Emplois

  • Internship project (master level)

    Programming a model-driven framework for ribosome
    profiling analysis

     UM CBS

    What

    Expression of genes is one of the most essential biological processes underlying life. One fundamental part of this process is the translation of proteins from mRNAs, mediated by molecular machines called ribosomes. Despite that, how the codon choice or the transcript's sequences determine protein synthesis rates remains one of the major open questions in biology.
    Recent technical advances, such as ribosome profiling, allow probing translation at codon resolution, making quantitative studies of transcript efficiency more accessible.


    How

    We recently developed NEAR (Non-Equilibrium Analysis of Ribo-seq), a method to analyse experimental ribosome profiling data and based on a well known mathematical
    model of unidimensional traffic [1].
    We now look to make the method more accessible by developing a code in python that will be freely distributed. The intern will adapt and re-write part of the code previously developed in another language, also developing GUIs or web-based interfaces to make it easily usable for the large community. There is possibility to further extensions in the method for the interested candidates.


    Who
    Students with an experience in coding in Python, with graphical or web interfaces, possibly with training in RNA-seq data analysis. A strong background in Physics/Mathematics is not needed, but motivation to understand the underlying biophysical model will be considered as a plus.


    When
    - 4/6-month scholarship (preferably starting from January 2022) for master students.


    Where
    The project is funded by the ANR (MAGEEc 2022-2026). Students will be based at the Centre de Biologie Structurale (CBS), University of Montpellier, in the Multiscale Biomolecular Modelling team. The project will also be developed in collaboration with international partners (with potential visits).


    Contact: Luca Ciandrini (Cette adresse e-mail est protégée contre les robots spammeurs. Vous devez activer le JavaScript pour la visualiser.).


    Related readings:

    [1] Juraj Szavits-Nossan, Luca Ciandrini, Inferring efficiency of translation initiation and elongation fromribosome profiling, Nucleic Acids Research 48 (17), (2020) https://doi.org/10.1093/nar/gkaa678

    [2] Juraj Szavits-Nossan, Luca Ciandrini, M. Carmen Romano, Deciphering mRNA Sequence Determinants of Protein Production Rate, Phys Rev Lett (2018)

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  • Internship and PhD project

    Modelling Gene Expression Economy

     UM CBS

    What

    The dream of every cell is to become two cells (F. Jacob). However, in order to create a copy of themselves, cells must respect economical tradeoffs between the production of their building blocks and resource consumption. The precise biophysical principles governing the interdependence between cell growth, gene expression (biomass production via protein synthesis) and the allocation of cellular resources are still elusive.
    We aim at understanding the regulation of the complex cellular economy and the interplay with physiology by new theoretical approaches and model-driven data analyses (omics level).


    How
    We will establish a multi-scale and comprehensive framework built on (nonequilibrium) statistical mechanical approaches to quantify the usage of cellular resources in gene expression, and throughly investigate the role of each potential bottleneck in the process. We will develop analytical models, as well as simulations (kinetic Monte Carlo).
    The outcomes will provide a more refined interpretation of our current understanding of growth laws, and provide new quantitative relationships that will be tested with either experiments or available datasets.


    Who
    Students willing to study biological questions, having a background in Physics/Mathematics and with an experience in programming. No prior biological training needed, but motivation to understand the underlying biological mechanisms is requested.


    When
    - 6-month scholarship (preferably starting from January 2022) for master students.
    - PhD position (3 years) to be filled in 2022.


    Where
    The project is funded by the ANR (MAGEEc 2022-2026). Students will be based at the Centre de Biologie Structurale (CBS), University of Montpellier, in the Multiscale Biomolecular Modelling team. The project will also be developed in collaboration with international partners (with potential visits).


    Contact: Luca Ciandrini (Cette adresse e-mail est protégée contre les robots spammeurs. Vous devez activer le JavaScript pour la visualiser.).


    Related readings:

    - Ludovico Calabrese, Jacopo Grilli, Matteo Osella, Christopher P Kempes, Marco Cosentino Lagomarsino, Luca Ciandrini, Role of protein degradation in growth laws, bioRxiv, doi.org/10.1101/2021.03.25.436692

    - Juraj Szavits-Nossan, Luca Ciandrini, M. Carmen Romano, Deciphering mRNA Sequence Determinants of Protein Production Rate, Phys Rev Lett (2018)

    - Lucas D. Fernandes, Alessandro P.S. de Moura, Luca Ciandrini, Gene length as a regulator for ribosome recruitment and protein synthesis: theoretical insights, Sci Rep (2017)

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  • 1

Stages

stages2

Le CBS accueille chaque année de nombreux stagiaires de tout niveau, de la 3ème au post-doctorat. Les candidatures (CV et lettre de motivation) sont à adresser directement aux chercheurs des équipes du CBS.

Le recrutement des étudiants en Thèse se fait par l'intermédiaire de l'Ecole Doctorale CBS2.

Les sujets de Thèse proposés par les chercheurs du CBS sont à consulter ici.

 

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