Interdisciplinary PhD at the Turing Centre for Living Systems (Marseille, France)
A bioinformatician with skills in programming (Python and R) and data analysis, with the taste and the will to perform experimental work of biochemistry and molecular biology,
Ref offer: PHD2018-03
Understanding uORF functions through dendritic cells biology and computational approaches
Upstream open reading frames (uORFs) are known as gene expression cis-regulatory elements. In half of eukaryotic mRNAs, one or more uORFs precede the initition codon of the main coding region. By reducing the efficiency of translation initiation of the main downstream ORF or by triggering mRNA decay, uORFs participate to the translation regulatory mechanisms, notably during stress. However, translation of small peptides encoded by uORFs led to the assumption that they may play additional functional roles in trans beside their regulatory functions, calling for further studies. In this context, the Center for Immunology (CIML) and the Theories and Approaches of Genomic Complexity (TAGC) institutes on the Marseille-Luminy campus will combine their efforts in an interdisciplinary project aiming at understanding the nature, the regulation and the functions of uORFs in the context of dendritic cells development and activation, in the light of a thorough computational predictive analysis of their pattern of expression and macromolecular interactions. The project will require developing computational biology approaches and analyses, complemented with experimental biology to identify uORFs and predict their expression and function in dendritic cells (DC), an important professional antigen presenting cell type that orchestrates both the innate and adaptive immune responses. We are interested in understanding the nature, the regulation and the function of uORFs in the context of DC development and activation and the successful applicant will achieve these main objectives by performing both in silico analyses and working at the bench.
Upstream open reading frames (uORFs) are known as gene expression cis-regulatory elements. In half of eukaryotic mRNAs, one or more uORFs precede the initition codon of the main coding region. By reducing the efficiency of translation initiation of the main downstream ORF or by triggering mRNA decay, uORFs participate to the translation regulatory mechanisms, notably during stress. However, translation of small peptides encoded by uORFs led to the assumption that they may play additional functional roles in trans beside their regulatory functions, calling for further studies. In this context, the Center for Immunology (CIML) and the Theories and Approaches of Genomic Complexity (TAGC) institutes on the Marseille-Luminy campus will combine their efforts in an interdisciplinary project aiming at understanding the nature, the regulation and the functions of uORFs in the context of dendritic cells development and activation, in the light of a thorough computational predictive analysis of their pattern of expression and macromolecular interactions. The project will require developing computational biology approaches and analyses, complemented with experimental biology to identify uORFs and predict their expression and function in dendritic cells (DC), an important professional antigen presenting cell type that orchestrates both the innate and adaptive immune responses. We are interested in understanding the nature, the regulation and the function of uORFs in the context of DC development and activation and the successful applicant will achieve these main objectives by performing both in silico analyses and working at the bench.
Expected profile – Selected applicants should either be:
A bioinformatician with skills in programming (Python and R) and data analysis, with the taste and the will to perform experimental work of biochemistry and molecular biology,
or
A biologist with skills in biochemistry and molecular biology, with the taste and the will to perform bioinformatics data analysis.
More details: http://centuri-livingsystems.org/wp-content/uploads/2018/02/PHD2018-03-.pdf
More details: http://centuri-livingsystems.org/wp-content/uploads/2018/02/PHD2018-03-.pdf
Supervisors and contacts:
Christine Brun - christine-g.brun@inserm.fr, TAGC, UMR 1090 - Bioinformatics and genomics of molecular networks, https://tagc.univ-amu.fr/
Philippe Pierre - pierre@ciml.univ-mrs.fr, CIML, UMR 7280 - Dendritic cell biology, http://www.ciml.univ-mrs.fr/fr
Ref offer: PHD2018-03
Application site: http://centuri-livingsystems.org/recruitment/
Deadline: 15th April 2018.
Short-listed candidates will interviewed in mid-June.
