Séminaire Mensuel / Monthly seminar

Mardi 10 Mars / March 10 (MaIAGE, salle 142, bâtiment 210)

14h00: Magali Champion (IMT/INSA Toulouse)

Statistical causal inference of Gene Regulatory Networks using l_1 penalized likelihood.

Les réseaux de régulation de gènes sont des outils permettant de modéliser sous forme de graphes les interactions qui existent entre un groupe de gènes donnés. Afin d'estimer des relations causales au sein de ces réseaux, on se place dans le cadre de modèles à équations structurelles gaussiennes, pour lesquels on cherche à maximiser la log-vraisemblance pénalisée. Nous proposons une réécriture originale de la matrice d'adjacence associée à un graphe qui nous permet d'une part d'obtenir des garanties théoriques de l'estimateur (inégalités oracles), d'autre part de mettre en place un algorithme hybride pour inférer ces réseaux. Pour finir, nous proposons une application numérique à des jeux de données simulés.

15h00: Flora Jay (MNHN)

Inbreeding and admixture inferred from the complete genome of Altai Neandertal.

In the last years several studies of archaic homminin genome sequences have been published. I will give an overview of previous findings about Neandertal and its sister group Denisova, and present new insights from a bone found in the Altai Mountains, Siberia. This bone was discovered in the same cave as the Denisova individual and was sequenced to 50-fold coverage. The genome is more closely related to Neandertal genomes from Croatia, Spain, and Caucasus than to Denisova, and provides evidence that both Neandertal and Denisova inhabited the Altai Mountains.
I will briefly present findings about the complex population history of these two archaic groups and modern humans, which is characterized by several episodes of gene flow. I will talk in further details about inbreeding in the Altai Neandertal sequence: we detected long runs of homozygosity (ROH) that suggest that this individual was highly inbred. We compared the number of long ROH and the overall coverage to those found when simulating different inbreeding scenarios. We found evidence for both recent and background inbreeding.