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The aim of this study is to investigate the relation that can be found between the phylogeny of a large set of complete chloroplast genomes, and the evolution of gene content inside these sequences. Core and pan genomes have been computed on textit{de novo} annotation of these 845 genomes, the former being used for producing well-supported phylogenetic tree while the latter provides information regarding the evolution of gene contents over time. It details too the specificity of some branches of the tree, when specificity is obtained on accessory genes. After having detailed the material and methods, we emphasize some remarkable relation between well-known events of the chloroplast history, like endosymbiosis, and the evolution of gene contents over the phylogenetic tree.
The Dissertation is focused on the studies of associations between functional elements in human genome and their nucleotide structure. The asymmetry in nucleotide content (skew, bias) was chosen as the main feature for nucleotide structure. A signifi
We train a neural network to predict human gene expression levels based on experimental data for rat cells. The network is trained with paired human/rat samples from the Open TG-GATES database, where paired samples were treated with the same compound
Gene-gene interactions have long been recognized to be fundamentally important to understand genetic causes of complex disease traits. At present, identifying gene-gene interactions from genome-wide case-control studies is computationally and methodo
Precision medicine is a paradigm shift in healthcare relying heavily on genomics data. However, the complexity of biological interactions, the large number of genes as well as the lack of comparisons on the analysis of data, remain a tremendous bottl
Summary: Interpretation and prioritization of candidate hits from genome-scale screening experiments represent a significant analytical challenge, particularly when it comes to an understanding of cancer relevance. We have developed a flexible tool t