Post-doctoral researcher in bio-informatics W/M

Employeur

The University of Bordeaux is a great dynamic and responsible university that cares about the well-being of its staff. Joining us means working in a privileged environment within a particularly diverse and open professional community, benefiting from welcome and inclusion schemes, training and internal mobility. It means participating in an academic, scientific and human adventure. It means committing to meeting the challenges of the 21st century.

Join the Centre de Résonance Magnétique des Systèmes Biologiques (CRMSB) – of the University of Bordeaux! The CRMSB develops research themes around MRI and its applications in biology and health. The laboratory is located at the interface of Engineering Sciences and Biological Sciences.

As part of the ABCardionostics project, funded by the European Union, we are recruiting a Post-Doctoral Researcher W/M whose work will focus on antibody biology and bioinformatics.

The objective of this project is to find a revolutionary solution to improve diagnosis and treatment. Our approach uses fully human antibodies, developed from cutting-edge research, to detect and treat atherosclerosis. By targeting specific immune cells involved in the disease, we aim to stop its progression and even reverse its effects. It involves 8 partners: the University of Bordeaux, the CNRS, the Polytechnic Institute of Bordeaux, The Carlos III national center for Cardiovascular research, BIOTEM, MAbSilico, Pie Medical Imaging, the University of Maastricht.

Votre mission

Your mission will consist of carrying out NGS sequence analyses of human antibodies (HuAb) anti-Mo/MP (monocyte/macrophage) or in silico analysis of the main VH-VL genes in collaboration with MabSilico and IMGT.

The aim is to identify, among millions of sequences, those that have been selected during successive cycles of phage display. Biological validations will further corroborate the bioinformatic analyses. The strength of these physiological selections without knowledge of the target is to obtain insight into the relevant biomarkers targeted in vivo. These biomarkers will be identified through proteomic analyses and IPA (Ingenuity Pathway Analysis) or R of proteins differentially expressed in the culpable Mo/MP subsets compared to the protective ones.

Bioinformatic analyses

With PhD students, you analyze the NGS sequences and identify the occurrence of Sanger sequences of individual clones within the NGS sequence library for leading antibodies

- diagnostic antibodies distinguishing macrophage subtypes
- therapeutic antibodies selected by FACS from pathogenic Mo/MP subsets

You compare the sequences obtained by Sanger sequencing to the NGS datasets in order to:

o validate that the biologically selected human antibodies are indeed present in the NGS data, confirming their specificity for biomarkers overexpressed in the atherosclerotic plaque

o confirm that this selection accurately reflects the recognition of the targeted biomarkers

You identify antibody clonotypes in the NGS data (most frequent VH-VL combinations, or dominant individual VH or VL sequences)

Identification of pathology-relevant biomarkers

You identify molecular targets of the leading human antibodies through proteomic analyses in order to identify proteins differentially expressed between pathogenic and protective Mo/MP subpopulations

You perform biological network analyses with the Ingenuity Pathway Analysis software (or other software such as KEGG, STRING) for the identification of relevant biomarkers

These biomarkers

• will guide the prediction of human antibody targets by computational methods (MabSelect and MabTarget AI software developed by MabSilico) applied to NGS sequencing data

• will be used for the construction of biochips

Vos atouts / Vos talents

Holder of a PhD in PhD in Biological or bioinformatics sciences, you have a first successful experience in NGS analysis or proteomics.

•        You are organized, methodical and rigorous

•        You demonstrate abilities to work in a team and take initiatives

•        You are proficient in programming on Python and/or R, Git versioning and the use of NextFlow

•        You are also familiar with biostatistics and have an ease in adopting new computer tools

•        You master English (oral, written) in a multicultural work context (level C1/B2)

Do you recognize yourself? Apply!

More information:

An international openness is essential for the realization of this project. Within the consortium are gathered people recognized for their expertise in:

-  atherosclerosis, study of macrophages and implementation of models and imaging of precise animal models

-  the engineering of original antibody formats

-  the in silico identification of the antibody target via artificial intelligence

Based in Bordeaux, Gironde, FRANCE – access by tramway line A (stop « Hôpital Pellegrin ») buses, bike.

The laboratory is near the city-centre of Bordeaux and about 60 Km of the Atlantic coast.

24-month fixed-term contract

Gross monthly salary: 2750€

Job Benefits:

50 days of annual leave from the first year

75% of the cost of a Gironde public transport pass covered

contribution to private healthcare insurance of 15€ / month

Subsidised meals

Leisure, sports and cultural activities for all staff

Disabled-friendly establishment

Possibility of staff parking

Sustainable mobility package for commuting between home and work

Welcome programme and training courses

Recruitment process: Applications are reviewed as they arrive.

Candidates selected for an interview will be contacted by the Recruitment Officer for a first pre-qualification phone conversation. An interview with the supervisor will then be organised by videoconference.

Interested applicants should send a CV, brief statement of qualifications and basis for interest in the position, list of  your relevant publications, and the email addresses of at least 2 appropriate references.