Equipe ComBi - sujet de thèse -2011

LABORATOIRE D’INFORMATIQUE DE NANTES-ATLANTIQUE ÉCOLE DOCTORALE STIM, N. 503UMR 6241 « Sciences et technologiesde l’information et des mathématiques »Ph. D. Proposal for 2011NGS : fast and furious genomic data analysisPh. D. Thesis DirectorNAME, Surname : RUSU, IrenaResearch Team : ComBiLaboratory : LINA (UMR 6241)Affiliation : Univ. NantesE-mail : Irena.Rusu (at) univ-nantes.frPhone : (+33/0) 2 51 12 58 16Advising Rate : 50 %Current Ph. D. Students : 3Ph. D. adviserNAME, Surname : FERTIN, GuillaumeResearch Team : LINALaboratory : LINA (UMR 6241)Affiliation : Univ. NantesE-mail : Guillaume.Fertin (at) univ-nantes.frPhone : (+33/0) 2 51 12 58 14Advising Rate : 50 %Current Ph. D. Students : 3Possible Funding : MESRPh. D. Proposal for 2011NGS : fast and furious genomic data analysisAbstract. The analysis of partially sequenced (or draft) genomes is one of the very recentproblems brought in by the next generation sequencing technologies. We address here threeclasses of problems related to draft genomes: (1) Recovering mapping errors of fragments along adraft genome and correcting them; (2) Improving the assembly of draft genomes, by filling in thegaps between the fragments; (3) Designing algorithms for identifying genome rearrangements indraft genomes. These three classes of problems will be addressed using comparison, thatneeds to be reinvented within this new context.Keywords. next generation sequencing, draft genomes, genome ...