Description of the thesis topic

The use of AI methods and tools has had a substantial impact on the field of proteomics (Neely et al., 2023 - https://doi.org/10.1021/acs.jproteome.2c00711).

The PhD will be attached to the Doctoral School of Chemical Sciences of the University of Strasbourg (ED222).

The goal of this thesis project is to develop novel ways of interpreting large-scale proteomics data using such AI-based models to extract interesting new biological information. Moreover, special attention will be given to the incorporation of protein post-translational modifications in these AI-based models, to unravel their specific roles and contributions to the (dys-)function of cells and tissues at the molecular level.

Work Context

The Institut Pluridisciplinaire Hubert CURIEN (IPHC), a joint research unit under the joint supervision of CNRS and the University of Strasbourg (UMR7178), is a multidisciplinary laboratory where research teams from different scientific cultures (ecology, physiology and ethology, chemistry and subatomic physics) develop very high level programs based on scientific instrumentation. The IPHC is structured into 4 departments and has a total staff of 393 staff including 257 permanent staff (ie 119 researchers and teachers / researchers and 138 engineers and technicians), 46 staff on fixed-term contracts and 102 doctoral students.

The PhD student will join the "Laboratoire de Spectrométrie de Masse Bio-Organique" (LSMBO) team of the IPHC comprised 9 researchers and teacher-researchers (M/F), 11 engineers (M/F), post-docs and PhD students and will benefit from all the material conditions (LC-MS / MS instrumentation), human support (sharing of expertise), and (bio-)IT (access to powerful compute hardware, and software tools for the (re-)processing of LC-MS / MS data) necessary for the successful completion of this thesis project.

The candidate must hold a master's and/or engineering degree.
He/she will need to prove a solid knowledge of (bio-)informatics data analysis and programming languages (notably Python), and will need to have some prior experience with the application of machine learning or AI methods. A strong interest in biology and/or biochemistry will be an advantage.
The candidate must have a good command of written and spoken English (at level B2 according to the Common European Framework of Reference for Languages) to be able to report regularly and present his/her results to the collaborators and at conferences.
Applications should include a detailed CV, a letter of motivation, a summary of the Master's thesis, as well as the grades of Master 1 and 2.
The candidate will benefit from access to an administrative restaurant, partial reimbursement of travel expenses, a works council, the possibility of teleworking and training to adapt to the job.

The position is located in a sector under the protection of scientific and technical potential (PPST), and therefore requires, in accordance with the regulations, that your arrival is authorized by the competent authority of the MESR.

Constraints and risks

-Casual work in staggered schedule
-Work in an ISO 9001 certified environment