Skip to Main content Skip to Navigation
Theses

Modélisation du déséquilibre de liaison en génomique des populations par méthodes d'optimisation

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.
Complete list of metadatas

Cited literature [104 references]  Display  Hide  Download

https://tel.archives-ouvertes.fr/tel-01758037
Contributor : Abes Star :  Contact
Submitted on : Wednesday, April 4, 2018 - 11:10:14 AM
Last modification on : Wednesday, October 7, 2020 - 1:20:04 PM

File

DIAS-ALVES_2017_diffusion.pdf
Version validated by the jury (STAR)

Identifiers

  • HAL Id : tel-01758037, version 1

Citation

Thomas Dias Alves. Modélisation du déséquilibre de liaison en génomique des populations par méthodes d'optimisation. Statistiques [math.ST]. Université Grenoble Alpes, 2017. Français. ⟨NNT : 2017GREAS052⟩. ⟨tel-01758037⟩

Share

Metrics

Record views

749

Files downloads

798