Extraction de connaissances à partir de données de protéomique de découverte haut-débit

Ce memoire presente mon travail d'encadrement d'activites de recherche pour les annees 2012-2016, ainsi que des perspectives pour les cinq annees a venir. Au travers de la presentation de deux de mes projets de recherche, j'analyse les differentes questions suscitees par l'animation d'un groupe de recherche dont l'objectif est le developpement d'outils et de methodes permettant l'extraction de connaissances automatisees a partir de donnees de quantification relative en proteomique label-free obtenues par spectrometrie de masse haut-debit. Ces questions concernent notamment (i) l'encadrement de jeunes chercheurs et la valorisation de leurs activites; (ii) la recherche de financements; et surtout (iii) la gestion des difficultes specifiques au contexte interdisciplinaire (mode de diffusion/valorisation, equilibre entre recherche et ingenierie, pilotage et priorisation des sujets de recherche, etc.). Le premier projet presente, ProStaR, est un outil logiciel permettant de faciliter l'analyse statistique de donnees proteomiques. Au-dela de l'important travail d'ingenierie que sa realisation a necessite, je montre qu'il peut etre le support de nombreux petits projets relativement independants mais novateurs en science des donnees. Le second projet, Reveal-MS, propose de resoudre le demultiplexage de spectres de peptides par des methodes innovantes de factorisation non-negative de matrices de grandes tailles. A l'inverse du precedent projet et dans une logique complementaire, celui-ci est moins motive par les besoins quotidiens de la proteomique que par la possibilite a long terme de permettre une rupture dans l'etat de l'art.

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