Sèverine Bérard

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In the class of repeated sequences that occur in DNA, minisatellites have been found polymorphic and became useful tools in genetic mapping and forensic studies. They consist of a heterogeneous tandem array of a short repeat unit. The slightly different units along the array are called variants. Minisatellites evolve mainly through tandem duplications and(More)
We propose new algorithms for computing pairwise rearrangement scenarios that conserve the combinatorial structure of genomes. More precisely, we investigate the problem of sorting signed permutations by reversals without breaking common intervals. We describe a combinatorial framework for this problem that allows us to characterize classes of signed(More)
MOTIVATION Most models of genome evolution integrating gene duplications, losses and chromosomal rearrangements are computationally intract able, even when comparing only two genomes. This prevents large-scale studies that consider different types of genome structural variations. RESULTS We define an 'adjacency phylogenetic tree' that describes the(More)
BACKGROUND Variable minisatellites count among the most polymorphic markers of eukaryotic and prokaryotic genomes. This variability can affect gene coding regions, like in the prion protein gene, or gene regulation regions, like for the cystatin B gene, and be associated or implicated in diseases: the Creutzfeld-Jakob disease and the myoclonus epilepsy type(More)
We describe a new algorithm for the problem of perfect sorting a signed permutation by reversals. The worst-case time complexity of this algorithm is parameterized by the maximum prime degree d of the strong interval tree, i.e. f (d).n O(1). This improves the best known algorithm which complexity was based on a parameter always larger than or equal to d.
We study the problem of transforming a multichromosomal genome into another using Double-Cut-and-Join (DCJ) operations. We introduce the notion of DCJ scenario that does not break families of common intervals (groups of genes co-localized in both genomes). Such scenarios are called perfect, and generalize the notion of perfect reversal scenarios. While(More)
UNLABELLED We present a web-based service, SimCT, which allows to graphically display the relationships between biological objects (e.g. genes or proteins) based on their annotations to a biomedical ontology. The result is presented as a tree of these objects, which can be viewed and explored through a specific java applet designed to highlight relevant(More)
We study the problem of transforming a multichromosomal genome into another using Double Cut-and-Join (DCJ) operations, which simulates several types of rearrangements, as reversals, translocations, and block-interchanges. We introduce the notion of a DCJ scenario that does not break families of common intervals (groups of genes co-localized in both(More)
We studied four formulae used to predict the accuracy of genomic selection prior to genotyping. The objectives of our study were to investigate the impact of the parameters of each formula on the values of accuracy calculated using these formulae, and to check whether the accuracies reported in the literature are in agreement with the formulae. First, we(More)