La mise en oeuvre de méthodes bioinformatiques pour la classification de viromes

par Grigorii Sukhorukov

Projet de thèse en Informatique

Sous la direction de Macha Nikolski.

Thèses en préparation à Bordeaux , dans le cadre de École doctorale de mathématiques et informatique , en partenariat avec Institut de Biochimie et Génétique Cellulaires (laboratoire) et de Computational Biology and Bioinformatics (equipe de recherche) depuis le 14-10-2019 .


  • Résumé

    Développement de méthodes machine learning pour l'analyse de données de séquençage de virome de plantes.

  • Titre traduit

    Bioinformatics pipelines development for virome classification


  • Résumé

    The project aims to develop bioinformaric computational methods for the analysis of HTS data in the context of plant virome studies. More precisely, the PhD candidate will 1) Define and apply bioinformatic pipelines to detect viruses from HTS datasets in a computationally efficient manner. 2) Design and develop new methods for homology free machine-learning specifically tailored for virome classification and for virome / microbiome interaction analysis; 3) Integrate the resulting pipeline within a user-friendly graphical system (such as Galaxy) providing a complete bioinformatics analysis workflow from raw sequencing reads. Relevance for the career development: The applicant will learn and become autonomous in the use and development of bioinformatic algorithms, tools and classification methods for virome high-throughput data, in particular concerning the development and validation of efficient computational methods for viral diagnostics and characterization. Team: The candidate will join the Bordeaux Bioinformatics Center team at the University of Bordeaux (https://www.cbib.u-bordeaux.fr/en), a dynamic and multidisciplinary research environment offering state of the art facilities. Requirements: Masters or equivalent, preferably in bioinformatics, computer science or data science Good mastery of English, strong communication skills and teamwork ability, dynamism, thoroughness and curiosity, basic French is a plus ELIGIBILITY CRITERIA The Marie Curie funding is available for researchers that move, both within Europe and globally. The following criteria apply: • Nationals from any country may apply. • Mobility: at the time of the recruitment, the researcher must not have resided or carried out his/her main activity (work, studies, etc.), in the country of the chosen host institution (recruiting beneficiary) for more than 12 months in the 3 years immediately prior to the date of the recruitment. • Research category of Early Stage Researcher (ESR): researchers who, at the time of the recruitment, have not yet been awarded a doctorate degree and are in the first 4 years (full-time equivalent) of their research careers, including the research training period that would entitle them to a doctorate. GENERAL EVALUATION CRITERIA • Educational background relevant for the chosen position (individual research project) • High proficiency in spoken and written English • Networking and communication skills (to be evaluated in the interview). • Previous research experience, relevant to the chosen position is desirable.