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Comparative genomics has revealed that some species have exceptional genomes, compared to their closest relatives. For instance, some species have undergone a strong reduction of their genome with a drastic reduction of their genic repertoire. Deciphering the causes of these atypical trajectories can be very difficult because of the many phenomena that are(More)
Abstract Systems biology invites us to consider the dynamic interactions between the components of a living cell. Here, by evolving artificial organisms whose genomes encode protein networks, we show that a coupling emerges at the evolutionary time scale between the protein network and the structure of the genome. Gene order is more stable when the protein(More)
We propose here a new evolutionary algorithm, the RBF-Gene algorithm, to optimize Radial Basis Function Neural Networks. Unlike other works on this subject, our algorithm can evolve both the structure and the numerical parameters of the network: it is able to evolve the number of neurons and their weights. The RBF-Gene algorithm's behavior is shown on a(More)
In the past few years, numerous research projects have focused on identifying and understanding scaling properties in the gene content of prokaryote genomes and the intricacy of their regulation networks. Yet, and despite the increasing amount of data available, the origins of these scalings remain an open question. The RAevol model, a digital genetics(More)
The organization of genomes shows striking differences among the different life forms. These differences come along with important variations in the way genomes are transcribed, operon structures being frequent in short genomes and the exception in large ones, while ncRNAs are frequent in large genomes but rare in short ones. Here, we use the digital(More)
By using Aevol, a simulation framework designed to study the evolution of genome structure, we investigate the effect of homologous rearrangements on the course of evolution. We designed an efficient model of rearrangements based on an intermittent search algorithm. Then, using experimental in silico evolution, we explore the effect of rearrangement rates(More)
Models of evolution by genome rearrangements are prone to two types of flaws: One is to ignore the diversity of susceptibility to breakage across genomic regions, and the other is to suppose that susceptibility values are given. Without necessarily supposing their precise localization, we call "solid" the regions that are improbably broken by rearrangements(More)