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PhD defended novembre 3^rd, 2014
Direction: Jacques Nicolas & Denis Tagu

Abstract:

This thesis aims to discriminate between embryos development towards either sexual or asexual reproduction types in pea aphids, Acyrthosiphon pisum, at the genomic level. This discrimination involves the creation of a post-transcriptional regulation network between microRNAs and mRNAs whose kinetic expressions change depending on the embryogenesis. It also involves a study of this network's interaction modules using formal concept analysis. To do so, a three-step strategy was set up. First the creation of an interaction network between the pea aphid's microRNAs and mRNAs. The network is then reduced by keeping only microRNAs and mRNAs which possess differential kinetics between the two embryogeneses, these are obtained using high-throughput sequencing data. Finally the remaining network is analysed using formal concept analysis. Analysing the network allowed for the identification of several functions of potential interest such as oogenesis, transcriptional regulation or even neuroendocrine system. In addition to network analysis, formal concept analysis was used to create a new method to repair a bipartite graph based on its topology and a method to visualise a bipartite graph using its formal concepts.