PhD defence of Thomas Dias-Alves on 12/18/17
Thesis defense of Thomas Dias-Alves , from BCM team, on 12/18/2017 1:30pm.
“ Modeling the linkage disequilibrium in population genomics with optimization methods ”
Supervisor :
- Michael BLUM, CNRS Research Director, UGA, TIMC-IMAG, Grenoble
Jury :
- Emmanuelle Génin, INSERM Research Director, UMR 1078 ’Genetics, functional genomics and biotechnology’, UBO, Brest, Reviewer
- Julien Chiquet, Research fellow, UMR AgroParisTech / INRA, MIA, Paris, Reviewer
- Franck Picard, CNRS Research Director, UMR LBBE "Biométrie et Biologie Évolutive", UCB, Lyon, Examiner
- Étienne Patin, Research fellow, CNRS URA3012 / Institut Pasteur, Paris, Examiner
- Bertrand Servin, Research fellow, INRA Unité GenPhySE "Génétique, Physiologie et Systèmes d’Élevage", Toulouse, Examiner
Place : Bâtiment Boucherle, 109 Faculté de Médecine et de Pharmacie, 38700 La Tronche
Detailed information:
Key-words : optimization, linkage disequillibrium, haplotype
Abstract : We present a new formalism and new methods to model linkage disequilibrium and to account for haplotype structure of population genomics data. Modeling relies on an optimization problem with constraints that is solved using dynamic programming. The algorithmic cost of proposed methods is linear, which is a desirable property to process large datasets.
First, we applied our framework to study admixed populations and perform local ancestry inference. Our method is applied to simulated genotypes of admixed human populations and to real genotypes from admixed Populus species.
Second, we developed our optimization framework to perform haploptype phasing and imputation based on a population of genotypes. All optimization methods have been developed in a Python package called Loter.
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