHU Lille, Université de Lille) in Lille, France.
The selected candidate will join Dr Francesc Puig-Castellvi and the research group “Metabolome, Microbiome and Metabolic diseases” within UMR 1283/8199 and will play a critical role in ensuring the efficient implementation of artificial intelligence (AI) strategies for predicting the chemical structure of small metabolites implicated in metabolic and cardiovascular diseases from mass fragmentation (MS/MS) spectra. They will work closely with members of the research group “Artificial Intelligence for precision medicine of cardiometabolic disorders” supervised by Dr. Nicolas Gambardella.
Activities
• Implementation and benchmarking of AI strategies workflows for predicting and ranking chemical structures from mass fragmentation mass spectroscopy data generated at the metabolomics platform from UMR 1283/8199.
• Development of strategies for comparison of experimental MS/MS spectra against large-scale open libraries based on molecular networking, calculation of spectral entropy, mass differences between fragments.
• Work closely with colleagues from the metabolomics platform to develop and implement strategies for annotation of metabolomics data based on database search.
• Management of project data.
• Maintain detailed records of the technical settings and results.
• Participation in research meetings and internal seminars.
Skills
• PhD / MEng in Artificial Intelligence, Bioinformatics, or similar
• Practical experience with artificial intelligence projects
• Knowledge of Python, R, SQL
• Experience with MS/MS structural identification
• Experience with metabolomics
• Ability to work independently
• Ability to prioritize tasks
• Ability to communicate in English in an international team
• Ability to write project updates and research papers
Work Context
The selected candidate will join the research group “Metabolome, Microbiome and Metabolic diseases” as part of the “ANR Jeunes Chercheurs” project led by Dr. Puig- Castellví and funded by the Agence Nationale de la Recherche. The group’s research focused on the study of the human metabolome and the identification of gut microbial metabolites involved in metabolic diseases. It is part of UMR 1283/8199 at the European Genomics Institute for Diabetes (Egid), recognised by a ‘Laboratory of Excellence’ award.The Institute provides an excellent intellectual environment and infrastructure for metabolomics (IMPACT-PM), sequencing (LIGAN-PM, ‘Equipment of Excellence’ platform award), animal facilities (metabolic cages, treadmill, CTscan, PET scan, MRI), cell imaging facility (confocal microscopy, electron microscopy), flow (INFLUX BD) and mass (CyTOF) cytometry.