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Reference : UMR5525-ROMCIM-009
Workplace : LA TRONCHE
Date of publication : Tuesday, July 30, 2019
Scientific Responsible name : Ivan Junier (advisor), Ralf Everaers (co-advisor)
Type of Contract : PhD Student contract / Thesis offer
Contract Period : 36 months
Start date of the thesis : 1 October 2019
Proportion of work : Full time
Remuneration : 2 135,00 € gross monthly
Description of the thesis topic
Engineering genetic information requires having a good understanding of the physical structuring of genomes. In bacteria, this structuring is affected at multiple physical scales, from base pair pairing to the spatial organization of chromosome, by the underwinding of DNA – called negative supercoiling. In vivo DNA supercoiling thus plays a crucial role in multiple fundamental processes such as gene transcription, DNA replication and the segregation of replicated chromosomes. This ubiquity nevertheless makes difficult to consider the impact of DNA supercoiling quantitatively.
In this context, the PhD will consist in developing a multi-scale polymer physics framework by combining various coarse-graining techniques and by integrating data about the functional organization of the bacterial genome. Generated data will then be used to rationalize data obtained by experimental groups working on various aspects of gene regulation and chromosome structuring in bacteria.
The PhD will take place in the team « Genomics and Evolution of Microorganisms » (GEM) in the laboratory TIMC-IMAG. It is funded by the Centre National de la Recherche Scientifique (CNRS) in France, which is the largest fundamental science agency in Europe.
TIMC-IMAG gathers scientists and clinicians towards the use of computer science and computational biology for understanding and controlling normal and pathological processes in biology and healthcare. It is based in Grenoble, one of the biggest student and academic cities in France, and located nearby the French Alpes.
Within the TIMC-IMAG, the GEM team aims at developing an evolutionary systems biology framework through interdisciplinary expertise including experimental evolution, cell biology, genetics, biochemistry, comparative genomics, phylogenomics and biophysical modeling to rationalize the behavior of microbial systems.
The PhD will be part of the doctoral school « Health, cognition and environmental engineering » (ED ISCE), which aims at providing research training courses in the fields of modeling, methods and algorithms in biology, health and environment.
Ivan Junier (advisor) is a biophysicist who has been working in the field of chromosome structuring and genome organisation in bacteria for 10 years. He is an expert in polymer modeling as well as comparative genomics (bioinformatics).
Ralf Everaers (ENS Lyon, France, co-advisor) is a physicist working in the fields of soft matter and biophysics. He is an expert of the coarse-grained modeling of polymers, with a strong focus on the spatial organisation of DNA.
Finally, the PhD will be realized in close collaboration with the polymer physicist Angelo Rosa (SISSA, Trieste, Italy), who is an expert in the polymer modeling of the spatial organisation of chromosomes, and with experimental groups working on various aspects of gene regulation and chromosome structuring in bacteria, more particularly with the group of Frédéric Boccard (I2BC, Paris- Saclay, France).
We are looking for a highly motivated candidate with a strong background in statistical and polymer physics, with an interest to apply computational tools to understand the functioning of living organisms. Advanced skills in programming are required and a previous interdisciplinary experience in connection with biological issues is a plus, although not necessary.
Constraints and risks
The PhD will involve extensive sojourns in the lab of Ralf Everaers (ENS Lyon, France) and sojourns as well in the lab of Angelo Rosa (SISSA, Trieste, Italy).
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