2 Sep 2023
Job InformationOrganisation/Company
CNRS
Department
Centre de Recherche en Informatique, Signal et Automatique de Lille
Research Field
Biological sciences
Computer science
Mathematics
Researcher Profile
First Stage Researcher (R1)
Country
France
Application Deadline
22 Sep 2023 - 23:59 (UTC)
Type of Contract
Temporary
Job Status
Full-time
Hours Per Week
35
Offer Starting Date
1 Jan 2024
Is the job funded through the EU Research Framework Programme?
Not funded by an EU programme
Is the Job related to staff position within a Research Infrastructure?
No
Offer DescriptionThe project is funded by the CNRS 80PRIME initiative and will be developed in an inter-institutional and interdisciplinary collaboration between the UMR CRIStAL and UMR EEP of the CNRS and the University of Lille. Furthermore, this project is realized in close collaboration with the ZooMS platform in Lille (MSAP).
In recent years, the analysis of ancient biological samples has changed our understanding of the evolution of life on Earth, renewing the approaches previously used in paleontology based on the study of fossils or carbon-14 dating. At the forefront of new molecular techniques is paleogenomics (sequencing of ancient DNA), although DNA degrades relatively quickly. More recently, paleoproteomics via ZooArchaeology by mass spectrometry (ZooMS) offers a possibility to identify morphologically ambiguous or unidentifiable bone fragments from bone assemblages. Identification of bones with ZooMS results from the sequencing of a target protein, such as collagen, which is abundant in bone fragments. The collagen present in the samples is digested and the mass of the peptides obtained by spectrometry gives indirect information on the amino acid sequence of the protein studied. To exploit this data, the community works with marker peptides, which serve as a sort of molecular barcode for taxonomic assignment. But the use of these marker peptides suffers from two limitations: it remains manual and it neglects the evolutionary dimension of the data.
There is therefore a real need to formalize and automate the methods in order to obtain robust and reproducible assignments, even on a large scale. This raises multiple questions: How can the marker peptide approach be generalized towards the combination of marker peptides or consensus marker peptides to take full advantage of the phylogenetic signal contained in the data? How to infer marker peptides at different taxonomic levels ? How to measure the phylogenetic signal contained in the target protein and its peptides ? How to reconstruct ancestral protein sequences from spectra and contemporary sequences to enrich contemporary data sets ?
The methods developed will combine sequence algorithmic approaches and a probabilistic framework using protein sequence evolution models to reconstruct phylogenetic trees and ancestral sequences. The expected results are twofold: to develop a toolbox for data analysis, and to propose a methodological framework for an informed use of marker peptides in ZooMS.
RequirementsResearch Field
Biological sciences
Education Level
PhD or equivalent
Research Field
Computer science
Education Level
PhD or equivalent
Research Field
Mathematics
Education Level
PhD or equivalent
Languages
FRENCH
Level
Basic
Research Field
Biological sciences
Years of Research Experience
None
Research Field
Computer science
Years of Research Experience
None
Research Field
Mathematics
Years of Research Experience
None
Website for additional job details
https: // emploi.cnrs.fr/Offres/Doctorant/UMR9189-HELTOU-002/Default.aspx
Work Location(s)Number of offers available
1
Company/Institute
Centre de Recherche en Informatique, Signal et Automatique de Lille
Country
France
City
VILLENEUVE D ASCQ
Website
https: // emploi.cnrs.fr/Candidat/Offre/UMR9189-HELTOU-002/Candidater.aspx
ContactCity
VILLENEUVE D ASCQ
Website
https:// cristal.univ-lille.fr/
STATUS: EXPIRED